1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
4 ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
5 ;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
6 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
7 ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
8 ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
9 ;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net>
10 ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
11 ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
12 ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
13 ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
14 ;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com>
15 ;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
16 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
17 ;;; Copyright © 2018 Eric Brown <brown@fastmail.com>
18 ;;; Copyright © 2018, 2019 Brett Gilio <brettg@posteo.net>
19 ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
20 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
22 ;;; This file is part of GNU Guix.
24 ;;; GNU Guix is free software; you can redistribute it and/or modify it
25 ;;; under the terms of the GNU General Public License as published by
26 ;;; the Free Software Foundation; either version 3 of the License, or (at
27 ;;; your option) any later version.
29 ;;; GNU Guix is distributed in the hope that it will be useful, but
30 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
31 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
32 ;;; GNU General Public License for more details.
34 ;;; You should have received a copy of the GNU General Public License
35 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
37 (define-module (gnu packages cran)
38 #:use-module ((guix licenses) #:prefix license:)
39 #:use-module (guix packages)
40 #:use-module (guix download)
41 #:use-module (guix git-download)
42 #:use-module (guix utils)
43 #:use-module (guix build-system r)
44 #:use-module (gnu packages algebra)
45 #:use-module (gnu packages base)
46 #:use-module (gnu packages bioinformatics)
47 #:use-module (gnu packages c)
48 #:use-module (gnu packages compression)
49 #:use-module (gnu packages curl)
50 #:use-module (gnu packages databases)
51 #:use-module (gnu packages fontutils)
52 #:use-module (gnu packages gcc)
53 #:use-module (gnu packages geo)
54 #:use-module (gnu packages ghostscript)
55 #:use-module (gnu packages gl)
56 #:use-module (gnu packages gnome)
57 #:use-module (gnu packages graph)
58 #:use-module (gnu packages gtk)
59 #:use-module (gnu packages haskell-xyz)
60 #:use-module (gnu packages icu4c)
61 #:use-module (gnu packages image)
62 #:use-module (gnu packages imagemagick)
63 #:use-module (gnu packages java)
64 #:use-module (gnu packages javascript)
65 #:use-module (gnu packages machine-learning)
66 #:use-module (gnu packages maths)
67 #:use-module (gnu packages mpi)
68 #:use-module (gnu packages multiprecision)
69 #:use-module (gnu packages networking)
70 #:use-module (gnu packages pcre)
71 #:use-module (gnu packages perl)
72 #:use-module (gnu packages pkg-config)
73 #:use-module (gnu packages python)
74 #:use-module (gnu packages python-xyz)
75 #:use-module (gnu packages statistics)
76 #:use-module (gnu packages 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 "1hvxw2glizq8g0qnxakcxh8jc5scn0hp1x8i70fdpqwwbgx49slr"))))
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 "0g9r156k9yl1f092hfw3b9wjx11akf0shbi3x0d0mvpnflvc8nfl"))))
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 "1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl"))))
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-fastmap
739 (uri (cran-uri "fastmap" version))
742 "1v7sp56xiha0bh78g3w92k52p9vkp7ryzpw0z66nyddxzrfv0y27"))))
743 (properties `((upstream-name . "fastmap")))
744 (build-system r-build-system)
745 (home-page "https://r-lib.github.io/fastmap/")
746 (synopsis "Fast implementation of a key-value store")
748 "This package provides a fast implementation of a key-value store.
749 Environments are commonly used as key-value stores, but every time a new key
750 is used, it is added to R's global symbol table, causing a small amount of
751 memory leakage. This can be problematic in cases where many different keys
752 are used. Fastmap avoids this memory leak issue by implementing the map using
753 data structures in C++.")
754 (license license:expat)))
756 (define-public r-shiny
764 (url "https://github.com/rstudio/shiny.git")
765 (commit (string-append "v" version))))
766 (file-name (git-file-name name version))
769 "17ac48g414h9dhi0k4wrah4gyik0q5r0xw3kc01c02qfjwimqsx7"))))
770 (build-system r-build-system)
772 `(#:modules ((guix build r-build-system)
773 (guix build minify-build-system)
776 #:imported-modules (,@%r-build-system-modules
777 (guix build minify-build-system))
779 (modify-phases (@ (guix build r-build-system) %standard-phases)
780 (add-after 'unpack 'replace-bundled-minified-JavaScript
781 (lambda* (#:key inputs #:allow-other-keys)
782 (let ((replace-file (lambda (old new)
783 (format #t "replacing ~a with ~a\n" old new)
786 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
787 ;; contain just data. They are not minified code, so we don't
789 (with-directory-excursion "inst/www/shared"
790 (replace-file "bootstrap/shim/respond.min.js"
791 (string-append (assoc-ref inputs "js-respond")
792 "/share/javascript/respond.min.js"))
793 (replace-file "bootstrap/shim/html5shiv.min.js"
794 (string-append (assoc-ref inputs "js-html5shiv")
795 "/share/javascript/html5shiv.min.js"))
796 (replace-file "json2-min.js"
797 (string-append (assoc-ref inputs "js-json2")
798 "/share/javascript/json2-min.js"))
799 (replace-file "strftime/strftime-min.js"
800 (string-append (assoc-ref inputs "js-strftime")
801 "/share/javascript/strftime.min.js"))
802 (replace-file "highlight/highlight.pack.js"
803 (string-append (assoc-ref inputs "js-highlight")
804 "/share/javascript/highlight.min.js"))
805 (replace-file "datatables/js/jquery.dataTables.min.js"
806 (string-append (assoc-ref inputs "js-datatables")
807 "/share/javascript/jquery.dataTables.min.js"))
808 (replace-file "selectize/js/selectize.min.js"
809 (string-append (assoc-ref inputs "js-selectize")
810 "/share/javascript/selectize.min.js"))
811 (replace-file "selectize/js/es5-shim.min.js"
812 (string-append (assoc-ref inputs "js-es5-shim")
813 "/share/javascript/es5-shim.min.js"))
814 (for-each (match-lambda
817 (minify source #:target target)))
818 '(("jqueryui/jquery-ui.js" .
819 "jqueryui/jquery-ui.min.js")
820 ("datepicker/js/bootstrap-datepicker.js" .
821 "datepicker/js/bootstrap-datepicker.min.js")
822 ("ionrangeslider/js/ion.rangeSlider.js" .
823 "ionrangeslider/js/ion.rangeSlider.min.js")
824 ("bootstrap/js/bootstrap.js" .
825 "bootstrap/js/bootstrap.min.js")
830 ("legacy/jquery.js" .
831 "legacy/jquery.min.js")
832 ("showdown/src/showdown.js" .
833 "showdown/compressed/showdown.js")))))
836 `(("r-crayon" ,r-crayon)
837 ("r-fastmap" ,r-fastmap)
838 ("r-httpuv" ,r-httpuv)
840 ("r-jsonlite" ,r-jsonlite)
841 ("r-xtable" ,r-xtable)
842 ("r-digest" ,r-digest)
843 ("r-htmltools" ,r-htmltools)
845 ("r-sourcetools" ,r-sourcetools)))
847 `(("js-datatables" ,js-datatables)
848 ("js-html5shiv" ,js-html5shiv)
849 ("js-json2" ,js-json2)
850 ("js-respond" ,js-respond)
851 ("js-selectize" ,js-selectize)
852 ("js-strftime" ,js-strftime)
853 ("js-highlight" ,js-highlight)
854 ("js-es5-shim" ,js-es5-shim)))
856 `(("uglify-js" ,uglify-js)))
857 (home-page "http://shiny.rstudio.com")
858 (synopsis "Easy interactive web applications with R")
860 "Makes it incredibly easy to build interactive web applications
861 with R. Automatic \"reactive\" binding between inputs and outputs and
862 extensive prebuilt widgets make it possible to build beautiful,
863 responsive, and powerful applications with minimal effort.")
864 (license license:artistic2.0)))
866 ;; This package includes minified JavaScript files. When upgrading please
867 ;; check that there are no new minified JavaScript files.
868 (define-public r-shinytree
875 (uri (cran-uri "shinyTree" version))
878 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
879 (modules '((guix build utils)))
882 ;; Delete minified JavaScript
883 (for-each delete-file
884 '("inst/www/jsTree-3.3.7/libs/require.js"
885 "inst/www/jsTree-3.3.7/libs/jquery.js"
886 "inst/www/jsTree-3.3.7/jstree.min.js"))
888 (properties `((upstream-name . "shinyTree")))
889 (build-system r-build-system)
891 `(#:modules ((guix build utils)
892 (guix build r-build-system)
896 (modify-phases %standard-phases
897 (add-after 'unpack 'replace-minified-javascript
898 (lambda* (#:key inputs #:allow-other-keys)
899 (with-directory-excursion "inst/www/jsTree-3.3.7/"
900 (symlink (string-append (assoc-ref inputs "js-requirejs")
901 "/share/javascript/require.min.js")
906 `((,(assoc-ref inputs "js-jquery")
910 (lambda (sources targets)
911 (for-each (lambda (source target)
912 (format #t "Processing ~a --> ~a~%"
914 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
915 (call-with-output-file target
917 (dump-port minified port)))))
921 `(("r-htmlwidgets" ,r-htmlwidgets)
922 ("r-jsonlite" ,r-jsonlite)
923 ("r-promises" ,r-promises)
925 ("r-stringr" ,r-stringr)))
927 `(("js-requirejs" ,js-requirejs)))
929 `(("uglify-js" ,uglify-js)
933 (uri "https://code.jquery.com/jquery-3.3.1.js")
936 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
937 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
938 (synopsis "jsTree bindings for Shiny")
940 "This package exposes R bindings to jsTree, a JavaScript library that
941 supports interactive trees, to enable rich, editable trees in Shiny.")
942 (license license:expat)))
944 (define-public r-shinydashboard
946 (name "r-shinydashboard")
950 (uri (cran-uri "shinydashboard" version))
953 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
954 (build-system r-build-system)
955 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
956 ;; Regenerate it from the included sources.
958 `(#:modules ((guix build utils)
959 (guix build r-build-system)
962 (modify-phases %standard-phases
963 (add-after 'unpack 'generate-minified-javascript
965 (with-directory-excursion "inst/AdminLTE"
966 (delete-file "app.min.js")
967 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
968 (call-with-output-file "app.min.js"
970 (dump-port minified port))))))))))
972 `(("r-htmltools" ,r-htmltools)
973 ("r-promises" ,r-promises)
974 ("r-shiny" ,r-shiny)))
976 `(("uglify-js" ,uglify-js)))
977 (home-page "http://rstudio.github.io/shinydashboard/")
978 (synopsis "Create dashboards with shiny")
979 (description "This package provides an extension to the Shiny web
980 application framework for R, making it easy to create attractive dashboards.")
981 ;; This package includes software that was released under the Expat
982 ;; license, but the whole package is released under GPL version 2 or
984 (license license:gpl2+)))
986 (define-public r-shinyfiles
988 (name "r-shinyfiles")
993 (uri (cran-uri "shinyFiles" version))
995 (base32 "1143m941hma9hc77c3xcw26c0ygfhn9ii2sbp9wrydxv4gc7mr8a"))))
996 (properties `((upstream-name . "shinyFiles")))
997 (build-system r-build-system)
1000 ("r-htmltools" ,r-htmltools)
1001 ("r-jsonlite" ,r-jsonlite)
1002 ("r-shiny" ,r-shiny)
1003 ("r-tibble" ,r-tibble)))
1004 (home-page "https://github.com/thomasp85/shinyFiles")
1005 (synopsis "Server-side file system viewer for Shiny")
1007 "This package provides functionality for client-side navigation of the
1008 server side file system in shiny apps. In case the app is running locally
1009 this gives the user direct access to the file system without the need to
1010 \"download\" files to a temporary location. Both file and folder selection as
1011 well as file saving is available.")
1012 (license license:gpl2+)))
1014 (define-public r-shinythemes
1016 (name "r-shinythemes")
1021 (uri (cran-uri "shinythemes" version))
1024 "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf"))))
1025 (properties `((upstream-name . "shinythemes")))
1026 (build-system r-build-system)
1027 (propagated-inputs `(("r-shiny" ,r-shiny)))
1028 (home-page "http://rstudio.github.io/shinythemes/")
1029 (synopsis "Themes for Shiny")
1031 "This package provides themes for use with Shiny. It includes several
1032 Bootstrap themes, which are packaged for use with Shiny applications.")
1033 ;; The package is released under version 3 of the GPL, but it includes
1034 ;; source files that are covered by the Expat license. It also includes
1035 ;; fonts under SIL or the ASL.
1036 (license (list license:gpl3 license:expat
1037 license:silofl1.1 license:asl2.0))))
1039 ;; The package sources include minified variants of d3.js and non-minified
1040 ;; source code of d3-jetpack.
1041 (define-public r-d3r
1048 (uri (cran-uri "d3r" version))
1051 "0xl3im76lp7pd5lhp8jfyqdm4j4zvjrx5a5fl81xv2cf7x3n4f2a"))))
1052 (build-system r-build-system)
1054 `(#:modules ((guix build utils)
1055 (guix build r-build-system)
1059 (modify-phases %standard-phases
1060 (add-after 'unpack 'process-javascript
1061 (lambda* (#:key inputs #:allow-other-keys)
1062 (with-directory-excursion "inst/www/d3/"
1066 `((,(assoc-ref inputs "d3.v3.js")
1067 "v3/dist/d3.min.js")
1068 (,(assoc-ref inputs "d3.v4.js")
1069 "v4/dist/d3.min.js")
1070 (,(assoc-ref inputs "d3.v5.js")
1071 "v5/dist/d3.min.js"))))
1072 (lambda (sources targets)
1073 (for-each (lambda (source target)
1074 (format #t "Processing ~a --> ~a~%"
1076 (delete-file target)
1077 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1078 (call-with-output-file target
1080 (dump-port minified port)))))
1084 `(("r-dplyr" ,r-dplyr)
1085 ("r-htmltools" ,r-htmltools)
1086 ("r-tidyr" ,r-tidyr)))
1088 `(("uglify-js" ,uglify-js)
1092 (uri "https://d3js.org/d3.v3.js")
1095 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
1099 (uri "https://d3js.org/d3.v4.js")
1102 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
1106 (uri "https://d3js.org/d3.v5.js")
1109 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))))
1110 (home-page "https://github.com/timelyportfolio/d3r")
1111 (synopsis "d3.js utilities for R")
1113 "This package provides a suite of functions to help ease the use of the
1114 d3.js visualization library in R. These helpers include
1115 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
1116 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
1117 R objects into the JSON format that the d3.js library expects.")
1118 (license license:bsd-3)))
1120 ;; We use the latest commit here because the last release was in 2016 while
1121 ;; the latest commit was in 2018.
1122 (define-public r-sankeyd3
1123 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
1127 (version (git-version "0.3.2" revision commit))
1132 (url "https://github.com/fbreitwieser/sankeyD3.git")
1134 (file-name (git-file-name name version))
1137 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
1138 (build-system r-build-system)
1141 ("r-htmlwidgets" ,r-htmlwidgets)
1142 ("r-shiny" ,r-shiny)
1143 ("r-magrittr" ,r-magrittr)))
1144 (home-page "https://github.com/fbreitwieser/sankeyD3")
1145 (synopsis "Sankey network graphs from R")
1147 "This package provides an R library to generate Sankey network graphs
1148 in R and Shiny via the D3 visualization library.")
1149 ;; The R code is licensed under GPLv3+. It includes the non-minified
1150 ;; JavaScript source code of d3-sankey, which is released under the
1151 ;; 3-clause BSD license.
1152 (license (list license:gpl3+ license:bsd-3)))))
1154 (define-public r-crosstalk
1156 (name "r-crosstalk")
1161 (uri (cran-uri "crosstalk" version))
1164 "0lfa89vhrzi7a1rghmygcjr8gzddw35sinb3jx6g49mc9jias7mk"))))
1165 (build-system r-build-system)
1167 `(("r-ggplot2" ,r-ggplot2)
1168 ("r-htmltools" ,r-htmltools)
1169 ("r-jsonlite" ,r-jsonlite)
1170 ("r-lazyeval" ,r-lazyeval)
1172 ("r-shiny" ,r-shiny)))
1173 (home-page "https://rstudio.github.io/crosstalk/")
1174 (synopsis "Inter-widget interactivity for HTML widgets")
1176 "This package provides building blocks for allowing HTML widgets to
1177 communicate with each other, with Shiny or without (i.e. static @code{.html}
1178 files). It currently supports linked brushing and filtering.")
1179 (license license:expat)))
1181 (define-public r-rook
1188 (uri (cran-uri "Rook" version))
1191 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
1192 (properties `((upstream-name . "Rook")))
1193 (build-system r-build-system)
1194 (propagated-inputs `(("r-brew" ,r-brew)))
1195 (home-page "https://cran.r-project.org/web/packages/Rook")
1196 (synopsis "Web server interface for R")
1198 "This package contains the Rook specification and convenience software
1199 for building and running Rook applications. A Rook application is an R
1200 reference class object that implements a @code{call} method or an R closure
1201 that takes exactly one argument, an environment, and returns a list with three
1202 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
1203 (license license:gpl2)))
1205 (define-public r-miniui
1212 (uri (cran-uri "miniUI" version))
1215 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
1216 (properties `((upstream-name . "miniUI")))
1217 (build-system r-build-system)
1219 `(("r-htmltools" ,r-htmltools)
1220 ("r-shiny" ,r-shiny)))
1221 (home-page "https://cran.r-project.org/web/packages/miniUI/")
1222 (synopsis "Shiny UI widgets for small screens")
1224 "This package provides UI widget and layout functions for writing Shiny apps that
1225 work well on small screens.")
1226 (license license:gpl3)))
1228 (define-public r-feather
1235 (uri (cran-uri "feather" version))
1238 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
1239 (build-system r-build-system)
1243 ("r-tibble" ,r-tibble)))
1244 (home-page "https://github.com/wesm/feather")
1245 (synopsis "R Bindings to the Feather API")
1246 (description "Read and write feather files, a lightweight binary columnar
1247 data store designed for maximum speed.")
1248 (license license:asl2.0)))
1250 (define-public r-maps
1257 (uri (cran-uri "maps" version))
1260 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
1261 (build-system r-build-system)
1262 (home-page "https://cran.r-project.org/web/packages/maps")
1263 (synopsis "Draw geographical maps")
1264 (description "This package provides an R module for display of maps.
1265 Projection code and larger maps are in separate packages (@code{mapproj} and
1267 (license license:gpl2)))
1269 (define-public r-mapproj
1276 (uri (cran-uri "mapproj" version))
1279 "1rggww8cbwv0vzlj5afzhbsbngg4bzj5znbkz7wmxsbshfbsm9b2"))))
1280 (build-system r-build-system)
1281 (propagated-inputs `(("r-maps" ,r-maps)))
1282 (home-page "https://cran.r-project.org/web/packages/mapproj")
1283 (synopsis "Map projection in R")
1284 (description "This package converts latitude/longitude into projected
1286 (license (list license:gpl2 ; The R interface
1287 (license:non-copyleft ; The C code
1288 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
1289 "Lucent Public License Version 1.02")))))
1291 (define-public r-rgooglemaps
1293 (name "r-rgooglemaps")
1298 (uri (cran-uri "RgoogleMaps" version))
1301 "0sbklacc4jl5524ixhc11mh6smrzdz4l9pji6cn402i6zdn9z05x"))))
1302 (properties `((upstream-name . "RgoogleMaps")))
1303 (build-system r-build-system)
1304 (propagated-inputs `(("r-png" ,r-png)))
1305 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
1306 (synopsis "Use Google Maps in R")
1307 (description "This package serves two purposes:
1309 @item Provide a comfortable R interface to query the Google server for static
1311 @item Use the map as a background image to overlay plots within R. This
1312 requires proper coordinate scaling.
1314 (license license:gpl2+)))
1316 (define-public r-geosphere
1318 (name "r-geosphere")
1323 (uri (cran-uri "geosphere" version))
1326 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
1327 (build-system r-build-system)
1328 (propagated-inputs `(("r-sp" ,r-sp)))
1329 (home-page "https://cran.r-project.org/web/packages/geosphere")
1330 (synopsis "Spherical trigonometry")
1331 (description "This package computes spherical trigonometry for geographic
1332 applications. That is, compute distances and related measures for angular
1333 (longitude/latitude) locations.")
1334 (license license:gpl3+)))
1336 (define-public r-jpeg
1343 (uri (cran-uri "jpeg" version))
1346 "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
1347 (build-system r-build-system)
1348 (inputs `(("libjpeg" ,libjpeg)))
1349 (home-page "http://www.rforge.net/jpeg/")
1350 (synopsis "Read and write JPEG images with R")
1351 (description "This package provides a way to read, write and display
1352 bitmap images stored in the JPEG format with R. It can read and write both
1353 files and in-memory raw vectors.")
1354 (license license:gpl2+)))
1356 (define-public r-ggmap
1363 (uri (cran-uri "ggmap" version))
1366 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
1367 (build-system r-build-system)
1369 `(("r-bitops" ,r-bitops)
1370 ("r-digest" ,r-digest)
1371 ("r-dplyr" ,r-dplyr)
1372 ("r-ggplot2" ,r-ggplot2)
1376 ("r-magrittr" ,r-magrittr)
1379 ("r-purrr" ,r-purrr)
1380 ("r-rgooglemaps" ,r-rgooglemaps)
1381 ("r-rjson" ,r-rjson)
1382 ("r-scales" ,r-scales)
1383 ("r-stringr" ,r-stringr)
1384 ("r-tibble" ,r-tibble)
1385 ("r-tidyr" ,r-tidyr)))
1386 (home-page "https://github.com/dkahle/ggmap")
1387 (synopsis "Spatial visualization with ggplot2")
1388 (description "This package provides a collection of functions to visualize
1389 spatial data and models on top of static maps from various online sources (e.g
1390 Google Maps and Stamen Maps). It includes tools common to those tasks,
1391 including functions for geolocation and routing.")
1392 (license license:gpl2)))
1394 (define-public r-haven
1401 (uri (cran-uri "haven" version))
1404 "0g9d6mxqmrw2zdms78jpx2sx73pczlyy771v1h5hmxqz9sqyk7hr"))))
1405 (build-system r-build-system)
1409 `(("r-forcats" ,r-forcats)
1412 ("r-rlang" ,r-rlang)
1413 ("r-readr" ,r-readr)
1414 ("r-tibble" ,r-tibble)
1415 ("r-tidyselect" ,r-tidyselect)))
1416 (home-page "https://haven.tidyverse.org")
1417 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
1419 "This package lets you mport foreign statistical formats into R via the
1420 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
1421 (license license:expat)))
1423 (define-public r-amap
1429 (uri (cran-uri "amap" version))
1432 "1il94bkhl8192vawq4gr2gwyhqhid27jr2312rhvr72ssg8p713b"))))
1433 (build-system r-build-system)
1435 `(("gfortran" ,gfortran)))
1436 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
1437 (synopsis "Another multidimensional analysis package")
1438 (description "This package provides tools for clustering and principal
1439 component analysis (with robust methods, and parallelized functions).")
1440 (license license:gpl2+)))
1442 (define-public r-ape
1449 (uri (cran-uri "ape" version))
1452 "08wbk1kxhs32bmmvqlqanbdg1w235amd35k8m00fngsj9h9xzc08"))))
1453 (build-system r-build-system)
1455 `(("r-lattice" ,r-lattice)
1457 ("r-rcpp" ,r-rcpp)))
1458 (home-page "http://ape-package.ird.fr/")
1459 (synopsis "Analyses of phylogenetics and evolution")
1461 "This package provides functions for reading, writing, plotting, and
1462 manipulating phylogenetic trees, analyses of comparative data in a
1463 phylogenetic framework, ancestral character analyses, analyses of
1464 diversification and macroevolution, computing distances from DNA sequences,
1465 and several other tools.")
1466 (license license:gpl2+)))
1468 (define-public r-abbyyr
1475 (uri (cran-uri "abbyyR" version))
1478 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
1479 (properties `((upstream-name . "abbyyR")))
1480 (build-system r-build-system)
1482 `(("r-curl" ,r-curl)
1485 ("r-progress" ,r-progress)
1486 ("r-readr" ,r-readr)
1488 (home-page "https://github.com/soodoku/abbyyR")
1489 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
1491 "This package provides tools to get text from images of text using Abbyy
1492 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
1493 OCR images, barcodes, forms, documents with machine readable zones, e.g.
1494 passports and get the results in a variety of formats including plain text and
1495 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
1496 (license license:expat)))
1498 (define-public r-colorspace
1500 (name "r-colorspace")
1505 (uri (cran-uri "colorspace" version))
1507 (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9"))))
1508 (build-system r-build-system)
1509 (home-page "https://cran.r-project.org/web/packages/colorspace")
1510 (synopsis "Color space manipulation")
1512 "This package carries out a mapping between assorted color spaces
1513 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
1514 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
1515 colors are provided.")
1516 (license license:bsd-3)))
1518 (define-public r-glue
1525 (uri (cran-uri "glue" version))
1528 "1a1ycg9r3gd91visp49q49rsrdgyf8kr9dxdy3hk99kikn4z5hag"))))
1529 (build-system r-build-system)
1530 (home-page "https://github.com/tidyverse/glue")
1531 (synopsis "Interpreted string literals")
1533 "This package provides an implementation of interpreted string literals,
1534 inspired by Python's Literal String Interpolation (PEP-0498) and
1535 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
1536 (license license:expat)))
1538 (define-public r-pastecs
1544 (uri (cran-uri "pastecs" version))
1547 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
1548 (build-system r-build-system)
1550 `(("r-boot" ,r-boot)))
1551 (home-page "http://www.sciviews.org/pastecs")
1552 (synopsis "Analysis of space-time ecological series")
1554 "This package provides functions for regulation, decomposition and analysis
1555 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
1556 initiative to bring PASSTEC 2000 functionalities to R.")
1557 (license license:gpl2+)))
1559 (define-public r-plogr
1566 (uri (cran-uri "plogr" version))
1569 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
1570 (build-system r-build-system)
1571 (home-page "https://github.com/krlmlr/plogr")
1572 (synopsis "R bindings for the plog C++ logging library")
1574 "This package provides the header files for a stripped-down version of
1575 the plog header-only C++ logging library, and a method to log to R's standard
1577 (license license:expat)))
1579 (define-public r-pls
1586 (uri (cran-uri "pls" version))
1588 (base32 "121byimd6bg7jbrq5wz5fpi0vxq0vh8g724vkhnjzszbvcv1xsb7"))))
1589 (build-system r-build-system)
1590 (home-page "http://mevik.net/work/software/pls.html")
1591 (synopsis "Partial Least Squares and Principal Component Regression")
1593 "The pls package implements multivariate regression methods: Partial Least
1594 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
1595 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
1598 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
1599 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
1600 @item multi-response models (or @dfn{PLS2})
1601 @item flexible cross-validation
1602 @item Jackknife variance estimates of regression coefficients
1603 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
1604 (R)MSEP, R², and correlation loadings
1605 @item formula interface, modelled after @code{lm()}, with methods for predict,
1606 print, summary, plot, update, etc.
1607 @item extraction functions for coefficients, scores, and loadings
1608 @item MSEP, RMSEP, and R² estimates
1609 @item multiplicative scatter correction (@dfn{MSC})
1611 (license license:gpl2)))
1620 (uri (cran-uri "ps" version))
1622 (base32 "1lcq7r0q4jb8x6k023zr2ydj2dg925bqqbkhx1phpnyjrk897498"))))
1623 (build-system r-build-system)
1624 (home-page "http://ps.r-lib.org")
1625 (synopsis "List, query, and manipulate system processes")
1627 "The ps package implements an API to list, query, and manipulate system
1628 processes. Most of its code is based on the @code{psutil} Python package.")
1629 (license license:bsd-3)))
1631 (define-public r-pkgbuild
1638 (uri (cran-uri "pkgbuild" version))
1640 (base32 "0xnlz6ivhkbmncg9hfw5p69lm4rjy3wn5lyxmygxyf4rrfnnqwxx"))))
1641 (build-system r-build-system)
1643 `(("r-callr" ,r-callr)
1645 ("r-crayon" ,r-crayon)
1647 ("r-prettyunits" ,r-prettyunits)
1649 ("r-rprojroot" ,r-rprojroot)
1650 ("r-withr" ,r-withr)))
1651 (home-page "https://github.com/r-pkgs/pkgbuild")
1652 (synopsis "Find tools needed to build R packages")
1654 "This package provides functions used to build R packages. It locates
1655 compilers needed to build R packages on various platforms and ensures the PATH
1656 is configured appropriately so R can use them.")
1657 (license license:gpl3)))
1659 (define-public r-pkgload
1666 (uri (cran-uri "pkgload" version))
1669 "0z7jvharafahi2gv5547mk1n499isjzw06kfwymmxc0gd575d1ii"))))
1670 (build-system r-build-system)
1672 `(("r-desc" ,r-desc)
1673 ("r-pkgbuild" ,r-pkgbuild)
1674 ("r-rlang" ,r-rlang)
1675 ("r-rprojroot" ,r-rprojroot)
1676 ("r-rstudioapi" ,r-rstudioapi)
1677 ("r-withr" ,r-withr)))
1678 (home-page "https://github.com/r-lib/pkgload")
1679 (synopsis "Simulate package installation and attach")
1681 "This package simulates the process of installing a package and then
1682 attaching it. This is a key part of the @code{devtools} package as it allows
1683 you to rapidly iterate while developing a package.")
1684 (license license:gpl3)))
1686 (define-public r-rcpp
1693 (uri (cran-uri "Rcpp" version))
1695 (base32 "03h3zyjq948y0hrrs95lfk4zgx6wfrg64hjlrfrzf5na7bfh0d9b"))))
1696 (build-system r-build-system)
1698 `(("r-knitr" ,r-knitr))) ; for vignettes
1699 (home-page "http://www.rcpp.org")
1700 (synopsis "Seamless R and C++ integration")
1702 "The Rcpp package provides R functions as well as C++ classes which offer
1703 a seamless integration of R and C++. Many R data types and objects can be
1704 mapped back and forth to C++ equivalents which facilitates both writing of new
1705 code as well as easier integration of third-party libraries. Documentation
1706 about Rcpp is provided by several vignettes included in this package, via the
1707 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
1708 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
1709 @code{citation(\"Rcpp\")} for details on these last two.")
1710 (license license:gpl2+)))
1712 (define-public r-bindr
1719 (uri (cran-uri "bindr" version))
1722 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
1723 (build-system r-build-system)
1724 (home-page "https://github.com/krlmlr/bindr")
1725 (synopsis "Parametrized active bindings")
1727 "This package provides a simple interface for creating active bindings
1728 where the bound function accepts additional arguments.")
1729 (license license:expat)))
1731 (define-public r-bindrcpp
1738 (uri (cran-uri "bindrcpp" version))
1741 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
1742 (build-system r-build-system)
1744 `(("r-bindr" ,r-bindr)
1745 ("r-plogr" ,r-plogr)
1746 ("r-rcpp" ,r-rcpp)))
1747 (home-page "https://github.com/krlmlr/bindrcpp")
1748 (synopsis "Rcpp interface to active bindings")
1750 "This package provides an easy way to fill an environment with active
1751 bindings that call a C++ function.")
1752 (license license:expat)))
1754 (define-public r-auc
1761 (uri (cran-uri "AUC" version))
1764 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
1765 (properties `((upstream-name . "AUC")))
1766 (build-system r-build-system)
1767 (home-page "https://cran.r-project.org/web/packages/AUC")
1768 (synopsis "Compute the area under the curve of selected measures")
1770 "This package includes functions to compute the area under the curve of
1771 selected measures: the area under the sensitivity curve (AUSEC), the area
1772 under the specificity curve (AUSPC), the area under the accuracy
1773 curve (AUACC), and the area under the receiver operating characteristic
1774 curve (AUROC). The curves can also be visualized. Support for partial areas
1776 (license license:gpl2+)))
1778 (define-public r-calibrate
1780 (name "r-calibrate")
1785 (uri (cran-uri "calibrate" version))
1787 (base32 "1s423nr176l2sc66wp7hzgqkv7c2bq8d2bjrrvrrm5qa9y3zdx1k"))))
1788 (build-system r-build-system)
1790 `(("r-mass" ,r-mass)))
1791 (home-page "https://cran.r-project.org/web/packages/calibrate")
1792 (synopsis "Calibration of scatterplot and biplot axes")
1794 "This is a package for drawing calibrated scales with tick marks
1795 on (non-orthogonal) variable vectors in scatterplots and biplots.")
1796 (license license:gpl2)))
1798 (define-public r-shape
1805 (uri (cran-uri "shape" version))
1808 "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
1809 (build-system r-build-system)
1810 (home-page "https://cran.r-project.org/web/packages/shape")
1811 (synopsis "Functions for plotting graphical shapes")
1813 "This package provides functions for plotting graphical shapes such as
1814 ellipses, circles, cylinders, arrows, ...")
1815 (license license:gpl3+)))
1817 (define-public r-globaloptions
1819 (name "r-globaloptions")
1824 (uri (cran-uri "GlobalOptions" version))
1826 (base32 "0x89hfz80avq4zcskxl71i4zi0mgniqqxfrvz050aa2189wfyja2"))))
1827 (properties `((upstream-name . "GlobalOptions")))
1828 (build-system r-build-system)
1829 (home-page "https://github.com/jokergoo/GlobalOptions")
1830 (synopsis "Generate functions to get or set global options")
1832 "This package provides more controls on the option values such as
1833 validation and filtering on the values, making options invisible or private.")
1834 (license license:gpl2+)))
1836 (define-public r-circlize
1843 (uri (cran-uri "circlize" version))
1846 "0jvr9hmxyhg0zx101iiqkrg8wfaj86kp62xpv42n2j9fkn5r1mi2"))))
1847 (build-system r-build-system)
1849 `(("r-colorspace" ,r-colorspace)
1850 ("r-globaloptions" ,r-globaloptions)
1851 ("r-shape" ,r-shape)))
1852 (home-page "https://github.com/jokergoo/circlize")
1853 (synopsis "Circular visualization")
1855 "Circular layout is an efficient way to visualise huge amounts of
1856 information. This package provides an implementation of circular layout
1857 generation in R as well as an enhancement of available software. Its
1858 flexibility is based on the usage of low-level graphics functions such that
1859 self-defined high-level graphics can be easily implemented by users for
1860 specific purposes. Together with the seamless connection between the powerful
1861 computational and visual environment in R, it gives users more convenience and
1862 freedom to design figures for better understanding complex patterns behind
1863 multi-dimensional data.")
1864 (license license:gpl2+)))
1866 (define-public r-powerlaw
1873 (uri (cran-uri "poweRlaw" version))
1876 "1asr6ikr7hmj78jyg8r1gwvcjg14addkxdiz92nh06lv71a183r4"))))
1877 (properties `((upstream-name . "poweRlaw")))
1878 (build-system r-build-system)
1880 `(("r-vgam" ,r-vgam)))
1881 (home-page "https://github.com/csgillespie/poweRlaw")
1882 (synopsis "Tools for the analysis of heavy tailed distributions")
1884 "This package provides an implementation of maximum likelihood estimators
1885 for a variety of heavy tailed distributions, including both the discrete and
1886 continuous power law distributions. Additionally, a goodness-of-fit based
1887 approach is used to estimate the lower cut-off for the scaling region.")
1888 ;; Any of these GPL versions.
1889 (license (list license:gpl2 license:gpl3))))
1891 (define-public r-compare
1898 (uri (cran-uri "compare" version))
1901 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
1902 (build-system r-build-system)
1903 (home-page "https://cran.r-project.org/web/packages/compare")
1904 (synopsis "Comparing objects for differences")
1906 "This package provides functions to compare a model object to a
1907 comparison object. If the objects are not identical, the functions can be
1908 instructed to explore various modifications of the objects (e.g., sorting
1909 rows, dropping names) to see if the modified versions are identical.")
1910 (license license:gpl2+)))
1912 (define-public r-dendextend
1914 (name "r-dendextend")
1919 (uri (cran-uri "dendextend" version))
1922 "1iclvd9cyckd4djpa87ynm05fk6zl4b4m735za1w4irimc130m3r"))))
1923 (build-system r-build-system)
1925 `(("r-ggplot2" ,r-ggplot2)
1926 ("r-magrittr" ,r-magrittr)
1927 ("r-viridis" ,r-viridis)))
1928 (home-page "https://cran.r-project.org/web/packages/dendextend")
1929 (synopsis "Extending 'dendrogram' functionality in R")
1931 "This package offers a set of functions for extending @code{dendrogram}
1932 objects in R, letting you visualize and compare trees of hierarchical
1933 clusterings. You can adjust a tree's graphical parameters (the color, size,
1934 type, etc of its branches, nodes and labels) and visually and statistically
1935 compare different dendrograms to one another.")
1936 ;; Any of these versions
1937 (license (list license:gpl2 license:gpl3))))
1939 (define-public r-getoptlong
1941 (name "r-getoptlong")
1946 (uri (cran-uri "GetoptLong" version))
1949 "1fl3w2n602ldybc5qj7qw4xmzzb804bsjkqwf6dswzj0vf0qiadr"))))
1950 (properties `((upstream-name . "GetoptLong")))
1951 (build-system r-build-system)
1955 `(("r-globaloptions" ,r-globaloptions)
1956 ("r-rjson" ,r-rjson)))
1957 (home-page "https://github.com/jokergoo/GetoptLong")
1958 (synopsis "Parsing command-line arguments and variable interpolation")
1960 "This is yet another command-line argument parser which wraps the
1961 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
1962 use in R. It also provides a simple way for variable interpolation in R.")
1963 (license license:gpl2+)))
1965 (define-public r-fastmatch
1967 (name "r-fastmatch")
1972 (uri (cran-uri "fastmatch" version))
1975 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
1976 (build-system r-build-system)
1977 (home-page "http://www.rforge.net/fastmatch")
1978 (synopsis "Fast match function")
1980 "This package provides a fast @code{match} replacement for cases that
1981 require repeated look-ups. It is slightly faster that R's built-in
1982 @code{match} function on first match against a table, but extremely fast on
1983 any subsequent lookup as it keeps the hash table in memory.")
1984 (license license:gpl2)))
1993 (uri (cran-uri "ff" version))
1996 "1w724q4jpzbvzpilb2ifviaxkjgk9lzwxz9gksnvicbmfa20fqqw"))))
1997 (build-system r-build-system)
1998 (propagated-inputs `(("r-bit" ,r-bit)))
1999 (home-page "http://ff.r-forge.r-project.org/")
2000 (synopsis "Memory-efficient storage of large data on disk and access functions")
2002 "This package provides data structures that are stored on disk but
2003 behave (almost) as if they were in RAM by transparently mapping only a section
2005 ;; error Architecture not supported.
2006 (supported-systems (delete "aarch64-linux" %supported-systems))
2007 (license license:gpl2)))
2009 (define-public r-ffbase
2016 (uri (cran-uri "ffbase" version))
2019 "04kxx2f3f0743c5nvpb7x1x0pcd220dazpd5ag1pidxbz3xa85nw"))))
2020 (build-system r-build-system)
2023 ("r-fastmatch" ,r-fastmatch)
2025 (home-page "http://github.com/edwindj/ffbase")
2026 (synopsis "Basic statistical functions for package 'ff'")
2028 "This package extends the out of memory vectors of @code{ff} with
2029 statistical functions and other utilities to ease their usage.")
2030 (license license:gpl3)))
2032 (define-public r-prettyunits
2034 (name "r-prettyunits")
2039 (uri (cran-uri "prettyunits" version))
2042 "0p3z42hnk53x7ky4d1dr2brf7p8gv3agxr71i99m01n2hq2ri91m"))))
2043 (build-system r-build-system)
2045 `(("r-assertthat" ,r-assertthat)
2046 ("r-magrittr" ,r-magrittr)))
2047 (home-page "https://github.com/gaborcsardi/prettyunits")
2048 (synopsis "Pretty, human readable formatting of quantities")
2050 "This package provides tools for pretty, human readable formatting of
2052 (license license:expat)))
2054 (define-public r-reshape
2061 (uri (cran-uri "reshape" version))
2064 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
2065 (build-system r-build-system)
2067 `(("r-plyr" ,r-plyr)
2068 ("r-rcpp" ,r-rcpp)))
2069 (home-page "http://had.co.nz/reshape")
2070 (synopsis "Flexibly reshape data")
2072 "Flexibly restructure and aggregate data using just two functions:
2073 @code{melt} and @code{cast}. This package provides them.")
2074 (license license:expat)))
2076 (define-public r-progress
2083 (uri (cran-uri "progress" version))
2086 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
2087 (build-system r-build-system)
2089 `(("r-crayon" ,r-crayon)
2091 ("r-prettyunits" ,r-prettyunits)
2093 (home-page "https://github.com/gaborcsardi/progress")
2094 (synopsis "Terminal progress bars")
2096 "This package provides configurable progress bars. They may include
2097 percentage, elapsed time, and/or the estimated completion time. They work in
2098 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
2099 package also provides a C++ API, that works with or without Rcpp.")
2100 (license license:expat)))
2102 (define-public r-ggally
2109 (uri (cran-uri "GGally" version))
2112 "1zjmcc5bzagvy7c5cmdcl39xmx07fwi98yrj4i05w7y40kqcsiws"))))
2113 (properties `((upstream-name . "GGally")))
2114 (build-system r-build-system)
2116 `(("libressl" ,libressl)))
2118 `(("r-ggplot2" ,r-ggplot2)
2119 ("r-gtable" ,r-gtable)
2121 ("r-progress" ,r-progress)
2122 ("r-rcolorbrewer" ,r-rcolorbrewer)
2123 ("r-reshape" ,r-reshape)
2124 ("r-rlang" ,r-rlang)))
2125 (home-page "https://ggobi.github.io/ggally")
2126 (synopsis "Extension to ggplot2")
2128 "The R package ggplot2 is a plotting system based on the grammar of
2129 graphics. GGally extends ggplot2 by adding several functions to reduce the
2130 complexity of combining geometric objects with transformed data. Some of
2131 these functions include a pairwise plot matrix, a two group pairwise plot
2132 matrix, a parallel coordinates plot, a survival plot, and several functions to
2134 (license license:gpl2+)))
2136 (define-public r-proxy
2143 (uri (cran-uri "proxy" version))
2146 "17b6qfllqrhzrxqgx7dccffgybnkcria5a68ap5ly3plg04ypm4x"))))
2147 (build-system r-build-system)
2148 (home-page "https://cran.r-project.org/web/packages/proxy")
2149 (synopsis "Distance and similarity measures")
2151 "This package provides an extensible framework for the efficient
2152 calculation of auto- and cross-proximities, along with implementations of the
2153 most popular ones.")
2154 (license license:gpl2)))
2163 (uri (cran-uri "sp" version))
2165 (base32 "0kpjsqh3lzqp1m0avsvm54lazlgwfx3hyf0av3mvbyslsanj42ll"))))
2166 (build-system r-build-system)
2168 `(("r-lattice" ,r-lattice)))
2169 (home-page "https://cran.r-project.org/web/packages/sp")
2170 (synopsis "Classes and methods for spatial data")
2172 "This package provides classes and methods for spatial data; the classes
2173 document where the spatial location information resides, for 2D or 3D data.
2174 Utility functions are provided, e.g. for plotting data as maps, spatial
2175 selection, as well as methods for retrieving coordinates, for subsetting,
2176 print, summary, etc.")
2177 (license license:gpl2+)))
2179 (define-public r-rmtstat
2186 (uri (cran-uri "RMTstat" version))
2189 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
2190 (properties `((upstream-name . "RMTstat")))
2191 (build-system r-build-system)
2192 (home-page "https://cran.r-project.org/web/packages/RMTstat")
2193 (synopsis "Distributions, statistics and tests derived from random matrix theory")
2195 "This package provides functions for working with the Tracy-Widom laws
2196 and other distributions related to the eigenvalues of large Wishart
2198 (license license:bsd-3)))
2200 (define-public r-rmpi
2206 (uri (cran-uri "Rmpi" version))
2209 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
2210 (properties `((upstream-name . "Rmpi")))
2211 (build-system r-build-system)
2213 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
2214 #:phases (modify-phases %standard-phases
2215 (add-before 'install 'mpi-setup
2218 `(("openmpi" ,openmpi)))
2220 `(("pkg-config" ,pkg-config)))
2221 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
2222 (synopsis "R interface to message-passing interface (MPI)")
2224 "This package provides an interface (wrapper) to MPI APIs. It also
2225 provides an interactive R manager and worker environment.")
2226 (license license:gpl2+)))
2228 (define-public r-lmoments
2235 (uri (cran-uri "Lmoments" version))
2238 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
2239 (properties `((upstream-name . "Lmoments")))
2240 (build-system r-build-system)
2242 `(("r-rcpp" ,r-rcpp)
2243 ("r-rcpparmadillo" ,r-rcpparmadillo)))
2244 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
2245 (synopsis "L-moments and quantile mixtures")
2247 "This package contains functions to estimate L-moments and trimmed
2248 L-moments from the data. It also contains functions to estimate the
2249 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
2250 quantile mixture from L-moments and trimmed L-moments.")
2251 (license license:gpl2)))
2253 (define-public r-distillery
2255 (name "r-distillery")
2260 (uri (cran-uri "distillery" version))
2263 "1mi3ig9jq0kd7yrwc5m37lmrw04p1b4lirnbsxi10z3n5yay4429"))))
2264 (build-system r-build-system)
2265 (home-page "http://www.ral.ucar.edu/staff/ericg")
2266 (synopsis "Functions for confidence intervals and object information")
2268 "This package provides some very simple method functions for confidence
2269 interval calculation and to distill pertinent information from a potentially
2270 complex object; primarily used in common with the packages extRemes and
2272 (license license:gpl2+)))
2274 (define-public r-extremes
2281 (uri (cran-uri "extRemes" version))
2284 "0hmgynxhzswqnhwb2sxrkczgam8c17s3vpxqc5bcz0bwczpxxyvm"))))
2285 (properties `((upstream-name . "extRemes")))
2286 (build-system r-build-system)
2288 `(("r-distillery" ,r-distillery)
2289 ("r-lmoments" ,r-lmoments)))
2290 (home-page "http://www.assessment.ucar.edu/toolkit/")
2291 (synopsis "Extreme value analysis")
2293 "ExtRemes is a suite of functions for carrying out analyses on the
2294 extreme values of a process of interest; be they block maxima over long blocks
2295 or excesses over a high threshold.")
2296 (license license:gpl2+)))
2298 (define-public r-lmtest
2305 (uri (cran-uri "lmtest" version))
2308 "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx"))))
2309 (build-system r-build-system)
2311 `(("r-zoo" ,r-zoo)))
2313 `(("gfortran" ,gfortran)))
2314 (home-page "https://cran.r-project.org/web/packages/lmtest")
2315 (synopsis "Testing linear regression models")
2317 "This package provides a collection of tests, data sets, and examples for
2318 diagnostic checking in linear regression models. Furthermore, some generic
2319 tools for inference in parametric models are provided.")
2320 ;; Either version is okay
2321 (license (list license:gpl2 license:gpl3))))
2323 (define-public r-idr
2329 (uri (cran-uri "idr" version))
2332 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
2333 (build-system r-build-system)
2334 (home-page "https://cran.r-project.org/web/packages/idr/")
2335 (synopsis "Irreproducible discovery rate")
2337 "This is a package for estimating the copula mixture model and plotting
2338 correspondence curves in \"Measuring reproducibility of high-throughput
2339 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
2340 by Li, Brown, Huang, and Bickel")
2341 (license license:gpl2+)))
2343 (define-public r-inline
2349 (uri (cran-uri "inline" version))
2352 "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
2353 (build-system r-build-system)
2354 (home-page "https://cran.r-project.org/web/packages/inline")
2355 (synopsis "Functions to inline C, C++, Fortran function calls from R")
2357 "This package provides functionality to dynamically define R functions
2358 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
2359 @code{.Call} calling conventions.")
2360 ;; Any version of the LGPL.
2361 (license license:lgpl3+)))
2363 (define-public r-bbmle
2370 (uri (cran-uri "bbmle" version))
2373 "1xzij7swrrzl5ly8l3lw6awh486zcm00251dwqws1y23fbgyh3vc"))))
2374 (build-system r-build-system)
2376 `(("r-lattice" ,r-lattice)
2378 ("r-numderiv" ,r-numderiv)))
2379 (home-page "https://cran.r-project.org/web/packages/bbmle")
2380 (synopsis "Tools for General Maximum Likelihood Estimation")
2382 "This package provides methods and functions for fitting maximum
2383 likelihood models in R. This package modifies and extends the @code{mle}
2384 classes in the @code{stats4} package.")
2385 ;; Any version of the GPL
2386 (license license:gpl2+)))
2388 (define-public r-emdbook
2395 (uri (cran-uri "emdbook" version))
2398 "0a515jdzvg87npvrh7md7zp0v5nlz7c2jr7pba5dql6slb0d8j7q"))))
2399 (build-system r-build-system)
2401 `(("r-bbmle" ,r-bbmle)
2403 ("r-lattice" ,r-lattice)
2406 ("r-rcpp" ,r-rcpp)))
2407 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
2408 (synopsis "Support functions and data for \"Ecological Models and Data\"")
2410 "This package provides auxiliary functions and data sets for \"Ecological
2411 Models and Data\", a book presenting maximum likelihood estimation and related
2412 topics for ecologists (ISBN 978-0-691-12522-0).")
2414 (license (list license:gpl2 license:gpl3))))
2416 (define-public r-lpsolve
2419 (version "5.6.13.3")
2423 (uri (cran-uri "lpSolve" version))
2426 "1xazby8amb47vw5n12k13awv7x3bjci3q8vdd3vk1ms0ii16ahg6"))))
2427 (properties `((upstream-name . "lpSolve")))
2428 (build-system r-build-system)
2429 (home-page "https://cran.r-project.org/web/packages/lpSolve")
2430 (synopsis "R interface to Lp_solve to solve linear/integer programs")
2432 "Lp_solve is software for solving linear, integer and mixed integer
2433 programs. This implementation supplies a \"wrapper\" function in C and some R
2434 functions that solve general linear/integer problems, assignment problems, and
2435 transportation problems.")
2436 (license license:lgpl2.0)))
2438 (define-public r-limsolve
2445 (uri (cran-uri "limSolve" version))
2448 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
2449 (properties `((upstream-name . "limSolve")))
2450 (build-system r-build-system)
2452 `(("r-lpsolve" ,r-lpsolve)
2454 ("r-quadprog" ,r-quadprog)))
2455 (native-inputs `(("gfortran" ,gfortran)))
2456 (home-page "https://cran.r-project.org/web/packages/limSolve")
2457 (synopsis "Solving linear inverse models")
2459 "This package provides functions that:
2462 @item find the minimum/maximum of a linear or quadratic function,
2463 @item sample an underdetermined or overdetermined system,
2464 @item solve a linear system Ax=B for the unknown x.
2467 It includes banded and tridiagonal linear systems. The package calls Fortran
2468 functions from LINPACK.")
2470 (license (list license:gpl2+ license:gpl3+))))
2472 (define-public r-fitdistrplus
2474 (name "r-fitdistrplus")
2479 (uri (cran-uri "fitdistrplus" version))
2482 "10q08wsv8v3w7797jdvvv60bgrf1bi6438wf0jcqv81ays82a245"))))
2483 (build-system r-build-system)
2485 `(("r-mass" ,r-mass)
2486 ("r-npsurv" ,r-npsurv)
2487 ("r-survival" ,r-survival)))
2488 (home-page "http://riskassessment.r-forge.r-project.org")
2489 (synopsis "Fitting a parametric distribution from data")
2491 "This package extends the @code{fitdistr} function of the MASS package
2492 with several functions to help the fit of a parametric distribution to
2493 non-censored or censored data. Censored data may contain left-censored,
2494 right-censored and interval-censored values, with several lower and upper
2495 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
2496 provides moment matching (MME), quantile matching (QME) and maximum
2497 goodness-of-fit estimation (MGE) methods (available only for non-censored
2498 data). Weighted versions of MLE, MME and QME are available.")
2499 (license license:gpl2+)))
2501 (define-public r-energy
2508 (uri (cran-uri "energy" version))
2511 "13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37"))))
2512 (build-system r-build-system)
2514 `(("r-boot" ,r-boot)
2515 ("r-rcpp" ,r-rcpp)))
2516 (home-page "https://cran.r-project.org/web/packages/energy")
2517 (synopsis "Multivariate inference via the energy of data")
2519 "This package provides e-statistics (energy) tests and statistics for
2520 multivariate and univariate inference, including distance correlation,
2521 one-sample, two-sample, and multi-sample tests for comparing multivariate
2522 distributions, are implemented. Measuring and testing multivariate
2523 independence based on distance correlation, partial distance correlation,
2524 multivariate goodness-of-fit tests, clustering based on energy distance,
2525 testing for multivariate normality, distance components (disco) for
2526 non-parametric analysis of structured data, and other energy
2527 statistics/methods are implemented.")
2528 (license license:gpl2+)))
2530 (define-public r-suppdists
2532 (name "r-suppdists")
2537 (uri (cran-uri "SuppDists" version))
2540 "1ffx8wigqqvz2pnh06jjc0fnf4vq9z2rhwk2y3f9aszn18ap3dgw"))))
2541 (properties `((upstream-name . "SuppDists")))
2542 (build-system r-build-system)
2543 (home-page "https://cran.r-project.org/web/packages/SuppDists")
2544 (synopsis "Supplementary distributions")
2546 "This package provides ten distributions supplementing those built into
2547 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
2548 Spearman's rho, maximum F ratio, the Pearson product moment correlation
2549 coefficient, Johnson distributions, normal scores and generalized
2550 hypergeometric distributions. In addition two random number generators of
2551 George Marsaglia are included.")
2552 (license license:gpl2+)))
2554 (define-public r-ksamples
2561 (uri (cran-uri "kSamples" version))
2564 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
2565 (properties `((upstream-name . "kSamples")))
2566 (build-system r-build-system)
2568 `(("r-suppdists" ,r-suppdists)))
2569 (home-page "https://cran.r-project.org/web/packages/kSamples")
2570 (synopsis "K-Sample rank tests and their combinations")
2572 "This package provides tools to compares k samples using the
2573 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
2574 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
2575 test. It computes asymptotic, simulated or (limited) exact P-values, all
2576 valid under randomization, with or without ties, or conditionally under random
2577 sampling from populations, given the observed tie pattern. Except for Steel's
2578 test and the JT test it also combines these tests across several blocks of
2580 (license license:gpl2+)))
2582 (define-public r-cvst
2589 (uri (cran-uri "CVST" version))
2592 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
2593 (properties `((upstream-name . "CVST")))
2594 (build-system r-build-system)
2596 `(("r-kernlab" ,r-kernlab)
2597 ("r-matrix" ,r-matrix)))
2598 (home-page "https://cran.r-project.org/web/packages/CVST")
2599 (synopsis "Fast cross-validation via sequential testing")
2601 "This package implements the fast cross-validation via sequential
2602 testing (CVST) procedure. CVST is an improved cross-validation procedure
2603 which uses non-parametric testing coupled with sequential analysis to
2604 determine the best parameter set on linearly increasing subsets of the data.
2605 Additionally to the CVST the package contains an implementation of the
2606 ordinary k-fold cross-validation with a flexible and powerful set of helper
2607 objects and methods to handle the overall model selection process. The
2608 implementations of the Cochran's Q test with permutations and the sequential
2609 testing framework of Wald are generic and can therefore also be used in other
2611 (license license:gpl2+)))
2613 (define-public r-squarem
2616 (version "2017.10-1")
2620 (uri (cran-uri "SQUAREM" version))
2623 "10xj26x7qjyvzndnbjl5krr9wabnb9cbrnp3m7xg673g8ddr12cv"))))
2624 (properties `((upstream-name . "SQUAREM")))
2625 (build-system r-build-system)
2626 (home-page "http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.html")
2627 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
2629 "This package provides algorithms for accelerating the convergence of
2630 slow, monotone sequences from smooth, contraction mapping such as the EM
2631 algorithm. It can be used to accelerate any smooth, linearly convergent
2632 acceleration scheme. A tutorial style introduction to this package is
2633 available in a vignette.")
2634 (license license:gpl2+)))
2636 (define-public r-lava
2643 (uri (cran-uri "lava" version))
2646 "0nfab5fgnmxh8cplg8rd8cp34fny5j0k5wn4baj51r6ck7fq9g3s"))))
2647 (build-system r-build-system)
2649 `(("r-numderiv" ,r-numderiv)
2650 ("r-squarem" ,r-squarem)
2651 ("r-survival" ,r-survival)))
2652 (home-page "https://github.com/kkholst/lava")
2653 (synopsis "Latent variable models")
2655 "This package provides tools for the estimation and simulation of latent
2657 (license license:gpl3)))
2659 (define-public r-drr
2666 (uri (cran-uri "DRR" version))
2669 "1yd1fvllfkcrwg9v322n4wkk4q4q84nvy58y4vac9pdr3yf3i4vl"))))
2670 (properties `((upstream-name . "DRR")))
2671 (build-system r-build-system)
2673 `(("r-cvst" ,r-cvst)
2674 ("r-kernlab" ,r-kernlab)
2675 ("r-matrix" ,r-matrix)))
2676 (home-page "https://cran.r-project.org/web/packages/DRR")
2677 (synopsis "Dimensionality reduction via regression")
2679 "This package provides an implementation of dimensionality reduction via
2680 regression using Kernel Ridge Regression.")
2681 (license license:gpl3)))
2683 (define-public r-prodlim
2686 (version "2019.11.13")
2690 (uri (cran-uri "prodlim" version))
2693 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
2694 (build-system r-build-system)
2696 `(("r-kernsmooth" ,r-kernsmooth)
2699 ("r-survival" ,r-survival)))
2700 (home-page "https://cran.r-project.org/web/packages/prodlim")
2701 (synopsis "Product-limit estimation for censored event history analysis")
2703 "This package provides a fast and user-friendly implementation of
2704 nonparametric estimators for censored event history (survival) analysis with
2705 the Kaplan-Meier and Aalen-Johansen methods.")
2706 (license license:gpl2+)))
2708 (define-public r-dimred
2715 (uri (cran-uri "dimRed" version))
2718 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
2719 (properties `((upstream-name . "dimRed")))
2720 (build-system r-build-system)
2723 ("r-magrittr" ,r-magrittr)))
2724 (home-page "https://github.com/gdkrmr/dimRed")
2725 (synopsis "Framework for dimensionality reduction")
2727 "This package provides a collection of dimensionality reduction
2728 techniques from R packages and provides a common interface for calling the
2730 (license license:gpl3)))
2732 (define-public r-timedate
2735 (version "3043.102")
2739 (uri (cran-uri "timeDate" version))
2742 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
2743 (properties `((upstream-name . "timeDate")))
2744 (build-system r-build-system)
2745 (home-page "https://www.rmetrics.org")
2746 (synopsis "Chronological and calendar objects")
2748 "This package provides an environment for teaching \"Financial
2749 Engineering and Computational Finance\" and for managing chronological and
2751 (license license:gpl2+)))
2753 (define-public r-magic
2760 (uri (cran-uri "magic" version))
2763 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
2764 (build-system r-build-system)
2766 `(("r-abind" ,r-abind)))
2767 (home-page "https://github.com/RobinHankin/magic.git")
2768 (synopsis "Create and investigate magic squares")
2770 "This package provides a collection of efficient, vectorized algorithms
2771 for the creation and investigation of magic squares and hypercubes, including
2772 a variety of functions for the manipulation and analysis of arbitrarily
2773 dimensioned arrays.")
2774 (license license:gpl2)))
2776 (define-public r-rmysql
2783 (uri (cran-uri "RMySQL" version))
2786 "1xamf99ih44dvaxg5x4ivj0hkqssmabgqd7gh8b8q1srw7yg8kbm"))))
2787 (properties `((upstream-name . "RMySQL")))
2788 (build-system r-build-system)
2790 `(("mariadb" ,mariadb "lib")
2791 ("mariadb-dev" ,mariadb "dev")
2794 `(("r-dbi" ,r-dbi)))
2795 (home-page "https://github.com/r-dbi/RMySQL")
2796 (synopsis "Database interface and MySQL driver for R")
2798 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
2799 package contains an old implementation based on legacy code from S-PLUS which
2800 is being phased out. A modern MySQL client based on Rcpp is available from
2801 the RMariaDB package.")
2802 (license license:gpl2)))
2804 (define-public r-rpostgresql
2806 (name "r-rpostgresql")
2811 (uri (cran-uri "RPostgreSQL" version))
2814 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
2815 (properties `((upstream-name . "RPostgreSQL")))
2816 (build-system r-build-system)
2818 `(("postgresql" ,postgresql)))
2820 `(("r-dbi" ,r-dbi)))
2821 (home-page "https://github.com/tomoakin/RPostgreSQL")
2822 (synopsis "R interface to the PostgreSQL database system")
2824 "This package provides a Database Interface (DBI) compliant driver for R
2825 to access PostgreSQL database systems.")
2826 ;; The whole package is released under GPL version 2. It includes code
2827 ;; under the PostgreSQL license.
2828 (license license:gpl2)))
2830 (define-public r-linprog
2837 (uri (cran-uri "linprog" version))
2840 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
2841 (build-system r-build-system)
2842 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
2843 (home-page "http://linprog.r-forge.r-project.org/")
2844 (synopsis "Linear programming and optimization")
2846 "This package can be used to solve Linear Programming / Linear
2847 Optimization problems by using the simplex algorithm.")
2848 (license license:gpl2+)))
2850 (define-public r-geometry
2857 (uri (cran-uri "geometry" version))
2860 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
2861 (build-system r-build-system)
2863 `(("r-magic" ,r-magic)
2864 ("r-linprog" ,r-linprog)
2865 ("r-lpsolve" ,r-lpsolve)
2867 ("r-rcppprogress" ,r-rcppprogress)))
2868 (home-page "http://geometry.r-forge.r-project.org/")
2869 (synopsis "Mesh generation and surface tesselation")
2871 "This package makes the qhull library available in R, in a similar manner
2872 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
2873 intersections about a point, Voronoi diagrams, furthest-site Delaunay
2874 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
2875 and higher dimensions. It implements the Quickhull algorithm for computing
2876 the convex hull. Qhull does not support constrained Delaunay triangulations,
2877 or mesh generation of non-convex objects, but the package does include some R
2878 functions that allow for this. Currently the package only gives access to
2879 Delaunay triangulation and convex hull computation.")
2880 ;; The Qhull sources are included and are distributed under a custom
2881 ;; non-copyleft license. The R sources are released under GPL version 2.
2882 (license (list license:gpl2
2883 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
2885 (define-public r-ddalpha
2892 (uri (cran-uri "ddalpha" version))
2895 "1064g7y8d7kmvd5kjc2m48yvidmh2ci1y0xgil3pcx4ix6mf0ljz"))))
2896 (build-system r-build-system)
2899 ("r-class" ,r-class)
2900 ("r-geometry" ,r-geometry)
2903 ("r-robustbase" ,r-robustbase)
2904 ("r-sfsmisc" ,r-sfsmisc)))
2906 `(("gfortran" ,gfortran)))
2907 (home-page "https://cran.r-project.org/web/packages/ddalpha")
2908 (synopsis "Depth-Based classification and calculation of data depth")
2910 "This package contains procedures for depth-based supervised learning,
2911 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
2912 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
2913 statistical depth function to a compact low-dimensional space, where the final
2914 classification is done. It also offers an extension to functional data and
2915 routines for calculating certain notions of statistical depth functions. 50
2916 multivariate and 5 functional classification problems are included.")
2917 (license license:gpl2)))
2919 (define-public r-gower
2926 (uri (cran-uri "gower" version))
2929 "007ivwn1nagpi26qq8iih1c2l61c53glvv60n90hi341ry8vwgxg"))))
2930 (build-system r-build-system)
2931 (home-page "https://github.com/markvanderloo/gower")
2932 (synopsis "Gower's distance")
2934 "This package provides tools to compute Gower's distance (or similarity)
2935 coefficient between records, and to compute the top-n matches between records.
2936 Core algorithms are executed in parallel on systems supporting OpenMP.")
2937 (license license:gpl3)))
2939 (define-public r-rcpproll
2946 (uri (cran-uri "RcppRoll" version))
2949 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
2950 (properties `((upstream-name . "RcppRoll")))
2951 (build-system r-build-system)
2953 `(("r-rcpp" ,r-rcpp)))
2954 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
2955 (synopsis "Efficient rolling and windowed operations")
2957 "This package provides fast and efficient routines for common rolling /
2958 windowed operations. Routines for the efficient computation of windowed mean,
2959 median, sum, product, minimum, maximum, standard deviation and variance are
2961 (license license:gpl2+)))
2963 (define-public r-ipred
2970 (uri (cran-uri "ipred" version))
2973 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
2974 (build-system r-build-system)
2976 `(("r-class" ,r-class)
2979 ("r-prodlim" ,r-prodlim)
2980 ("r-rpart" ,r-rpart)
2981 ("r-survival" ,r-survival)))
2982 (home-page "https://cran.r-project.org/web/packages/ipred")
2983 (synopsis "Improved predictors")
2985 "This package provides improved predictive models by indirect
2986 classification and bagging for classification, regression and survival
2987 problems as well as resampling based estimators of prediction error.")
2988 (license license:gpl2+)))
2990 (define-public r-psych
2997 (uri (cran-uri "psych" version))
3000 "0hvp0dkkkn0szaf5rkirr3kb8qmr4bxwl775m5wmpvn1kc25w5vf"))))
3001 (build-system r-build-system)
3003 `(("r-foreign" ,r-foreign)
3004 ("r-lattice" ,r-lattice)
3005 ("r-mnormt" ,r-mnormt)
3006 ("r-nlme" ,r-nlme)))
3007 (home-page "https://cran.r-project.org/web/packages/psych/")
3008 (synopsis "Procedures for psychological, psychometric, and personality research")
3010 "This package provides a general purpose toolbox for personality,
3011 psychometric theory and experimental psychology. Functions are primarily for
3012 multivariate analysis and scale construction using factor analysis, principal
3013 component analysis, cluster analysis and reliability analysis, although others
3014 provide basic descriptive statistics. Item Response Theory is done using
3015 factor analysis of tetrachoric and polychoric correlations. Functions for
3016 analyzing data at multiple levels include within and between group statistics,
3017 including correlations and factor analysis. Functions for simulating and
3018 testing particular item and test structures are included. Several functions
3019 serve as a useful front end for structural equation modeling. Graphical
3020 displays of path diagrams, factor analysis and structural equation models are
3021 created using basic graphics.")
3022 (license license:gpl2+)))
3024 (define-public r-generics
3031 (uri (cran-uri "generics" version))
3034 "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi"))))
3035 (build-system r-build-system)
3036 (home-page "https://github.com/r-lib/generics")
3037 (synopsis "Common S3 generics not provided by base R methods")
3039 "In order to reduce potential package dependencies and conflicts,
3040 generics provides a number of commonly used S3 generics that are not provided
3041 by base R methods related to model fitting.")
3042 (license license:gpl2)))
3044 (define-public r-broom
3051 (uri (cran-uri "broom" version))
3054 "0qmclih5dm5sqzy4hplcfy677kr12pm9pnpv3r319g14dd27pbqn"))))
3055 (build-system r-build-system)
3057 `(("r-backports" ,r-backports)
3058 ("r-dplyr" ,r-dplyr)
3059 ("r-generics" ,r-generics)
3061 ("r-purrr" ,r-purrr)
3062 ("r-reshape2" ,r-reshape2)
3063 ("r-stringr" ,r-stringr)
3064 ("r-tibble" ,r-tibble)
3065 ("r-tidyr" ,r-tidyr)))
3066 (home-page "https://github.com/tidyverse/broom")
3067 (synopsis "Convert statistical analysis objects into tidy data frames")
3069 "This package provides tools to convert statistical analysis objects from
3070 R into tidy data frames, so that they can more easily be combined, reshaped
3071 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
3072 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
3073 summarizes a model's statistical findings such as coefficients of a
3074 regression; @code{augment}, which adds columns to the original data such as
3075 predictions, residuals and cluster assignments; and @code{glance}, which
3076 provides a one-row summary of model-level statistics.")
3077 (license license:expat)))
3079 (define-public r-recipes
3086 (uri (cran-uri "recipes" version))
3089 "1gw8x7vqj7k18mfpiqinyfwzv9i5r0pb51k7xcfxsjap6m9nks98"))))
3090 (build-system r-build-system)
3092 `(("r-dplyr" ,r-dplyr)
3093 ("r-generics" ,r-generics)
3095 ("r-gower" ,r-gower)
3096 ("r-ipred" ,r-ipred)
3097 ("r-lubridate" ,r-lubridate)
3098 ("r-magrittr" ,r-magrittr)
3099 ("r-matrix" ,r-matrix)
3100 ("r-purrr" ,r-purrr)
3101 ("r-rlang" ,r-rlang)
3102 ("r-tibble" ,r-tibble)
3103 ("r-tidyr" ,r-tidyr)
3104 ("r-tidyselect" ,r-tidyselect)
3105 ("r-timedate" ,r-timedate)
3106 ("r-withr" ,r-withr)))
3107 (home-page "https://github.com/topepo/recipes")
3108 (synopsis "Preprocessing tools to create design matrices")
3110 "Recipes is an extensible framework to create and preprocess design
3111 matrices. Recipes consist of one or more data manipulation and analysis
3112 \"steps\". Statistical parameters for the steps can be estimated from an
3113 initial data set and then applied to other data sets. The resulting design
3114 matrices can then be used as inputs into statistical or machine learning
3116 (license license:gpl2)))
3118 (define-public r-pdist
3125 (uri (cran-uri "pdist" version))
3128 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
3129 (build-system r-build-system)
3130 (home-page "https://github.com/jeffwong/pdist")
3131 (synopsis "Partitioned distance function")
3133 "Pdist computes the euclidean distance between rows of a matrix X and
3134 rows of another matrix Y. Previously, this could be done by binding the two
3135 matrices together and calling @code{dist}, but this creates unnecessary
3136 computation by computing the distances between a row of X and another row of
3137 X, and likewise for Y. Pdist strictly computes distances across the two
3138 matrices, not within the same matrix, making computations significantly faster
3139 for certain use cases.")
3140 (license license:gpl3+)))
3142 (define-public r-ggrepel
3149 (uri (cran-uri "ggrepel" version))
3152 "10vjrcmx8yknfbx93d9a4y3z8gafri0fhimw6hcq733dmdvkml6m"))))
3153 (build-system r-build-system)
3155 `(("r-ggplot2" ,r-ggplot2)
3157 ("r-scales" ,r-scales)))
3158 (home-page "http://github.com/slowkow/ggrepel")
3159 (synopsis "Repulsive text and label geometries for ggplot2")
3161 "This package provides text and label geometries for ggplot2 that help to
3162 avoid overlapping text labels. Labels repel away from each other and away
3163 from the data points.")
3164 (license license:gpl3)))
3166 (define-public r-corrplot
3173 (uri (cran-uri "corrplot" version))
3176 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
3177 (build-system r-build-system)
3178 (home-page "https://github.com/taiyun/corrplot")
3179 (synopsis "Visualization of a correlation matrix")
3181 "This package provides a graphical display of a correlation matrix or
3182 general matrix. It also contains some algorithms to do matrix reordering. In
3183 addition, corrplot is good at details, including choosing color, text labels,
3184 color labels, layout, etc.")
3185 ;; Any version of the GPL
3186 (license license:gpl2+)))
3188 (define-public r-stringdist
3190 (name "r-stringdist")
3195 (uri (cran-uri "stringdist" version))
3197 (base32 "1dqfakclzaf878x7mhwmqrcpcql2h9cv19fz5f3ygpajf3si5kqi"))))
3198 (build-system r-build-system)
3199 (home-page "https://github.com/markvanderloo/stringdist")
3200 (synopsis "Approximate string matching and string distance functions")
3202 "This package implements an approximate string matching version of R's
3203 native @code{match} function. It can calculate various string distances based
3204 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
3205 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
3206 Jaro-Winkler). An implementation of soundex is provided as well. Distances
3207 can be computed between character vectors while taking proper care of encoding
3208 or between integer vectors representing generic sequences.")
3209 (license license:gpl3+)))
3211 (define-public r-ucminf
3218 (uri (cran-uri "ucminf" version))
3221 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
3222 (build-system r-build-system)
3223 (native-inputs `(("gfortran" ,gfortran)))
3224 (home-page "https://cran.r-project.org/web/packages/ucminf/")
3225 (synopsis "General-purpose unconstrained non-linear optimization")
3227 "This package provides an implementation of an algorithm for
3228 general-purpose unconstrained non-linear optimization. The algorithm is of
3229 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
3230 search with a trust region type monitoring of the input to the line search
3231 algorithm. The interface of @code{ucminf} is designed for easy interchange
3232 with the package @code{optim}.")
3233 (license license:gpl2+)))
3235 (define-public r-ordinal
3238 (version "2019.4-25")
3242 (uri (cran-uri "ordinal" version))
3245 "1pvrkly4x12w32n7w1qljdwzqnlkv7rfa7rx0nz5vbiw29xas4i8"))))
3246 (build-system r-build-system)
3248 `(("r-mass" ,r-mass)
3249 ("r-matrix" ,r-matrix)
3250 ("r-numderiv" ,r-numderiv)
3251 ("r-ucminf" ,r-ucminf)))
3252 (home-page "https://github.com/runehaubo/ordinal")
3253 (synopsis "Regression models for ordinal data")
3255 "This package provides an implementation of cumulative link (mixed)
3256 models also known as ordered regression models, proportional odds models,
3257 proportional hazards models for grouped survival times and ordered models.
3258 Estimation is via maximum likelihood and mixed models are fitted with the
3259 Laplace approximation and adaptive Gauss-Hermite quadrature.")
3260 (license license:gpl2+)))
3262 (define-public r-jomo
3269 (uri (cran-uri "jomo" version))
3272 "1k9l4290g350zbw1pjs871q9bxj3j2h1dilxpp06v4wy4n7d8qs0"))))
3273 (build-system r-build-system)
3275 `(("r-lme4" ,r-lme4)
3277 ("r-ordinal" ,r-ordinal)
3278 ("r-survival" ,r-survival)))
3279 (home-page "https://cran.r-project.org/web/packages/jomo/")
3280 (synopsis "Multilevel Joint Modelling Multiple Imputation")
3282 "Similarly to Schafer's package pan, jomo is a package for multilevel
3283 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
3284 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
3285 possibility of handling binary and categorical data through latent normal
3286 variables, the option to use cluster-specific covariance matrices and to
3287 impute compatibly with the substantive model.")
3288 (license license:gpl2)))
3290 (define-public r-pan
3297 (uri (cran-uri "pan" version))
3300 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
3301 (build-system r-build-system)
3302 (native-inputs `(("gfortran" ,gfortran)))
3303 (home-page "https://cran.r-project.org/web/packages/pan/")
3304 (synopsis "Multiple imputation for multivariate panel or clustered data")
3306 "This package implements multiple imputation for multivariate panel or
3308 (license license:gpl3)))
3310 (define-public r-mitml
3317 (uri (cran-uri "mitml" version))
3320 "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
3321 (build-system r-build-system)
3323 `(("r-haven" ,r-haven)
3326 (home-page "https://cran.r-project.org/web/packages/mitml/")
3327 (synopsis "Tools for multiple imputation in multilevel modeling")
3329 "This package provides tools for multiple imputation of missing data in
3330 multilevel modeling. It includes a user-friendly interface to the packages
3331 pan and jomo, and several functions for visualization, data management and the
3332 analysis of multiply imputed data sets.")
3333 (license license:gpl2+)))
3335 (define-public r-mice
3342 (uri (cran-uri "mice" version))
3345 "0pgcxdmp77604h6f4x8hhs6j4xdjgf5b9zvnixyzdj8vcgdjpivv"))))
3346 (build-system r-build-system)
3348 `(("r-broom" ,r-broom)
3349 ("r-dplyr" ,r-dplyr)
3350 ("r-lattice" ,r-lattice)
3352 ("r-mitml" ,r-mitml)
3355 ("r-rlang" ,r-rlang)
3356 ("r-rpart" ,r-rpart)
3357 ("r-survival" ,r-survival)))
3358 (home-page "https://cran.r-project.org/web/packages/mice/")
3359 (synopsis "Multivariate imputation by chained equations")
3361 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
3362 implemented by the MICE algorithm as described in @url{Van Buuren and
3363 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
3364 variable has its own imputation model. Built-in imputation models are
3365 provided for continuous data (predictive mean matching, normal), binary
3366 data (logistic regression), unordered categorical data (polytomous logistic
3367 regression) and ordered categorical data (proportional odds). MICE can also
3368 impute continuous two-level data (normal model, pan, second-level variables).
3369 Passive imputation can be used to maintain consistency between variables.
3370 Various diagnostic plots are available to inspect the quality of the
3372 ;; Any of these two versions.
3373 (license (list license:gpl2 license:gpl3))))
3375 (define-public r-truncnorm
3377 (name "r-truncnorm")
3382 (uri (cran-uri "truncnorm" version))
3385 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
3386 (build-system r-build-system)
3387 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
3388 (synopsis "Truncated normal distribution")
3389 (description "This package provides functions for the truncated normal
3390 distribution with mean equal to @code{mean} and standard deviation equal to
3391 @code{sd}. It includes density, distribution, quantile, and expected value
3392 functions, as well as a random generation function.")
3393 (license license:gpl2)))
3395 (define-public r-rsolnp
3402 (uri (cran-uri "Rsolnp" version))
3405 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
3406 (properties `((upstream-name . "Rsolnp")))
3407 (build-system r-build-system)
3409 `(("r-truncnorm" ,r-truncnorm)))
3410 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
3411 (synopsis "General non-linear optimization")
3412 (description "The Rsolnp package implements a general non-linear augmented
3413 Lagrange multiplier method solver, a @dfn{sequential quadratic
3414 programming} (SQP) based solver).")
3415 ;; Any version of the GPL.
3416 (license license:gpl2+)))
3418 (define-public r-hardyweinberg
3420 (name "r-hardyweinberg")
3425 (uri (cran-uri "HardyWeinberg" version))
3428 "1irz44q6nf95h37av868f47aakwv3jgwgw217xfsfw0afkm7s25f"))))
3429 (properties `((upstream-name . "HardyWeinberg")))
3430 (build-system r-build-system)
3432 `(("r-mice" ,r-mice)
3434 ("r-rsolnp" ,r-rsolnp)))
3435 (home-page "https://cran.r-project.org/package=HardyWeinberg")
3436 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
3438 "This package contains tools for exploring Hardy-Weinberg equilibrium for
3439 diallelic genetic marker data. All classical tests (chi-square, exact,
3440 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
3441 included in the package, as well as functions for power computation and for
3442 the simulation of marker data under equilibrium and disequilibrium. Routines
3443 for dealing with markers on the X-chromosome are included. Functions for
3444 testing equilibrium in the presence of missing data by using multiple
3445 imputation are also provided. Implements several graphics for exploring the
3446 equilibrium status of a large set of diallelic markers: ternary plots with
3447 acceptance regions, log-ratio plots and Q-Q plots.")
3448 (license license:gpl2+)))
3457 (uri (cran-uri "sm" version))
3460 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
3461 (build-system r-build-system)
3462 (native-inputs `(("gfortran" ,gfortran)))
3463 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
3464 (synopsis "Smoothing methods for nonparametric regression and density estimation")
3466 "This is software accompanying the book 'Applied Smoothing Techniques for
3467 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
3468 University Press. It provides smoothing methods for nonparametric regression
3469 and density estimation")
3470 (license license:gpl2+)))
3472 (define-public r-venndiagram
3474 (name "r-venndiagram")
3478 (uri (cran-uri "VennDiagram" version))
3481 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
3482 (properties `((upstream-name . "VennDiagram")))
3483 (build-system r-build-system)
3485 `(("r-futile-logger" ,r-futile-logger)))
3486 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
3487 (synopsis "Generate High-Resolution Venn and Euler Plots")
3489 "This package provides a set of functions to generate high-resolution
3490 Venn and Euler plots. It includes handling for several special cases,
3491 including two-case scaling, and extensive customization of plot shape and
3493 (license license:gpl2+)))
3495 (define-public r-vioplot
3502 (uri (cran-uri "vioplot" version))
3505 "1fsklymilspzz5fzlj7666x09aglaw0v4x0yfjjzy4vr5qpjc529"))))
3506 (build-system r-build-system)
3510 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
3511 (synopsis "Violin plot")
3513 "This package provides a violin plot, which is a combination of a box
3514 plot and a kernel density plot.")
3515 (license license:bsd-3)))
3517 (define-public r-rsofia
3523 ;; This package has been removed from CRAN, so we can
3524 ;; only fetch it from the archives.
3525 (uri (string-append "https://cran.r-project.org/src/"
3526 "contrib/Archive/RSofia/RSofia_"
3530 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
3531 (properties `((upstream-name . "RSofia")))
3532 (build-system r-build-system)
3534 `(("r-rcpp" ,r-rcpp)))
3535 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
3536 (synopsis "Port of sofia-ml to R")
3537 (description "This package is a port of sofia-ml to R. Sofia-ml is a
3538 suite of fast incremental algorithms for machine learning that can be used for
3539 training models for classification or ranking.")
3540 (license license:asl2.0)))
3542 (define-public r-xts
3549 (uri (cran-uri "xts" version))
3552 "1f0kxrvn13py3hk2gh2m56cqm39x3bqp1i350r5viddacrm2yxqj"))))
3553 (build-system r-build-system)
3554 (propagated-inputs `(("r-zoo" ,r-zoo)))
3555 (home-page "https://github.com/joshuaulrich/xts")
3556 (synopsis "Extensible time series")
3558 "This package provides for uniform handling of R's different time-based
3559 data classes by extending @code{zoo}, maximizing native format information
3560 preservation and allowing for user-level customization and extension, while
3561 simplifying cross-class interoperability.")
3562 (license license:gpl2+)))
3564 (define-public r-performanceanalytics
3566 (name "r-performanceanalytics")
3571 (uri (cran-uri "PerformanceAnalytics" version))
3574 "0jhjldwyxwq7a47zmk5y1jjck7hvq92p8rlgjvdfy51hx2dmlqqd"))))
3576 `((upstream-name . "PerformanceAnalytics")))
3577 (build-system r-build-system)
3579 `(("r-quadprog" ,r-quadprog)
3582 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
3583 (synopsis "Econometric tools for performance and risk analysis")
3584 (description "This is a collection of econometric functions for
3585 performance and risk analysis. This package aims to aid practitioners and
3586 researchers in utilizing the latest research in analysis of non-normal return
3587 streams. In general, it is most tested on return (rather than price) data on
3588 a regular scale, but most functions will work with irregular return data as
3589 well, and increasing numbers of functions will work with P&L or price data
3591 ;; Either version may be picked.
3592 (license (list license:gpl2 license:gpl3))))
3594 (define-public r-laeken
3601 (uri (cran-uri "laeken" version))
3604 "1g9r3y7b0gl91hijk9awa8rjk97mqpkxinzq2cgmx0m38ng9ylpa"))))
3605 (build-system r-build-system)
3607 `(("r-boot" ,r-boot)
3608 ("r-mass" ,r-mass)))
3609 (home-page "https://cran.r-project.org/web/packages/laeken/")
3610 (synopsis "Estimation of indicators on social exclusion and poverty")
3611 (description "This package provides tools for the estimation of indicators
3612 on social exclusion and poverty, as well as an implementation of Pareto tail
3613 modeling for empirical income distributions.")
3614 (license license:gpl2+)))
3616 (define-public r-vcd
3623 (uri (cran-uri "vcd" version))
3626 "1lp99h0wvsc61l1dgcqjxdrcgpgw88ak430cdsv43kmm43qssqd5"))))
3627 (build-system r-build-system)
3629 `(("r-colorspace" ,r-colorspace)
3630 ("r-lmtest" ,r-lmtest)
3631 ("r-mass" ,r-mass)))
3632 (home-page "https://cran.r-project.org/web/packages/vcd/")
3633 (synopsis "Visualizing categorical data")
3634 (description "This package provides visualization techniques, data sets,
3635 summary and inference procedures aimed particularly at categorical data.
3636 Special emphasis is given to highly extensible grid graphics. The package was
3637 originally inspired by the book \"Visualizing Categorical Data\" by Michael
3638 Friendly and is now the main support package for a new book, \"Discrete Data
3639 Analysis with R\" by Michael Friendly and David Meyer (2015).")
3640 (license license:gpl2)))
3642 (define-public r-ica
3649 (uri (cran-uri "ica" version))
3652 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
3653 (build-system r-build-system)
3654 (home-page "https://cran.r-project.org/web/packages/ica/")
3655 (synopsis "Independent component analysis")
3656 (description "This package provides tools for @dfn{Independent Component
3657 Analysis} (ICA) using various algorithms: FastICA,
3658 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
3659 of Eigenmatrices} (JADE).")
3660 (license license:gpl2+)))
3662 (define-public r-dtw
3669 (uri (cran-uri "dtw" version))
3672 "02hyhx1sy5h3vzh9zixy18a7d47df4k5d0wyflcvlcbsbcl6p90s"))))
3673 (build-system r-build-system)
3674 (propagated-inputs `(("r-proxy" ,r-proxy)))
3675 (home-page "http://dtw.r-forge.r-project.org/")
3676 (synopsis "Dynamic Time Warping Algorithms")
3677 (description "This package provides a comprehensive implementation of
3678 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
3679 optimal (least cumulative distance) alignment between points of two time
3680 series. Common DTW variants covered include local (slope) and global (window)
3681 constraints, subsequence matches, arbitrary distance definitions,
3682 normalizations, minimum variance matching, and so on.")
3683 (license license:gpl2+)))
3685 (define-public r-sdmtools
3688 (version "1.1-221.2")
3692 (uri (cran-uri "SDMTools" version))
3695 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
3696 (properties `((upstream-name . "SDMTools")))
3697 (build-system r-build-system)
3698 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
3699 (home-page "http://www.rforge.net/SDMTools/")
3700 (synopsis "Species distribution modelling tools")
3701 (description "This package provides a set of tools for post processing
3702 the outcomes of species distribution modeling exercises. It includes novel
3703 methods for comparing models and tracking changes in distributions through
3704 time. It further includes methods for visualizing outcomes, selecting
3705 thresholds, calculating measures of accuracy and landscape fragmentation
3707 (license license:gpl3+)))
3709 (define-public r-scatterplot3d
3711 (name "r-scatterplot3d")
3716 (uri (cran-uri "scatterplot3d" version))
3719 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
3720 (build-system r-build-system)
3721 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
3722 (synopsis "3D scatter plot")
3723 (description "This package provides an implementation of scatter plots for
3724 plotting. a three dimensional point cloud.")
3725 (license license:gpl2)))
3727 (define-public r-ggridges
3734 (uri (cran-uri "ggridges" version))
3737 "0dhwcpy785ac2ny5bjp284595nnybi3554wd0yffsli0vzf7ry01"))))
3738 (build-system r-build-system)
3740 `(("r-ggplot2" ,r-ggplot2)
3742 ("r-scales" ,r-scales)
3743 ("r-withr" ,r-withr)))
3744 (home-page "https://github.com/clauswilke/ggridges")
3745 (synopsis "Ridgeline plots in ggplot2")
3747 "Ridgeline plots provide a convenient way of visualizing changes in
3748 distributions over time or space. This package enables the creation of such
3749 plots in @code{ggplot2}.")
3750 (license license:gpl2)))
3752 (define-public r-ggjoy
3759 (uri (cran-uri "ggjoy" version))
3762 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
3763 (build-system r-build-system)
3765 `(("r-ggplot2" ,r-ggplot2)
3766 ("r-ggridges" ,r-ggridges)))
3767 (home-page "https://github.com/clauswilke/ggjoy")
3768 (synopsis "Joyplots in ggplot2")
3769 (description "Joyplots provide a convenient way of visualizing changes in
3770 distributions over time or space. This package enables the creation of such
3771 plots in @code{ggplot2}.")
3772 (license license:gpl2)))
3774 (define-public r-cli
3781 (uri (cran-uri "cli" version))
3784 "1gv3zqdipj29ivkw5dsi1qdlra7q4lcrcqvlg9fns7d670yglfki"))))
3785 (build-system r-build-system)
3787 `(("r-assertthat" ,r-assertthat)
3788 ("r-crayon" ,r-crayon)
3789 ("r-fansi" ,r-fansi)
3790 ("r-glue" ,r-glue)))
3791 (home-page "https://github.com/r-lib/cli#readme")
3792 (synopsis "Helpers for developing command line interfaces")
3793 (description "This package provides a suite of tools designed to build
3794 attractive command line interfaces (CLIs). It includes tools for drawing
3795 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
3796 (license license:expat)))
3798 (define-public r-argparser
3800 (name "r-argparser")
3805 (uri (cran-uri "argparser" version))
3808 "0s1wxshx4jk69wfxhycx973q6y8cmqrfymyjklhq1i8xrj0kmmx9"))))
3809 (build-system r-build-system)
3810 (home-page "https://bitbucket.org/djhshih/argparser")
3811 (synopsis "Command-line argument parser")
3813 "This package provides a cross-platform command-line argument parser
3814 written purely in R with no external dependencies. It is useful with the
3815 Rscript front-end and facilitates turning an R script into an executable
3817 (license license:gpl3+)))
3819 (define-public r-debugme
3826 (uri (cran-uri "debugme" version))
3829 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
3830 (build-system r-build-system)
3831 (propagated-inputs `(("r-crayon" ,r-crayon)))
3832 (home-page "https://github.com/r-lib/debugme#readme")
3833 (synopsis "Debug R packages")
3835 "This package allows the user to specify debug messages as special string
3836 constants, and control debugging of packages via environment variables.")
3837 (license license:expat)))
3839 (define-public r-processx
3846 (uri (cran-uri "processx" version))
3849 "1g6ipcaxg9y94lyrnbp7kkbqfkcdh1fyrqjjclbjp3x7iysdvazi"))))
3850 (build-system r-build-system)
3854 (home-page "https://github.com/r-lib/processx3")
3855 (synopsis "Execute and control system processes")
3857 "This package provides portable tools to run system processes in the
3858 background. It can check if a background process is running; wait on a
3859 background process to finish; get the exit status of finished processes; kill
3860 background processes and their children; restart processes. It can read the
3861 standard output and error of the processes, using non-blocking connections.
3862 @code{processx} can poll a process for standard output or error, with a
3863 timeout. It can also poll several processes at once.")
3864 (license license:expat)))
3866 (define-public r-tsp
3873 (uri (cran-uri "TSP" version))
3876 "0rxxhvqi55869dg2p82hzg5kvgcqf9h60cjcg00k3pv9aw4x07kb"))))
3877 (properties `((upstream-name . "TSP")))
3878 (build-system r-build-system)
3879 (propagated-inputs `(("r-foreach" ,r-foreach)))
3880 (home-page "https://cran.r-project.org/web/packages/TSP/")
3881 (synopsis "Traveling salesperson problem (TSP)")
3882 (description "This package provides basic infrastructure and some
3883 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
3884 traveling salesman problem).")
3885 (license license:gpl3)))
3887 (define-public r-qap
3894 (uri (cran-uri "qap" version))
3897 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
3898 (build-system r-build-system)
3899 (native-inputs `(("gfortran" ,gfortran)))
3900 (home-page "https://cran.r-project.org/web/packages/qap/")
3901 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
3902 (description "This package implements heuristics for the @dfn{quadratic
3903 assignment problem} (QAP). Currently only a simulated annealing heuristic is
3905 (license license:gpl3)))
3907 (define-public r-gclus
3914 (uri (cran-uri "gclus" version))
3917 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
3918 (build-system r-build-system)
3919 (propagated-inputs `(("r-cluster" ,r-cluster)))
3920 (home-page "https://cran.r-project.org/web/packages/gclus/")
3921 (synopsis "Clustering graphics")
3922 (description "This package orders panels in scatterplot matrices and
3923 parallel coordinate displays by some merit index. It contains various indices
3924 of merit, ordering functions, and enhanced versions of @code{pairs} and
3925 @code{parcoord} which color panels according to their merit level.")
3926 (license license:gpl2+)))
3928 (define-public r-webshot
3935 (uri (cran-uri "webshot" version))
3938 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
3939 (build-system r-build-system)
3941 `(("r-callr" ,r-callr)
3942 ("r-jsonlite" ,r-jsonlite)
3943 ("r-magrittr" ,r-magrittr)))
3944 (home-page "https://github.com/wch/webshot/")
3945 (synopsis "Take screenshots of web pages")
3947 "Webshot makes it easy to take screenshots of web pages from within R.
3948 It can also run Shiny applications locally and take screenshots of the
3949 application; and it can render and screenshot static as well as interactive R
3950 Markdown documents.")
3951 (license license:gpl2)))
3953 (define-public r-seriation
3955 (name "r-seriation")
3960 (uri (cran-uri "seriation" version))
3963 "1zbdxq0s5rc5v307b69fw9k52m0654ls7pf22lh35ggirig6lwsk"))))
3964 (build-system r-build-system)
3966 `(("r-cluster" ,r-cluster)
3967 ("r-colorspace" ,r-colorspace)
3968 ("r-dendextend" ,r-dendextend)
3969 ("r-gclus" ,r-gclus)
3970 ("r-gplots" ,r-gplots)
3973 ("r-registry" ,r-registry)
3975 (native-inputs `(("gfortran" ,gfortran)))
3976 (home-page "http://s2.smu.edu/IDA/seriation/")
3977 (synopsis "Infrastructure for ordering objects using seriation")
3979 "This package provides infrastructure for seriation with an
3980 implementation of several seriation/sequencing techniques to reorder matrices,
3981 dissimilarity matrices, and dendrograms. It also provides (optimally)
3982 reordered heatmaps, color images and clustering visualizations like
3983 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
3985 (license license:gpl3)))
3987 (define-public r-xfun
3994 (uri (cran-uri "xfun" version))
3996 (base32 "0dncw6bqkal7nyarrrrj9arxy0y3nkdzmrbibcjh84m1cxd4phiw"))))
3997 (build-system r-build-system)
3998 (home-page "https://github.com/yihui/xfun")
3999 (synopsis "Miscellaneous functions")
4001 "This package provides miscellaneous functions commonly used in other
4002 packages maintained by Yihui Xie.")
4003 (license license:expat)))
4005 (define-public r-utf8
4012 (uri (cran-uri "utf8" version))
4015 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
4016 (build-system r-build-system)
4017 (home-page "https://github.com/patperry/r-utf8")
4018 (synopsis "Unicode text processing")
4020 "This package provides tools to process and print UTF-8 encoded
4021 international text (Unicode). Input, validate, normalize, encode, format, and
4023 (license license:asl2.0)))
4025 (define-public r-zeallot
4032 (uri (cran-uri "zeallot" version))
4035 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
4036 (build-system r-build-system)
4037 (home-page "https://github.com/nteetor/zeallot")
4038 (synopsis "Multiple, unpacking, and destructuring assignment")
4040 "This package provides a @code{%<-%} operator to perform multiple,
4041 unpacking, and destructuring assignment in R. The operator unpacks the
4042 right-hand side of an assignment into multiple values and assigns these values
4043 to variables on the left-hand side of the assignment.")
4044 (license license:expat)))
4046 (define-public r-vctrs
4053 (uri (cran-uri "vctrs" version))
4056 "05h0y8qzwc899qj84gkhg4jwzscd065as00d4d8smv42h4i8zkjv"))))
4057 (build-system r-build-system)
4059 `(("r-backports" ,r-backports)
4060 ("r-digest" ,r-digest)
4061 ("r-ellipsis" ,r-ellipsis)
4063 ("r-rlang" ,r-rlang)
4064 ("r-zeallot" ,r-zeallot)))
4065 (home-page "https://github.com/r-lib/vctrs")
4066 (synopsis "Vector helpers")
4068 "There are three main goals to the @code{vctrs} package:
4071 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
4072 @code{length()} and @code{class()}. These definitions are paired with a
4073 framework for type-coercion and size-recycling.
4074 @item To define type- and size-stability as desirable function properties, use
4075 them to analyse existing base function, and to propose better alternatives.
4076 This work has been particularly motivated by thinking about the ideal
4077 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
4078 @item To provide a new @code{vctr} base class that makes it easy to create new
4079 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
4080 a few new @code{vctrs} generics, making implementation considerably simpler
4083 (license license:gpl3)))
4085 (define-public r-pillar
4092 (uri (cran-uri "pillar" version))
4095 "0988047mf0xdhdkqqmavzx4ifjhndjnxniyrrhrdq1nvnrvbpfms"))))
4096 (build-system r-build-system)
4099 ("r-crayon" ,r-crayon)
4100 ("r-fansi" ,r-fansi)
4101 ("r-rlang" ,r-rlang)
4103 ("r-vctrs" ,r-vctrs)))
4104 (home-page "https://github.com/r-lib/pillar")
4105 (synopsis "Coloured formatting for columns")
4107 "This package provides a @code{pillar} generic designed for formatting
4108 columns of data using the full range of colours provided by modern
4110 (license license:gpl3)))
4112 (define-public r-uuid
4119 (uri (cran-uri "uuid" version))
4122 "1gmisd630fc8ybg845hbg13wmm3pk3npaamrh5wqbc1nqd6p0wfx"))))
4123 (build-system r-build-system)
4124 (home-page "http://www.rforge.net/uuid")
4125 (synopsis "Tools for generating and handling of UUIDs")
4127 "This package provides tools for generating and handling of
4128 @dfn{Universally Unique Identifiers} (UUIDs).")
4129 (license license:expat)))
4131 (define-public r-tinytex
4138 (uri (cran-uri "tinytex" version))
4141 "0mgxrbj4gam2gvxfk26nq820vsfjggj81m2l7j9m8vp361k15r0w"))))
4142 (build-system r-build-system)
4144 `(("r-xfun" ,r-xfun)))
4145 (home-page "https://github.com/yihui/tinytex")
4146 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
4148 "This package provides helper functions to install and maintain the LaTeX
4149 distribution named TinyTeX, a lightweight, cross-platform, portable, and
4150 easy-to-maintain version of TeX Live. This package also contains helper
4151 functions to compile LaTeX documents, and install missing LaTeX packages
4153 (license license:expat)))
4155 (define-public r-network
4162 (uri (cran-uri "network" version))
4165 "0dnf1wl3za2lhx2lwd8smhlijl1cfhckgr8zz9piiirrfi2m2kx2"))))
4166 (build-system r-build-system)
4168 `(("r-magrittr" ,r-magrittr)
4169 ("r-tibble" ,r-tibble)))
4170 (home-page "https://statnet.org/")
4171 (synopsis "Classes for relational data")
4173 "This package provides tools to create and modify network objects. The
4174 @code{network} class can represent a range of relational data types, and
4175 supports arbitrary vertex/edge/graph attributes.")
4176 (license license:gpl2+)))
4178 (define-public r-statnet-common
4180 (name "r-statnet-common")
4185 (uri (cran-uri "statnet.common" version))
4188 "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3"))))
4190 `((upstream-name . "statnet.common")))
4191 (build-system r-build-system)
4193 `(("r-coda" ,r-coda)))
4194 (home-page "https://statnet.org")
4195 (synopsis "R scripts and utilities used by the Statnet software")
4196 (description "This package provides non-statistical utilities used by the
4197 software developed by the Statnet Project.")
4198 (license license:gpl3)))
4200 (define-public r-statcheck
4202 (name "r-statcheck")
4207 (uri (cran-uri "statcheck" version))
4210 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
4211 (build-system r-build-system)
4213 `(("r-ggplot2" ,r-ggplot2)
4215 ("r-rmarkdown" ,r-rmarkdown)))
4216 (home-page "https://cran.r-project.org/web/packages/statcheck/")
4217 (synopsis "Extract statistics from articles and recompute p-values")
4218 (description "This package can automatically extract statistical
4219 null-hypothesis significant testing (NHST) results from articles and recompute
4220 the p-values based on the reported test statistic and degrees of freedom to
4221 detect possible inconsistencies.")
4222 (license license:gpl2)))
4224 (define-public r-sna
4231 (uri (cran-uri "sna" version))
4234 "1ks8819qvpdfansfqj9p32s1rhvl26frvbi78m4rx1wd1qcv74i2"))))
4235 (build-system r-build-system)
4237 `(("r-network" ,r-network)
4238 ("r-statnet-common" ,r-statnet-common)))
4239 (home-page "https://statnet.org")
4240 (synopsis "Tools for social network analysis")
4242 "This package provides a range of tools for social network analysis,
4243 including node and graph-level indices, structural distance and covariance
4244 methods, structural equivalence detection, network regression, random graph
4245 generation, and 2D/3D network visualization.")
4246 (license license:gpl2+)))
4248 (define-public r-tfisher
4255 (uri (cran-uri "TFisher" version))
4258 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
4259 (properties `((upstream-name . "TFisher")))
4260 (build-system r-build-system)
4262 `(("r-matrix" ,r-matrix)
4263 ("r-mvtnorm" ,r-mvtnorm)
4265 (home-page "https://cran.r-project.org/web/packages/TFisher/")
4266 (synopsis "Optimal thresholding Fisher's p-value combination method")
4268 "This package provides the @dfn{cumulative distribution function} (CDF),
4269 quantile, and statistical power calculator for a collection of thresholding
4270 Fisher's p-value combination methods, including Fisher's p-value combination
4271 method, truncated product method and, in particular, soft-thresholding
4272 Fisher's p-value combination method which is proven to be optimal in some
4273 context of signal detection. The p-value calculator for the omnibus version
4274 of these tests are also included.")
4275 (license license:gpl2)))
4277 (define-public r-ttr
4284 (uri (cran-uri "TTR" version))
4287 "0fxipnyxaz55n4camrk9cs71x9w4dsmjrihysv8i1s6khf825rg6"))))
4288 (properties `((upstream-name . "TTR")))
4289 (build-system r-build-system)
4291 `(("r-curl" ,r-curl)
4294 (home-page "https://github.com/joshuaulrich/TTR")
4295 (synopsis "Technical trading rules")
4297 "This package provides functions and data to construct technical trading
4299 (license license:gpl2)))
4301 (define-public r-leaps
4308 (uri (cran-uri "leaps" version))
4311 "11gjmn1azrjw5xlvdb4gknj9985kck9x8zb9np1rnk2smp6pka2m"))))
4312 (build-system r-build-system)
4313 (native-inputs `(("gfortran" ,gfortran)))
4314 (home-page "https://cran.r-project.org/web/packages/leaps/")
4315 (synopsis "Regression subset selection")
4317 "This package provides tools for regression subset selection, including
4318 exhaustive search.")
4319 (license license:gpl2+)))
4321 (define-public r-splus2r
4328 (uri (cran-uri "splus2R" version))
4331 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
4332 (properties `((upstream-name . "splus2R")))
4333 (build-system r-build-system)
4334 (native-inputs `(("gfortran" ,gfortran)))
4335 (home-page "https://cran.r-project.org/web/packages/splus2R/")
4336 (synopsis "Supplemental S-PLUS functionality in R")
4338 "Currently there are many functions in S-PLUS that are missing in R. To
4339 facilitate the conversion of S-PLUS packages to R packages, this package
4340 provides some missing S-PLUS functionality in R.")
4341 (license license:gpl2)))
4343 (define-public r-ifultools
4345 (name "r-ifultools")
4350 (uri (cran-uri "ifultools" version))
4353 "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j"))))
4354 (build-system r-build-system)
4356 `(("r-mass" ,r-mass)
4357 ("r-splus2r" ,r-splus2r)))
4358 (home-page "https://cran.r-project.org/web/packages/ifultools/")
4359 (synopsis "Insightful research tools")
4360 (description "This package provides C code used by the wmtsa, fractal, and
4362 (license license:gpl2)))
4364 (define-public r-sapa
4371 (uri (cran-uri "sapa" version))
4374 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
4375 (build-system r-build-system)
4377 `(("r-ifultools" ,r-ifultools)
4378 ("r-splus2r" ,r-splus2r)))
4379 (home-page "https://cran.r-project.org/web/packages/sapa/")
4380 (synopsis "Spectral analysis for physical applications")
4381 (description "This package provides software for the book Spectral
4382 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
4383 Cambridge University Press, 1993.")
4384 (license license:gpl2)))
4386 (define-public r-aggregation
4388 (name "r-aggregation")
4393 (uri (cran-uri "aggregation" version))
4396 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
4397 (build-system r-build-system)
4398 (home-page "https://cran.r-project.org/web/packages/aggregation/")
4399 (synopsis "Methods for p-value aggregation")
4401 "This package contains functionality for performing the following methods
4402 of p-value aggregation: Fisher's method, the Lancaster method (weighted
4403 Fisher's method), and Sidak correction.")
4404 (license license:gpl3)))
4406 (define-public r-quantmod
4413 (uri (cran-uri "quantmod" version))
4416 "0lyzaf5ypk93v6zj9gdghy05cc7cxgn9yasv1apx5r6qsjcfgwky"))))
4417 (build-system r-build-system)
4419 `(("r-curl" ,r-curl)
4423 (home-page "https://cran.r-project.org/web/packages/quantmod/")
4424 (synopsis "Quantitative financial modelling framework")
4425 (description "This package provides a quantitative financial modelling
4426 framework to allow users to specify, build, trade, and analyse quantitative
4427 financial trading strategies.")
4428 (license license:gpl3)))
4430 (define-public r-tseries
4437 (uri (cran-uri "tseries" version))
4440 "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
4441 (build-system r-build-system)
4443 `(("r-quadprog" ,r-quadprog)
4444 ("r-quantmod" ,r-quantmod)
4447 `(("gfortran" ,gfortran)))
4448 (home-page "https://cran.r-project.org/web/packages/tseries/")
4449 (synopsis "Time series analysis and computational finance")
4451 "This package provides functions relating to time series analysis and
4452 computational finance.")
4453 (license license:gpl2)))
4455 (define-public r-wmtsa
4462 (uri (cran-uri "wmtsa" version))
4465 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
4466 (build-system r-build-system)
4468 `(("r-ifultools" ,r-ifultools)
4470 ("r-splus2r" ,r-splus2r)))
4471 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
4472 (synopsis "Wavelet methods for time series analysis")
4474 "This package provides software to accompany the book \"Wavelet Methods
4475 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
4476 University Press, 2000.")
4477 (license license:gpl2)))
4479 (define-public r-tsa
4486 (uri (cran-uri "TSA" version))
4489 "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q"))))
4490 (properties `((upstream-name . "TSA")))
4491 (build-system r-build-system)
4493 `(("r-leaps" ,r-leaps)
4494 ("r-locfit" ,r-locfit)
4495 ("r-mgcv" ,r-mgcv)))
4496 (home-page "http://www.stat.uiowa.edu/~kchan/TSA.htm")
4497 (synopsis "Time series analysis")
4499 "This package contains R functions and datasets detailed in the book
4500 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
4501 Cryer and Kung-Sik Chan.")
4502 (license license:gpl2+)))
4504 (define-public r-extradistr
4506 (name "r-extradistr")
4511 (uri (cran-uri "extraDistr" version))
4514 "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3"))))
4515 (properties `((upstream-name . "extraDistr")))
4516 (build-system r-build-system)
4518 `(("r-rcpp" ,r-rcpp)))
4519 (home-page "https://github.com/twolodzko/extraDistr")
4520 (synopsis "Additional univariate and multivariate distributions")
4522 "This package implements density, distribution functions, quantile
4523 functions and random generation functions for a large number of univariate and
4524 multivariate distributions.")
4525 (license license:gpl2)))
4527 (define-public r-fractal
4534 (uri (cran-uri "fractal" version))
4537 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
4538 (build-system r-build-system)
4540 `(("r-ifultools" ,r-ifultools)
4543 ("r-scatterplot3d" ,r-scatterplot3d)
4544 ("r-splus2r" ,r-splus2r)
4545 ("r-wmtsa" ,r-wmtsa)))
4546 (home-page "https://cran.r-project.org/web/packages/fractal/")
4547 (synopsis "Fractal time series modeling and analysis")
4549 "This package provides tools for stochastic fractal and deterministic
4550 chaotic time series analysis.")
4551 (license license:gpl2)))
4553 (define-public r-urca
4560 (uri (cran-uri "urca" version))
4563 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
4564 (build-system r-build-system)
4565 (propagated-inputs `(("r-nlme" ,r-nlme)))
4566 (native-inputs `(("gfortran" ,gfortran)))
4567 (home-page "https://cran.r-project.org/web/packages/urca/")
4568 (synopsis "Unit root and cointegration tests for time series data")
4570 "This package provides unit root and cointegration tests encountered in
4571 applied econometric analysis.")
4572 (license license:gpl2+)))
4574 (define-public r-cubature
4581 (uri (cran-uri "cubature" version))
4584 "0jpyq8j7x06dpiz29w48av879ygldzgls9z810192hsymkmfaz6r"))))
4585 (build-system r-build-system)
4587 `(("r-rcpp" ,r-rcpp)))
4588 (home-page "https://github.com/bnaras/cubature")
4589 (synopsis "Adaptive multivariate integration over hypercubes")
4591 "This package is an R wrapper around the cubature C library for adaptive
4592 multivariate integration over hypercubes. This version provides both
4593 @code{hcubature} and @code{pcubature} routines in addition to a vector
4595 ;; The included cubature C library is released under GPLv2+, but the
4596 ;; wrapper declares the license to be GPLv3+.
4597 (license (list license:gpl2+ license:gpl3+))))
4599 (define-public r-trend
4606 (uri (cran-uri "trend" version))
4609 "1bd567n15k2vpmgbx02584k5kglrc58mlb5kgd07wdss3knpa48q"))))
4610 (build-system r-build-system)
4612 `(("r-extradistr" ,r-extradistr)))
4614 `(("gfortran" ,gfortran)))
4615 (home-page "https://cran.r-project.org/web/packages/trend/")
4616 (synopsis "Non-parametric trend tests and change-point detection")
4618 "The analysis of environmental data often requires the detection of
4619 trends and change-points. This package includes tests for trend
4620 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
4621 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
4622 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
4623 correlation trend test), change-point detection (Lanzante's test procedures,
4624 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
4625 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
4626 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
4627 sample Robust Rank-Order Distributional Test.")
4628 (license license:gpl3)))
4630 (define-public r-expm
4637 (uri (cran-uri "expm" version))
4640 "15k0acg2aqb2ajhwal6l7vhhp03m4lg579805d34554cl0kn9l2q"))))
4641 (build-system r-build-system)
4642 (propagated-inputs `(("r-matrix" ,r-matrix)))
4643 (native-inputs `(("gfortran" ,gfortran)))
4644 (home-page "https://r-forge.r-project.org/projects/expm/")
4645 (synopsis "Tools for matrix exponentials and related quantities")
4647 "This package provides tools for the computation of the matrix
4648 exponential, logarithm, square root, and related quantities.")
4649 (license license:gpl2+)))
4651 (define-public r-complexplus
4653 (name "r-complexplus")
4658 (uri (cran-uri "complexplus" version))
4661 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
4662 (build-system r-build-system)
4664 `(("r-expm" ,r-expm)
4665 ("r-matrix" ,r-matrix)))
4666 (home-page "https://cran.r-project.org/web/packages/complexplus/")
4667 (synopsis "Functions of complex or real variables")
4669 "This package extends several functions to the complex domain, including
4670 the matrix exponential and logarithm, and the determinant.")
4671 (license license:gpl2)))
4673 (define-public r-phontools
4675 (name "r-phontools")
4680 (uri (cran-uri "phonTools" version))
4683 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
4684 (properties `((upstream-name . "phonTools")))
4685 (build-system r-build-system)
4686 (home-page "http://www.santiagobarreda.com/rscripts.html")
4687 (synopsis "Tools for phonetic and acoustic analyses")
4689 "This package contains tools for the organization, display, and analysis
4690 of the sorts of data frequently encountered in phonetics research and
4691 experimentation, including the easy creation of IPA vowel plots, and the
4692 creation and manipulation of WAVE audio files.")
4693 (license license:bsd-2)))
4702 (uri (cran-uri "np" version))
4705 "1z4jcpx8bbgwslv42wrphfd1qfq965qjn0kmfxm5f6hbbycahcgy"))))
4706 (build-system r-build-system)
4708 `(("r-boot" ,r-boot)
4709 ("r-cubature" ,r-cubature)
4710 ("r-quadprog" ,r-quadprog)
4711 ("r-quantreg" ,r-quantreg)))
4712 (home-page "https://github.com/JeffreyRacine/R-Package-np")
4713 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
4714 (description "This package provides non-parametric (and semi-parametric)
4715 kernel methods that seamlessly handle a mix of continuous, unordered, and
4716 ordered factor data types.")
4717 ;; Any version of the GPL.
4718 (license license:gpl3+)))
4720 (define-public r-powerplus
4722 (name "r-powerplus")
4727 (uri (cran-uri "powerplus" version))
4730 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
4731 (build-system r-build-system)
4733 `(("r-complexplus" ,r-complexplus)
4736 ("r-matrix" ,r-matrix)
4737 ("r-phontools" ,r-phontools)))
4738 (home-page "https://cran.r-project.org/web/packages/powerplus/")
4739 (synopsis "Exponentiation operations")
4741 "This package provides tools for the computation of matrix and scalar
4743 (license license:gpl2)))
4745 (define-public r-egg
4752 (uri (cran-uri "egg" version))
4755 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
4756 (properties `((upstream-name . "egg")))
4757 (build-system r-build-system)
4759 `(("r-ggplot2" ,r-ggplot2)
4760 ("r-gridextra" ,r-gridextra)
4761 ("r-gtable" ,r-gtable)))
4762 (home-page "https://cran.r-project.org/web/packages/egg")
4763 (synopsis "Extensions for ggplot2")
4765 "This package provides miscellaneous functions to help customize ggplot2
4766 objects. High-level functions are provided to post-process ggplot2 layouts
4767 and allow alignment between plot panels, as well as setting panel sizes to
4768 fixed values. Other functions include a custom @code{geom}, and helper
4769 functions to enforce symmetric scales or add tags to facetted plots.")
4770 (license license:gpl3)))
4772 (define-public r-heatmaply
4774 (name "r-heatmaply")
4779 (uri (cran-uri "heatmaply" version))
4782 "0576gml3bcl7r1biigzj1rag2xzz422knbw7arc8d2gsakjj757g"))))
4783 (build-system r-build-system)
4785 `(("r-assertthat" ,r-assertthat)
4786 ("r-colorspace" ,r-colorspace)
4787 ("r-dendextend" ,r-dendextend)
4789 ("r-ggplot2" ,r-ggplot2)
4790 ("r-htmlwidgets" ,r-htmlwidgets)
4791 ("r-magrittr" ,r-magrittr)
4792 ("r-plotly" ,r-plotly)
4793 ("r-rcolorbrewer" ,r-rcolorbrewer)
4794 ("r-reshape2" ,r-reshape2)
4795 ("r-scales" ,r-scales)
4796 ("r-seriation" ,r-seriation)
4797 ("r-viridis" ,r-viridis)
4798 ("r-webshot" ,r-webshot)))
4799 (home-page "https://cran.r-project.org/package=heatmaply")
4800 (synopsis "Interactive cluster heat maps using plotly")
4802 "This package enables you to create interactive cluster heatmaps that can
4803 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
4804 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
4805 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
4806 a popular graphical method for visualizing high-dimensional data, in which a
4807 table of numbers is encoded as a grid of colored cells. The rows and columns
4808 of the matrix are ordered to highlight patterns and are often accompanied by
4810 ;; Either version of the license.
4811 (license (list license:gpl2 license:gpl3))))
4820 (uri (cran-uri "h5" version))
4823 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
4824 (build-system r-build-system)
4829 `(("which" ,which)))
4831 `(("r-rcpp" ,r-rcpp)))
4832 (home-page "https://github.com/mannau/h5")
4833 (synopsis "Interface to the HDF5 Library")
4835 "This package provides an S4 interface to the HDF5 library supporting
4836 fast storage and retrieval of R-objects like vectors, matrices and arrays to
4837 binary files in a language independent format. The HDF5 format can therefore
4838 be used as an alternative to R's save/load mechanism. Since h5 is able to
4839 access only subsets of stored data it can also handle data sets which do not
4841 (license license:bsd-2)))
4843 (define-public r-cgdsr
4850 (uri (cran-uri "cgdsr" version))
4853 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
4854 (build-system r-build-system)
4856 `(("r-httr" ,r-httr)
4857 ("r-r-methodss3" ,r-r-methodss3)
4858 ("r-r-oo" ,r-r-oo)))
4859 (home-page "https://github.com/cBioPortal/cgdsr")
4860 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
4862 "This package provides a basic set of R functions for querying the Cancer
4863 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
4864 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
4865 (license license:lgpl3)))
4867 (define-public r-import
4874 (uri (cran-uri "import" version))
4877 "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
4878 (build-system r-build-system)
4879 (home-page "https://github.com/smbache/import")
4880 (synopsis "Import mechanism for R")
4882 "This is an alternative mechanism for importing objects from packages.
4883 The syntax allows for importing multiple objects from a package with a single
4884 command in an expressive way. The import package bridges some of the gap
4885 between using @code{library} (or @code{require}) and direct (single-object)
4886 imports. Furthermore the imported objects are not placed in the current
4887 environment. It is also possible to import objects from stand-alone @code{.R}
4889 (license license:expat)))
4891 (define-public r-shinyace
4898 (uri (cran-uri "shinyAce" version))
4901 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
4902 (properties `((upstream-name . "shinyAce")))
4903 (build-system r-build-system)
4905 `(("r-shiny" ,r-shiny)
4906 ("r-jsonlite" ,r-jsonlite)))
4907 (home-page "http://cran.r-project.org/web/packages/shinyAce")
4908 (synopsis "Ace editor bindings for Shiny")
4910 "This package provides Ace editor bindings to enable a rich text editing
4911 environment within Shiny.")
4912 (license license:expat)))
4914 (define-public r-base64url
4916 (name "r-base64url")
4921 (uri (cran-uri "base64url" version))
4924 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
4925 (build-system r-build-system)
4927 `(("r-backports" ,r-backports)))
4928 (home-page "https://github.com/mllg/base64url")
4929 (synopsis "Fast and URL-safe base64 encoder and decoder")
4931 "This package provides a URL-safe base64 encoder and decoder. In
4932 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
4933 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
4934 encoder does not fill the string with trailing @code{=}. The resulting
4935 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
4936 and thus are safe to use in URLs or for file names. The package also comes
4937 with a simple base32 encoder/decoder suited for case insensitive file
4939 (license license:gpl3)))
4941 (define-public r-radiant-data
4943 (name "r-radiant-data")
4948 (uri (cran-uri "radiant.data" version))
4951 "08x7zasxf429m021482p86lx3zc6dqz2mih0id8s34isg4gafapg"))
4952 (modules '((guix build utils)))
4955 ;; Delete files that are under CC-NC-SA.
4956 (delete-file-recursively "inst/app/tools/help")
4958 (properties `((upstream-name . "radiant.data")))
4959 (build-system r-build-system)
4961 `(("r-base64enc" ,r-base64enc)
4962 ("r-broom" ,r-broom)
4965 ("r-dplyr" ,r-dplyr)
4968 ("r-ggplot2" ,r-ggplot2)
4969 ("r-gridextra" ,r-gridextra)
4970 ("r-import" ,r-import)
4971 ("r-jsonlite" ,r-jsonlite)
4972 ("r-knitr" ,r-knitr)
4973 ("r-lubridate" ,r-lubridate)
4974 ("r-magrittr" ,r-magrittr)
4975 ("r-markdown" ,r-markdown)
4976 ("r-plotly" ,r-plotly)
4977 ("r-psych" ,r-psych)
4978 ("r-readr" ,r-readr)
4979 ("r-readxl" ,r-readxl)
4980 ("r-rlang" ,r-rlang)
4981 ("r-rmarkdown" ,r-rmarkdown)
4982 ("r-rstudioapi" ,r-rstudioapi)
4983 ("r-scales" ,r-scales)
4984 ("r-shiny" ,r-shiny)
4985 ("r-shinyfiles" ,r-shinyfiles)
4986 ("r-shinyace" ,r-shinyace)
4987 ("r-stringi" ,r-stringi)
4988 ("r-tibble" ,r-tibble)
4989 ("r-tidyr" ,r-tidyr)
4990 ("r-writexl" ,r-writexl)))
4991 (home-page "https://github.com/radiant-rstats/radiant.data")
4992 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
4994 "The Radiant Data menu includes interfaces for loading, saving, viewing,
4995 visualizing, summarizing, transforming, and combining data. It also contains
4996 functionality to generate reproducible reports of the analyses conducted in
4998 (license license:agpl3)))
5000 (define-public r-algdesign
5002 (name "r-algdesign")
5007 (uri (cran-uri "AlgDesign" version))
5009 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
5010 (properties `((upstream-name . "AlgDesign")))
5011 (build-system r-build-system)
5012 (home-page "https://github.com/jvbraun/AlgDesign")
5013 (synopsis "Algorithmic experimental design")
5015 "This package provides tools to calculate exact and approximate theory
5016 experimental designs for D, A, and I criteria. Very large designs may be
5017 created. Experimental designs may be blocked or blocked designs created from
5018 a candidate list, using several criteria. The blocking can be done when whole
5019 and within plot factors interact.")
5020 (license license:gpl2+)))
5022 (define-public r-signal
5029 (uri (cran-uri "signal" version))
5032 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
5033 (build-system r-build-system)
5034 (propagated-inputs `(("r-mass" ,r-mass)))
5035 (native-inputs `(("gfortran" ,gfortran)))
5036 (home-page "https://cran.r-project.org/web/packages/signal/")
5037 (synopsis "Signal processing")
5039 "This package provides a set of signal processing functions originally
5040 written for Matlab and GNU Octave. It includes filter generation utilities,
5041 filtering functions, resampling routines, and visualization of filter models.
5042 It also includes interpolation functions.")
5043 (license license:gpl2)))
5045 (define-public r-gsubfn
5052 (uri (cran-uri "gsubfn" version))
5055 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
5056 (build-system r-build-system)
5057 (propagated-inputs `(("r-proto" ,r-proto)))
5058 (home-page "http://gsubfn.googlecode.com")
5059 (synopsis "Utilities for strings and function arguments.")
5061 "This package provides @code{gsubfn} which is like @code{gsub} but can
5062 take a replacement function or certain other objects instead of the
5063 replacement string. Matches and back references are input to the replacement
5064 function and replaced by the function output. @code{gsubfn} can be used to
5065 split strings based on content rather than delimiters and for quasi-perl-style
5066 string interpolation. The package also has facilities for translating
5067 formulas to functions and allowing such formulas in function calls instead of
5069 (license license:gpl2+)))
5071 (define-public r-sqldf
5078 (uri (cran-uri "sqldf" version))
5081 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
5082 (build-system r-build-system)
5084 `(("r-chron" ,r-chron)
5086 ("r-gsubfn" ,r-gsubfn)
5087 ("r-proto" ,r-proto)
5088 ("r-rsqlite" ,r-rsqlite)))
5089 (home-page "https://github.com/ggrothendieck/sqldf")
5090 (synopsis "Manipulate R data frames using SQL")
5092 "The @code{sqldf} function is typically passed a single argument which is
5093 an SQL select statement where the table names are ordinary R data frame names.
5094 @code{sqldf} transparently sets up a database, imports the data frames into
5095 that database, performs the SQL statement and returns the result using a
5096 heuristic to determine which class to assign to each column of the returned
5097 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
5098 used to read filtered files into R even if the original files are larger than
5099 R itself can handle.")
5100 (license license:gpl2)))
5102 (define-public r-abind
5109 (uri (cran-uri "abind" version))
5112 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
5113 (build-system r-build-system)
5114 (home-page "https://cran.r-project.org/web/packages/abind/")
5115 (synopsis "Combine multidimensional arrays")
5117 "This package provides tools to combine multidimensional arrays into a
5118 single array. This is a generalization of @code{cbind} and @code{rbind}. It
5119 works with vectors, matrices, and higher-dimensional arrays. It also provides
5120 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
5121 extracting and replacing data in arrays.")
5122 (license license:lgpl2.0+)))
5124 (define-public r-prroc
5131 (uri (cran-uri "PRROC" version))
5134 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
5135 (properties `((upstream-name . "PRROC")))
5136 (build-system r-build-system)
5137 (home-page "https://cran.r-project.org/web/packages/PRROC/")
5138 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
5140 "This package computes the areas under the @dfn{precision-recall} (PR)
5141 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
5142 contrast to other implementations, the interpolation between points of the PR
5143 curve is done by a non-linear piecewise function. In addition to the areas
5144 under the curves, the curves themselves can also be computed and plotted by a
5145 specific S3-method.")
5146 (license license:gpl3)))
5148 (define-public r-vim
5155 (uri (cran-uri "VIM" version))
5158 "08x4a4yzgp8adgrv7a3666yma4b60n64mcsnvhzmwdy023f4ysrw"))))
5159 (properties `((upstream-name . "VIM")))
5160 (build-system r-build-system)
5163 ("r-colorspace" ,r-colorspace)
5164 ("r-data-table" ,r-data-table)
5165 ("r-e1071" ,r-e1071)
5166 ("r-laeken" ,r-laeken)
5169 ("r-ranger" ,r-ranger)
5171 ("r-robustbase" ,r-robustbase)
5174 (home-page "https://github.com/alexkowa/VIM")
5175 (synopsis "Visualization and imputation of missing values")
5177 "This package provides tools for the visualization of missing and/or
5178 imputed values are introduced, which can be used for exploring the data and
5179 the structure of the missing and/or imputed values. Depending on this
5180 structure of the missing values, the corresponding methods may help to
5181 identify the mechanism generating the missing values and allows to explore the
5182 data including missing values. In addition, the quality of imputation can be
5183 visually explored using various univariate, bivariate, multiple and
5184 multivariate plot methods.")
5185 (license license:gpl2+)))
5187 (define-public r-fnn
5194 (uri (cran-uri "FNN" version))
5197 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
5198 (properties `((upstream-name . "FNN")))
5199 (build-system r-build-system)
5200 (home-page "https://cran.r-project.org/web/packages/FNN")
5201 (synopsis "Fast nearest neighbor search algorithms and applications")
5203 "This package provides cover-tree and kd-tree fast k-nearest neighbor
5204 search algorithms. Related applications including KNN classification,
5205 regression and information measures are implemented.")
5206 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
5207 ;; later can be used.
5208 (license license:gpl2+)))
5210 (define-public r-smoother
5217 (uri (cran-uri "smoother" version))
5220 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
5221 (build-system r-build-system)
5223 `(("r-ttr" ,r-ttr)))
5224 (home-page "http://cran.r-project.org/web/packages/smoother")
5225 (synopsis "Functions relating to the smoothing of numerical data")
5227 "This package provides a collection of methods for smoothing numerical
5228 data, commencing with a port of the Matlab gaussian window smoothing function.
5229 In addition, several functions typically used in smoothing of financial data
5231 (license license:gpl2)))
5233 (define-public r-riverplot
5235 (name "r-riverplot")
5240 (uri (cran-uri "riverplot" version))
5243 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
5244 (build-system r-build-system)
5245 (home-page "https://logfc.wordpress.com")
5246 (synopsis "Sankey or ribbon plots")
5248 "Sankey plots are a type of diagram that is convenient to illustrate how
5249 flow of information, resources etc. separates and joins, much like observing
5250 how rivers split and merge. For example, they can be used to compare
5251 different clusterings. This package provides an implementation of Sankey
5253 (license license:gpl2+)))
5255 (define-public r-dyn
5262 (uri (cran-uri "dyn" version))
5265 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
5266 (build-system r-build-system)
5268 `(("r-zoo" ,r-zoo)))
5269 (home-page "https://cran.r-project.org/web/packages/dyn")
5270 (synopsis "Time series regression")
5272 "This package provides the dyn class interfaces @code{ts}, @code{irts},
5273 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
5274 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
5275 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
5276 @code{randomForest::randomForest()} and other regression functions, allowing
5277 those functions to be used with time series including specifications that may
5278 contain lags, diffs and missing values.")
5280 (license license:gpl2+)))
5282 (define-public r-catdap
5289 (uri (cran-uri "catdap" version))
5292 "0i877l61f6c75pczi235rzci67w29zv1d7z5zn5p5ymndclvlpl2"))))
5293 (build-system r-build-system)
5295 `(("gfortran" ,gfortran)))
5296 (home-page "https://cran.r-project.org/web/packages/catdap/")
5297 (synopsis "Tools for categorical data analysis")
5299 "This package provides functions for analyzing multivariate data.
5300 Dependencies of the distribution of the specified variable (response
5301 variable) to other variables (explanatory variables) are derived and
5302 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
5303 (license license:gpl2+)))
5305 (define-public r-arules
5312 (uri (cran-uri "arules" version))
5315 "003c5cd3xzq39h7c19px077ygm0n1v7k83icy5zzrnkagyds2p8n"))))
5316 (build-system r-build-system)
5318 `(("r-matrix" ,r-matrix)))
5319 (home-page "https://github.com/mhahsler/arules")
5320 (synopsis "Mining association rules and frequent itemsets")
5322 "This package provides an infrastructure for representing, manipulating
5323 and analyzing transaction data and patterns (frequent itemsets and association rules).
5324 It also provides C implementations of the association mining algorithms Apriori
5326 (license license:gpl3)))
5328 (define-public r-parsedate
5330 (name "r-parsedate")
5335 (uri (cran-uri "parsedate" version))
5338 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
5339 (build-system r-build-system)
5341 `(("r-rematch2" ,r-rematch2)))
5342 (home-page "https://github.com/gaborcsardi/parsedate")
5344 "Recognize and parse dates in various formats")
5346 "This package provides three functions for dealing with dates:
5347 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
5348 time formats, @code{parse_date} parses dates in unspecified formats,
5349 and @code{format_iso_8601} formats a date in ISO 8601 format.")
5350 (license license:gpl2)))
5352 (define-public r-abc-data
5359 (uri (cran-uri "abc.data" version))
5362 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
5363 (properties `((upstream-name . "abc.data")))
5364 (build-system r-build-system)
5365 (home-page "https://cran.r-project.org/web/packages/abc.data/")
5366 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
5368 "This package contains data which are used by functions of the abc
5369 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
5370 algorithms for performing parameter estimation, model selection, and
5372 (license license:gpl3+)))
5374 (define-public r-abc
5381 (uri (cran-uri "abc" version))
5384 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
5385 (build-system r-build-system)
5387 `(("r-abc-data" ,r-abc-data)
5388 ("r-locfit" ,r-locfit)
5391 ("r-quantreg" ,r-quantreg)))
5392 (home-page "https://cran.r-project.org/web/packages/abc/")
5393 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
5395 "This package implements several @dfn{Approximate Bayesian
5396 Computation} (ABC) algorithms for performing parameter estimation, model
5397 selection, and goodness-of-fit. Cross-validation tools are also available for
5398 measuring the accuracy of ABC estimates, and to calculate the
5399 misclassification probabilities of different models.")
5400 (license license:gpl3+)))
5402 (define-public r-zip
5409 (uri (cran-uri "zip" version))
5412 "1c02amk3pl6xir5jnbfiwiv2wvpkpbkkb1w71y6lf2yk7g3d0pdb"))))
5413 (build-system r-build-system)
5414 (home-page "https://github.com/gaborcsardi/zip")
5415 (synopsis "Cross-platform Zip compression")
5417 "This package provides a cross-platform Zip compression library for R.
5418 It is a replacement for the @code{zip} function, that does not require any
5419 additional external tools on any platform.")
5420 (license license:cc0)))
5422 (define-public r-openxlsx
5429 (uri (cran-uri "openxlsx" version))
5432 "1mwxldw9i9nfksx1i6h1kfs7vmsz9fgyllbsipar4vnfyqhqp8q7"))))
5433 (build-system r-build-system)
5435 `(("r-rcpp" ,r-rcpp)
5436 ("r-stringi" ,r-stringi)
5438 (home-page "https://github.com/awalker89/openxlsx")
5439 (synopsis "Read, write and edit XLSX files")
5441 "This package simplifies the creation of Excel @code{.xlsx} files by
5442 providing a high level interface to writing, styling and editing worksheets.
5443 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
5444 and @code{XLConnect} packages with the added benefit of removing the
5445 dependency on Java.")
5446 (license license:gpl3)))
5448 (define-public r-rio
5455 (uri (cran-uri "rio" version))
5458 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
5459 (build-system r-build-system)
5461 `(("r-curl" ,r-curl)
5462 ("r-data-table" ,r-data-table)
5463 ("r-foreign" ,r-foreign)
5464 ("r-haven" ,r-haven)
5465 ("r-openxlsx" ,r-openxlsx)
5466 ("r-readxl" ,r-readxl)
5467 ("r-tibble" ,r-tibble)))
5468 (home-page "https://github.com/leeper/rio")
5469 (synopsis "Swiss-army knife for data I/O")
5471 "This package provides streamlined data import and export infrastructure
5472 by making assumptions that the user is probably willing to make: @code{import}
5473 and @code{export} determine the data structure from the file extension,
5474 reasonable defaults are used for data import and export (e.g.,
5475 @code{stringsAsFactors=FALSE}), web-based import is natively
5476 supported (including from SSL/HTTPS), compressed files can be read directly
5477 without explicit decompression, and fast import packages are used where
5478 appropriate. An additional convenience function, @code{convert}, provides a
5479 simple method for converting between file types.")
5480 (license license:gpl2)))
5482 (define-public r-maptools
5489 (uri (cran-uri "maptools" version))
5492 "0v4llkxk8qs61vq4ykvaim4k23aagdaz0p62ns7zfq02sln3pfk9"))))
5493 (build-system r-build-system)
5495 `(("r-foreign" ,r-foreign)
5496 ("r-lattice" ,r-lattice)
5498 (home-page "http://r-forge.r-project.org/projects/maptools/")
5499 (synopsis "Tools for reading and handling spatial objects")
5501 "This package provides a set of tools for manipulating and reading
5502 geographic data, in particular ESRI Shapefiles. It includes binary access to
5503 GSHHG shoreline files. The package also provides interface wrappers for
5504 exchanging spatial objects with other R packages.")
5505 ;; The C source files from shapelib are released under the Expat license.
5506 ;; The R code is released under GPL version 2 or later.
5507 (license (list license:gpl2+
5510 (define-public r-later
5517 (uri (cran-uri "later" version))
5520 "11xjavj7siz0xv2ffq1ld4bwl35jyrcfpvvs4p3ilpifxx49hyr7"))))
5521 (build-system r-build-system)
5525 ("r-rlang" ,r-rlang)))
5526 (home-page "https://github.com/r-lib/later")
5527 (synopsis "Utilities for delaying function execution")
5529 "This package provides tools to execute arbitrary R or C functions some
5530 time after the current time, after the R execution stack has emptied.")
5531 (license license:gpl2+)))
5533 (define-public r-promises
5540 (uri (cran-uri "promises" version))
5543 "01l0ydjvvy6afcg5d6pzvk1ikd3djq8n2flv8c831ksn68z0zsn8"))))
5544 (build-system r-build-system)
5546 `(("r-later" ,r-later)
5547 ("r-magrittr" ,r-magrittr)
5550 ("r-rlang" ,r-rlang)))
5551 (home-page "https://rstudio.github.io/promises")
5552 (synopsis "Abstractions for promise-based asynchronous programming")
5554 "This package provides fundamental abstractions for doing asynchronous
5555 programming in R using promises. Asynchronous programming is useful for
5556 allowing a single R process to orchestrate multiple tasks in the background
5557 while also attending to something else. Semantics are similar to JavaScript
5558 promises, but with a syntax that is idiomatic R.")
5559 (license license:expat)))
5561 (define-public r-dosnow
5568 (uri (cran-uri "doSNOW" version))
5571 "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh"))))
5572 (properties `((upstream-name . "doSNOW")))
5573 (build-system r-build-system)
5575 `(("r-foreach" ,r-foreach)
5576 ("r-iterators" ,r-iterators)
5577 ("r-snow" ,r-snow)))
5578 (home-page "https://cran.r-project.org/web/packages/doSNOW")
5579 (synopsis "Foreach parallel adaptor for the snow package")
5581 "This package provides a parallel backend for the @code{%dopar%} function
5582 using the @code{snow} package.")
5583 (license license:gpl2)))
5585 (define-public r-snowfall
5588 (version "1.84-6.1")
5591 (uri (cran-uri "snowfall" version))
5593 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
5594 (build-system r-build-system)
5596 `(("r-snow" ,r-snow)))
5597 (home-page "http://cran.r-project.org/web/packages/snowfall/")
5598 (synopsis "Easier cluster computing")
5599 (description "This package is a usability wrapper around snow for easier
5600 development of parallel R programs. This package offers e.g. extended error
5601 checks, and additional functions. All functions work in sequential mode, too,
5602 if no cluster is present or wished. The package is also designed as connector
5603 to the cluster management tool @code{sfCluster}, but can also used without
5605 (license license:gpl2+)))
5607 (define-public r-rappdirs
5614 (uri (cran-uri "rappdirs" version))
5617 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
5618 (build-system r-build-system)
5619 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
5620 (synopsis "Determine where to save data, caches, and logs")
5622 "This package provides an easy way to determine which directories on the
5623 user's computer should be used to save data, caches and logs. It is a port of
5624 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
5625 (license license:expat)))
5627 (define-public r-renv
5634 (uri (cran-uri "renv" version))
5637 "0mwqpcay6v1hnvhggsrn1chvdlhi9hwvsswas8ysygfy5wxxz1sm"))))
5638 (properties `((upstream-name . "renv")))
5639 (build-system r-build-system)
5640 (home-page "https://rstudio.github.io/renv")
5641 (synopsis "Project environments")
5643 "This package provides a dependency management toolkit for R. Using
5644 renv, you can create and manage project-local R libraries, save the state of
5645 these libraries to a lockfile, and later restore your library as required.
5646 Together, these tools can help make your projects more isolated, portable, and
5648 (license license:expat)))
5650 (define-public r-learnr
5657 (uri (cran-uri "learnr" version))
5660 "0278q9nbkc4nb0rp930kjrwyidf0v7y38d1s187m4f4bs7ha82k6"))))
5661 (build-system r-build-system)
5663 `(("r-checkmate" ,r-checkmate)
5664 ("r-ellipsis" ,r-ellipsis)
5665 ("r-evaluate" ,r-evaluate)
5666 ("r-htmltools" ,r-htmltools)
5667 ("r-htmlwidgets" ,r-htmlwidgets)
5668 ("r-jsonlite" ,r-jsonlite)
5669 ("r-knitr" ,r-knitr)
5670 ("r-markdown" ,r-markdown)
5671 ("r-rappdirs" ,r-rappdirs)
5673 ("r-rmarkdown" ,r-rmarkdown)
5674 ("r-rprojroot" ,r-rprojroot)
5675 ("r-shiny" ,r-shiny)
5676 ("r-withr" ,r-withr)))
5677 (home-page "https://rstudio.github.io/learnr/")
5678 (synopsis "Interactive tutorials for R")
5680 "This package provides tools to create interactive tutorials using R
5681 Markdown. Use a combination of narrative, figures, videos, exercises, and
5682 quizzes to create self-paced tutorials for learning about R and R packages.")
5683 (license license:asl2.0)))
5685 (define-public r-analytics
5687 (name "r-analytics")
5692 (uri (cran-uri "analytics" version))
5695 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
5696 (build-system r-build-system)
5699 ("r-cluster" ,r-cluster)
5700 ("r-fractal" ,r-fractal)
5701 ("r-lmtest" ,r-lmtest)
5704 ("r-powerplus" ,r-powerplus)
5705 ("r-robust" ,r-robust)
5706 ("r-trend" ,r-trend)
5710 (home-page "https://cran.r-project.org/web/packages/analytics/")
5711 (synopsis "Collection of data analysis tools")
5713 "This package is a collection of data analysis tools. It includes tools
5714 for regression outlier detection in a fitted linear model, stationary
5715 bootstrap using a truncated geometric distribution, a comprehensive test for
5716 weak stationarity, column means by group, weighted biplots, and a heuristic to
5717 obtain a better initial configuration in non-metric MDS.")
5718 (license license:gpl2)))
5720 (define-public r-reticulate
5722 (name "r-reticulate")
5727 (uri (cran-uri "reticulate" version))
5730 "1qwxh7zq9igl7dxl5g5qjbvv0mlac3w80djnkm0w8rxnaval3gmd"))))
5731 (build-system r-build-system)
5732 (inputs `(("python" ,python)))
5734 `(("r-jsonlite" ,r-jsonlite)
5735 ("r-matrix" ,r-matrix)
5736 ("r-rcpp" ,r-rcpp)))
5737 (home-page "https://github.com/rstudio/reticulate")
5738 (synopsis "R interface to Python")
5740 "This package provides an interface from R to Python modules, classes,
5741 and functions. When calling into Python, R data types are automatically
5742 converted to their equivalent Python types. When values are returned from
5743 Python to R they are converted back to R types.")
5744 (license license:asl2.0)))
5746 (define-public r-bibtex
5753 (uri (cran-uri "bibtex" version))
5756 "0wl3925ryd54g1nv3ncwllc493d39dpgy5md61940h69c0van1hz"))))
5757 (build-system r-build-system)
5758 (propagated-inputs `(("r-stringr" ,r-stringr)))
5759 (home-page "https://github.com/romainfrancois/bibtex")
5760 (synopsis "Bibtex parser")
5761 (description "This package provides a utility for R to parse a bibtex
5763 (license license:gpl2+)))
5765 (define-public r-ggseqlogo
5767 (name "r-ggseqlogo")
5772 (uri (cran-uri "ggseqlogo" version))
5775 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
5776 (build-system r-build-system)
5777 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
5778 (home-page "https://github.com/omarwagih/ggseqlogo")
5779 (synopsis "ggplot2 extension for drawing genetic sequence logos")
5781 "The range of functions provided by this package makes it possible to
5782 draw highly versatile genomic sequence logos. Features include, but are not
5783 limited to, modifying colour schemes and fonts used to draw the logo,
5784 generating multiple logo plots, and aiding the visualisation with annotations.
5785 Sequence logos can easily be combined with other ggplot2 plots.")
5786 ;; Unspecified version of the LGPL.
5787 (license license:lgpl3+)))
5789 (define-public r-ggsci
5796 (uri (cran-uri "ggsci" version))
5799 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
5800 (build-system r-build-system)
5802 `(("r-ggplot2" ,r-ggplot2)
5803 ("r-scales" ,r-scales)))
5804 (home-page "https://nanx.me/ggsci/")
5805 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
5807 "This package provides a collection of ggplot2 color palettes inspired by
5808 plots in scientific journals, data visualization libraries, science fiction
5809 movies, and TV shows.")
5810 (license license:gpl3)))
5812 (define-public r-ggsignif
5819 (uri (cran-uri "ggsignif" version))
5822 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
5823 (build-system r-build-system)
5825 `(("r-ggplot2" ,r-ggplot2)))
5826 (home-page "https://github.com/const-ae/ggsignif")
5827 (synopsis "Significance brackets for ggplot2")
5829 "Enrich your ggplots with group-wise comparisons. This package provides
5830 an easy way to indicate if two groups are significantly different. Commonly
5831 this is shown by a bracket on top connecting the groups of interest which
5832 itself is annotated with the level of significance. The package provides a
5833 single layer that takes the groups for comparison and the test as arguments
5834 and adds the annotation to the plot.")
5835 (license license:gpl3)))
5837 (define-public r-ggpubr
5844 (uri (cran-uri "ggpubr" version))
5847 "0ln1gh3zlfx5s7zqcpvfdiksq74v1pma5kwkhc6r0riqnjjd19pf"))))
5848 (build-system r-build-system)
5850 `(("r-cowplot" ,r-cowplot)
5851 ("r-dplyr" ,r-dplyr)
5852 ("r-ggplot2" ,r-ggplot2)
5853 ("r-ggrepel" ,r-ggrepel)
5854 ("r-ggsci" ,r-ggsci)
5855 ("r-ggsignif" ,r-ggsignif)
5857 ("r-gridextra" ,r-gridextra)
5858 ("r-magrittr" ,r-magrittr)
5859 ("r-polynom" ,r-polynom)
5860 ("r-purrr" ,r-purrr)
5861 ("r-rlang" ,r-rlang)
5862 ("r-scales" ,r-scales)
5863 ("r-tidyr" ,r-tidyr)))
5864 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
5865 (synopsis "ggplot2-based publication-ready plots")
5867 "The ggplot2 package is an excellent and flexible package for elegant
5868 data visualization in R. However the default generated plots require some
5869 formatting before we can send them for publication. The ggpubr package
5870 provides some easy-to-use functions for creating and customizing ggplot2-based
5871 publication-ready plots.")
5872 (license license:gpl2)))
5874 (define-public r-ellipse
5881 (uri (cran-uri "ellipse" version))
5884 "0g82vc51m3c1k0hnpp2zla6amxxgk2mmkl8ssnsc49jv3599r6hs"))))
5885 (build-system r-build-system)
5886 (home-page "https://cran.r-project.org/web/packages/ellipse/")
5887 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
5889 "This package contains various routines for drawing ellipses and
5890 ellipse-like confidence regions, implementing the plots described in Murdoch
5891 and Chow (1996), A graphical display of large correlation matrices, The
5892 American Statistician 50, 178-180. There are also routines implementing the
5893 profile plots described in Bates and Watts (1988), Nonlinear Regression
5894 Analysis and its Applications.")
5895 (license license:gpl2+)))
5897 (define-public r-flashclust
5899 (name "r-flashclust")
5904 (uri (cran-uri "flashClust" version))
5907 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
5908 (properties `((upstream-name . "flashClust")))
5909 (build-system r-build-system)
5910 (native-inputs `(("gfortran" ,gfortran)))
5911 (home-page "https://cran.r-project.org/web/packages/flashClust/")
5912 (synopsis "Implementation of optimal hierarchical clustering")
5914 "This package provides a fast implementation of hierarchical
5916 (license license:gpl2+)))
5918 (define-public r-factominer
5920 (name "r-factominer")
5925 (uri (cran-uri "FactoMineR" version))
5928 "0qiw60ypf3bf5xsqz2b9l82i4jvprjm8lzpp12lhl8d9j5s8m0j8"))))
5929 (properties `((upstream-name . "FactoMineR")))
5930 (build-system r-build-system)
5933 ("r-cluster" ,r-cluster)
5934 ("r-ellipse" ,r-ellipse)
5935 ("r-flashclust" ,r-flashclust)
5936 ("r-ggplot2" ,r-ggplot2)
5937 ("r-ggrepel" ,r-ggrepel)
5938 ("r-lattice" ,r-lattice)
5939 ("r-leaps" ,r-leaps)
5941 ("r-scatterplot3d" ,r-scatterplot3d)))
5942 (home-page "http://factominer.free.fr")
5943 (synopsis "Multivariate exploratory data analysis and data mining")
5945 "This package provides exploratory data analysis methods to summarize,
5946 visualize and describe datasets. The main principal component methods are
5947 available, those with the largest potential in terms of applications:
5948 principal component analysis (PCA) when variables are quantitative,
5949 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
5950 variables are categorical, Multiple Factor Analysis when variables are
5951 structured in groups, etc. and hierarchical cluster analysis.")
5952 (license license:gpl2+)))
5954 (define-public r-factoextra
5956 (name "r-factoextra")
5961 (uri (cran-uri "factoextra" version))
5964 "0bpsbcmp6jpa9qk53dhfzghrz98dh0h0n68brl7rjz724yjbvhn8"))))
5965 (build-system r-build-system)
5967 `(("r-abind" ,r-abind)
5968 ("r-cluster" ,r-cluster)
5969 ("r-dendextend" ,r-dendextend)
5970 ("r-factominer" ,r-factominer)
5971 ("r-ggplot2" ,r-ggplot2)
5972 ("r-ggpubr" ,r-ggpubr)
5973 ("r-ggrepel" ,r-ggrepel)
5974 ("r-reshape2" ,r-reshape2)
5975 ("r-tidyr" ,r-tidyr)))
5976 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
5977 (synopsis "Extract and visualize the results of multivariate data analyses")
5979 "This package provides some easy-to-use functions to extract and
5980 visualize the output of multivariate data analyses, including
5981 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
5982 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
5983 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
5984 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
5985 packages. It contains also functions for simplifying some clustering analysis
5986 steps and provides ggplot2-based elegant data visualization.")
5987 (license license:gpl2)))
5989 (define-public r-fansi
5996 (uri (cran-uri "fansi" version))
5999 "02f2rx7v7wz6w97m2slwky2i5y8f9iafycmkyr3siy3z3k8fj171"))))
6000 (build-system r-build-system)
6002 `(("r-knitr" ,r-knitr))) ; for vignettes
6003 (home-page "https://github.com/brodieG/fansi")
6004 (synopsis "ANSI control sequence aware string functions")
6006 "This package provides counterparts to R string manipulation functions
6007 that account for the effects of ANSI text formatting control sequences.")
6008 (license license:gpl2+)))
6010 (define-public r-nbclust
6017 (uri (cran-uri "NbClust" version))
6020 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
6021 (properties `((upstream-name . "NbClust")))
6022 (build-system r-build-system)
6023 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
6024 (synopsis "Determine the best number of clusters in a data set")
6026 "NbClust provides 30 indexes for determining the optimal number of
6027 clusters in a data set and offers the best clustering scheme from different
6028 results to the user.")
6029 (license license:gpl2)))
6031 (define-public r-hdf5r
6038 (uri (cran-uri "hdf5r" version))
6041 "1pq12vkfqxvcaznwaxvjdg3acimk5a20m8h18sixvxc34vnqxw8f"))))
6042 (build-system r-build-system)
6047 `(("r-bit64" ,r-bit64)
6049 (home-page "https://hhoeflin.github.io/hdf5r")
6050 (synopsis "Interface to the HDF5 binary data format")
6052 "HDF5 is a data model, library and file format for storing and managing
6053 large amounts of data. This package provides a nearly feature complete,
6054 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
6055 functionality is added so that HDF5 objects behave very similar to their
6056 corresponding R counterparts.")
6057 (license license:asl2.0)))
6059 (define-public r-itertools
6061 (name "r-itertools")
6066 (uri (cran-uri "itertools" version))
6069 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
6070 (build-system r-build-system)
6072 `(("r-iterators" ,r-iterators)))
6073 (home-page "https://cran.r-project.org/web/packages/itertools/")
6074 (synopsis "Iterator tools")
6076 "This package provides various tools for creating iterators, many
6077 patterned after functions in the Python @code{itertools} module, and others
6078 patterned after functions in the snow package.")
6079 (license license:gpl2)))
6081 (define-public r-polynom
6088 (uri (cran-uri "polynom" version))
6091 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
6092 (build-system r-build-system)
6093 (home-page "https://cran.r-project.org/web/packages/polynom/")
6094 (synopsis "Functions for univariate polynomial manipulations")
6096 "This package provides a collection of functions to implement a class for
6097 univariate polynomial manipulations.")
6098 (license license:gpl2)))
6100 (define-public r-gbrd
6107 (uri (cran-uri "gbRd" version))
6110 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
6111 (properties `((upstream-name . "gbRd")))
6112 (build-system r-build-system)
6113 (home-page "https://cran.r-project.org/web/packages/gbRd/")
6114 (synopsis "Utilities for processing Rd objects and files")
6116 "This package provides utilities for processing Rd objects and files.
6117 Extract argument descriptions and other parts of the help pages of
6119 (license license:gpl2+)))
6121 (define-public r-rjags
6128 (uri (cran-uri "rjags" version))
6131 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
6132 (build-system r-build-system)
6134 `(("r-coda" ,r-coda)))
6138 `(("pkg-config" ,pkg-config)))
6139 (home-page "http://mcmc-jags.sourceforge.net")
6140 (synopsis "Bayesian graphical models using MCMC")
6142 "This package provides an R interface to the JAGS MCMC library. JAGS is
6143 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
6144 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
6145 (license license:gpl2)))
6147 (define-public r-rdpack
6154 (uri (cran-uri "Rdpack" version))
6157 "11cd27s6zp5cxnwxcvz6rjf00y0r7aq8ywhzwpf1r4xy1z44kd4g"))))
6158 (properties `((upstream-name . "Rdpack")))
6159 (build-system r-build-system)
6161 `(("r-bibtex" ,r-bibtex)
6162 ("r-gbrd" ,r-gbrd)))
6163 (home-page "https://github.com/GeoBosh/Rdpack")
6164 (synopsis "Update and manipulate Rd documentation objects")
6166 "This package provides functions for manipulation of R documentation
6167 objects, including functions @code{reprompt()} and @code{ereprompt()} for
6168 updating Rd documentation for functions, methods and classes; it also includes
6169 Rd macros for citations and import of references from bibtex files for use in
6170 Rd files and roxygen2 comments, as well as many functions for manipulation of
6171 references and Rd files.")
6172 (license license:gpl2+)))
6174 (define-public r-officer
6181 (uri (cran-uri "officer" version))
6184 "1i6jmnbkx7gd0qyf6akhizmxp7y1dh3h7a886mcbmrzka9d60zh4"))))
6185 (build-system r-build-system)
6187 `(("r-base64enc" ,r-base64enc)
6188 ("r-digest" ,r-digest)
6189 ("r-htmltools" ,r-htmltools)
6190 ("r-magrittr" ,r-magrittr)
6193 ("r-rlang" ,r-rlang)
6197 (home-page "https://davidgohel.github.io/officer")
6198 (synopsis "Manipulation of Word and PowerPoint documents")
6200 "This package provides tools to access and manipulate Word and PowerPoint
6201 documents from R. The package focuses on tabular and graphical reporting from
6202 R; it also provides two functions that let users get document content into
6203 data objects. A set of functions lets add and remove images, tables and
6204 paragraphs of text in new or existing documents. When working with PowerPoint
6205 presentations, slides can be added or removed; shapes inside slides can also
6206 be added or removed. When working with Word documents, a cursor can be used
6207 to help insert or delete content at a specific location in the document.")
6208 (license license:gpl3)))
6210 (define-public r-abn
6217 (uri (cran-uri "abn" version))
6220 "19w6bdjyp4zwqs6p0flry4qxqynf9rh8ykdrfrp61wrdf7kysw0d"))))
6221 (build-system r-build-system)
6225 `(("r-lme4" ,r-lme4)
6229 ("r-rcpparmadillo" ,r-rcpparmadillo)
6230 ("r-rjags" ,r-rjags)))
6231 (home-page "http://www.r-bayesian-networks.org")
6232 (synopsis "Modelling multivariate data with additive bayesian networks")
6234 "Bayesian network analysis is a form of probabilistic graphical models
6235 which derives from empirical data a directed acyclic graph, DAG, describing
6236 the dependency structure between random variables. An additive Bayesian
6237 network model consists of a form of a DAG where each node comprises a
6238 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
6239 equivalent to Bayesian multivariate regression using graphical modelling, they
6240 generalises the usual multivariable regression, GLM, to multiple dependent
6241 variables. This package provides routines to help determine optimal Bayesian
6242 network models for a given data set, where these models are used to identify
6243 statistical dependencies in messy, complex data.")
6244 (license license:gpl2+)))
6246 (define-public r-acd
6253 (uri (cran-uri "ACD" version))
6256 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
6257 (properties `((upstream-name . "ACD")))
6258 (build-system r-build-system)
6259 (home-page "https://cran.r-project.org/web/packages/ACD/")
6260 (synopsis "Categorical data analysis with complete or missing responses")
6262 "This package provides tools for categorical data analysis with complete
6263 or missing responses.")
6264 (license license:gpl2+)))
6266 (define-public r-acdm
6273 (uri (cran-uri "ACDm" version))
6276 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
6277 (properties `((upstream-name . "ACDm")))
6278 (build-system r-build-system)
6280 `(("r-dplyr" ,r-dplyr)
6281 ("r-ggplot2" ,r-ggplot2)
6283 ("r-rsolnp" ,r-rsolnp)
6285 (home-page "https://cran.r-project.org/web/packages/ACDm/")
6286 (synopsis "Tools for Autoregressive Conditional Duration Models")
6288 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
6289 and Russell, 1998) models. It creates trade, price or volume durations from
6290 transactions (tic) data, performs diurnal adjustments, fits various ACD models
6292 (license license:gpl2+)))
6294 (define-public r-overlap
6301 (uri (cran-uri "overlap" version))
6304 "1j3m6ir1chdz0si2fhcw6gs7c9h09bv0chz18rpzxsywww6d4rzy"))))
6305 (build-system r-build-system)
6306 (home-page "https://cran.r-project.org/web/packages/overlap/")
6307 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
6309 "This package provides functions to fit kernel density functions to data
6310 on temporal activity patterns of animals; estimate coefficients of overlapping
6311 of densities for two species; and calculate bootstrap estimates of confidence
6313 (license license:gpl3+)))
6315 (define-public r-snakecase
6317 (name "r-snakecase")
6322 (uri (cran-uri "snakecase" version))
6325 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
6326 (build-system r-build-system)
6328 `(("r-stringi" ,r-stringi)
6329 ("r-stringr" ,r-stringr)))
6330 (home-page "https://github.com/Tazinho/snakecase")
6331 (synopsis "Convert strings into any case")
6333 "This package provides a consistent, flexible and easy to use tool to
6334 parse and convert strings into cases like snake or camel among others.")
6335 (license license:gpl3)))
6337 (define-public r-prediction
6339 (name "r-prediction")
6344 (uri (cran-uri "prediction" version))
6347 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
6348 (build-system r-build-system)
6350 `(("r-data-table" ,r-data-table)))
6351 (home-page "https://github.com/leeper/prediction")
6352 (synopsis "Tidy, type-safe prediction methods")
6354 "This package provides the @code{prediction()} function, a type-safe
6355 alternative to @code{predict()} that always returns a data frame. The package
6356 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
6357 from the @code{stats} package, as well as numerous other model classes from
6358 other add-on packages.")
6359 (license license:expat)))
6361 (define-public r-insight
6368 (uri (cran-uri "insight" version))
6371 "0scjmr8qvwaswb9wfq2lxp1v5fl72way8cid9agrf0z1agp0adad"))))
6372 (build-system r-build-system)
6373 (home-page "https://easystats.github.io/insight/")
6374 (synopsis "Easy access to model information for various model objects")
6376 "This package provides a tool to provide an easy, intuitive and
6377 consistent access to information contained in various R models, like model
6378 formulas, model terms, information about random effects, data that was used to
6379 fit the model or data from response variables. The package mainly revolves
6380 around two types of functions: Functions that find (the names of) information,
6381 starting with @code{find_}, and functions that get the underlying data,
6382 starting with @code{get_}. The package has a consistent syntax and works with
6383 many different model objects, where otherwise functions to access these
6384 information are missing.")
6385 (license license:gpl3)))
6387 (define-public r-sjlabelled
6389 (name "r-sjlabelled")
6394 (uri (cran-uri "sjlabelled" version))
6397 "0c9wy0gsr2sbkrv2638xbi7qm0gl6jyr6sfricavhkm7l4hljjkz"))))
6398 (build-system r-build-system)
6400 `(("r-haven" ,r-haven)
6401 ("r-insight" ,r-insight)
6402 ("r-magrittr" ,r-magrittr)
6403 ("r-purrr" ,r-purrr)
6404 ("r-rlang" ,r-rlang)
6405 ("r-tidyselect" ,r-tidyselect)))
6406 (home-page "https://github.com/strengejacke/sjlabelled")
6407 (synopsis "Labelled data utility functions")
6409 "This package provides a collection of functions dealing with labelled
6410 data, like reading and writing data between R and other statistical software
6411 packages. This includes easy ways to get, set or change value and variable
6412 label attributes, to convert labelled vectors into factors or numeric (and
6413 vice versa), or to deal with multiple declared missing values.")
6414 (license license:gpl3)))
6416 (define-public r-sjmisc
6423 (uri (cran-uri "sjmisc" version))
6426 "0rl0bmk91wc4dxdgy008fl0dwkx3ffvys30vgpnr78lb4pk45nb2"))))
6427 (build-system r-build-system)
6429 `(("r-dplyr" ,r-dplyr)
6430 ("r-insight" ,r-insight)
6431 ("r-magrittr" ,r-magrittr)
6432 ("r-purrr" ,r-purrr)
6433 ("r-rlang" ,r-rlang)
6434 ("r-sjlabelled" ,r-sjlabelled)
6435 ("r-tidyselect" ,r-tidyselect)))
6436 (home-page "https://github.com/strengejacke/sjmisc")
6437 (synopsis "Data and variable transformation functions")
6439 "This package is a collection of miscellaneous utility functions,
6440 supporting data transformation tasks like recoding, dichotomizing or grouping
6441 variables, setting and replacing missing values. The data transformation
6442 functions also support labelled data, and all integrate seamlessly into a
6443 tidyverse workflow.")
6444 (license license:gpl3)))
6446 (define-public r-nortest
6453 (uri (cran-uri "nortest" version))
6456 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
6457 (build-system r-build-system)
6458 (home-page "https://cran.r-project.org/web/packages/nortest/")
6459 (synopsis "Tests for normality")
6461 "This package provides five omnibus tests for testing the composite
6462 hypothesis of normality.")
6463 (license license:gpl2+)))
6465 (define-public r-moonbook
6472 (uri (cran-uri "moonBook" version))
6475 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
6476 (properties `((upstream-name . "moonBook")))
6477 (build-system r-build-system)
6479 `(("r-magrittr" ,r-magrittr)
6480 ("r-nortest" ,r-nortest)
6481 ("r-purrr" ,r-purrr)
6482 ("r-sjmisc" ,r-sjmisc)
6483 ("r-stringr" ,r-stringr)
6484 ("r-survival" ,r-survival)))
6485 (home-page "https://github.com/cardiomoon/moonBook")
6486 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
6488 "This package provides several analysis-related functions for the book
6489 entitled \"R statistics and graph for medical articles\" (written in Korean),
6490 version 1, by Keon-Woong Moon with Korean demographic data with several plot
6492 (license license:gpl2)))
6494 (define-public r-flextable
6496 (name "r-flextable")
6501 (uri (cran-uri "flextable" version))
6504 "1f869f2dfqkzhf6yix7xcbs8rn1nwq3sg623h74zg6h1pl6px66w"))))
6505 (build-system r-build-system)
6507 `(("r-base64enc" ,r-base64enc)
6508 ("r-data-table" ,r-data-table)
6509 ("r-gdtools" ,r-gdtools)
6510 ("r-htmltools" ,r-htmltools)
6511 ("r-knitr" ,r-knitr)
6512 ("r-officer" ,r-officer)
6513 ("r-rlang" ,r-rlang)
6514 ("r-rmarkdown" ,r-rmarkdown)
6515 ("r-xml2" ,r-xml2)))
6516 (home-page "https://davidgohel.github.io/flextable")
6517 (synopsis "Functions for tabular reporting")
6519 "This package provides tools to create pretty tables for HTML documents
6520 and other formats. Functions are provided to let users create tables, modify
6521 and format their content. It extends the @code{officer} package and can be
6522 used within R markdown documents when rendering to HTML and to Word
6524 (license license:gpl3)))
6526 (define-public r-writexl
6533 (uri (cran-uri "writexl" version))
6536 "09fhdip6igcg97fjx4c7727cx2lb49l4d74l4i8rg2bag2s5lrj3"))))
6537 (build-system r-build-system)
6538 (inputs `(("zlib" ,zlib)))
6539 (home-page "https://github.com/ropensci/writexl")
6540 (synopsis "Export data frames to xlsx format")
6542 "This package provides a data frame to xlsx exporter based on
6544 (license license:bsd-2)))
6546 (define-public r-biasedurn
6548 (name "r-biasedurn")
6553 (uri (cran-uri "BiasedUrn" version))
6556 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
6557 (properties `((upstream-name . "BiasedUrn")))
6558 (build-system r-build-system)
6559 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
6560 (synopsis "Biased Urn model distributions")
6562 "This package provides statistical models of biased sampling in the form
6563 of univariate and multivariate noncentral hypergeometric distributions,
6564 including Wallenius' noncentral hypergeometric distribution and Fisher's
6565 noncentral hypergeometric distribution (also called extended hypergeometric
6567 (license license:gpl3)))
6569 (define-public r-goplot
6576 (uri (cran-uri "GOplot" version))
6579 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
6580 (properties `((upstream-name . "GOplot")))
6581 (build-system r-build-system)
6583 `(("r-ggdendro" ,r-ggdendro)
6584 ("r-ggplot2" ,r-ggplot2)
6585 ("r-gridextra" ,r-gridextra)
6586 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6587 (home-page "https://github.com/wencke/wencke.github.io")
6588 (synopsis "Visualization of functional analysis data")
6590 "This package provides an implementation of multilayered visualizations
6591 for enhanced graphical representation of functional analysis data. It
6592 combines and integrates omics data derived from expression and functional
6593 annotation enrichment analyses. Its plotting functions have been developed
6594 with an hierarchical structure in mind: starting from a general overview to
6595 identify the most enriched categories (modified bar plot, bubble plot) to a
6596 more detailed one displaying different types of relevant information for the
6597 molecules in a given set of categories (circle plot, chord plot, cluster plot,
6598 Venn diagram, heatmap).")
6599 (license license:gpl2)))
6601 (define-public r-getopt
6608 (uri (cran-uri "getopt" version))
6611 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
6612 (build-system r-build-system)
6613 (home-page "https://github.com/trevorld/getopt")
6614 (synopsis "Command-line option processor for R")
6616 "This package is designed to be used with Rscript to write shebang
6617 scripts that accept short and long options. Many users will prefer to
6618 use the packages @code{optparse} or @code{argparse} which add extra
6619 features like automatically generated help options and usage texts,
6620 support for default values, positional argument support, etc.")
6621 (license license:gpl2+)))
6623 (define-public r-findpython
6625 (name "r-findpython")
6630 (uri (cran-uri "findpython" version))
6633 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
6634 (build-system r-build-system)
6635 (home-page "https://github.com/trevorld/findpython")
6636 (synopsis "Functions to find an acceptable Python binary")
6638 "This package was designed to find an acceptable Python binary that
6639 matches version and feature constraints.")
6640 (license license:expat)))
6642 ;; This in not the same as "r-argparser"
6643 (define-public r-argparse
6650 (uri (cran-uri "argparse" version))
6653 "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l"))))
6654 (build-system r-build-system)
6655 (inputs `(("python" ,python)))
6657 `(("r-findpython" ,r-findpython)
6658 ("r-jsonlite" ,r-jsonlite)
6660 (home-page "https://github.com/trevorld/argparse")
6661 (synopsis "Command line optional and positional argument parser")
6663 "This package provides a command line parser to be used with Rscript to
6664 write shebang scripts that gracefully accept positional and optional arguments
6665 and automatically generate usage notices.")
6666 (license license:gpl2+)))
6668 (define-public r-hash
6675 (uri (cran-uri "hash" version))
6678 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
6679 (build-system r-build-system)
6680 (home-page "https://cran.r-project.org/web/packages/hash/")
6681 (synopsis "Implementation of hash/associated arrays/dictionaries")
6683 "This package implements a data structure similar to hashes in Perl and
6684 dictionaries in Python but with a purposefully R flavor. For objects of
6685 appreciable size, access using hashes outperforms native named lists and
6687 (license license:gpl2+)))
6689 (define-public r-orddom
6696 (uri (cran-uri "orddom" version))
6699 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
6700 (build-system r-build-system)
6701 (propagated-inputs `(("r-psych" ,r-psych)))
6702 (home-page "https://cran.r-project.org/web/packages/orddom/")
6703 (synopsis "Ordinal dominance statistics")
6705 "This package provides tools to compute ordinal, statistics and effect
6706 sizes as an alternative to mean comparison: Cliff's delta or success rate
6707 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
6708 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
6709 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
6710 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
6711 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
6712 Group (Non-)Overlap considerations.")
6713 (license license:gpl2)))
6715 (define-public r-deriv
6722 (uri (cran-uri "Deriv" version))
6725 "0hlqm216bg3l79gq6m0am0xz6vd3l2hgjnjm6lym3mkmgkka4kxw"))))
6726 (properties `((upstream-name . "Deriv")))
6727 (build-system r-build-system)
6728 (home-page "https://cran.r-project.org/web/packages/Deriv")
6729 (synopsis "Symbolic differentiation")
6731 "This package provides an R-based solution for symbolic differentiation.
6732 It admits user-defined functions as well as function substitution in arguments
6733 of functions to be differentiated. Some symbolic simplification is part of
6735 (license license:gpl3+)))
6737 (define-public r-doby
6744 (uri (cran-uri "doBy" version))
6747 "1d0d6pwai1g4i5jls0jm9va29ci5hy92n5957608f3fzi1jwy635"))))
6748 (properties `((upstream-name . "doBy")))
6749 (build-system r-build-system)
6751 `(("r-broom" ,r-broom)
6752 ("r-deriv" ,r-deriv)
6753 ("r-dplyr" ,r-dplyr)
6754 ("r-magrittr" ,r-magrittr)
6756 ("r-matrix" ,r-matrix)
6758 ("r-pbkrtest" ,r-pbkrtest)
6759 ("r-tibble" ,r-tibble)))
6760 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
6761 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
6763 "This package contains:
6766 @item facilities for working with grouped data: @code{do}
6767 something to data stratified @code{by} some variables.
6768 @item implementations of least-squares means, general linear contrasts, and
6769 @item miscellaneous other utilities.
6771 (license license:gpl2+)))
6773 (define-public r-refgenome
6775 (name "r-refgenome")
6780 (uri (cran-uri "refGenome" version))
6783 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
6784 (properties `((upstream-name . "refGenome")))
6785 (build-system r-build-system)
6789 ("r-rsqlite" ,r-rsqlite)))
6790 (home-page "https://cran.r-project.org/web/packages/refGenome/")
6792 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
6794 "This package contains functionality for importing and managing of
6795 downloaded genome annotation data from the Ensembl genome browser (European
6796 Bioinformatics Institute) and from the UCSC genome browser (University of
6797 California, Santa Cruz) and annotation routines for genomic positions and
6798 splice site positions.")
6799 (license license:gpl2)))
6801 (define-public r-basix
6808 (uri (cran-uri "BASIX" version))
6811 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
6812 (properties `((upstream-name . "BASIX")))
6813 (build-system r-build-system)
6814 (home-page "https://cran.r-project.org/web/packages/BASIX/")
6815 (synopsis "Efficient C/C++ toolset for R")
6817 "BASIX provides some efficient C/C++ implementations of native R
6818 procedures to speed up calculations in R.")
6819 (license license:gpl2)))
6821 (define-public r-blockfest
6823 (name "r-blockfest")
6828 (uri (cran-uri "BlockFeST" version))
6831 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
6832 (properties `((upstream-name . "BlockFeST")))
6833 (build-system r-build-system)
6834 (propagated-inputs `(("r-basix" ,r-basix)))
6835 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
6836 (synopsis "Bayesian calculation of region-specific fixation index")
6838 "This package provides an R implementation of an extension of the
6839 BayeScan software for codominant markers, adding the option to group
6840 individual SNPs into pre-defined blocks. A typical application of this new
6841 approach is the identification of genomic regions, genes, or gene sets
6842 containing one or more SNPs that evolved under directional selection.")
6843 (license license:gpl2)))
6845 (define-public r-proc
6852 (uri (cran-uri "pROC" version))
6855 "1jx8af9p6sxbypqvj1cci7q9sbyaw310inbjxibjcr3acj59h45h"))))
6856 (properties `((upstream-name . "pROC")))
6857 (build-system r-build-system)
6859 `(("r-plyr" ,r-plyr)
6860 ("r-rcpp" ,r-rcpp)))
6861 (home-page "http://expasy.org/tools/pROC/")
6862 (synopsis "Display and analyze ROC curves")
6864 "This package provides tools for visualizing, smoothing and comparing
6865 receiver operating characteristic (ROC curves). The area under the
6866 curve (AUC) can be compared with statistical tests based on U-statistics or
6867 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
6868 (license license:gpl3+)))
6870 (define-public r-rootsolve
6872 (name "r-rootsolve")
6877 (uri (cran-uri "rootSolve" version))
6880 "0skrspq7sd7gaq73w91km14v8znc8chncgy64hvjgcng2xw15phx"))))
6881 (properties `((upstream-name . "rootSolve")))
6882 (build-system r-build-system)
6883 (native-inputs `(("gfortran" ,gfortran)))
6884 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
6885 (synopsis "Tools for the analysis of ordinary differential equations")
6887 "This package provides routines to find the root of nonlinear functions,
6888 and to perform steady-state and equilibrium analysis of @dfn{ordinary
6889 differential equations} (ODE). It includes routines that:
6892 @item generate gradient and jacobian matrices (full and banded),
6893 @item find roots of non-linear equations by the Newton-Raphson method,
6894 @item estimate steady-state conditions of a system of (differential) equations
6895 in full, banded or sparse form, using the Newton-Raphson method, or by
6896 dynamically running,
6897 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
6898 and 3-D partial differential equations, that have been converted to ordinary
6899 differential equations by numerical differencing (using the method-of-lines
6902 (license license:gpl2+)))
6904 (define-public r-abcanalysis
6906 (name "r-abcanalysis")
6911 (uri (cran-uri "ABCanalysis" version))
6913 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
6914 (properties `((upstream-name . "ABCanalysis")))
6915 (build-system r-build-system)
6916 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
6917 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
6918 (synopsis "Computed ABC Analysis")
6920 "Multivariate data sets often differ in several factors or derived statistical
6921 parameters, which have to be selected for a valid interpretation. Basing this
6922 selection on traditional statistical limits leads occasionally to the perception
6923 of losing information from a data set. This package provides tools to calculate
6924 these limits on the basis of the mathematical properties of the distribution of
6925 the analyzed items.")
6926 (license license:gpl3)))
6928 (define-public r-slam
6935 (uri (cran-uri "slam" version))
6937 (base32 "1ihhbx76miwys35gsbhijriadvrw4f51lc3v45pnn6cvcfd9hr0b"))))
6938 (build-system r-build-system)
6939 (home-page "https://cran.r-project.org/web/packages/slam/")
6940 (synopsis "Sparse lightweight arrays and matrices")
6942 "This package contains data structures and algorithms for sparse arrays and matrices,
6943 based on index arrays and simple triplet representations, respectively.")
6944 (license license:gpl2)))
6946 (define-public r-manipulatewidget
6948 (name "r-manipulatewidget")
6953 (uri (cran-uri "manipulateWidget" version))
6955 (base32 "1zagrbwkn2d50zzw8i2vyb1hsq4cydmfsqiy1a2qlp6zrv8a6q9x"))))
6957 `((upstream-name . "manipulateWidget")))
6958 (build-system r-build-system)
6960 `(("r-base64enc" ,r-base64enc)
6961 ("r-codetools" ,r-codetools)
6962 ("r-htmltools" ,r-htmltools)
6963 ("r-htmlwidgets" ,r-htmlwidgets)
6964 ("r-knitr" ,r-knitr)
6965 ("r-miniui" ,r-miniui)
6966 ("r-shiny" ,r-shiny)
6967 ("r-webshot" ,r-webshot)))
6968 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
6969 (synopsis "Add even more interactivity to interactive charts")
6971 "This package lets you create in just a few lines of R code a nice user interface to
6972 modify the data or the graphical parameters of one or multiple interactive
6973 charts. It is useful to quickly explore visually some data or for package
6974 developers to generate user interfaces easy to maintain.")
6975 (license license:gpl2+)))
6984 (uri (cran-uri "A3" version))
6986 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
6987 (properties `((upstream-name . "A3")))
6988 (build-system r-build-system)
6990 `(("r-pbapply" ,r-pbapply)
6991 ("r-xtable" ,r-xtable)))
6992 (home-page "https://cran.r-project.org/web/packages/A3/")
6993 (synopsis "Error metrics for predictive models")
6995 "This package supplies tools for tabulating and analyzing the results of predictive
6996 models. The methods employed are applicable to virtually any predictive model
6997 and make comparisons between different methodologies straightforward.")
6998 (license license:gpl2+)))
7000 (define-public r-infotheo
7007 (uri (cran-uri "infotheo" version))
7010 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
7011 (build-system r-build-system)
7012 (home-page "http://homepage.meyerp.com/software")
7013 (synopsis "Information-theoretic measures")
7015 "This package implements various measures of information theory based on
7016 several entropy estimators.")
7017 (license license:gpl3+)))
7019 (define-public r-abcoptim
7026 (uri (cran-uri "ABCoptim" version))
7028 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
7029 (properties `((upstream-name . "ABCoptim")))
7030 (build-system r-build-system)
7031 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
7032 (home-page "https://github.com/gvegayon/ABCoptim/")
7033 (synopsis "Optimization of Artificial Bee Colony algorithm")
7035 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
7036 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
7037 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
7038 algorithms, and uses only common control parameters such as colony size and
7039 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
7040 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
7041 This version is a work-in-progress and is written in R code.")
7042 (license license:expat)))
7044 (define-public r-abcp2
7051 (uri (cran-uri "ABCp2" version))
7053 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
7054 (properties `((upstream-name . "ABCp2")))
7055 (build-system r-build-system)
7056 (propagated-inputs `(("r-mass" ,r-mass)))
7057 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
7058 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
7060 "This package tests the goodness of fit of a distribution of offspring to the Normal,
7061 Poisson, and Gamma distribution and estimates the proportional paternity of the
7062 second male (P2) based on the best fit distribution.")
7063 (license license:gpl2)))
7065 (define-public r-abcrf
7072 (uri (cran-uri "abcrf" version))
7074 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
7075 (build-system r-build-system)
7077 `(("r-doparallel" ,r-doparallel)
7078 ("r-foreach" ,r-foreach)
7080 ("r-matrixstats" ,r-matrixstats)
7081 ("r-ranger" ,r-ranger)
7083 ("r-rcpparmadillo" ,r-rcpparmadillo)
7084 ("r-readr" ,r-readr)
7085 ("r-stringr" ,r-stringr)))
7086 (home-page "https://cran.r-project.org/web/packages/abcrf/")
7087 (synopsis "Approximate bayesian computation via random forests")
7089 "This package performs approximate bayesian computation (ABC) model choice and
7090 parameter inference via random forests. This machine learning tool named random
7091 forests (RF) can conduct selection among the highly complex models covered by
7093 (license license:gpl2+)))
7095 (define-public r-abctools
7102 (uri (cran-uri "abctools" version))
7104 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
7105 (build-system r-build-system)
7108 ("r-abind" ,r-abind)
7109 ("r-hmisc" ,r-hmisc)
7110 ("r-plyr" ,r-plyr)))
7111 (home-page "https://github.com/dennisprangle/abctools/")
7112 (synopsis "Tools for ABC analyses")
7114 "This @code{r-abctools} package provides tools for approximate Bayesian computation
7115 including summary statistic selection and assessing coverage. This includes
7116 recent dimension reduction algorithms to tune the choice of summary statistics,
7117 and coverage methods to tune the choice of threshold.")
7118 (license license:gpl2+)))
7120 (define-public r-ggstance
7127 (uri (cran-uri "ggstance" version))
7129 (base32 "0kdksay61hyb6612b07r84chh7a9aibjyclk3qcypvr9aang8hkh"))))
7130 (build-system r-build-system)
7132 `(("r-ggplot2" ,r-ggplot2)
7134 ("r-rlang" ,r-rlang)
7135 ("r-withr" ,r-withr)))
7136 (home-page "https://cran.r-project.org/web/packages/ggstance/")
7137 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
7139 "This package is a @code{r-ggplot2} extension that provides flipped components:
7141 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
7142 @item vertical versions of @code{r-ggplot2} positions.
7144 (license license:gpl3)))
7146 (define-public r-mosaiccore
7148 (name "r-mosaiccore")
7153 (uri (cran-uri "mosaicCore" version))
7155 (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
7156 (properties `((upstream-name . "mosaicCore")))
7157 (build-system r-build-system)
7159 `(("r-dplyr" ,r-dplyr)
7160 ("r-lazyeval" ,r-lazyeval)
7162 ("r-rlang" ,r-rlang)
7163 ("r-tidyr" ,r-tidyr)))
7164 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
7165 (synopsis "Common utilities for mosaic family packages")
7167 "Common utilities used in other Mosaic family packages are collected here.")
7168 (license license:gpl2+)))
7170 (define-public r-ggformula
7172 (name "r-ggformula")
7177 (uri (cran-uri "ggformula" version))
7179 (base32 "16ycabhnp78fsiv1dc63ccgh9gmpsy2683vbmq0fdzl6w3pd87sr"))))
7180 (build-system r-build-system)
7182 `(("r-ggplot2" ,r-ggplot2)
7183 ("r-ggstance" ,r-ggstance)
7184 ("r-magrittr" ,r-magrittr)
7185 ("r-mosaiccore" ,r-mosaiccore)
7186 ("r-rlang" ,r-rlang)
7187 ("r-stringr" ,r-stringr)
7188 ("r-tibble" ,r-tibble)
7189 ("r-tidyr" ,r-tidyr)))
7190 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
7191 (synopsis "Formula interface for the @code{r-ggplot2}")
7193 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
7194 gf_density(), and so on, bring the formula interface to ggplot(). This captures
7195 and extends the excellent simplicity of the lattice-graphics formula interface,
7196 while providing the intuitive capabilities of @code{r-ggplot2}.")
7197 (license license:expat)))
7199 (define-public r-mosaicdata
7201 (name "r-mosaicdata")
7206 (uri (cran-uri "mosaicData" version))
7208 (base32 "04z0mdm52mykqsxsinhmsihn181zf6cw321gayk2rjp7lj7mwdq9"))))
7209 (properties `((upstream-name . "mosaicData")))
7210 (build-system r-build-system)
7211 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
7212 (synopsis "Data sets for project Mosaic")
7214 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
7215 used to teach mathematics, statistics, computation and modeling.")
7216 (license license:gpl2+)))
7218 (define-public r-raster
7225 (uri (cran-uri "raster" version))
7228 "0faxv71hlxkblvbi3ps1vfzm3wwi0brwzmpsr5114bddcqyiqkvn"))))
7229 (build-system r-build-system)
7231 `(("r-rcpp" ,r-rcpp)
7233 (home-page "https://www.rspatial.org/")
7234 (synopsis "Geographic data analysis and modeling")
7236 "The package implements basic and high-level functions for reading,
7237 writing, manipulating, analyzing and modeling of gridded spatial data.
7238 Processing of very large files is supported.")
7239 (license license:gpl3+)))
7241 (define-public r-mosaic
7248 (uri (cran-uri "mosaic" version))
7250 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
7251 (build-system r-build-system)
7253 `(("r-broom" ,r-broom)
7254 ("r-dplyr" ,r-dplyr)
7255 ("r-ggdendro" ,r-ggdendro)
7256 ("r-ggformula" ,r-ggformula)
7257 ("r-ggplot2" ,r-ggplot2)
7258 ("r-ggrepel" ,r-ggrepel)
7260 ("r-gridextra" ,r-gridextra)
7261 ("r-lattice" ,r-lattice)
7262 ("r-latticeextra" ,r-latticeextra)
7263 ("r-lazyeval" ,r-lazyeval)
7265 ("r-matrix" ,r-matrix)
7266 ("r-mosaiccore" ,r-mosaiccore)
7267 ("r-mosaicdata" ,r-mosaicdata)
7268 ("r-readr" ,r-readr)
7269 ("r-tidyr" ,r-tidyr)))
7270 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
7271 (synopsis "Mathematics, statistics, and computation teaching utilities")
7273 "This package contain data sets and utilities from
7274 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
7275 statistics, computation and modeling. Project MOSAIC is a community of
7276 educators working to tie together aspects of quantitative work that students
7277 in science, technology, engineering and mathematics will need in their
7278 professional lives, but which are usually taught in isolation, if at all.")
7279 (license license:gpl2+)))
7281 (define-public r-abd
7288 (uri (cran-uri "abd" version))
7290 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
7291 (build-system r-build-system)
7293 `(("r-lattice" ,r-lattice)
7294 ("r-mosaic" ,r-mosaic)
7295 ("r-nlme" ,r-nlme)))
7296 (home-page "https://cran.r-project.org/web/packages/abd/")
7297 (synopsis "Analysis of biological data")
7299 "The @code{r-abd} package contains data sets and sample code for the Analysis of
7300 biological data by Michael Whitlock and Dolph Schluter.")
7301 (license license:gpl2)))
7303 (define-public r-svgui
7310 (uri (cran-uri "svGUI" version))
7312 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
7313 (properties `((upstream-name . "svGUI")))
7314 (build-system r-build-system)
7315 (home-page "https://github.com/SciViews/svGUI/")
7316 (synopsis "Functions for managing GUI clients in R")
7318 "The SciViews @code{svGUI} package eases the management of Graphical User
7319 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
7320 centralizes info about GUI elements currently used, and it dispatches GUI
7321 calls to the particular toolkits in use in function of the context.")
7322 (license license:gpl2)))
7324 (define-public r-svdialogs
7326 (name "r-svdialogs")
7331 (uri (cran-uri "svDialogs" version))
7333 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
7334 (properties `((upstream-name . "svDialogs")))
7335 (build-system r-build-system)
7338 ("zenity" ,zenity)))
7340 `(("r-rstudioapi" ,r-rstudioapi)
7341 ("r-svgui" ,r-svgui)))
7342 (home-page "https://github.com/SciViews/svDialogs/")
7343 (synopsis "Portable dialog boxes")
7345 "This package helps to construct standard dialog boxes for your GUI, including
7346 message boxes, input boxes, list, file or directory selection, and others. In
7347 case R cannot display GUI dialog boxes, a simpler command line version of these
7348 interactive elements is also provided as a fallback solution.")
7349 (license license:gpl2)))
7351 (define-public r-abe
7358 (uri (cran-uri "abe" version))
7361 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
7362 (build-system r-build-system)
7363 (home-page "https://cran.r-project.org/web/packages/abe/")
7364 (synopsis "Augmented backward elimination")
7366 "This package performs augmented backward elimination and checks the
7367 stability of the obtained model. Augmented backward elimination combines
7368 significance or information based criteria with the change in estimate to
7369 either select the optimal model for prediction purposes or to serve as a tool
7370 to obtain a practically sound, highly interpretable model.")
7371 (license license:gpl2+)))
7373 (define-public r-abf2
7380 (uri (cran-uri "abf2" version))
7382 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
7383 (build-system r-build-system)
7384 (home-page "https://cran.r-project.org/web/packages/abf2/")
7385 (synopsis "Load gap-free axon @code{r-abf2} files")
7387 "This package loads electrophysiology data from ABF2 files, as created by
7388 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
7389 mode are currently supported.")
7390 (license license:artistic2.0)))
7392 (define-public r-abhgenotyper
7394 (name "r-abhgenotyper")
7399 (uri (cran-uri "ABHgenotypeR" version))
7401 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
7402 (properties `((upstream-name . "ABHgenotypeR")))
7403 (build-system r-build-system)
7405 `(("r-ggplot2" ,r-ggplot2)
7406 ("r-reshape2" ,r-reshape2)))
7407 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
7408 (synopsis "Visualize and manipulate ABH genotypes")
7410 "The @code{r-abhgenotyper} package provides simple imputation,
7411 error-correction and plotting capacities for genotype data. The package is
7412 supposed to serve as an intermediate but independent analysis tool between the
7413 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
7414 not found in either TASSEL or @code{r-qtl} in addition to visualization of
7415 genotypes as \"graphical genotypes\".")
7416 (license license:gpl3)))
7418 (define-public r-furrr
7425 (uri (cran-uri "furrr" version))
7428 "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx"))))
7429 (build-system r-build-system)
7431 `(("r-future" ,r-future)
7432 ("r-globals" ,r-globals)
7433 ("r-purrr" ,r-purrr)
7434 ("r-rlang" ,r-rlang)))
7435 (home-page "https://github.com/DavisVaughan/furrr")
7436 (synopsis "Apply mapping functions in parallel using futures")
7438 "This package provides implementations of the family of @code{map()}
7439 functions from the @code{purrr} package that can be resolved using any
7440 @code{future}-supported backend, e.g. parallel on the local machine or
7441 distributed on a compute cluster.")
7442 (license license:lgpl2.1+)))
7444 (define-public r-abjutils
7451 (uri (cran-uri "abjutils" version))
7453 (base32 "0n4zps65y3zg0gfzlv97w91si52a9izkncirskbkj5x9hk0nhxcv"))))
7454 (build-system r-build-system)
7456 `(("r-devtools" ,r-devtools)
7457 ("r-dplyr" ,r-dplyr)
7458 ("r-furrr" ,r-furrr)
7459 ("r-future" ,r-future)
7462 ("r-magrittr" ,r-magrittr)
7463 ("r-progress" ,r-progress)
7464 ("r-purrr" ,r-purrr)
7465 ("r-readr" ,r-readr)
7466 ("r-rlang" ,r-rlang)
7467 ("r-rstudioapi" ,r-rstudioapi)
7468 ("r-scales" ,r-scales)
7469 ("r-stringi" ,r-stringi)
7470 ("r-stringr" ,r-stringr)
7471 ("r-tibble" ,r-tibble)
7472 ("r-tidyr" ,r-tidyr)))
7473 (home-page "https://github.com/abjur/abjutils/")
7474 (synopsis "Collection of tools for jurimetrical analysis")
7476 "This package implements general purpose tools, such as functions for
7477 sampling and basic manipulation of Brazilian lawsuits identification number.
7478 It also implements functions for text cleaning, such as accentuation
7480 (license license:expat)))
7482 (define-public r-abnormality
7484 (name "r-abnormality")
7489 (uri (cran-uri "abnormality" version))
7491 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
7492 (build-system r-build-system)
7494 `(("r-mass" ,r-mass)
7495 ("r-matrix" ,r-matrix)))
7496 (home-page "https://cran.r-project.org/web/packages/abnormality/")
7497 (synopsis "Measure a subject's abnormality with respect to a reference population")
7499 "This package contains functions to implement the methodology and
7500 considerations laid out by Marks et al. in the article \"Measuring abnormality
7501 in high dimensional spaces: applications in biomechanical gait analysis\".
7502 Using high-dimensional datasets to measure a subject's overall level of
7503 abnormality as compared to a reference population is often needed in outcomes
7505 (license license:expat)))
7507 (define-public r-abodoutlier
7509 (name "r-abodoutlier")
7514 (uri (cran-uri "abodOutlier" version))
7516 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
7517 (properties `((upstream-name . "abodOutlier")))
7518 (build-system r-build-system)
7520 `(("r-cluster" ,r-cluster)))
7521 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
7522 (synopsis "Angle-based outlier detection")
7524 "This package performs angle-based outlier detection on a given data
7525 frame. It offers three methods to process data:
7527 @item full but slow implementation using all the data that has cubic
7529 @item a fully randomized method;
7530 @item a method using k-nearest neighbours.
7532 These algorithms are well suited for high dimensional data outlier
7534 (license license:expat)))
7536 (define-public r-abps
7543 (uri (cran-uri "ABPS" version))
7545 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
7546 (properties `((upstream-name . "ABPS")))
7547 (build-system r-build-system)
7548 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
7549 (home-page "https://cran.r-project.org/web/packages/ABPS/")
7550 (synopsis "Abnormal blood profile score to detect blood doping")
7552 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
7553 The ABPS is a part of the Athlete biological passport program of the World
7554 anti-doping agency, which combines several blood parameters into a single
7555 score in order to detect blood doping. The package also contains functions to
7556 calculate other scores used in anti-doping programs, such as the ratio of
7557 hemoglobin to reticulocytes (OFF-score), as well as example data.")
7558 (license license:gpl2+)))
7560 (define-public r-parmigene
7562 (name "r-parmigene")
7567 (uri (cran-uri "parmigene" version))
7570 "1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d"))))
7571 (build-system r-build-system)
7572 (home-page "https://cran.r-project.org/web/packages/parmigene/")
7573 (synopsis "Mutual information estimation for gene network reconstruction")
7575 "This package provides a parallel estimation of the mutual information
7576 based on entropy estimates from k-nearest neighbors distances and algorithms
7577 for the reconstruction of gene regulatory networks.")
7578 (license license:agpl3+)))
7580 (define-public r-pscl
7587 (uri (cran-uri "pscl" version))
7589 (base32 "1phf3awsfr4ncqfqzin5m1pz0g7y1zhbcm2sz7358ssw914fd7rc"))))
7590 (build-system r-build-system)
7592 `(("r-mass" ,r-mass)))
7593 (home-page "https://github.com/atahk/pscl/")
7594 (synopsis "Political science computational laboratory")
7596 "The @code{pscl} is an R package providing classes and methods for:
7598 @item Bayesian analysis of roll call data (item-response models);
7599 @item elementary Bayesian statistics;
7600 @item maximum likelihood estimation of zero-inflated and hurdle models for count
7602 @item utility functions.
7604 (license license:gpl2)))
7606 (define-public r-accelmissing
7608 (name "r-accelmissing")
7613 (uri (cran-uri "accelmissing" version))
7615 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
7616 (build-system r-build-system)
7618 `(("r-mice" ,r-mice)
7619 ("r-pscl" ,r-pscl)))
7620 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
7621 (synopsis "Missing value imputation for accelerometer data")
7623 "This package provides a statistical method to impute the missing values in
7624 accelerometer data. The methodology includes both parametric and
7625 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
7626 model. It also provides multiple functions to preprocess the accelerometer data
7627 previous to the missing data imputation. These include detecting the wearing
7628 and the non-wearing time, selecting valid days and subjects, and creating plots.")
7629 (license license:gpl2+)))
7631 (define-public r-mhsmm
7638 (uri (cran-uri "mhsmm" version))
7640 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
7641 (build-system r-build-system)
7642 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
7643 (home-page "https://github.com/jaredo/mhsmm/")
7644 (synopsis "Inference for hidden Markov and semi-Markov models")
7646 "The @code{r-mhsmm} package implements estimation and prediction methods for
7647 hidden Markov and semi-Markov models for multiple observation sequences. Such
7648 techniques are of interest when observed data is thought to be dependent on some
7649 unobserved (or hidden) state. Also, this package is suitable for equidistant
7650 time series data, with multivariate and/or missing data. Allows user defined
7651 emission distributions.")
7652 (license license:gpl2+)))
7654 (define-public r-nleqslv
7661 (uri (cran-uri "nleqslv" version))
7663 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
7664 (build-system r-build-system)
7665 (native-inputs `(("gfortran" ,gfortran)))
7666 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
7667 (synopsis "Solve systems of nonlinear equations")
7669 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
7670 Broyden or a Newton method with a choice of global strategies such as line
7671 search and trust region. There are options for using a numerical or user
7672 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
7673 singular or ill-conditioned Jacobian.")
7674 (license license:gpl2+)))
7676 (define-public r-physicalactivity
7678 (name "r-physicalactivity")
7683 (uri (cran-uri "PhysicalActivity" version))
7685 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
7687 `((upstream-name . "PhysicalActivity")))
7688 (build-system r-build-system)
7689 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
7690 (synopsis "Procesing accelerometer data for physical activity measurement")
7692 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
7693 for classification of monitor wear and nonwear time intervals in accelerometer
7694 data collected to assess physical activity. The package also contains functions
7695 for making plots of accelerometer data and obtaining the summary of various
7696 information including daily monitor wear time and the mean monitor wear time
7697 during valid days. The revised package version 0.2-1 improved the functions
7698 regarding speed, robustness and add better support for time zones and daylight
7699 saving. In addition, several functions were added:
7701 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
7702 @item the @code{markPAI} can categorize physical activity intensity level based
7703 on user-defined cut-points of accelerometer counts.
7705 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
7706 @code{queryActigraph} functions.")
7707 (license license:gpl3+)))
7709 (define-public r-acc
7716 (uri (cran-uri "acc" version))
7718 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
7719 (build-system r-build-system)
7721 `(("r-circlize" ,r-circlize)
7723 ("r-ggplot2" ,r-ggplot2)
7724 ("r-iterators" ,r-iterators)
7725 ("r-mhsmm" ,r-mhsmm)
7726 ("r-nleqslv" ,r-nleqslv)
7727 ("r-physicalactivity" ,r-physicalactivity)
7729 ("r-r-utils" ,r-r-utils)
7731 ("r-rcpparmadillo" ,r-rcpparmadillo)
7732 ("r-rsqlite" ,r-rsqlite)
7734 (home-page "https://cran.r-project.org/web/packages/acc/")
7735 (synopsis "Exploring accelerometer data")
7737 "This package processes accelerometer data from uni-axial and tri-axial devices
7738 and generates data summaries. Also, includes functions to plot, analyze, and
7739 simulate accelerometer data.")
7740 (license license:gpl2+)))
7742 (define-public r-rbenchmark
7744 (name "r-rbenchmark")
7749 (uri (cran-uri "rbenchmark" version))
7751 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
7752 (build-system r-build-system)
7753 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
7754 (synopsis "Benchmarking routine for R")
7756 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
7757 and is intended to facilitate benchmarking of arbitrary R code. The library
7758 consists of just one function, benchmark, which is a simple wrapper around
7759 system.time. Given a specification of the benchmarking process (counts of
7760 replications, evaluation environment) and an arbitrary number of expressions,
7761 benchmark evaluates each of the expressions in the specified environment,
7762 replicating the evaluation as many times as specified, and returning the results
7763 conveniently wrapped into a data frame.")
7764 (license license:gpl2+)))
7766 (define-public r-mitools
7773 (uri (cran-uri "mitools" version))
7776 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
7777 (build-system r-build-system)
7778 (propagated-inputs `(("r-dbi" ,r-dbi)))
7779 (home-page "https://cran.r-project.org/web/packages/mitools/")
7780 (synopsis "Tools for multiple imputation of missing data")
7782 "This package provides tools to perform analyses and combine results from
7783 multiple-imputation datasets.")
7784 (license license:gpl2)))
7786 (define-public r-magick
7793 (uri (cran-uri "magick" version))
7796 "1xh5mhaks3wk1iwqs9d3lnbfv121lc1yz5fqdzk5il9ppr831l85"))))
7797 (build-system r-build-system)
7799 `(("imagemagick" ,imagemagick)
7802 `(("r-curl" ,r-curl)
7803 ("r-magrittr" ,r-magrittr)
7804 ("r-rcpp" ,r-rcpp)))
7806 `(("pkg-config" ,pkg-config)))
7807 (home-page "https://github.com/ropensci/magick")
7808 (synopsis "Advanced graphics and image-processing in R")
7810 "This package provides bindings to ImageMagick, a comprehensive image
7811 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
7812 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
7813 operations are vectorized via the Magick++ STL meaning they operate either on
7814 a single frame or a series of frames for working with layers, collages, or
7815 animation. In RStudio, images are automatically previewed when printed to the
7816 console, resulting in an interactive editing environment.")
7817 (license license:expat)))
7819 (define-public r-survey
7826 (uri (cran-uri "survey" version))
7829 "0xclsy4ram4k48vzh5m5bpmknnpwxnss85v73s4czsjj5ffjxwwh"))))
7830 (build-system r-build-system)
7832 `(("r-lattice" ,r-lattice)
7833 ("r-matrix" ,r-matrix)
7834 ("r-minqa" ,r-minqa)
7835 ("r-mitools" ,r-mitools)
7836 ("r-numderiv" ,r-numderiv)
7837 ("r-survival" ,r-survival)))
7838 (home-page "http://r-survey.r-forge.r-project.org/survey/")
7839 (synopsis "Analysis of complex survey samples")
7841 "This package provides tools for the analysis of complex survey samples.
7842 The provided features include: summary statistics, two-sample tests, rank
7843 tests, generalised linear models, cumulative link models, Cox models,
7844 loglinear models, and general maximum pseudolikelihood estimation for
7845 multistage stratified, cluster-sampled, unequally weighted survey samples;
7846 variances by Taylor series linearisation or replicate weights;
7847 post-stratification, calibration, and raking; two-phase subsampling designs;
7848 graphics; PPS sampling without replacement; principal components, and factor
7850 ;; Either version of the GPL.
7851 (license (list license:gpl2 license:gpl3))))
7853 (define-public r-dvmisc
7860 (uri (cran-uri "dvmisc" version))
7862 (base32 "0x391pxg5mqgp5xxc8qwhwxky8ds7d9gr9iwmsb12c92kxfk00bv"))))
7863 (build-system r-build-system)
7865 `(("r-cubature" ,r-cubature)
7866 ("r-data-table" ,r-data-table)
7867 ("r-dplyr" ,r-dplyr)
7868 ("r-ggplot2" ,r-ggplot2)
7870 ("r-mvtnorm" ,r-mvtnorm)
7871 ("r-pracma" ,r-pracma)
7872 ("r-purrr" ,r-purrr)
7873 ("r-rbenchmark" ,r-rbenchmark)
7875 ("r-survey" ,r-survey)))
7876 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
7877 (synopsis "Faster computation of common statistics and miscellaneous functions")
7879 "This package implements faster versions of base R functions (e.g. mean, standard
7880 deviation, covariance, weighted mean), mostly written in C++, along with
7881 miscellaneous functions for various purposes (e.g. create the histogram with
7882 fitted probability density function or probability mass function curve, create
7883 the body mass index groups, assess the linearity assumption in logistic
7885 (license license:gpl2)))
7887 (define-public r-accelerometry
7889 (name "r-accelerometry")
7894 (uri (cran-uri "accelerometry" version))
7896 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
7897 (build-system r-build-system)
7899 `(("r-dvmisc" ,r-dvmisc)
7900 ("r-rcpp" ,r-rcpp)))
7901 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
7902 (synopsis "Functions for processing accelerometer data")
7904 "This package provides a collection of functions that perform operations on
7905 time-series accelerometer data, such as identify the non-wear time, flag minutes
7906 that are part of an activity bout, and find the maximum 10-minute average count
7907 value. The functions are generally very flexible, allowing for a variety of
7908 algorithms to be implemented.")
7909 (license license:gpl3)))
7911 (define-public r-absim
7918 (uri (cran-uri "AbSim" version))
7920 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
7921 (properties `((upstream-name . "AbSim")))
7922 (build-system r-build-system)
7925 ("r-powerlaw" ,r-powerlaw)))
7926 (home-page "https://cran.r-project.org/web/packages/AbSim/")
7927 (synopsis "Time resolved simulations of antibody repertoires")
7929 "This package provides simulation methods for the evolution of antibody repertoires.
7930 The heavy and light chain variable region of both human and C57BL/6 mice can
7931 be simulated in a time-dependent fashion. Both single lineages using one set of
7932 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
7933 with an initial V-D-J recombination event, starting the first phylogenetic tree.
7934 Upon completion, the main loop of the algorithm begins, with each iteration
7935 representing one simulated time step. Various mutation events are possible at
7936 each time step, contributing to a diverse final repertoire.")
7937 (license license:gpl2)))
7939 (define-public r-quic
7946 (uri (cran-uri "QUIC" version))
7948 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
7949 (properties `((upstream-name . "QUIC")))
7950 (build-system r-build-system)
7951 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
7952 (synopsis "Regularized sparse inverse covariance matrix estimation")
7954 "This package implements the regularized Gaussian maximum likelihood
7955 estimation of the inverse of a covariance matrix. It uses Newton's method and
7956 coordinate descent to solve the regularized inverse covariance matrix
7957 estimation problem.")
7958 ;; The project home page states that the release is under GPLv3 or later.
7959 ;; The CRAN page only says GPL-3.
7960 (license license:gpl3+)))
7962 (define-public r-abundant
7969 (uri (cran-uri "abundant" version))
7971 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
7972 (build-system r-build-system)
7974 `(("r-quic" ,r-quic)))
7975 (home-page "https://cran.r-project.org/web/packages/abundant/")
7976 (synopsis "Abundant regression and high-dimensional principal fitted components")
7978 "This package provides tools to fit and predict with the high-dimensional
7979 principal fitted components model. This model is described by Cook, Forzani,
7980 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
7981 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
7982 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
7983 (license license:gpl2+)))
7985 (define-public r-ac3net
7992 (uri (cran-uri "Ac3net" version))
7994 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
7995 (properties `((upstream-name . "Ac3net")))
7996 (build-system r-build-system)
7998 `(("r-data-table" ,r-data-table)))
7999 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
8000 (synopsis "Inferring directional conservative causal core gene networks")
8001 (description "This package infers directional Conservative causal core
8002 (gene) networks (C3NET). This is a version of the algorithm C3NET with
8003 directional network.")
8004 (license license:gpl3+)))
8006 (define-public r-aca
8013 (uri (cran-uri "ACA" version))
8015 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
8016 (properties `((upstream-name . "ACA")))
8017 (build-system r-build-system)
8018 (home-page "https://cran.r-project.org/web/packages/ACA/")
8019 (synopsis "Abrupt change-point or aberration detection in point series")
8021 "This package offers an interactive function for the detection of breakpoints in
8023 ;; Any version of the GPL
8024 (license (list license:gpl2+ license:gpl3+))))
8026 (define-public r-acceptancesampling
8028 (name "r-acceptancesampling")
8033 (uri (cran-uri "AcceptanceSampling" version))
8035 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
8037 `((upstream-name . "AcceptanceSampling")))
8038 (build-system r-build-system)
8039 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
8040 (synopsis "Creation and evaluation of acceptance sampling plans")
8042 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
8043 acceptance sampling plans. Acceptance sampling is a methodology commonly used
8044 in quality control and improvement. International standards of acceptance
8045 sampling provide sampling plans for specific circumstances. The aim of this
8046 package is to provide an easy-to-use interface to visualize single, double or
8047 multiple sampling plans. In addition, methods have been provided to enable the
8048 user to assess sampling plans against pre-specified levels of performance, as
8049 measured by the probability of acceptance for a given level of quality in the
8051 (license license:gpl3+)))
8053 (define-public r-acclma
8060 (uri (cran-uri "ACCLMA" version))
8062 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
8063 (properties `((upstream-name . "ACCLMA")))
8064 (build-system r-build-system)
8065 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
8066 (synopsis "ACC & LMA graph plotting")
8068 "This package contains a function that imports data from a @acronym{CSV,
8069 Comma-Separated Values} file, or uses manually entered data from the format (x,
8070 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
8071 Curve} vs @acronym{LOI, Line of Independence} graph and
8072 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
8073 function is @code{plotLMA} (source file, header) that takes a data set and plots the
8074 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
8075 string) was passed, a manual data entry window is opened. The header parameter
8076 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
8077 a header row or not. The dataset should contain only one independent variable
8078 (x) and one dependent variable (y) and can contain a weight for each
8080 (license license:gpl2)))
8082 (define-public r-aspi
8089 (uri (cran-uri "aspi" version))
8091 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
8092 (build-system r-build-system)
8094 "https://cran.r-project.org/web/packages/aspi/")
8096 "Analysis of symmetry of parasitic infections")
8098 "This package provides tools for the analysis and visualization of bilateral
8099 asymmetry in parasitic infections.")
8100 (license license:gpl3+)))
8102 (define-public r-sandwich
8109 (uri (cran-uri "sandwich" version))
8112 "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv"))))
8113 (build-system r-build-system)
8115 `(("r-zoo" ,r-zoo)))
8116 (home-page "https://cran.r-project.org/web/packages/sandwich/")
8117 (synopsis "Robust Covariance Matrix Estimators")
8119 "This package provides model-robust standard error estimators for
8120 cross-sectional, time series, clustered, panel, and longitudinal data.")
8121 ;; Either version of the license.
8122 (license (list license:gpl2 license:gpl3))))
8124 (define-public r-th-data
8131 (uri (cran-uri "TH.data" version))
8134 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
8135 (properties `((upstream-name . "TH.data")))
8136 (build-system r-build-system)
8138 `(("r-mass" ,r-mass)
8139 ("r-survival" ,r-survival)))
8140 (home-page "https://cran.r-project.org/web/packages/TH.data/")
8141 (synopsis "Shared data sets")
8143 "This package contains supporting data sets that are used in other
8144 packages maintained by Torsten Hothorn.")
8145 (license license:gpl3)))
8147 (define-public r-multcomp
8154 (uri (cran-uri "multcomp" version))
8157 "1kzmdn9jmz5bmhf3wsfr12ljbasmwsgcsfdia52k0bi6q0swdg19"))))
8158 (build-system r-build-system)
8160 `(("r-codetools" ,r-codetools)
8161 ("r-mvtnorm" ,r-mvtnorm)
8162 ("r-sandwich" ,r-sandwich)
8163 ("r-survival" ,r-survival)
8164 ("r-th-data" ,r-th-data)))
8165 (home-page "https://cran.r-project.org/web/packages/multcomp/")
8166 (synopsis "Simultaneous inference in general parametric models")
8168 "Simultaneous tests and confidence intervals for general linear
8169 hypotheses in parametric models, including linear, generalized linear, linear
8170 mixed effects, and survival models. The package includes demos reproducing
8171 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
8172 Hothorn, Westfall, 2010, CRC Press).")
8173 (license license:gpl2)))
8175 (define-public r-emmeans
8178 (version "1.4.3.01")
8182 (uri (cran-uri "emmeans" version))
8185 "16v5j31516nbqnj2zhgqvyp5yxd4zcs5zi0aspa5plr2qikvrkmg"))))
8186 (build-system r-build-system)
8188 `(("r-estimability" ,r-estimability)
8189 ("r-mvtnorm" ,r-mvtnorm)
8190 ("r-numderiv" ,r-numderiv)
8192 ("r-xtable" ,r-xtable)))
8193 (home-page "https://github.com/rvlenth/emmeans")
8194 (synopsis "Estimated marginal means, aka least-squares means")
8196 "This package provides tools to obtain @dfn{estimated marginal
8197 means} (EMMs) for many linear, generalized linear, and mixed models. It can
8198 be used to compute contrasts or linear functions of EMMs, trends, and
8199 comparisons of slopes.")
8200 ;; Either version of the license.
8201 (license (list license:gpl2 license:gpl3))))
8203 (define-public r-pwr
8210 (uri (cran-uri "pwr" version))
8213 "0r5g781lr677vp3zyhgmi7r68c87l8gd05l1s3ffnxgn5wf043sm"))))
8214 (build-system r-build-system)
8216 `(("r-knitr" ,r-knitr)))
8217 (home-page "https://github.com/heliosdrm/pwr")
8218 (synopsis "Basic functions for power analysis")
8220 "This package provides power analysis functions along the lines of
8222 (license license:gpl3+)))
8224 (define-public r-libcoin
8231 (uri (cran-uri "libcoin" version))
8234 "1cm9x1dlg9f7fh7n5nw3x4a7rl88c7ylrlc8x3rx4mq5w1j42x0a"))))
8235 (build-system r-build-system)
8236 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8237 (home-page "https://cran.r-project.org/web/packages/libcoin")
8238 (synopsis "Linear test statistics for permutation inference")
8240 "This package provides basic infrastructure for linear test statistics
8241 and permutation inference in the framework of Strasser and Weber (1999).")
8242 (license license:gpl2)))
8244 (define-public r-coin
8251 (uri (cran-uri "coin" version))
8254 "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx"))))
8255 (build-system r-build-system)
8257 `(("r-libcoin" ,r-libcoin)
8258 ("r-matrixstats" ,r-matrixstats)
8259 ("r-modeltools" ,r-modeltools)
8260 ("r-multcomp" ,r-multcomp)
8261 ("r-mvtnorm" ,r-mvtnorm)
8262 ("r-survival" ,r-survival)))
8263 (home-page "http://coin.r-forge.r-project.org")
8264 (synopsis "Conditional inference procedures in a permutation test framework")
8266 "This package provides conditional inference procedures for the general
8267 independence problem including two-sample, K-sample (non-parametric ANOVA),
8268 correlation, censored, ordered and multivariate problems.")
8269 (license license:gpl2)))
8271 (define-public r-bayesplot
8273 (name "r-bayesplot")
8278 (uri (cran-uri "bayesplot" version))
8281 "0sq0ajnm96hmlqf1cv5n2gshh3qdij4n1zbm7qrniz2q6b5aj342"))))
8282 (build-system r-build-system)
8284 `(("pandoc" ,ghc-pandoc)
8285 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
8287 `(("r-dplyr" ,r-dplyr)
8288 ("r-ggplot2" ,r-ggplot2)
8289 ("r-ggridges" ,r-ggridges)
8291 ("r-reshape2" ,r-reshape2)
8292 ("r-rlang" ,r-rlang)
8293 ("r-tibble" ,r-tibble)
8294 ("r-tidyselect" ,r-tidyselect)))
8295 (home-page "http://mc-stan.org/bayesplot")
8296 (synopsis "Plotting for Bayesian models")
8298 "This package provides plotting functions for posterior analysis, model
8299 checking, and MCMC diagnostics. The package is designed not only to provide
8300 convenient functionality for users, but also a common set of functions that
8301 can be easily used by developers working on a variety of R packages for
8302 Bayesian modeling.")
8303 (license license:gpl3+)))
8305 (define-public r-tmb
8312 (uri (cran-uri "TMB" version))
8315 "1r2d8c5iazihba42sn33yarv0dcfiy989sx64zcf14zr8k6cgjzs"))))
8316 (properties `((upstream-name . "TMB")))
8317 (build-system r-build-system)
8319 `(("r-matrix" ,r-matrix)
8320 ("r-rcppeigen" ,r-rcppeigen)))
8321 (home-page "http://tmb-project.org")
8322 (synopsis "Template model builder: a general random effect tool")
8324 "With this tool, a user should be able to quickly implement complex
8325 random effect models through simple C++ templates. The package combines
8326 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
8327 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
8328 from R) to obtain an efficient implementation of the applied Laplace
8329 approximation with exact derivatives. Key features are: Automatic sparseness
8330 detection, parallelism through BLAS and parallel user templates.")
8331 (license license:gpl2)))
8333 (define-public r-sjstats
8340 (uri (cran-uri "sjstats" version))
8342 (base32 "029rl05p88bp01favz300m980r1khcx2a2kn88yqbnbgkjjgqqc6"))))
8343 (build-system r-build-system)
8345 `(("r-bayestestr" ,r-bayestestr)
8346 ("r-broom" ,r-broom)
8347 ("r-dplyr" ,r-dplyr)
8348 ("r-emmeans" ,r-emmeans)
8349 ("r-insight" ,r-insight)
8351 ("r-magrittr" ,r-magrittr)
8353 ("r-modelr" ,r-modelr)
8354 ("r-parameters" ,r-parameters)
8355 ("r-performance" ,r-performance)
8356 ("r-purrr" ,r-purrr)
8357 ("r-rlang" ,r-rlang)
8358 ("r-sjlabelled" ,r-sjlabelled)
8359 ("r-sjmisc" ,r-sjmisc)
8360 ("r-tidyr" ,r-tidyr)))
8361 (home-page "https://github.com/strengejacke/sjstats")
8362 (synopsis "Functions for common statistical computations")
8364 "This package provides a collection of convenient functions for common
8365 statistical computations, which are not directly provided by R's @code{base}
8366 or @code{stats} packages. This package aims at providing, first, shortcuts
8367 for statistical measures, which otherwise could only be calculated with
8368 additional effort. Second, these shortcut functions are generic, and can be
8369 applied not only to vectors, but also to other objects as well. The focus of
8370 most functions lies on summary statistics or fit measures for regression
8371 models, including generalized linear models, mixed effects models and Bayesian
8373 (license license:gpl3)))
8375 (define-public r-glmmtmb
8382 (uri (cran-uri "glmmTMB" version))
8385 "035hkywa37bz555fv6znxd4hfcs5w884365wfnwk4jx5vann4vvb"))))
8386 (properties `((upstream-name . "glmmTMB")))
8387 (build-system r-build-system)
8389 `(("r-lme4" ,r-lme4)
8390 ("r-matrix" ,r-matrix)
8392 ("r-rcppeigen" ,r-rcppeigen)
8395 `(("r-knitr" ,r-knitr))) ; for vignettes
8396 (home-page "https://github.com/glmmTMB")
8397 (synopsis "Generalized linear mixed models")
8399 "Fit linear and generalized linear mixed models with various extensions,
8400 including zero-inflation. The models are fitted using maximum likelihood
8401 estimation via the Template Model Builder. Random effects are assumed to be
8402 Gaussian on the scale of the linear predictor and are integrated out using the
8403 Laplace approximation. Gradients are calculated using automatic
8405 (license license:agpl3+)))
8407 (define-public r-bayestestr
8409 (name "r-bayestestr")
8414 (uri (cran-uri "bayestestR" version))
8417 "1d3f50rzjzgzclwd6j887dssyhv7hdq7pik9nnlr3w775v3f69zc"))))
8418 (properties `((upstream-name . "bayestestR")))
8419 (build-system r-build-system)
8421 `(("r-insight" ,r-insight)))
8422 (home-page "https://github.com/easystats/bayestestR")
8423 (synopsis "Describe Bayesian models and posterior distributions")
8425 "This package provides utilities to understand and describe posterior
8426 distributions and Bayesian models. It includes point-estimates such as
8427 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
8428 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
8429 ROPE percentage and pd).")
8430 (license license:gpl3)))
8432 (define-public r-performance
8434 (name "r-performance")
8439 (uri (cran-uri "performance" version))
8442 "0lxpmp9smn5r3xvfik36nr608wcpmmximjh0v2sckyvjf7hnb4s0"))))
8443 (build-system r-build-system)
8445 `(("r-bayestestr" ,r-bayestestr)
8446 ("r-insight" ,r-insight)))
8447 (home-page "https://easystats.github.io/performance/")
8448 (synopsis "Assessment of regression models performance")
8450 "This package provides utilities for computing measures to assess model
8451 quality, which are not directly provided by R's @code{base} or @code{stats}
8452 packages. These include e.g. measures like r-squared, intraclass correlation
8453 coefficient, root mean squared error or functions to check models for
8454 overdispersion, singularity or zero-inflation and more. Functions apply to a
8455 large variety of regression models, including generalized linear models, mixed
8456 effects models and Bayesian models.")
8457 (license license:gpl3)))
8459 (define-public r-ggeffects
8461 (name "r-ggeffects")
8466 (uri (cran-uri "ggeffects" version))
8469 "0ryfbaav0k874kbwmhbiv7fan93dmkpaimm1iw5kryjhhs3917lb"))))
8470 (build-system r-build-system)
8472 `(("r-dplyr" ,r-dplyr)
8473 ("r-insight" ,r-insight)
8474 ("r-magrittr" ,r-magrittr)
8476 ("r-purrr" ,r-purrr)
8477 ("r-rlang" ,r-rlang)
8478 ("r-sjlabelled" ,r-sjlabelled)
8479 ("r-sjmisc" ,r-sjmisc)))
8480 (home-page "https://github.com/strengejacke/ggeffects")
8481 (synopsis "Create tidy data frames of marginal effects for ggplot")
8483 "This package provides tools to compute marginal effects from statistical
8484 models and return the result as tidy data frames. These data frames are ready
8485 to use with the @code{ggplot2} package. Marginal effects can be calculated
8486 for many different models. Interaction terms, splines and polynomial terms
8487 are also supported. The two main functions are @code{ggpredict()} and
8488 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
8489 results using @code{ggplot2}.")
8490 (license license:gpl3)))
8492 (define-public r-effectsize
8494 (name "r-effectsize")
8499 (uri (cran-uri "effectsize" version))
8502 "07vgmxdl75798hgdh90zysafjh97rmmj2wjjyr6xff4fbhi8rlkb"))))
8503 (properties `((upstream-name . "effectsize")))
8504 (build-system r-build-system)
8506 `(("r-bayestestr" ,r-bayestestr)
8507 ("r-insight" ,r-insight)
8508 ("r-parameters" ,r-parameters)))
8509 (home-page "https://github.com/easystats/effectsize")
8510 (synopsis "Indices of effect size and standardized parameters")
8512 "This package provides utilities to work with indices of effect size and
8513 standardized parameters for a wide variety of models, allowing computation and
8514 conversion of indices such as Cohen's d, r, odds, etc.")
8515 (license license:gpl3)))
8517 (define-public r-sjplot
8524 (uri (cran-uri "sjPlot" version))
8526 (base32 "0rmfc2pq80w0kxh6icljhqm31q580s0czvllsfxk6crmpyfgxkp7"))))
8527 (properties `((upstream-name . "sjPlot")))
8528 (build-system r-build-system)
8530 `(("r-bayestestr" ,r-bayestestr)
8531 ("r-dplyr" ,r-dplyr)
8532 ("r-effectsize" ,r-effectsize)
8533 ("r-forcats" ,r-forcats)
8534 ("r-ggeffects" ,r-ggeffects)
8535 ("r-ggplot2" ,r-ggplot2)
8536 ("r-ggrepel" ,r-ggrepel)
8537 ("r-glmmtmb" ,r-glmmtmb)
8538 ("r-insight" ,r-insight)
8539 ("r-knitr" ,r-knitr)
8541 ("r-magrittr" ,r-magrittr)
8543 ("r-modelr" ,r-modelr)
8544 ("r-parameters" ,r-parameters)
8545 ("r-performance" ,r-performance)
8546 ("r-psych" ,r-psych)
8547 ("r-purrr" ,r-purrr)
8548 ("r-rlang" ,r-rlang)
8549 ("r-scales" ,r-scales)
8550 ("r-sjlabelled" ,r-sjlabelled)
8551 ("r-sjmisc" ,r-sjmisc)
8552 ("r-sjstats" ,r-sjstats)
8553 ("r-tidyr" ,r-tidyr)))
8554 (home-page "https://strengejacke.github.io/sjPlot/")
8555 (synopsis "Data visualization for statistics in social science")
8557 "This package represents a collection of plotting and table output
8558 functions for data visualization. Results of various statistical
8559 analyses (that are commonly used in social sciences) can be visualized using
8560 this package, including simple and cross tabulated frequencies, histograms,
8561 box plots, (generalized) linear models, mixed effects models, principal
8562 component analysis and correlation matrices, cluster analyses, scatter plots,
8563 stacked scales, effects plots of regression models (including interaction
8564 terms) and much more. This package supports labelled data.")
8565 (license license:gpl3)))
8567 (define-public r-ini
8574 (uri (cran-uri "ini" version))
8577 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
8578 (build-system r-build-system)
8579 (home-page "https://github.com/dvdscripter/ini")
8580 (synopsis "Read and write configuration files")
8582 "This package provides tools to parse simple @code{.ini} configuration
8583 files to an structured list. Users can manipulate this resulting list with
8584 @code{lapply()} functions. This same structured list can be used to write
8585 back to file after modifications.")
8586 (license license:gpl3)))
8595 (uri (cran-uri "gh" version))
8598 "1llinfajb0g7006jd2w1hpskxpmkjhnqarcjb71r1qvsccb2ph7k"))))
8599 (build-system r-build-system)
8601 `(("r-httr" ,r-httr)
8603 ("r-jsonlite" ,r-jsonlite)))
8604 (home-page "https://github.com/r-lib/gh#readme")
8605 (synopsis "Access the GitHub API via R")
8607 "This package provides a minimal R client to access the GitHub API.")
8608 (license license:expat)))
8617 (uri (cran-uri "fs" version))
8620 "1g26rgx13dzigp2vrlld6h28q33lwbax97zvwdrq2pc3iz54v4yn"))))
8621 (build-system r-build-system)
8623 `(("r-rcpp" ,r-rcpp)))
8625 `(("pkg-config" ,pkg-config)))
8626 (home-page "http://fs.r-lib.org")
8627 (synopsis "Cross-platform file system operations based on libuv")
8629 "This package provides a cross-platform interface to file system
8630 operations, built on top of the libuv C library.")
8631 (license license:gpl3)))
8633 (define-public r-clisymbols
8635 (name "r-clisymbols")
8640 (uri (cran-uri "clisymbols" version))
8643 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
8644 (build-system r-build-system)
8645 (home-page "https://github.com/gaborcsardi/clisymbols")
8646 (synopsis "Unicode symbols at the R prompt")
8648 "This package provides a small subset of Unicode symbols, that are useful
8649 when building command line applications. They fall back to alternatives on
8650 terminals that do not support Unicode.")
8651 (license license:expat)))
8653 (define-public r-usethis
8660 (uri (cran-uri "usethis" version))
8663 "07an5wbikilg7cb3q6x5aykw8dfqnjrc3wpfb7gjmy0d9fh20fcy"))))
8664 (build-system r-build-system)
8666 `(("r-clipr" ,r-clipr)
8667 ("r-clisymbols" ,r-clisymbols)
8668 ("r-crayon" ,r-crayon)
8673 ("r-git2r" ,r-git2r)
8675 ("r-purrr" ,r-purrr)
8676 ("r-rlang" ,r-rlang)
8677 ("r-rprojroot" ,r-rprojroot)
8678 ("r-rstudioapi" ,r-rstudioapi)
8679 ("r-whisker" ,r-whisker)
8680 ("r-withr" ,r-withr)
8681 ("r-yaml" ,r-yaml)))
8682 (home-page "https://github.com/r-lib/usethis")
8683 (synopsis "Automate R package and project setup")
8685 "This package helps you to automate R package and project setup tasks
8686 that are otherwise performed manually. This includes setting up unit testing,
8687 test coverage, continuous integration, Git, GitHub integration, licenses,
8688 Rcpp, RStudio projects, and more.")
8689 (license license:gpl3)))
8691 (define-public r-sessioninfo
8693 (name "r-sessioninfo")
8698 (uri (cran-uri "sessioninfo" version))
8701 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
8702 (build-system r-build-system)
8705 ("r-withr" ,r-withr)))
8706 (home-page "https://github.com/r-lib/sessioninfo#readme")
8707 (synopsis "R session information")
8709 "This package provides tools to query and print information about the
8710 current R session. It is similar to @code{utils::sessionInfo()}, but includes
8711 more information about packages, and where they were installed from.")
8712 (license license:gpl2)))
8714 (define-public r-remotes
8721 (uri (cran-uri "remotes" version))
8724 "19v8dmnk9l4i9m64p7zgmj7y1vhnnwhi5kyn0k5d034zzkvchi49"))))
8725 (build-system r-build-system)
8726 (home-page "https://github.com/r-lib/remotes#readme")
8727 (synopsis "R package installation from remote repositories")
8729 "Download and install R packages stored in GitHub, BitBucket, or plain
8730 subversion or git repositories. This package is a lightweight replacement of
8731 the @code{install_*} functions in the @code{devtools} package. Indeed most of
8732 the code was copied over from @code{devtools}.")
8733 (license license:gpl2+)))
8735 (define-public r-xopen
8742 (uri (cran-uri "xopen" version))
8745 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
8746 (build-system r-build-system)
8748 `(("r-processx" ,r-processx)))
8749 (home-page "https://github.com/r-lib/xopen#readme")
8750 (synopsis "Open system files, URLs, anything")
8752 "This package provides a cross-platform solution to open files,
8753 directories or URLs with their associated programs.")
8754 (license license:expat)))
8756 (define-public r-rcmdcheck
8758 (name "r-rcmdcheck")
8763 (uri (cran-uri "rcmdcheck" version))
8766 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
8767 (build-system r-build-system)
8769 `(("r-callr" ,r-callr)
8771 ("r-crayon" ,r-crayon)
8773 ("r-digest" ,r-digest)
8774 ("r-pkgbuild" ,r-pkgbuild)
8775 ("r-prettyunits" ,r-prettyunits)
8777 ("r-rprojroot" ,r-rprojroot)
8778 ("r-sessioninfo" ,r-sessioninfo)
8779 ("r-withr" ,r-withr)
8780 ("r-xopen" ,r-xopen)))
8781 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
8782 (synopsis "Run R CMD check from R and capture results")
8784 "Run @code{R CMD check} from R programmatically, and capture the results
8785 of the individual checks.")
8786 (license license:expat)))
8788 (define-public r-rapportools
8790 (name "r-rapportools")
8795 (uri (cran-uri "rapportools" version))
8798 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
8799 (build-system r-build-system)
8801 `(("r-pander" ,r-pander)
8803 ("r-reshape" ,r-reshape)))
8804 (home-page "https://cran.r-project.org/web/packages/rapportools/")
8805 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
8807 "This package provides helper functions that act as wrappers to more
8808 advanced statistical methods with the advantage of having sane defaults for
8810 (license license:agpl3+)))
8812 (define-public r-pander
8819 (uri (cran-uri "pander" version))
8822 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
8823 (build-system r-build-system)
8825 `(("r-digest" ,r-digest)
8826 ("r-rcpp" ,r-rcpp)))
8827 (home-page "https://rapporter.github.io/pander")
8828 (synopsis "Render R objects into Pandoc's markdown")
8830 "The main aim of the pander R package is to provide a minimal and easy
8831 tool for rendering R objects into Pandoc's markdown. The package is also
8832 capable of exporting/converting complex Pandoc documents (reports) in various
8834 ;; This package is licensed under either the AGPLv3+ or the very rarely
8836 (license license:agpl3+)))
8838 (define-public r-summarytools
8840 (name "r-summarytools")
8845 (uri (cran-uri "summarytools" version))
8848 "1n695baz56mg4f13xjjadfq0xalw5xsn6xicil0yap5hgi8fsr3a"))))
8849 (build-system r-build-system)
8851 `(("r-checkmate" ,r-checkmate)
8852 ("r-dplyr" ,r-dplyr)
8853 ("r-htmltools" ,r-htmltools)
8854 ("r-lubridate" ,r-lubridate)
8855 ("r-magick" ,r-magick)
8856 ("r-matrixstats" ,r-matrixstats)
8857 ("r-pander" ,r-pander)
8859 ("r-rapportools" ,r-rapportools)
8860 ("r-rcurl" ,r-rcurl)
8861 ("r-tibble" ,r-tibble)
8862 ("r-tidyr" ,r-tidyr)))
8863 (home-page "https://github.com/dcomtois/summarytools")
8864 (synopsis "Tools to quickly and neatly summarize data")
8866 "This package provides tools for data frame summaries, cross-tabulations,
8867 weight-enabled frequency tables and common univariate statistics in concise
8868 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
8869 good point-of-entry for exploring data, both for experienced and new R
8871 (license license:gpl2)))
8873 (define-public r-lsei
8880 (uri (cran-uri "lsei" version))
8883 "1xl06fb3is744pxlh42wx5hn1h0ab1k31wnmsmh0524kxzcyp0a7"))))
8884 (build-system r-build-system)
8886 `(("gfortran" ,gfortran)))
8887 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
8888 (synopsis "Solve regression problems under equality/inequality constraints")
8890 "It contains functions that solve least squares linear regression
8891 problems under linear equality/inequality constraints. Functions for solving
8892 quadratic programming problems are also available, which transform such
8893 problems into least squares ones first.")
8894 (license license:gpl2+)))
8896 (define-public r-npsurv
8903 (uri (cran-uri "npsurv" version))
8906 "1wq4c9yfha5azjhrn40iiqkshmvh611sa90jp3lh82n4bl9zfk20"))))
8907 (build-system r-build-system)
8909 `(("r-lsei" ,r-lsei)))
8910 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
8911 (synopsis "Nonparametric survival analysis")
8913 "This package contains functions for non-parametric survival analysis of
8914 exact and interval-censored observations.")
8915 (license license:gpl2+)))
8917 (define-public r-clusteval
8919 (name "r-clusteval")
8924 (uri (cran-uri "clusteval" version))
8927 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
8928 (build-system r-build-system)
8930 `(("r-mvtnorm" ,r-mvtnorm)
8931 ("r-rcpp" ,r-rcpp)))
8932 (home-page "https://cran.r-project.org/web/packages/clusteval/")
8933 (synopsis "Evaluation of clustering algorithms")
8935 "This R package provides a suite of tools to evaluate clustering
8936 algorithms, clusterings, and individual clusters.")
8937 (license license:expat)))
8939 (define-public r-tweedie
8946 (uri (cran-uri "tweedie" version))
8949 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
8950 (build-system r-build-system)
8951 (native-inputs `(("gfortran" ,gfortran)))
8952 (home-page "https://cran.r-project.org/web/packages/tweedie/")
8953 (synopsis "Evaluation of Tweedie exponential family models")
8955 "Maximum likelihood computations for Tweedie families, including the
8956 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
8957 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
8958 and related methods.")
8959 (license license:gpl2+)))
8961 (define-public r-rcppgsl
8968 (uri (cran-uri "RcppGSL" version))
8970 (base32 "0cnw2k7cfqrm79r6j283aybflxig80x4n4rjkfp2317wf10mrsa5"))))
8971 (properties `((upstream-name . "RcppGSL")))
8972 (build-system r-build-system)
8974 `(("r-rcpp" ,r-rcpp)
8977 `(("r-knitr" ,r-knitr))) ; for vignettes
8978 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
8979 (synopsis "Rcpp integration for GSL vectors and matrices")
8981 "The GNU Scientific Library (or GSL) is a collection of numerical
8982 routines for scientific computing. It is particularly useful for C and C++
8983 programs as it provides a standard C interface to a wide range of mathematical
8984 routines. There are over 1000 functions in total with an extensive test
8985 suite. The RcppGSL package provides an easy-to-use interface between GSL data
8986 structures and R using concepts from Rcpp which is itself a package that eases
8987 the interfaces between R and C++.")
8988 (license license:gpl2+)))
8990 (define-public r-mvabund
8997 (uri (cran-uri "mvabund" version))
9000 "0la935gsiryfc0zixxr1dqj0av271x96pqxbi3bp6dksbw5gm68k"))))
9001 (build-system r-build-system)
9003 `(("r-mass" ,r-mass)
9005 ("r-rcppgsl" ,r-rcppgsl)
9006 ("r-statmod" ,r-statmod)
9007 ("r-tweedie" ,r-tweedie)))
9008 (home-page "https://cran.r-project.org/web/packages/mvabund/")
9009 (synopsis "Statistical methods for analysing multivariate abundance data")
9011 "This package provides a set of tools for displaying, modeling and
9012 analysing multivariate abundance data in community ecology.")
9013 (license license:lgpl2.1+)))
9015 (define-public r-afex
9022 (uri (cran-uri "afex" version))
9025 "12n020y7rjm7402940gkqxa5j901p093f381i23p66fa3fyrshkf"))))
9026 (build-system r-build-system)
9030 ("r-lmertest" ,r-lmertest)
9031 ("r-pbkrtest" ,r-pbkrtest)
9032 ("r-reshape2" ,r-reshape2)))
9033 (home-page "https://afex.singmann.science/")
9034 (synopsis "Analysis of factorial experiments")
9036 "This package provides convenience functions for analyzing factorial
9037 experiments using ANOVA or mixed models.")
9038 (license license:gpl2+)))
9040 (define-public r-lmertest
9047 (uri (cran-uri "lmerTest" version))
9050 "1nkz8cmxa5yb8q4i65bmhnn5pd4bhwcyjplyscynb24z3f64xp9b"))))
9051 (properties `((upstream-name . "lmerTest")))
9052 (build-system r-build-system)
9054 `(("r-ggplot2" ,r-ggplot2)
9057 ("r-numderiv" ,r-numderiv)))
9058 (home-page "https://github.com/runehaubo/lmerTestR")
9059 (synopsis "Tests in linear mixed effects models")
9061 "This package provides p-values in type I, II or III anova and summary
9062 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
9063 method. A Kenward-Roger method is also available via the @code{pbkrtest}
9064 package. Model selection methods include step, drop1 and anova-like tables
9065 for random effects (ranova). Methods for Least-Square means (LS-means) and
9066 tests of linear contrasts of fixed effects are also available.")
9067 (license license:gpl2+)))
9069 (define-public r-r2glmm
9076 (uri (cran-uri "r2glmm" version))
9079 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
9080 (build-system r-build-system)
9082 `(("r-afex" ,r-afex)
9083 ("r-data-table" ,r-data-table)
9084 ("r-dplyr" ,r-dplyr)
9085 ("r-ggplot2" ,r-ggplot2)
9086 ("r-gridextra" ,r-gridextra)
9087 ("r-lmertest" ,r-lmertest)
9089 ("r-matrix" ,r-matrix)
9091 ("r-pbkrtest" ,r-pbkrtest)))
9092 (home-page "https://github.com/bcjaeger/r2glmm")
9093 (synopsis "Compute R squared for mixed (multilevel) models")
9095 "This package computes model and semi partial R squared with confidence
9096 limits for the linear and generalized linear mixed model (LMM and GLMM). The
9097 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
9098 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
9100 (license license:gpl2)))
9102 (define-public r-weights
9109 (uri (cran-uri "weights" version))
9112 "0186bfpkhxngrshac6bpg37alp6slwhwd43inrm8hqg0vhpfgc4c"))))
9113 (build-system r-build-system)
9115 `(("r-gdata" ,r-gdata)
9116 ("r-hmisc" ,r-hmisc)
9117 ("r-mice" ,r-mice)))
9119 "https://cran.r-project.org/web/packages/weights/")
9120 (synopsis "Weighting and weighted statistics")
9121 (description "This package Provides a variety of functions for producing
9122 simple weighted statistics, such as weighted Pearson's correlations, partial
9123 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
9124 includes some software for quickly recoding survey data and plotting point
9125 estimates from interaction terms in regressions (and multiply imputed
9126 regressions). NOTE: Weighted partial correlation calculations pulled to
9128 (license license:gpl2+)))
9130 (define-public r-rcppannoy
9132 (name "r-rcppannoy")
9137 (uri (cran-uri "RcppAnnoy" version))
9140 "1wiigx5g5788j6lyc3f6bs1rsvc4alyc3052g35hxl1giinxmhn4"))))
9141 (properties `((upstream-name . "RcppAnnoy")))
9142 (build-system r-build-system)
9144 `(("r-rcpp" ,r-rcpp)))
9146 `(("r-knitr" ,r-knitr))) ; for vignettes
9147 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
9148 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
9150 "Annoy is a small C++ library for Approximate Nearest Neighbors written
9151 for efficient memory usage as well an ability to load from and save to disk.
9152 This package provides an R interface.")
9153 ;; Annoy is released under ASL 2.0, but this wrapper is released under
9155 (license (list license:gpl2+ license:asl2.0))))
9157 (define-public r-rcpphnsw
9164 (uri (cran-uri "RcppHNSW" version))
9167 "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv"))))
9168 (properties `((upstream-name . "RcppHNSW")))
9169 (build-system r-build-system)
9170 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9171 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
9172 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
9174 "Hnswlib is a C++ library for approximate nearest neighbors. This
9175 package provides a minimal R interface by relying on the Rcpp package.")
9176 ;; hnswlib is released under Version 2.0 of the Apache License.
9177 (license (list license:gpl3 license:asl2.0))))
9179 (define-public r-rcppparallel
9181 (name "r-rcppparallel")
9186 (uri (cran-uri "RcppParallel" version))
9189 "0p13f2mywjr7gmskf8ri4y8p5yr1bvr4xrpw2w11vdvafwz1vcia"))))
9190 (properties `((upstream-name . "RcppParallel")))
9191 (build-system r-build-system)
9192 (home-page "http://rcppcore.github.io/RcppParallel")
9193 (synopsis "Parallel programming tools for Rcpp")
9195 "This package provides high level functions for parallel programming with
9196 Rcpp. For example, the @code{parallelFor()} function can be used to convert
9197 the work of a standard serial @code{for} loop into a parallel one and the
9198 @code{parallelReduce()} function can be used for accumulating aggregates or
9200 (license license:gpl2)))
9202 (define-public r-ncdf4
9209 (uri (cran-uri "ncdf4" version))
9212 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
9213 (build-system r-build-system)
9215 `(("netcdf" ,netcdf)
9217 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
9218 (synopsis "R interface to Unidata netCDF format data files")
9220 "This package provides a high-level R interface to data files written
9221 using Unidata's netCDF library (version 4 or earlier), which are binary data
9222 files that are portable across platforms and include metadata information in
9223 addition to the data sets. Using this package, netCDF files can be opened and
9224 data sets read in easily. It is also easy to create new netCDF dimensions,
9225 variables, and files, in either version 3 or 4 format, and manipulate existing
9227 (license license:gpl3+)))
9229 (define-public r-biocmanager
9231 (name "r-biocmanager")
9236 (uri (cran-uri "BiocManager" version))
9238 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
9239 (properties `((upstream-name . "BiocManager")))
9240 (build-system r-build-system)
9241 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
9242 (synopsis "Access the Bioconductor project package repository")
9244 "This package provides a convenient tool to install and update
9245 Bioconductor packages.")
9246 (license license:artistic2.0)))
9248 (define-public r-rgl
9251 (version "0.100.30")
9255 (uri (cran-uri "rgl" version))
9258 "0rzqzskcwf2ah4yr62x5rjwf7yh90d43h39gk7jmfc5lc08zaxc5"))))
9259 (build-system r-build-system)
9261 `(("pkg-config" ,pkg-config)))
9263 `(("freetype" ,freetype)
9267 ("ghc-pandoc" ,ghc-pandoc)
9270 `(("r-crosstalk" ,r-crosstalk)
9271 ("r-htmltools" ,r-htmltools)
9272 ("r-htmlwidgets" ,r-htmlwidgets)
9273 ("r-jsonlite" ,r-jsonlite)
9274 ("r-knitr" ,r-knitr)
9275 ("r-magrittr" ,r-magrittr)
9276 ("r-manipulatewidget" ,r-manipulatewidget)
9277 ("r-shiny" ,r-shiny)))
9278 (home-page "https://r-forge.r-project.org/projects/rgl/")
9279 (synopsis "3D visualization using OpenGL")
9281 "This package provides medium to high level functions for 3D interactive graphics,
9282 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
9283 as functions for constructing representations of geometric
9284 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
9285 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
9286 image formats, including PNG, Postscript, SVG, PGF.")
9287 ;; Any version of the GPL.
9288 (license (list license:gpl2+ license:gpl3+))))
9290 (define-public r-multicool
9292 (name "r-multicool")
9297 (uri (cran-uri "multicool" version))
9300 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
9301 (build-system r-build-system)
9302 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9303 (home-page "https://cran.r-project.org/web/packages/multicool/")
9304 (synopsis "Permutations of multisets in cool-lex order")
9306 "This package provides a set of tools to permute multisets without loops
9307 or hash tables and to generate integer partitions. Cool-lex order is similar
9308 to colexicographical order.")
9309 (license license:gpl2)))
9311 (define-public r-misc3d
9318 (uri (cran-uri "misc3d" version))
9321 "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
9322 (build-system r-build-system)
9323 (home-page "https://cran.r-project.org/web/packages/misc3d/")
9324 (synopsis "Miscellaneous 3D Plots")
9326 "This package provides a collection of miscellaneous 3d plots, including
9328 ;; Any version of the GPL.
9329 (license (list license:gpl2+ license:gpl3+))))
9338 (uri (cran-uri "ks" version))
9340 (base32 "0hcccjfqnzdxkmnfzq8c5a7yhc138azwyl7rp29d1vl1jawwrwfq"))))
9341 (build-system r-build-system)
9344 ("r-kernlab" ,r-kernlab)
9345 ("r-kernsmooth" ,r-kernsmooth)
9346 ("r-matrix" ,r-matrix)
9347 ("r-mclust" ,r-mclust)
9349 ("r-multicool" ,r-multicool)
9350 ("r-mvtnorm" ,r-mvtnorm)))
9351 (home-page "http://www.mvstat.net/tduong/")
9352 (synopsis "Kernel smoothing")
9354 "This package provides kernel smoothers for univariate and multivariate
9355 data, including density functions, density derivatives, cumulative
9356 distributions, modal clustering, discriminant analysis, and two-sample
9357 hypothesis testing.")
9358 ;; Either version of the GPL.
9359 (license (list license:gpl2 license:gpl3))))
9361 (define-public r-feature
9368 (uri (cran-uri "feature" version))
9371 "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
9372 (build-system r-build-system)
9375 ("r-misc3d" ,r-misc3d)
9377 (home-page "http://www.mvstat.net/tduong/")
9378 (synopsis "Inferential feature significance for kernel density estimation")
9380 "The feature package contains functions to display and compute kernel
9381 density estimates, significant gradient and significant curvature regions.
9382 Significant gradient and/or curvature regions often correspond to significant
9383 features (e.g. local modes).")
9384 ;; Either version of the GPL.
9385 (license (list license:gpl2 license:gpl3))))
9387 (define-public r-arm
9394 (uri (cran-uri "arm" version))
9397 "0vvp90jygajd6ydky57z66wqjq9msfbl88irj5jbsray574mh4bg"))))
9398 (build-system r-build-system)
9400 `(("r-abind" ,r-abind)
9404 ("r-matrix" ,r-matrix)
9405 ("r-nlme" ,r-nlme)))
9406 (home-page "https://cran.r-project.org/web/packages/arm/")
9407 (synopsis "Data analysis using regression and multilevel/hierarchical models")
9409 "This package provides functions to accompany A. Gelman and J. Hill,
9410 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
9411 University Press, 2007.")
9412 (license license:gpl3+)))
9414 (define-public r-circular
9421 (uri (cran-uri "circular" version))
9424 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
9425 (build-system r-build-system)
9427 `(("r-boot" ,r-boot)
9428 ("r-mvtnorm" ,r-mvtnorm)))
9430 `(("gfortran" ,gfortran)))
9431 (home-page "https://cran.r-project.org/web/packages/circular/")
9432 (synopsis "Circular statistics")
9434 "This package provides tools for circular statistics, from \"Topics in
9435 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
9437 (license license:gpl2+)))
9439 (define-public r-activity
9446 (uri (cran-uri "activity" version))
9449 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
9450 (build-system r-build-system)
9452 `(("r-circular" ,r-circular)
9453 ("r-insol" ,r-insol)
9454 ("r-pbapply" ,r-pbapply)))
9455 (home-page "https://cran.r-project.org/web/packages/activity/")
9456 (synopsis "Animal activity statistics")
9458 "This package provides functions to fit kernel density functions to
9459 animal activity time data; plot activity distributions; quantify overall
9460 levels of activity; statistically compare activity metrics through
9461 bootstrapping; and evaluate variation in linear variables with time (or other
9462 circular variables).")
9463 (license license:gpl3)))
9465 (define-public r-ouch
9472 (uri (cran-uri "ouch" version))
9475 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
9476 (build-system r-build-system)
9477 (propagated-inputs `(("r-subplex" ,r-subplex)))
9478 (home-page "http://kingaa.github.io/ouch/")
9479 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
9481 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
9482 for evolution along a phylogenetic tree.")
9483 (license license:gpl2+)))
9485 (define-public r-fmsb
9492 (uri (cran-uri "fmsb" version))
9495 "1n29bnyp20pvpk2lsa9fblsj5w7amp14snc74pk5w3yr5y6rj0s5"))))
9496 (build-system r-build-system)
9497 (home-page "http://minato.sip21c.org/msb/")
9498 (synopsis "Functions for medical statistics book with demographic data")
9500 "This package provides several utility functions for the book entitled
9501 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
9502 Japan, 2007) with Japanese demographic data and some demographic analysis
9503 related functions.")
9504 (license license:gpl2+)))
9506 (define-public r-stabledist
9508 (name "r-stabledist")
9513 (uri (cran-uri "stabledist" version))
9516 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
9517 (build-system r-build-system)
9518 (home-page "http://www.rmetrics.org")
9519 (synopsis "Stable distribution functions")
9521 "This package provides density, probability and quantile functions, and
9522 random number generation for (skew) stable distributions, using the
9523 parametrizations of Nolan.")
9524 (license license:gpl2+)))
9526 (define-public r-gsl
9533 (uri (cran-uri "gsl" version))
9536 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
9537 (build-system r-build-system)
9540 (home-page "https://cran.r-project.org/web/packages/gsl")
9541 (synopsis "Wrapper for the GNU Scientific Library")
9543 "This package provides an R wrapper for the special functions and quasi
9544 random number generators of the GNU Scientific Library.")
9545 (license license:gpl2+)))
9547 (define-public r-adgoftest
9549 (name "r-adgoftest")
9554 (uri (cran-uri "ADGofTest" version))
9557 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
9558 (properties `((upstream-name . "ADGofTest")))
9559 (build-system r-build-system)
9560 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
9561 (synopsis "Anderson-Darling GoF test")
9563 "This package provides an implementation of the Anderson-Darling GoF test
9564 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
9565 Anderson-Darling Distribution\".")
9566 ;; Any version of the GPL.
9567 (license license:gpl3+)))
9569 (define-public r-softimpute
9571 (name "r-softimpute")
9576 (uri (cran-uri "softImpute" version))
9579 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
9580 (properties `((upstream-name . "softImpute")))
9581 (build-system r-build-system)
9583 `(("r-matrix" ,r-matrix)))
9585 `(("gfortran" ,gfortran)))
9586 (home-page "https://cran.r-project.org/web/packages/softImpute")
9587 (synopsis "Matrix completion via iterative soft-thresholded SVD")
9589 "This package provides iterative methods for matrix completion that use
9590 nuclear-norm regularization. The package includes procedures for centering
9591 and scaling rows, columns or both, and for computing low-rank @dfn{single
9592 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
9594 (license license:gpl2)))
9596 (define-public r-fftwtools
9598 (name "r-fftwtools")
9603 (uri (cran-uri "fftwtools" version))
9606 "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6"))))
9607 (build-system r-build-system)
9608 (inputs `(("fftw" ,fftw)))
9609 (home-page "https://github.com/krahim/fftwtools")
9610 (synopsis "Wrapper for FFTW3")
9612 "This package provides a wrapper for several FFTW functions. It provides
9613 access to the two-dimensional FFT, the multivariate FFT, and the
9614 one-dimensional real to complex FFT using the FFTW3 library. The package
9615 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
9616 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
9617 The FFT functions have a parameter that allows them to not return the
9618 redundant complex conjugate when the input is real data.")
9619 (license license:gpl2+)))
9621 (define-public r-tiff
9628 (uri (cran-uri "tiff" version))
9631 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
9632 (build-system r-build-system)
9634 `(("libtiff" ,libtiff)
9635 ("libjpeg" ,libjpeg)
9637 (home-page "http://www.rforge.net/tiff/")
9638 (synopsis "Read and write TIFF images")
9640 "This package provides an easy and simple way to read, write and display
9641 bitmap images stored in the TIFF format. It can read and write both files and
9642 in-memory raw vectors.")
9643 ;; Either of these two license versions.
9644 (license (list license:gpl2 license:gpl3))))
9646 (define-public r-nlp
9653 (uri (cran-uri "NLP" version))
9656 "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w"))))
9657 (properties `((upstream-name . "NLP")))
9658 (build-system r-build-system)
9659 (home-page "https://cran.r-project.org/web/packages/NLP/")
9660 (synopsis "Natural language processing infrastructure")
9662 "This package provides basic classes and methods for Natural Language
9664 (license license:gpl3)))
9673 (uri (cran-uri "tm" version))
9676 "0spv43kjbpxq3rdxx8ysgrncjyc35ydiwk7gp8n4sig45iqyz59r"))))
9677 (properties `((upstream-name . "tm")))
9678 (build-system r-build-system)
9684 ("r-xml2" ,r-xml2)))
9685 (home-page "http://tm.r-forge.r-project.org/")
9686 (synopsis "Text mining package")
9688 "This package provides a framework for text mining applications within R.")
9689 (license license:gpl3)))
9691 (define-public r-waveslim
9698 (uri (cran-uri "waveslim" version))
9701 "0mky0nb4xxp8rybp87mxw2f1q6k400wpxv01zr4injv7ja6028xk"))))
9702 (build-system r-build-system)
9704 `(("gfortran" ,gfortran)))
9705 (home-page "http://waveslim.blogspot.com")
9706 (synopsis "Basic wavelet routines for signal processing")
9708 "This package provides basic wavelet routines for time series (1D),
9709 image (2D) and array (3D) analysis. The code provided here is based on
9710 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
9711 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
9712 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
9713 pairs (Selesnick 2001, 2002).")
9714 (license license:bsd-3)))
9716 (define-public r-wordcloud
9718 (name "r-wordcloud")
9723 (uri (cran-uri "wordcloud" version))
9726 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
9727 (build-system r-build-system)
9729 `(("r-rcolorbrewer" ,r-rcolorbrewer)
9731 ;; The "tm" package is only "suggested" according to CRAN, but the
9732 ;; wordcloud package cannot be loaded without it.
9734 (home-page "https://cran.r-project.org/web/packages/wordcloud")
9735 (synopsis "Word clouds")
9737 "This package provides functionality to create pretty word clouds,
9738 visualize differences and similarity between documents, and avoid
9739 over-plotting in scatter plots with text.")
9740 (license license:lgpl2.1)))
9742 (define-public r-colorramps
9744 (name "r-colorramps")
9749 (uri (cran-uri "colorRamps" version))
9752 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
9753 (properties `((upstream-name . "colorRamps")))
9754 (build-system r-build-system)
9755 (home-page "https://cran.r-project.org/web/packages/colorRamps")
9756 (synopsis "Build color tables")
9757 (description "This package provides features to build gradient color
9759 ;; Any version of the GPL
9760 (license license:gpl3+)))
9762 (define-public r-tidytree
9769 (uri (cran-uri "tidytree" version))
9771 (base32 "1sbfwcxf9v1lhpa0392b49b6qfjrq7nlqz2djqzk5aknj9j64zvy"))))
9772 (build-system r-build-system)
9775 ("r-dplyr" ,r-dplyr)
9776 ("r-lazyeval" ,r-lazyeval)
9777 ("r-magrittr" ,r-magrittr)
9778 ("r-rlang" ,r-rlang)
9779 ("r-tibble" ,r-tibble)))
9780 (home-page "https://github.com/GuangchuangYu/tidytree")
9781 (synopsis "Tidy tool for phylogenetic tree data manipulation")
9783 "Phylogenetic trees generally contain multiple components including nodes,
9784 edges, branches and associated data. This package provides an approach to
9785 convert tree objects to tidy data frames. It also provides tidy interfaces to
9786 manipulate tree data.")
9787 (license license:artistic2.0)))
9789 (define-public r-rvcheck
9796 (uri (cran-uri "rvcheck" version))
9798 (base32 "1a3xlzi4n1rqiapfa180aif7n7nws8pbg8k3nk7ccaczvmni38aw"))))
9799 (build-system r-build-system)
9801 `(("r-biocmanager" ,r-biocmanager)
9802 ("r-rlang" ,r-rlang)))
9803 (home-page "https://cran.r-project.org/web/packages/rvcheck")
9804 (synopsis "R package version check")
9806 "This package provides tools to check the latest release version of R and
9807 R packages (on CRAN, Bioconductor or Github).")
9808 (license license:artistic2.0)))
9810 (define-public r-docopt
9817 (uri (cran-uri "docopt" version))
9820 "06zknnd0c5s2y0hbddzdlr3m63ib783izpck6pgz7sjbab5pd068"))))
9821 (build-system r-build-system)
9822 (home-page "https://github.com/docopt/docopt.R")
9823 (synopsis "Command-line interface specification language")
9825 "This package enables you to define a command-line interface by just
9826 giving it a description in the specific format.")
9827 (license license:expat)))
9829 (define-public r-sparsesvd
9831 (name "r-sparsesvd")
9836 (uri (cran-uri "sparsesvd" version))
9839 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
9840 (build-system r-build-system)
9841 (propagated-inputs `(("r-matrix" ,r-matrix)))
9842 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
9843 (synopsis "Sparse truncated singular value decomposition")
9845 "This package provides a Wrapper around the SVDLIBC library
9846 for (truncated) singular value decomposition of a sparse matrix. Currently,
9847 only sparse real matrices in Matrix package format are supported.")
9848 ;; SVDLIBC is released under BSD-2. The R interface is released under
9850 (license (list license:bsd-3 license:bsd-2))))
9852 (define-public r-speedglm
9859 (uri (cran-uri "speedglm" version))
9862 "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz"))))
9863 (build-system r-build-system)
9865 `(("r-mass" ,r-mass)
9866 ("r-matrix" ,r-matrix)))
9867 (home-page "https://cran.r-project.org/web/packages/speedglm")
9868 (synopsis "Fit linear and generalized linear models to large data sets")
9870 "This package provides tools for fitting linear models and generalized
9871 linear models to large data sets by updating algorithms.")
9872 ;; Any version of the GPL
9873 (license license:gpl2+)))
9875 (define-public r-densityclust
9877 (name "r-densityclust")
9882 (uri (cran-uri "densityClust" version))
9885 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
9886 (properties `((upstream-name . "densityClust")))
9887 (build-system r-build-system)
9890 ("r-ggplot2" ,r-ggplot2)
9891 ("r-ggrepel" ,r-ggrepel)
9892 ("r-gridextra" ,r-gridextra)
9893 ("r-rcolorbrewer" ,r-rcolorbrewer)
9895 ("r-rtsne" ,r-rtsne)))
9896 (home-page "https://cran.r-project.org/web/packages/densityClust")
9897 (synopsis "Clustering by fast search and find of density peaks")
9899 "This package provides an improved implementation (based on k-nearest
9900 neighbors) of the density peak clustering algorithm, originally described by
9901 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
9902 large datasets (> 100,000 samples) very efficiently.")
9903 (license license:gpl2+)))
9905 (define-public r-combinat
9912 (uri (cran-uri "combinat" version))
9915 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
9916 (build-system r-build-system)
9917 (home-page "https://cran.r-project.org/web/packages/combinat")
9918 (synopsis "Combinatorics utilities")
9919 (description "This package provides assorted routines for combinatorics.")
9920 (license license:gpl2)))
9922 (define-public r-qlcmatrix
9924 (name "r-qlcmatrix")
9929 (uri (cran-uri "qlcMatrix" version))
9932 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
9933 (properties `((upstream-name . "qlcMatrix")))
9934 (build-system r-build-system)
9936 `(("r-docopt" ,r-docopt)
9937 ("r-matrix" ,r-matrix)
9939 ("r-sparsesvd" ,r-sparsesvd)))
9940 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
9941 (synopsis "Sparse matrix functions for quantitative language comparison")
9943 "This package provides an extension of the functionality of the Matrix
9944 package for using sparse matrices. Some of the functions are very general,
9945 while other are highly specific for the special data format used for
9946 @dfn{quantitative language comparison} (QLC).")
9947 (license license:gpl3)))
9949 (define-public r-ddrtree
9956 (uri (cran-uri "DDRTree" version))
9959 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
9960 (properties `((upstream-name . "DDRTree")))
9961 (build-system r-build-system)
9964 ("r-irlba" ,r-irlba)
9966 ("r-rcppeigen" ,r-rcppeigen)))
9967 (home-page "https://cran.r-project.org/web/packages/DDRTree")
9968 (synopsis "Learning principal graphs with DDRTree")
9970 "This package provides an implementation of the framework of
9971 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
9972 dimensional space while constructs a principal tree which passes through the
9973 middle of the data simultaneously. DDRTree shows superiority to
9974 alternatives (Wishbone, DPT) for inferring the ordering as well as the
9975 intrinsic structure of single cell genomics data. In general, it could be
9976 used to reconstruct the temporal progression as well as the bifurcation
9977 structure of any data type.")
9978 (license license:asl2.0)))
9980 (define-public r-corpcor
9987 (uri (cran-uri "corpcor" version))
9990 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
9991 (build-system r-build-system)
9992 (home-page "http://strimmerlab.org/software/corpcor/")
9993 (synopsis "Efficient estimation of covariance and (partial) correlation")
9995 "This package implements a James-Stein-type shrinkage estimator for the
9996 covariance matrix, with separate shrinkage for variances and correlations.
9997 Furthermore, functions are available for fast singular value decomposition,
9998 for computing the pseudoinverse, and for checking the rank and positive
9999 definiteness of a matrix.")
10000 (license license:gpl3+)))
10002 (define-public r-rspectra
10004 (name "r-rspectra")
10009 (uri (cran-uri "RSpectra" version))
10012 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
10013 (properties `((upstream-name . "RSpectra")))
10014 (build-system r-build-system)
10016 `(("r-matrix" ,r-matrix)
10018 ("r-rcppeigen" ,r-rcppeigen)))
10019 (home-page "https://github.com/yixuan/RSpectra")
10020 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
10022 "This package provides an R interface to the Spectra library for
10023 large-scale eigenvalue and SVD problems. It is typically used to compute a
10024 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
10025 which is usually more efficient than @code{eigen()} if k << n.")
10027 (license license:mpl2.0)))
10029 (define-public r-vbsr
10036 (uri (cran-uri "vbsr" version))
10039 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
10040 (build-system r-build-system)
10041 (home-page "https://cran.r-project.org/web/packages/vbsr")
10042 (synopsis "Variational Bayes spike regression regularized linear models")
10044 "This package provides an efficient algorithm for solving ultra-sparse
10045 regularized regression models using a variational Bayes algorithm with a spike
10046 prior. The algorithm is solved on a path, with coordinate updates, and is
10047 capable of generating very sparse models. Very general model
10048 diagnostics for controlling type-1 errors are also provided.")
10049 (license license:gpl2)))
10051 (define-public r-flare
10054 (version "1.6.0.2")
10058 (uri (cran-uri "flare" version))
10061 "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
10062 (build-system r-build-system)
10064 `(("r-igraph" ,r-igraph)
10065 ("r-lattice" ,r-lattice)
10067 ("r-matrix" ,r-matrix)))
10068 (home-page "https://cran.r-project.org/web/packages/flare")
10069 (synopsis "Family of Lasso regression implementations")
10071 "This package provides implementations of a family of Lasso variants
10072 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
10073 high dimensional sparse linear models.")
10074 (license license:gpl2)))
10076 (define-public r-lassopv
10083 (uri (cran-uri "lassopv" version))
10086 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
10087 (build-system r-build-system)
10088 (propagated-inputs `(("r-lars" ,r-lars)))
10089 (home-page "https://github.com/lingfeiwang/lassopv")
10090 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
10092 "This package enables you to estimate the p-values for predictors x
10093 against target variable y in Lasso regression, using the regularization
10094 strength when each predictor enters the active set of regularization path for
10095 the first time as the statistic.")
10096 (license license:gpl3)))
10098 (define-public r-splitstackshape
10100 (name "r-splitstackshape")
10105 (uri (cran-uri "splitstackshape" version))
10108 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
10109 (build-system r-build-system)
10111 `(("r-data-table" ,r-data-table)))
10112 (home-page "https://github.com/mrdwab/splitstackshape")
10113 (synopsis "Stack and reshape datasets after splitting concatenated values")
10115 "Online data collection tools like Google Forms often export
10116 multiple-response questions with data concatenated in cells. The
10117 @code{concat.split} (cSplit) family of functions provided by this package
10118 splits such data into separate cells. This package also includes functions to
10119 stack groups of columns and to reshape wide data, even when the data are
10120 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
10121 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
10123 (license license:gpl3)))
10125 (define-public r-tfmpvalue
10127 (name "r-tfmpvalue")
10132 (uri (cran-uri "TFMPvalue" version))
10135 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
10136 (properties `((upstream-name . "TFMPvalue")))
10137 (build-system r-build-system)
10138 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10139 (home-page "https://github.com/ge11232002/TFMPvalue")
10140 (synopsis "P-value computation for position weight matrices")
10142 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
10143 identification from sequence/alignments, we are interested in the significance
10144 of certain match scores. TFMPvalue provides the accurate calculation of a
10145 p-value with a score threshold for position weight matrices, or the score with
10146 a given p-value. It is an interface to code originally made available by
10147 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
10148 Touzet and Varre (2007).")
10149 (license license:gpl2)))
10151 (define-public r-rnifti
10158 (uri (cran-uri "RNifti" version))
10161 "0hfid40pgfi1ykqka8y3v0m7h0iyd6fbvycvqlad3ibmbg621f0w"))))
10162 (properties `((upstream-name . "RNifti")))
10163 (build-system r-build-system)
10164 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10165 (home-page "https://github.com/jonclayden/RNifti")
10166 (synopsis "Fast R and C++ access to NIfTI images")
10168 "This package provides very fast read and write access to images stored
10169 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
10170 compiled C and interpreted R code. It also provides a C/C++ API that can be
10171 used by other packages.")
10172 (license license:gpl2)))
10174 (define-public r-shades
10181 (uri (cran-uri "shades" version))
10184 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
10185 (build-system r-build-system)
10186 (home-page "https://github.com/jonclayden/shades")
10187 (synopsis "Simple color manipulation")
10189 "This package provides functions for easily manipulating colors,
10190 creating color scales and calculating color distances.")
10191 (license license:bsd-3)))
10193 (define-public r-ore
10200 (uri (cran-uri "ore" version))
10202 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
10203 (build-system r-build-system)
10204 (home-page "https://github.com/jonclayden/ore")
10205 (synopsis "R interface to the Onigmo regular expression library")
10207 "This package provides an alternative to R's built-in functionality for
10208 handling regular expressions, based on the Onigmo library. It offers
10209 first-class compiled regex objects, partial matching and function-based
10210 substitutions, amongst other features.")
10211 (license license:bsd-3)))
10213 (define-public r-reportr
10220 (uri (cran-uri "reportr" version))
10223 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
10224 (build-system r-build-system)
10225 (propagated-inputs `(("r-ore" ,r-ore)))
10226 (home-page "https://github.com/jonclayden/reportr")
10227 (synopsis "General message and error reporting system")
10229 "This package provides a system for reporting messages, which offers
10230 certain useful features over the standard R system, such as the incorporation
10231 of output consolidation, message filtering, assertions, expression
10232 substitution, automatic generation of stack traces for debugging, and
10233 conditional reporting based on the current \"output level\".")
10234 (license license:gpl2)))
10236 (define-public r-tractor-base
10238 (name "r-tractor-base")
10243 (uri (cran-uri "tractor.base" version))
10246 "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i"))))
10247 (properties `((upstream-name . "tractor.base")))
10248 (build-system r-build-system)
10251 ("r-reportr" ,r-reportr)
10252 ("r-rnifti" ,r-rnifti)
10253 ("r-shades" ,r-shades)))
10254 (home-page "http://www.tractor-mri.org.uk")
10255 (synopsis "Read, manipulate and visualize magnetic resonance images")
10257 "This package provides functions for working with magnetic resonance
10258 images. It supports reading and writing of popular file formats (DICOM,
10259 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
10260 visualization; flexible image manipulation; metadata and sparse image
10262 (license license:gpl2)))
10264 (define-public r-grimport
10266 (name "r-grimport")
10271 (uri (cran-uri "grImport" version))
10274 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
10275 (properties `((upstream-name . "grImport")))
10276 (build-system r-build-system)
10278 `(("ghostscript" ,ghostscript)))
10280 `(("r-xml" ,r-xml)))
10281 (home-page "https://cran.r-project.org/web/packages/grImport")
10282 (synopsis "Convert, import, and draw PostScript pictures")
10284 "This package provides functions for converting, importing, and drawing
10285 PostScript pictures in R plots.")
10286 (license license:gpl2+)))
10288 (define-public r-grimport2
10290 (name "r-grimport2")
10295 (uri (cran-uri "grImport2" version))
10298 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
10299 (properties `((upstream-name . "grImport2")))
10300 (build-system r-build-system)
10302 `(("r-base64enc" ,r-base64enc)
10306 (home-page "https://cran.r-project.org/web/packages/grImport2/")
10307 (synopsis "Import SVG graphics")
10309 "This package provides functions for importing external vector images and
10310 drawing them as part of R plots. This package is different from the
10311 @code{grImport} package because, where that package imports PostScript format
10312 images, this package imports SVG format images. Furthermore, this package
10313 imports a specific subset of SVG, so external images must be preprocessed
10314 using a package like @code{rsvg} to produce SVG that this package can import.
10315 SVG features that are not supported by R graphics, such as gradient fills, can
10316 be imported and then exported via the @code{gridSVG} package.")
10317 (license license:gpl2+)))
10319 (define-public r-kohonen
10326 (uri (cran-uri "kohonen" version))
10329 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
10330 (build-system r-build-system)
10332 `(("r-rcpp" ,r-rcpp)))
10333 (home-page "https://cran.r-project.org/web/packages/kohonen")
10334 (synopsis "Supervised and unsupervised self-organising maps")
10336 "This package provides functions to train @dfn{self-organising
10337 maps} (SOMs). Also interrogation of the maps and prediction using trained
10338 maps are supported. The name of the package refers to Teuvo Kohonen, the
10339 inventor of the SOM.")
10340 (license license:gpl2+)))
10342 (define-public r-nnls
10349 (uri (cran-uri "nnls" version))
10352 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
10353 (build-system r-build-system)
10354 (native-inputs `(("gfortran" ,gfortran)))
10355 (home-page "https://cran.r-project.org/web/packages/nnls")
10356 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
10358 "This package provides an R interface to the Lawson-Hanson implementation
10359 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
10360 the combination of non-negative and non-positive constraints.")
10361 (license license:gpl2+)))
10363 (define-public r-iso
10370 (uri (cran-uri "Iso" version))
10373 "014mm5b1f7i6nwlz3kyg1biph0y542kcx5bd13p68cv5a928qzid"))))
10374 (properties `((upstream-name . "Iso")))
10375 (build-system r-build-system)
10376 (native-inputs `(("gfortran" ,gfortran)))
10377 (home-page "http://www.stat.auckland.ac.nz/~rolf/")
10378 (synopsis "Functions to perform isotonic regression")
10380 "This package provides support for linear order and unimodal
10381 order (univariate) isotonic regression and bivariate isotonic regression with
10382 linear order on both variables.")
10383 (license license:gpl2+)))
10385 (define-public r-chemometricswithr
10387 (name "r-chemometricswithr")
10392 (uri (cran-uri "ChemometricsWithR" version))
10395 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
10397 `((upstream-name . "ChemometricsWithR")))
10398 (build-system r-build-system)
10400 `(("r-devtools" ,r-devtools)
10401 ("r-kohonen" ,r-kohonen)
10404 (home-page "https://github.com/rwehrens/CWR")
10405 (synopsis "Chemometrics with R")
10407 "This package provides functions and scripts used in the book
10408 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
10409 Life Sciences\" by Ron Wehrens, Springer (2011).")
10410 (license license:gpl2+)))
10412 (define-public r-als
10419 (uri (cran-uri "ALS" version))
10422 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
10423 (properties `((upstream-name . "ALS")))
10424 (build-system r-build-system)
10427 ("r-nnls" ,r-nnls)))
10428 (home-page "https://cran.r-project.org/web/packages/ALS")
10429 (synopsis "Multivariate curve resolution alternating least squares")
10431 "Alternating least squares is often used to resolve components
10432 contributing to data with a bilinear structure; the basic technique may be
10433 extended to alternating constrained least squares. This package provides an
10434 implementation of @dfn{multivariate curve resolution alternating least
10435 squares} (MCR-ALS).
10437 Commonly applied constraints include unimodality, non-negativity, and
10438 normalization of components. Several data matrices may be decomposed
10439 simultaneously by assuming that one of the two matrices in the bilinear
10440 decomposition is shared between datasets.")
10441 (license license:gpl2+)))
10443 (define-public r-strucchange
10445 (name "r-strucchange")
10450 (uri (cran-uri "strucchange" version))
10453 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
10454 (build-system r-build-system)
10456 `(("r-sandwich" ,r-sandwich)
10458 (home-page "https://cran.r-project.org/web/packages/strucchange")
10459 (synopsis "Testing, monitoring, and dating structural changes")
10461 "This package provides tools for testing, monitoring and dating
10462 structural changes in (linear) regression models. It features tests/methods
10463 from the generalized fluctuation test framework as well as from the F
10464 test (Chow test) framework. This includes methods to fit, plot and test
10465 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
10466 statistics, respectively. It is possible to monitor incoming data online
10467 using fluctuation processes. Finally, the breakpoints in regression models
10468 with structural changes can be estimated together with confidence intervals.
10469 Emphasis is always given to methods for visualizing the data.")
10470 ;; Either of these two GPL versions
10471 (license (list license:gpl2 license:gpl3))))
10473 (define-public r-pixmap
10480 (uri (cran-uri "pixmap" version))
10483 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
10484 (build-system r-build-system)
10485 (home-page "https://cran.r-project.org/web/packages/pixmap")
10486 (synopsis "Tools for bitmap images")
10488 "This package provides functions for importing, exporting, plotting and
10489 other manipulations of bitmapped images.")
10490 (license license:gpl2)))
10492 (define-public r-rapidjsonr
10494 (name "r-rapidjsonr")
10499 (uri (cran-uri "rapidjsonr" version))
10502 "0h4phjjhykbb45rg5b1xn48vqxdcvcngbm0416ds8in7j469wbwd"))))
10503 (build-system r-build-system)
10504 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
10505 (synopsis "JSON parser")
10507 "This package provides JSON parsing capability through the Rapidjson
10509 (license license:expat)))
10511 (define-public r-ontologyindex
10513 (name "r-ontologyindex")
10518 (uri (cran-uri "ontologyIndex" version))
10521 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
10522 (properties `((upstream-name . "ontologyIndex")))
10523 (build-system r-build-system)
10524 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
10525 (synopsis "Functions for processing ontologies in R")
10527 "This package provides functions for reading ontologies into R as lists
10528 and manipulating sets of ontological terms.")
10529 (license license:gpl2+)))
10531 (define-public r-gargle
10538 (uri (cran-uri "gargle" version))
10541 "08zhfk2sl342w35i5n2c93ayypg3z0kbl0020l3y9adqka1vazgx"))))
10542 (build-system r-build-system)
10547 ("r-jsonlite" ,r-jsonlite)
10548 ("r-rlang" ,r-rlang)
10549 ("r-withr" ,r-withr)))
10550 (home-page "https://gargle.r-lib.org")
10551 (synopsis "Utilities for working with Google APIs")
10553 "This package provides utilities for working with Google APIs. This
10554 includes functions and classes for handling common credential types and for
10555 preparing, executing, and processing HTTP requests.")
10556 (license license:expat)))
10558 (define-public r-bigrquery
10560 (name "r-bigrquery")
10565 (uri (cran-uri "bigrquery" version))
10568 "1ggh2gngr5x0g6y7d55y6kvn94anf7qi1bkc28cjmw61hxjq38fb"))))
10569 (build-system r-build-system)
10571 `(("r-assertthat" ,r-assertthat)
10572 ("r-bit64" ,r-bit64)
10575 ("r-gargle" ,r-gargle)
10578 ("r-jsonlite" ,r-jsonlite)
10579 ("r-prettyunits" ,r-prettyunits)
10580 ("r-progress" ,r-progress)
10581 ("r-rapidjsonr" ,r-rapidjsonr)
10583 ("r-rlang" ,r-rlang)
10584 ("r-tibble" ,r-tibble)))
10585 (home-page "https://github.com/rstats-db/bigrquery")
10586 (synopsis "R interface to Google's BigQuery API")
10588 "This package provides an R interface to Google's BigQuery database.")
10589 (license license:gpl3)))
10591 (define-public r-gmp
10594 (version "0.5-13.5")
10598 (uri (cran-uri "gmp" version))
10601 "042mzsl6z6s61fy5m21yf9q83l08vnyqljn4iax7kqyiycpsp0gn"))))
10602 (build-system r-build-system)
10605 (modify-phases %standard-phases
10606 (add-after 'unpack 'set-CC
10607 (lambda _ (setenv "CC" "gcc") #t)))))
10608 (inputs `(("gmp" ,gmp)))
10609 (home-page "https://cran.r-project.org/web/packages/gmp")
10610 (synopsis "Multiple precision arithmetic")
10612 "This package supports multiple precision arithmetic (big integers and
10613 rationals, prime number tests, matrix computation), \"arithmetic without
10614 limitations\" using the GNU Multiple Precision library.")
10615 ;; Any version of the GPL.
10616 (license license:gpl3+)))
10618 (define-public r-rmpfr
10625 (uri (cran-uri "Rmpfr" version))
10628 "1zq3as34r27v2yc729731997wdhxb6cs5ilmak4nmsljabnac7gc"))))
10629 (properties `((upstream-name . "Rmpfr")))
10630 (build-system r-build-system)
10634 `(("r-gmp" ,r-gmp)))
10635 (home-page "http://rmpfr.r-forge.r-project.org/")
10636 (synopsis "R bindings to the MPFR library")
10638 "This package supports arithmetic (via S4 classes and methods) for
10639 arbitrary precision floating point numbers, including transcendental
10640 functions. To this end, the package interfaces with the @dfn{Multiple
10641 Precision Floating-Point Reliable} (MPFR) library.")
10642 (license license:gpl2+)))
10644 (define-public r-assertive-base
10646 (name "r-assertive-base")
10651 (uri (cran-uri "assertive.base" version))
10654 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
10656 `((upstream-name . "assertive.base")))
10657 (build-system r-build-system)
10658 (home-page "https://bitbucket.org/richierocks/assertive.base")
10659 (synopsis "Core of the assertive package")
10661 "This package provides a minimal set of predicates and assertions used by
10662 the assertive package. This is mainly for use by other package developers who
10663 want to include run-time testing features in their own packages.")
10664 (license license:gpl3+)))
10666 (define-public r-assertive-properties
10668 (name "r-assertive-properties")
10673 (uri (cran-uri "assertive.properties" version))
10676 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
10678 `((upstream-name . "assertive.properties")))
10679 (build-system r-build-system)
10681 `(("r-assertive-base" ,r-assertive-base)))
10682 (home-page "https://bitbucket.org/richierocks/assertive.properties")
10683 (synopsis "Assertions to check properties of variables")
10685 "This package provides a set of predicates and assertions for checking
10686 the properties of variables, such as length, names and attributes. This is
10687 mainly for use by other package developers who want to include run-time
10688 testing features in their own packages.")
10689 (license license:gpl3+)))
10691 (define-public r-assertive-numbers
10693 (name "r-assertive-numbers")
10698 (uri (cran-uri "assertive.numbers" version))
10701 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
10703 `((upstream-name . "assertive.numbers")))
10704 (build-system r-build-system)
10706 `(("r-assertive-base" ,r-assertive-base)))
10707 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
10708 (synopsis "Assertions to check properties of numbers")
10710 "This package provides a set of predicates and assertions for checking
10711 the properties of numbers. This is mainly for use by other package developers
10712 who want to include run-time testing features in their own packages.")
10713 (license license:gpl3+)))
10715 (define-public r-assertive-sets
10717 (name "r-assertive-sets")
10722 (uri (cran-uri "assertive.sets" version))
10725 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
10727 `((upstream-name . "assertive.sets")))
10728 (build-system r-build-system)
10730 `(("r-assertive-base" ,r-assertive-base)))
10731 (home-page "https://bitbucket.org/richierocks/assertive.sets")
10732 (synopsis "Assertions to check properties of sets")
10734 "This package provides a set of predicates and assertions for checking
10735 the properties of sets. This is mainly for use by other package developers
10736 who want to include run-time testing features in their own packages.")
10737 (license license:gpl3+)))
10739 (define-public r-assertive-matrices
10741 (name "r-assertive-matrices")
10746 (uri (cran-uri "assertive.matrices" version))
10749 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
10751 `((upstream-name . "assertive.matrices")))
10752 (build-system r-build-system)
10754 `(("r-assertive-base" ,r-assertive-base)))
10755 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
10756 (synopsis "Assertions to check properties of matrices")
10758 "This package provides a set of predicates and assertions for checking
10759 the properties of matrices. This is mainly for use by other package
10760 developers who want to include run-time testing features in their own
10762 (license license:gpl3+)))
10764 (define-public r-assertive-models
10766 (name "r-assertive-models")
10771 (uri (cran-uri "assertive.models" version))
10774 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
10776 `((upstream-name . "assertive.models")))
10777 (build-system r-build-system)
10779 `(("r-assertive-base" ,r-assertive-base)))
10780 (home-page "https://bitbucket.org/richierocks/assertive.models")
10781 (synopsis "Assertions to check properties of models")
10783 "This package provides a set of predicates and assertions for checking
10784 the properties of models. This is mainly for use by other package developers
10785 who want to include run-time testing features in their own packages.")
10786 (license license:gpl3+)))
10788 (define-public r-assertive-reflection
10790 (name "r-assertive-reflection")
10795 (uri (cran-uri "assertive.reflection" version))
10798 "19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj"))))
10800 `((upstream-name . "assertive.reflection")))
10801 (build-system r-build-system)
10803 `(("r-assertive-base" ,r-assertive-base)))
10804 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
10805 (synopsis "Assertions for checking the state of R")
10807 "This package provides a set of predicates and assertions for checking
10808 the state and capabilities of R, the operating system it is running on, and
10809 the IDE being used. This is mainly for use by other package developers who
10810 want to include run-time testing features in their own packages.")
10811 (license license:gpl3+)))
10813 (define-public r-assertive-types
10815 (name "r-assertive-types")
10820 (uri (cran-uri "assertive.types" version))
10823 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
10825 `((upstream-name . "assertive.types")))
10826 (build-system r-build-system)
10828 `(("r-assertive-base" ,r-assertive-base)
10829 ("r-assertive-properties" ,r-assertive-properties)
10830 ("r-codetools" ,r-codetools)))
10831 (home-page "https://bitbucket.org/richierocks/assertive.types")
10832 (synopsis "Assertions to check types of variables")
10834 "This package provides a set of predicates and assertions for checking
10835 the types of variables. This is mainly for use by other package developers
10836 who want to include run-time testing features in their own packages.")
10837 (license license:gpl3+)))
10839 (define-public r-assertive-files
10841 (name "r-assertive-files")
10846 (uri (cran-uri "assertive.files" version))
10849 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
10851 `((upstream-name . "assertive.files")))
10852 (build-system r-build-system)
10854 `(("r-assertive-base" ,r-assertive-base)
10855 ("r-assertive-numbers" ,r-assertive-numbers)))
10856 (home-page "https://bitbucket.org/richierocks/assertive.files")
10857 (synopsis "Assertions to check properties of files")
10859 "This package provides a set of predicates and assertions for checking
10860 the properties of files and connections. This is mainly for use by other
10861 package developers who want to include run-time testing features in their own
10863 (license license:gpl3+)))
10865 (define-public r-assertive-code
10867 (name "r-assertive-code")
10872 (uri (cran-uri "assertive.code" version))
10875 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
10877 `((upstream-name . "assertive.code")))
10878 (build-system r-build-system)
10880 `(("r-assertive-base" ,r-assertive-base)
10881 ("r-assertive-properties" ,r-assertive-properties)
10882 ("r-assertive-types" ,r-assertive-types)))
10883 (home-page "https://bitbucket.org/richierocks/assertive.code")
10884 (synopsis "Assertions to check properties of code")
10886 "This package provides a set of predicates and assertions for checking
10887 the properties of code. This is mainly for use by other package developers
10888 who want to include run-time testing features in their own packages.")
10889 (license license:gpl3+)))
10891 (define-public r-assertive-datetimes
10893 (name "r-assertive-datetimes")
10898 (uri (cran-uri "assertive.datetimes" version))
10901 "00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78"))))
10903 `((upstream-name . "assertive.datetimes")))
10904 (build-system r-build-system)
10906 `(("r-assertive-base" ,r-assertive-base)
10907 ("r-assertive-types" ,r-assertive-types)))
10908 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
10909 (synopsis "Assertions to check properties of dates and times")
10911 "This package provides a set of predicates and assertions for checking
10912 the properties of dates and times. This is mainly for use by other package
10913 developers who want to include run-time testing features in their own
10915 (license license:gpl3+)))
10917 (define-public r-assertive-strings
10919 (name "r-assertive-strings")
10924 (uri (cran-uri "assertive.strings" version))
10927 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
10929 `((upstream-name . "assertive.strings")))
10930 (build-system r-build-system)
10932 `(("r-assertive-base" ,r-assertive-base)
10933 ("r-assertive-types" ,r-assertive-types)
10934 ("r-stringi" ,r-stringi)))
10935 (home-page "https://bitbucket.org/richierocks/assertive.strings")
10936 (synopsis "Assertions to check properties of strings")
10938 "This package provides a set of predicates and assertions for checking
10939 the properties of strings. This is mainly for use by other package developers
10940 who want to include run-time testing features in their own packages.")
10941 (license license:gpl3+)))
10943 (define-public r-assertive-data-us
10945 (name "r-assertive-data-us")
10950 (uri (cran-uri "assertive.data.us" version))
10953 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
10955 `((upstream-name . "assertive.data.us")))
10956 (build-system r-build-system)
10958 `(("r-assertive-base" ,r-assertive-base)
10959 ("r-assertive-strings" ,r-assertive-strings)))
10960 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
10961 (synopsis "Assertions to check properties of strings")
10963 "This package provides a set of predicates and assertions for checking
10964 the properties of US-specific complex data types. This is mainly for use by
10965 other package developers who want to include run-time testing features in
10966 their own packages.")
10967 (license license:gpl3+)))
10969 (define-public r-assertive-data-uk
10971 (name "r-assertive-data-uk")
10976 (uri (cran-uri "assertive.data.uk" version))
10979 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
10981 `((upstream-name . "assertive.data.uk")))
10982 (build-system r-build-system)
10984 `(("r-assertive-base" ,r-assertive-base)
10985 ("r-assertive-strings" ,r-assertive-strings)))
10986 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
10987 (synopsis "Assertions to check properties of strings")
10989 "This package provides a set of predicates and assertions for checking
10990 the properties of UK-specific complex data types. This is mainly for use by
10991 other package developers who want to include run-time testing features in
10992 their own packages.")
10993 (license license:gpl3+)))
10995 (define-public r-assertive-data
10997 (name "r-assertive-data")
11002 (uri (cran-uri "assertive.data" version))
11005 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
11007 `((upstream-name . "assertive.data")))
11008 (build-system r-build-system)
11010 `(("r-assertive-base" ,r-assertive-base)
11011 ("r-assertive-strings" ,r-assertive-strings)))
11012 (home-page "https://bitbucket.org/richierocks/assertive.data")
11013 (synopsis "Assertions to check properties of data")
11015 "This package provides a set of predicates and assertions for checking
11016 the properties of (country independent) complex data types. This is mainly
11017 for use by other package developers who want to include run-time testing
11018 features in their own packages.")
11019 (license license:gpl3+)))
11021 (define-public r-assertive
11023 (name "r-assertive")
11028 (uri (cran-uri "assertive" version))
11031 "0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3"))))
11032 (build-system r-build-system)
11034 `(("r-assertive-base" ,r-assertive-base)
11035 ("r-assertive-code" ,r-assertive-code)
11036 ("r-assertive-data" ,r-assertive-data)
11037 ("r-assertive-data-uk" ,r-assertive-data-uk)
11038 ("r-assertive-data-us" ,r-assertive-data-us)
11039 ("r-assertive-datetimes" ,r-assertive-datetimes)
11040 ("r-assertive-files" ,r-assertive-files)
11041 ("r-assertive-matrices" ,r-assertive-matrices)
11042 ("r-assertive-models" ,r-assertive-models)
11043 ("r-assertive-numbers" ,r-assertive-numbers)
11044 ("r-assertive-properties" ,r-assertive-properties)
11045 ("r-assertive-reflection" ,r-assertive-reflection)
11046 ("r-assertive-sets" ,r-assertive-sets)
11047 ("r-assertive-strings" ,r-assertive-strings)
11048 ("r-assertive-types" ,r-assertive-types)
11049 ("r-knitr" ,r-knitr)))
11050 (home-page "https://bitbucket.org/richierocks/assertive")
11051 (synopsis "Readable check functions to ensure code integrity")
11053 "This package provides lots of predicates (@code{is_*} functions) to
11054 check the state of your variables, and assertions (@code{assert_*} functions)
11055 to throw errors if they aren't in the right form.")
11056 (license license:gpl3+)))
11058 (define-public r-dotcall64
11060 (name "r-dotcall64")
11065 (uri (cran-uri "dotCall64" version))
11068 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
11069 (properties `((upstream-name . "dotCall64")))
11070 (build-system r-build-system)
11071 (native-inputs `(("gfortran" ,gfortran)))
11072 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
11073 (synopsis "Enhanced foreign function interface supporting long vectors")
11075 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
11076 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
11077 supports long vectors, arguments of type 64-bit integer, and provides a
11078 mechanism to avoid unnecessary copies of read-only and write-only arguments.
11079 This makes it a convenient and fast interface to C/C++ and Fortran code.")
11080 (license license:gpl2+)))
11082 (define-public r-spam
11089 (uri (cran-uri "spam" version))
11091 (base32 "1wfv45jq8zy8kyjr308zicc1461y1777qll1cy6lw4071f9rvba2"))))
11092 (build-system r-build-system)
11094 `(("r-dotcall64" ,r-dotcall64)))
11095 (native-inputs `(("gfortran" ,gfortran)))
11096 (home-page "https://www.math.uzh.ch/pages/spam/")
11097 (synopsis "Sparse matrix algebra")
11099 "This package provides a set of functions for sparse matrix algebra.
11100 Differences with other sparse matrix packages are:
11103 @item it only supports (essentially) one sparse matrix format;
11104 @item it is based on transparent and simple structure(s);
11105 @item it is tailored for MCMC calculations within G(M)RF;
11106 @item and it is fast and scalable (with the extension package @code{spam64}).
11108 ;; Either of these licenses
11109 (license (list license:bsd-3 license:lgpl2.0))))
11111 (define-public r-fields
11118 (uri (cran-uri "fields" version))
11120 (base32 "173zm5vr236ydiq0v27qy0l3x7h9fc7jly38iakg77j26i0a01il"))))
11121 (build-system r-build-system)
11123 `(("r-maps" ,r-maps)
11124 ("r-spam" ,r-spam)))
11126 `(("gfortran" ,gfortran)))
11127 (home-page "https://www.image.ucar.edu/fields")
11128 (synopsis "Tools for spatial data")
11130 "This is a package for curve, surface and function fitting with an
11131 emphasis on splines, spatial data and spatial statistics. The major methods
11132 include cubic, and thin plate splines, Kriging, and compactly supported
11133 covariance functions for large data sets.")
11134 (license license:gpl2+)))
11136 (define-public r-spatialextremes
11138 (name "r-spatialextremes")
11139 (version "2.0-7.2")
11143 (uri (cran-uri "SpatialExtremes" version))
11146 "0aqq9ryxi4xsdqjhc1lhb7ai8szs7m2vys6nn0ygps1w3pm4xwj8"))))
11148 `((upstream-name . "SpatialExtremes")))
11149 (build-system r-build-system)
11151 `(("r-fields" ,r-fields)
11152 ("r-maps" ,r-maps)))
11153 (home-page "http://spatialextremes.r-forge.r-project.org/")
11154 (synopsis "Modelling spatial extremes")
11156 "This package provides tools for the statistical modelling of spatial
11157 extremes using max-stable processes, copula or Bayesian hierarchical models.
11158 More precisely, this package allows (conditional) simulations from various
11159 parametric max-stable models, analysis of the extremal spatial dependence, the
11160 fitting of such processes using composite likelihoods or least square (simple
11161 max-stable processes only), model checking and selection and prediction.")
11162 (license license:gpl2+)))
11164 (define-public r-drc
11171 (uri (cran-uri "drc" version))
11174 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
11175 (build-system r-build-system)
11178 ("r-gtools" ,r-gtools)
11180 ("r-multcomp" ,r-multcomp)
11181 ("r-plotrix" ,r-plotrix)
11182 ("r-scales" ,r-scales)))
11183 (home-page "https://cran.r-project.org/web/packages/drc")
11184 (synopsis "Analysis of dose-response curves")
11186 "This package provides a suite of flexible and versatile model fitting
11187 and after-fitting functions for the analysis of dose-response data.")
11188 (license license:gpl2+)))
11190 (define-public r-rmeta
11197 (uri (cran-uri "rmeta" version))
11200 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
11201 (build-system r-build-system)
11202 (home-page "https://cran.r-project.org/web/packages/rmeta")
11203 (synopsis "Tools for meta-analysis")
11205 "This package provides functions for simple fixed and random effects
11206 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
11207 draws standard summary plots, funnel plots, and computes summaries and tests
11208 for association and heterogeneity.")
11209 (license license:gpl2)))
11211 (define-public r-bootstrap
11213 (name "r-bootstrap")
11218 (uri (cran-uri "bootstrap" version))
11221 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
11222 (build-system r-build-system)
11223 (native-inputs `(("gfortran" ,gfortran)))
11224 (home-page "https://cran.r-project.org/web/packages/bootstrap")
11225 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
11227 "This package provides software and data for the book \"An Introduction
11228 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
11229 This package is primarily provided for projects already based on it, and for
11230 support of the book. New projects should preferentially use the recommended
11231 package \"boot\".")
11232 (license license:bsd-3)))
11234 (define-public r-survivalroc
11236 (name "r-survivalroc")
11241 (uri (cran-uri "survivalROC" version))
11244 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
11245 (properties `((upstream-name . "survivalROC")))
11246 (build-system r-build-system)
11247 (home-page "https://cran.r-project.org/web/packages/survivalROC")
11248 (synopsis "Time-dependent ROC curve estimation from censored survival data")
11250 "Compute time-dependent ROC curve from censored survival data using
11251 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
11252 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
11253 (license license:gpl2+)))
11255 (define-public r-longitudinal
11257 (name "r-longitudinal")
11262 (uri (cran-uri "longitudinal" version))
11265 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
11266 (build-system r-build-system)
11267 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
11268 (home-page "http://strimmerlab.org/software/longitudinal/")
11269 (synopsis "Analysis of multiple time course data")
11271 "This package contains general data structures and functions for
11272 longitudinal data with multiple variables, repeated measurements, and
11273 irregularly spaced time points. It also implements a shrinkage estimator of
11274 dynamical correlation and dynamical covariance.")
11275 (license license:gpl3+)))
11277 (define-public r-genenet
11284 (uri (cran-uri "GeneNet" version))
11287 "0w52apk0nnr8nsskf26ff7ana8xiksr8wqmkjxzwhzgg7fncm61p"))))
11288 (properties `((upstream-name . "GeneNet")))
11289 (build-system r-build-system)
11291 `(("r-corpcor" ,r-corpcor)
11292 ("r-fdrtool" ,r-fdrtool)
11293 ("r-longitudinal" ,r-longitudinal)))
11294 (home-page "http://strimmerlab.org/software/genenet/")
11295 (synopsis "Modeling and inferring gene networks")
11297 "This package analyzes gene expression (time series) data with focus on
11298 the inference of gene networks. In particular, GeneNet implements the methods
11299 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
11300 for learning large-scale gene association networks (including assignment of
11301 putative directions).")
11302 (license license:gpl3+)))
11304 (define-public r-rbamtools
11306 (name "r-rbamtools")
11307 (version "2.16.17")
11311 (uri (cran-uri "rbamtools" version))
11314 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
11315 (build-system r-build-system)
11316 (inputs `(("zlib" ,zlib)))
11318 `(("r-refgenome" ,r-refgenome)))
11319 (home-page "https://cran.r-project.org/web/packages/rbamtools")
11320 (synopsis "Read and write BAM (binary alignment) files")
11322 "This package provides an R interface to functions of the SAMtools
11324 (license license:artistic2.0)))
11326 (define-public r-protviz
11333 (uri (cran-uri "protViz" version))
11336 "0cznzm1ijlq33yd5wsa61prav77y2vi698w0n2fx1xcv504c4bjv"))))
11337 (properties `((upstream-name . "protViz")))
11338 (build-system r-build-system)
11339 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11340 (home-page "https://github.com/protViz/protViz/")
11341 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
11343 "This package helps with quality checks, visualizations and analysis of
11344 mass spectrometry data, coming from proteomics experiments. The package is
11345 developed, tested and used at the Functional Genomics Center Zurich, where it
11346 is used mainly for prototyping, teaching, and having fun with proteomics data.
11347 But it can also be used to do data analysis for small scale data sets.")
11348 (license license:gpl3)))
11350 (define-public r-cmprsk
11357 (uri (cran-uri "cmprsk" version))
11359 (base32 "0xhgfg5b4i9skkaxp7gzkafgg5bqs5q1rp4hpw2jjmykg2nifn99"))))
11360 (build-system r-build-system)
11362 `(("r-survival" ,r-survival)))
11364 `(("gfortran" ,gfortran)))
11365 (home-page "https://cran.r-project.org/web/packages/cmprsk")
11366 (synopsis "Subdistribution analysis of competing risks")
11368 "This package provides tool for estimation, testing and regression
11369 modeling of subdistribution functions in competing risks, as described in
11370 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
11371 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
11372 A proportional hazards model for the subdistribution of a competing risk,
11373 JASA, 94:496-509.")
11374 (license license:gpl2+)))
11376 (define-public r-etm
11383 (uri (cran-uri "etm" version))
11386 "1yivbq8y0ijcl1m4nir4q9hp4pi6iphwxgjprygsdf7vp98wq677"))))
11387 (build-system r-build-system)
11389 `(("r-data-table" ,r-data-table)
11390 ("r-lattice" ,r-lattice)
11392 ("r-rcpparmadillo" ,r-rcpparmadillo)
11393 ("r-survival" ,r-survival)))
11394 (home-page "https://cran.r-project.org/web/packages/etm")
11395 (synopsis "Empirical transition matrix")
11397 "The @dfn{empirical transition matrix} (etm) package permits to estimate
11398 the matrix of transition probabilities for any time-inhomogeneous multistate
11399 model with finite state space using the Aalen-Johansen estimator.")
11400 (license license:expat)))
11402 (define-public r-epi
11409 (uri (cran-uri "Epi" version))
11412 "046y10vwks5y84pzccmrn6d4pd6qz70imvp1hw5ywp8fnwzfh4g5"))))
11413 (properties `((upstream-name . "Epi")))
11414 (build-system r-build-system)
11416 `(("r-cmprsk" ,r-cmprsk)
11417 ("r-data-table" ,r-data-table)
11420 ("r-matrix" ,r-matrix)
11422 ("r-numderiv" ,r-numderiv)
11424 ("r-survival" ,r-survival)
11426 (home-page "http://BendixCarstensen.com/Epi/")
11427 (synopsis "Statistical analysis in epidemiology")
11429 "This package provides functions for demographic and epidemiological
11430 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
11431 particular representation, manipulation and simulation of multistate data -
11432 the Lexis suite of functions, which includes interfaces to the @code{mstate},
11433 @code{etm} and @code{cmprsk} packages. It also contains functions for
11434 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
11435 data and some useful functions for tabulation and plotting, as well as a
11436 number of epidemiological data sets.")
11437 (license license:gpl2)))
11439 (define-public r-ppls
11442 (version "1.6-1.1")
11446 (uri (cran-uri "ppls" version))
11449 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
11450 (build-system r-build-system)
11451 (propagated-inputs `(("r-mass" ,r-mass)))
11452 (home-page "https://cran.r-project.org/web/packages/ppls")
11453 (synopsis "Penalized partial least squares")
11455 "This package contains linear and nonlinear regression methods based on
11456 partial least squares and penalization techniques. Model parameters are
11457 selected via cross-validation, and confidence intervals ans tests for the
11458 regression coefficients can be conducted via jackknifing.")
11459 (license license:gpl2+)))
11461 (define-public r-huge
11468 (uri (cran-uri "huge" version))
11470 (base32 "07n3j1va2z4v30rj22cww72khgzbz2xsp0yc0qswlrwyxi4my5i3"))))
11471 (build-system r-build-system)
11473 `(("r-igraph" ,r-igraph)
11475 ("r-matrix" ,r-matrix)
11477 ("r-rcppeigen" ,r-rcppeigen)))
11478 (home-page "https://cran.r-project.org/web/packages/huge")
11479 (synopsis "High-dimensional undirected graph estimation")
11481 "This package provides a general framework for high-dimensional
11482 undirected graph estimation. It integrates data preprocessing, neighborhood
11483 screening, graph estimation, and model selection techniques into a pipeline.")
11484 (license license:gpl2)))
11486 (define-public r-parcor
11493 (uri (cran-uri "parcor" version))
11496 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
11497 (build-system r-build-system)
11500 ("r-genenet" ,r-genenet)
11501 ("r-glmnet" ,r-glmnet)
11503 ("r-ppls" ,r-ppls)))
11504 (home-page "https://cran.r-project.org/web/packages/parcor")
11505 (synopsis "Regularized estimation of partial correlation matrices")
11507 "This package estimates the matrix of partial correlations based on
11508 different regularized regression methods: lasso, adaptive lasso, PLS, and
11509 Ridge Regression. In addition, the package provides model selection for
11510 lasso, adaptive lasso and Ridge regression based on cross-validation.")
11511 (license license:gpl2+)))
11513 (define-public r-mcmc
11520 (uri (cran-uri "mcmc" version))
11523 "1fc6a6asn53lx7x7pnlb5mb716nv4pcmbp99f1i30y4hzygihfj4"))))
11524 (build-system r-build-system)
11525 (home-page "http://www.stat.umn.edu/geyer/mcmc/")
11526 (synopsis "Markov chain Monte Carlo")
11528 "This package simulates continuous distributions of random vectors using
11529 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
11530 function that evaluates the log unnormalized density. Algorithms are random
11531 walk Metropolis algorithm (function @code{metrop}), simulated
11532 tempering (function @code{temper}), and morphometric random walk
11533 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
11534 by change of variable.")
11535 (license license:expat)))
11537 (define-public r-listenv
11544 (uri (cran-uri "listenv" version))
11547 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
11548 (build-system r-build-system)
11550 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11551 (home-page "https://github.com/HenrikBengtsson/listenv")
11552 (synopsis "Environments behaving (almost) as lists")
11554 "This package implements list environments. List environments are
11555 environments that have list-like properties. For instance, the elements of a
11556 list environment are ordered and can be accessed and iterated over using index
11558 (license license:lgpl2.1+)))
11560 (define-public r-globals
11567 (uri (cran-uri "globals" version))
11570 "1ha8iasgijp4q3v2b0b17y1wh7cd3nvzd9b03w49qm2bidkaf68m"))))
11571 (build-system r-build-system)
11573 `(("r-codetools" ,r-codetools)))
11574 (home-page "https://github.com/HenrikBengtsson/globals")
11575 (synopsis "Identify global objects in R expressions")
11577 "This package provides tools to identify global (\"unknown\" or \"free\")
11578 objects in R expressions by code inspection using various strategies, e.g.
11579 conservative or liberal. The objective of this package is to make it as
11580 simple as possible to identify global objects for the purpose of exporting
11581 them in distributed compute environments.")
11582 (license license:lgpl2.1+)))
11584 (define-public r-future
11591 (uri (cran-uri "future" version))
11594 "101hi8warqa0py9l6c5p98f7i9xjhx01w655z6a35jx1dhspykzd"))))
11595 (build-system r-build-system)
11597 `(("r-digest" ,r-digest)
11598 ("r-globals" ,r-globals)
11599 ("r-listenv" ,r-listenv)))
11601 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11602 (home-page "https://github.com/HenrikBengtsson/future")
11603 (synopsis "Unified parallel and distributed processing in R")
11605 "The purpose of this package is to provide a lightweight and unified
11606 Future API for sequential and parallel processing of R expression via futures.
11607 This package implements sequential, multicore, multisession, and cluster
11608 futures. With these, R expressions can be evaluated on the local machine, in
11609 parallel a set of local machines, or distributed on a mix of local and remote
11610 machines. Extensions to this package implement additional backends for
11611 processing futures via compute cluster schedulers etc. Because of its unified
11612 API, there is no need to modify any code in order to switch from sequential on
11613 the local machine to, say, distributed processing on a remote compute cluster.")
11614 (license license:lgpl2.1+)))
11616 (define-public r-future-apply
11618 (name "r-future-apply")
11623 (uri (cran-uri "future.apply" version))
11626 "0wd3bh114zkvrqlpn8gqz4ix1igr9hr8x72h2g00a7mqkfjfqx33"))))
11627 (properties `((upstream-name . "future.apply")))
11628 (build-system r-build-system)
11630 `(("r-future" ,r-future)
11631 ("r-globals" ,r-globals)))
11633 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11634 (home-page "https://github.com/HenrikBengtsson/future.apply")
11635 (synopsis "Apply function to elements in parallel using futures")
11637 "This package provides implementations of @code{apply()},
11638 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
11639 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
11640 can be resolved using any future-supported backend, e.g. parallel on the local
11641 machine or distributed on a compute cluster.")
11642 (license license:gpl2+)))
11644 (define-public r-rsvd
11651 (uri (cran-uri "rsvd" version))
11654 "0fia77y5fxnhwkcxlgp98ygb8fdfraky75x80hkf7kvvpwc5rzn8"))))
11655 (build-system r-build-system)
11657 `(("r-matrix" ,r-matrix)))
11658 (home-page "https://github.com/erichson/rSVD")
11659 (synopsis "Randomized singular value decomposition")
11661 "Low-rank matrix decompositions are fundamental tools and widely used for
11662 data analysis, dimension reduction, and data compression. Classically, highly
11663 accurate deterministic matrix algorithms are used for this task. However, the
11664 emergence of large-scale data has severely challenged our computational
11665 ability to analyze big data. The concept of randomness has been demonstrated
11666 as an effective strategy to quickly produce approximate answers to familiar
11667 problems such as the @dfn{singular value decomposition} (SVD). This package
11668 provides several randomized matrix algorithms such as the randomized singular
11669 value decomposition (@code{rsvd}), randomized principal component
11670 analysis (@code{rpca}), randomized robust principal component
11671 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
11672 and the randomized CUR decomposition (@code{rcur}). In addition several plot
11673 functions are provided.")
11674 (license license:gpl3+)))
11676 (define-public r-sloop
11683 (uri (cran-uri "sloop" version))
11686 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
11687 (build-system r-build-system)
11689 `(("r-codetools" ,r-codetools)
11690 ("r-crayon" ,r-crayon)
11691 ("r-purrr" ,r-purrr)
11692 ("r-rlang" ,r-rlang)
11693 ("r-tibble" ,r-tibble)))
11694 (home-page "https://github.com/r-lib/sloop")
11695 (synopsis "Helpers for object-oriented programming in R")
11697 "This package provides a collection of helper functions designed to
11698 help you to better understand object oriented programming in R, particularly
11700 (license license:gpl3)))
11702 (define-public r-capushe
11709 (uri (cran-uri "capushe" version))
11712 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
11713 (build-system r-build-system)
11714 (propagated-inputs `(("r-mass" ,r-mass)))
11715 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
11716 (synopsis "Calibrating penalties using slope heuristics")
11718 "This package provides tools for the calibration of penalized criteria
11719 for model selection. The calibration methods available are based on the slope
11721 (license license:gpl2+)))
11723 (define-public r-dorng
11730 (uri (cran-uri "doRNG" version))
11733 "1sb75aqkliprglfxc4x4wds6alqgzhvl2n812g1d32a88ra3slr7"))))
11734 (properties `((upstream-name . "doRNG")))
11735 (build-system r-build-system)
11737 `(("r-foreach" ,r-foreach)
11738 ("r-iterators" ,r-iterators)
11739 ("r-pkgmaker" ,r-pkgmaker)
11740 ("r-rngtools" ,r-rngtools)))
11741 (home-page "https://renozao.github.io/doRNG/")
11742 (synopsis "Generic reproducible parallel backend for foreach loops")
11744 "This package provides functions to perform reproducible parallel
11745 @code{foreach} loops, using independent random streams as generated by
11746 L'Ecuyer's combined multiple-recursive generator. It enables to easily
11747 convert standard @code{%dopar%} loops into fully reproducible loops,
11748 independently of the number of workers, the task scheduling strategy, or the
11749 chosen parallel environment and associated foreach backend.")
11750 (license license:gpl2+)))
11752 (define-public r-blockmodeling
11754 (name "r-blockmodeling")
11759 (uri (cran-uri "blockmodeling" version))
11762 "11v9903y9dwlzaqp8sx0fsibcg82phvappddy37r8lnxd4vchsd2"))))
11763 (build-system r-build-system)
11765 `(("r-doparallel" ,r-doparallel)
11766 ("r-dorng" ,r-dorng)
11767 ("r-foreach" ,r-foreach)
11768 ("r-matrix" ,r-matrix)))
11769 (native-inputs `(("gfortran" ,gfortran)))
11770 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
11771 (synopsis "Generalized and classical blockmodeling of valued networks")
11773 "This package is primarily meant as an implementation of generalized
11774 blockmodeling for valued networks. In addition, measures of similarity or
11775 dissimilarity based on structural equivalence and regular equivalence (REGE
11776 algorithms) can be computed and partitioned matrices can be plotted.")
11777 (license license:gpl2+)))
11779 (define-public r-upsetr
11786 (uri (cran-uri "UpSetR" version))
11789 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
11790 (properties `((upstream-name . "UpSetR")))
11791 (build-system r-build-system)
11793 `(("r-ggplot2" ,r-ggplot2)
11794 ("r-gridextra" ,r-gridextra)
11796 ("r-scales" ,r-scales)))
11797 (home-page "https://github.com/hms-dbmi/UpSetR")
11798 (synopsis "Visualize intersecting sets")
11800 "This package provides a more scalable alternative to Venn and Euler
11801 diagrams for visualizing intersecting sets. Create visualizations of
11802 intersecting sets using a novel matrix design, along with visualizations of
11803 several common set, element and attribute related tasks.")
11804 (license license:expat)))
11806 ;; This package includes a JavaScript file, which is not minified. When
11807 ;; upgrading please check that there are no new minified JavaScript files.
11808 (define-public r-shinybs
11815 (uri (cran-uri "shinyBS" version))
11818 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
11819 (properties `((upstream-name . "shinyBS")))
11820 (build-system r-build-system)
11821 ;; The tests spawn Shiny browser apps. They cannot be run
11822 ;; non-interactively.
11823 (arguments '(#:tests? #f))
11825 `(("r-htmltools" ,r-htmltools)
11826 ("r-shiny" ,r-shiny)))
11827 (home-page "https://ebailey78.github.io/shinyBS/")
11828 (synopsis "Twitter Bootstrap components for Shiny")
11830 "This package adds additional Twitter Bootstrap components to Shiny.")
11831 (license license:gpl3)))
11833 (define-public r-outliers
11835 (name "r-outliers")
11840 (uri (cran-uri "outliers" version))
11843 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
11844 (build-system r-build-system)
11845 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
11846 (synopsis "Tests for outliers")
11848 "This package provides a collection of some tests commonly used for
11849 identifying outliers.")
11850 (license license:gpl2+)))
11852 (define-public r-bayesm
11859 (uri (cran-uri "bayesm" version))
11861 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
11862 (build-system r-build-system)
11864 `(("r-rcpp" ,r-rcpp)
11865 ("r-rcpparmadillo" ,r-rcpparmadillo)))
11866 (home-page "http://www.perossi.org/home/bsm-1")
11867 (synopsis "Bayesian inference for marketing/micro-econometrics")
11869 "This package covers many important models used in marketing and
11870 micro-econometrics applications, including Bayes Regression (univariate or
11871 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
11872 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
11873 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
11874 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
11875 Estimation with normal base, Hierarchical Linear Models with normal prior and
11876 covariates, Hierarchical Linear Models with a mixture of normals prior and
11877 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
11878 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
11879 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
11880 analysis of choice-based conjoint data, Bayesian treatment of linear
11881 instrumental variables models, Analysis of Multivariate Ordinal survey data
11882 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
11883 Coefficient Logit Models.")
11884 (license license:gpl2+)))
11886 (define-public r-tensora
11893 (uri (cran-uri "tensorA" version))
11896 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
11897 (properties `((upstream-name . "tensorA")))
11898 (build-system r-build-system)
11899 (home-page "http://www.stat.boogaart.de/tensorA")
11900 (synopsis "Advanced tensor arithmetic with named indices")
11902 "This package provides convenience functions for advanced linear algebra
11903 with tensors and computation with datasets of tensors on a higher level
11904 abstraction. It includes Einstein and Riemann summing conventions, dragging,
11905 co- and contravariate indices, and parallel computations on sequences of
11907 (license license:gpl2+)))
11909 (define-public r-rarpack
11916 (uri (cran-uri "rARPACK" version))
11919 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
11920 (properties `((upstream-name . "rARPACK")))
11921 (build-system r-build-system)
11922 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
11923 (home-page "https://github.com/yixuan/rARPACK")
11924 (synopsis "Solvers for large scale eigenvalue and SVD problems")
11926 "This package was previously an R wrapper of the ARPACK library, and now
11927 a shell of the R package RSpectra, an R interface to the Spectra library for
11928 solving large scale eigenvalue/vector problems. The current version of
11929 rARPACK simply imports and exports the functions provided by RSpectra. New
11930 users of rARPACK are advised to switch to the RSpectra package.")
11931 (license license:bsd-3)))
11933 (define-public r-compositions
11935 (name "r-compositions")
11940 (uri (cran-uri "compositions" version))
11943 "103hbmibrf1n333pn4xpll1gqqsv4szms0n5gdq7zak31aar0bg4"))))
11944 (build-system r-build-system)
11946 `(("r-bayesm" ,r-bayesm)
11947 ("r-robustbase" ,r-robustbase)
11948 ("r-tensora" ,r-tensora)))
11949 (home-page "http://www.stat.boogaart.de/compositions")
11950 (synopsis "Compositional data analysis")
11952 "This package provides functions for the consistent analysis of
11953 compositional data (e.g. portions of substances) and positive
11954 numbers (e.g. concentrations).")
11955 (license license:gpl2+)))
11957 (define-public r-cobs
11964 (uri (cran-uri "cobs" version))
11967 "1pqvz7czcchri4x79g78hbwyagb3bqzdqb047zkbdinyz067c7kb"))))
11968 (build-system r-build-system)
11970 `(("r-quantreg" ,r-quantreg)
11971 ("r-sparsem" ,r-sparsem)))
11972 (home-page "https://cran.r-project.org/web/packages/cobs")
11973 (synopsis "Constrained B-Splines (sparse matrix based)")
11975 "This package provides qualitatively constrained (regression) smoothing
11976 splines via linear programming and sparse matrices.")
11977 (license license:gpl2+)))
11979 (define-public r-drimpute
11981 (name "r-drimpute")
11986 (uri (cran-uri "DrImpute" version))
11989 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
11990 (properties `((upstream-name . "DrImpute")))
11991 (build-system r-build-system)
11993 `(("r-rcpp" ,r-rcpp)
11994 ("r-rcpparmadillo" ,r-rcpparmadillo)))
11995 (home-page "https://github.com/ikwak2/DrImpute")
11996 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
11998 "This is an R package for imputing dropout events. Many statistical
11999 methods in cell type identification, visualization and lineage reconstruction
12000 do not account for dropout events. DrImpute can improve the performance of
12001 such software by imputing dropout events.")
12002 (license license:gpl3)))
12004 (define-public r-gamlss-dist
12006 (name "r-gamlss-dist")
12011 (uri (cran-uri "gamlss.dist" version))
12013 (base32 "1rl7hzdg5xpvaq3yyzwxhsaqzzs0qidi3ibv454fisijgv8l4vqw"))))
12014 (properties `((upstream-name . "gamlss.dist")))
12015 (build-system r-build-system)
12016 (propagated-inputs `(("r-mass" ,r-mass)))
12017 (home-page "http://www.gamlss.org/")
12018 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
12020 "This package provides a set of distributions which can be used for
12021 modelling the response variables in Generalized Additive Models for Location
12022 Scale and Shape. The distributions can be continuous, discrete or mixed
12023 distributions. Extra distributions can be created, by transforming, any
12024 continuous distribution defined on the real line, to a distribution defined on
12025 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
12026 transformation, respectively.")
12027 ;; Either version of the GPL.
12028 (license (list license:gpl2 license:gpl3))))
12030 ;; This package includes JavaScript files, which are not minified. When
12031 ;; upgrading please check that there are no new minified JavaScript files.
12032 (define-public r-shinyjs
12039 (uri (cran-uri "shinyjs" version))
12042 "113zpijri0l80rlgrvqn6bxk0sdqgl79h7yhja2p76f9dc9i2sr8"))))
12043 (build-system r-build-system)
12045 `(("r-digest" ,r-digest)
12046 ("r-htmltools" ,r-htmltools)
12047 ("r-jsonlite" ,r-jsonlite)
12048 ("r-shiny" ,r-shiny)))
12049 (home-page "https://deanattali.com/shinyjs")
12050 (synopsis "Improve the user experience of your Shiny apps")
12052 "Perform common useful JavaScript operations in Shiny apps that will
12053 greatly improve your apps without having to know any JavaScript. Examples
12054 include: hiding an element, disabling an input, resetting an input back to its
12055 original value, delaying code execution by a few seconds, and many more useful
12056 functions for both the end user and the developer. Shinyjs can also be used
12057 to easily call your own custom JavaScript functions from R.")
12058 (license license:agpl3+)))
12060 ;; This package includes minified JavaScript files. When upgrading please
12061 ;; check that there are no new minified JavaScript files.
12062 (define-public r-colourpicker
12064 (name "r-colourpicker")
12069 (uri (cran-uri "colourpicker" version))
12072 "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
12073 (build-system r-build-system)
12075 `(#:modules ((guix build utils)
12076 (guix build r-build-system)
12080 (modify-phases %standard-phases
12081 (add-after 'unpack 'process-javascript
12082 (lambda* (#:key inputs #:allow-other-keys)
12083 (with-directory-excursion "inst"
12087 `((,(assoc-ref inputs "js-salvattore")
12088 "examples/colourInput/www/salvattore.min.js")
12089 (,(assoc-ref inputs "js-jquery")
12090 "htmlwidgets/lib/jquery/jquery.min.js")
12091 ("www/shared/colourpicker/js/colourpicker.js"
12092 "www/shared/colourpicker/js/colourpicker.min.js"))))
12093 (lambda (sources targets)
12094 (for-each (lambda (source target)
12095 (format #t "Processing ~a --> ~a~%"
12097 (delete-file target)
12098 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
12099 (call-with-output-file target
12101 (dump-port minified port)))))
12102 sources targets))))
12105 `(("r-ggplot2" ,r-ggplot2)
12106 ("r-htmltools" ,r-htmltools)
12107 ("r-htmlwidgets" ,r-htmlwidgets)
12108 ("r-jsonlite" ,r-jsonlite)
12109 ("r-miniui" ,r-miniui)
12110 ("r-shiny" ,r-shiny)
12111 ("r-shinyjs" ,r-shinyjs)))
12113 `(("uglify-js" ,uglify-js)
12117 (uri "https://code.jquery.com/jquery-3.3.1.js")
12120 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
12124 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
12127 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
12128 (home-page "https://github.com/daattali/colourpicker")
12129 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
12131 "This package provides a color picker that can be used as an input in
12132 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
12133 custom color palettes, and many more options. A plot color helper tool is
12134 available as an RStudio Addin, which helps you pick colors to use in your
12135 plots. A more generic color picker RStudio Addin is also provided to let you
12136 select colors to use in your R code.")
12137 (license license:expat)))
12139 (define-public r-ggextra
12146 (uri (cran-uri "ggExtra" version))
12149 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
12150 (properties `((upstream-name . "ggExtra")))
12151 (build-system r-build-system)
12153 `(("r-colourpicker" ,r-colourpicker)
12154 ("r-ggplot2" ,r-ggplot2)
12155 ("r-gtable" ,r-gtable)
12156 ("r-miniui" ,r-miniui)
12158 ("r-scales" ,r-scales)
12159 ("r-shiny" ,r-shiny)
12160 ("r-shinyjs" ,r-shinyjs)))
12161 (home-page "https://github.com/daattali/ggExtra")
12162 (synopsis "Marginal histograms for ggplot2 and other enhancements")
12164 "This package is a collection of functions and layers to enhance ggplot2.
12165 The flagship function is @code{ggMarginal()}, which can be used to add
12166 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
12167 (license license:expat)))
12169 (define-public r-minpack-lm
12171 (name "r-minpack-lm")
12176 (uri (cran-uri "minpack.lm" version))
12179 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
12180 (properties `((upstream-name . "minpack.lm")))
12181 (build-system r-build-system)
12182 (native-inputs `(("gfortran" ,gfortran)))
12183 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
12184 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
12186 "The @code{nls.lm} function provides an R interface to @code{lmder} and
12187 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
12188 problems by a modification of the Levenberg-Marquardt algorithm, with support
12189 for lower and upper parameter bounds. The implementation can be used via
12190 @code{nls}-like calls using the @code{nlsLM} function.")
12191 (license license:gpl3)))
12193 (define-public r-moments
12200 (uri (cran-uri "moments" version))
12203 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
12204 (build-system r-build-system)
12205 (home-page "https://cran.r-project.org/web/packages/moments")
12206 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
12208 "This package provides functions to calculate: moments, Pearson's
12209 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
12210 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
12211 (license license:gpl2+)))
12213 (define-public r-msir
12220 (uri (cran-uri "msir" version))
12223 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
12224 (build-system r-build-system)
12226 `(("r-mclust" ,r-mclust)))
12227 (home-page "https://cran.r-project.org/web/packages/msir")
12228 (synopsis "Model-based sliced inverse regression")
12230 "This is an R package for dimension reduction based on finite Gaussian
12231 mixture modeling of inverse regression.")
12232 (license license:gpl2+)))
12234 (define-public r-pbivnorm
12236 (name "r-pbivnorm")
12241 (uri (cran-uri "pbivnorm" version))
12244 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
12245 (build-system r-build-system)
12246 (native-inputs `(("gfortran" ,gfortran)))
12247 (home-page "https://github.com/brentonk/pbivnorm")
12248 (synopsis "Vectorized bivariate normal CDF")
12250 "This package provides a vectorized R function for calculating
12251 probabilities from a standard bivariate normal CDF.")
12252 (license license:gpl2+)))
12254 (define-public r-lavaan
12261 (uri (cran-uri "lavaan" version))
12264 "04kvsh2m6mnzlhv83phr3hjzy4sx1ck6f7dgsm7xb8cs84dnxszy"))))
12265 (build-system r-build-system)
12267 `(("r-mass" ,r-mass)
12268 ("r-mnormt" ,r-mnormt)
12269 ("r-numderiv" ,r-numderiv)
12270 ("r-pbivnorm" ,r-pbivnorm)))
12271 (home-page "http://lavaan.ugent.be")
12272 (synopsis "Latent variable analysis")
12274 "This package provides tools to fit a variety of latent variable models,
12275 including confirmatory factor analysis, structural equation modeling and
12276 latent growth curve models.")
12277 (license license:gpl2+)))
12279 (define-public r-nonnest2
12281 (name "r-nonnest2")
12286 (uri (cran-uri "nonnest2" version))
12289 "1bq44qqmm59j91m0sny4xnqmxqlga4cm48qdsw8xfs3x19xwmxk6"))))
12290 (build-system r-build-system)
12292 `(("r-compquadform" ,r-compquadform)
12293 ("r-lavaan" ,r-lavaan)
12294 ("r-mvtnorm" ,r-mvtnorm)
12295 ("r-sandwich" ,r-sandwich)))
12296 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
12297 (synopsis "Tests of non-nested models")
12299 "This package allows for testing of non-nested models. It includes tests
12300 of model distinguishability and of model fit that can be applied to both
12301 nested and non-nested models. The package also includes functionality to
12302 obtain confidence intervals associated with AIC and BIC.")
12303 ;; Either version of the GPL.
12304 (license (list license:gpl2 license:gpl3))))
12306 (define-public r-penalized
12308 (name "r-penalized")
12313 (uri (cran-uri "penalized" version))
12316 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
12317 (build-system r-build-system)
12319 `(("r-rcpp" ,r-rcpp)
12320 ("r-rcpparmadillo" ,r-rcpparmadillo)
12321 ("r-survival" ,r-survival)))
12322 (home-page "https://cran.r-project.org/web/packages/penalized/")
12323 (synopsis "Penalized estimation in GLMs and in the Cox model")
12325 "This package provides tools for fitting possibly high dimensional
12326 penalized regression models. The penalty structure can be any combination of
12327 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
12328 constraint on the regression coefficients. The supported regression models
12329 are linear, logistic and Poisson regression and the Cox Proportional Hazards
12330 model. Cross-validation routines allow optimization of the tuning
12332 (license license:gpl2+)))
12334 (define-public r-zim
12341 (uri (cran-uri "ZIM" version))
12344 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
12345 (properties `((upstream-name . "ZIM")))
12346 (build-system r-build-system)
12347 (propagated-inputs `(("r-mass" ,r-mass)))
12348 (home-page "https://github.com/biostatstudio/ZIM")
12349 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
12351 "Analyze count time series with excess zeros. Two types of statistical
12352 models are supported: Markov regression and state-space models. They are also
12353 known as observation-driven and parameter-driven models respectively in the
12354 time series literature. The functions used for Markov regression or
12355 observation-driven models can also be used to fit ordinary regression models
12356 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
12357 negative binomial (ZINB) assumption. The package also contains miscellaneous
12358 functions to compute density, distribution, quantile, and generate random
12359 numbers from ZIP and ZINB distributions.")
12360 (license license:gpl3)))
12362 (define-public r-nor1mix
12369 (uri (cran-uri "nor1mix" version))
12372 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
12373 (build-system r-build-system)
12374 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
12375 (synopsis "Normal (1-d) mixture models")
12377 "This package provides S3 classes and methods for one-dimensional normal
12378 mixture models, for, e.g., density estimation or clustering algorithms
12379 research and teaching; it provides the widely used Marron-Wand densities. It
12380 also provides tools for efficient random number generation and graphics.")
12381 (license license:gpl2+)))
12383 (define-public r-beanplot
12385 (name "r-beanplot")
12390 (uri (cran-uri "beanplot" version))
12393 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
12394 (build-system r-build-system)
12395 (home-page "https://cran.r-project.org/web/packages/beanplot/")
12396 (synopsis "Visualization via beanplots")
12398 "This package provides beanplots, an alternative to
12399 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
12401 (license license:gpl2)))
12403 (define-public r-pbdzmq
12410 (uri (cran-uri "pbdZMQ" version))
12413 "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
12414 (properties `((upstream-name . "pbdZMQ")))
12415 (build-system r-build-system)
12417 `(("zeromq" ,zeromq)
12420 `(("pkg-config" ,pkg-config)))
12421 (home-page "https://pbdr.org/")
12422 (synopsis "R interface to ZeroMQ")
12424 "ZeroMQ is a well-known library for high-performance asynchronous
12425 messaging in scalable, distributed applications. This package provides high
12426 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
12427 interactive client/server programming frameworks. A few wrapper functions
12428 compatible with @code{rzmq} are also provided.")
12429 (license license:gpl3)))
12431 (define-public r-repr
12438 (uri (cran-uri "repr" version))
12441 "0jy43g34r38fqprcdys0p9pliahrj5l64a9bbkzy206qgz0j5ppc"))))
12442 (build-system r-build-system)
12444 `(("r-base64enc" ,r-base64enc)
12445 ("r-htmltools" ,r-htmltools)
12446 ("r-jsonlite" ,r-jsonlite)
12447 ("r-pillar" ,r-pillar)))
12448 (home-page "https://cran.r-project.org/web/packages/repr/")
12449 (synopsis "Serializable representations")
12451 "This package provides string and binary representations of objects for
12452 several formats and MIME types.")
12453 (license license:gpl3)))
12455 (define-public r-irdisplay
12457 (name "r-irdisplay")
12462 (uri (cran-uri "IRdisplay" version))
12465 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
12466 (properties `((upstream-name . "IRdisplay")))
12467 (build-system r-build-system)
12469 `(("r-repr" ,r-repr)))
12470 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
12471 (synopsis "Jupyter display machinery")
12473 "This package provides an interface to the rich display capabilities of
12474 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
12475 running IRkernel session.")
12476 (license license:expat)))
12478 (define-public r-irkernel
12480 (name "r-irkernel")
12485 (uri (cran-uri "IRkernel" version))
12488 "1viqxs91dys1z4cf7gb59rmqvzb8lc7jdp4azrpmhgwa8qf46s94"))))
12489 (properties `((upstream-name . "IRkernel")))
12490 (build-system r-build-system)
12493 (modify-phases %standard-phases
12494 (add-after 'install 'install-kernelspec
12495 (lambda* (#:key outputs #:allow-other-keys)
12496 (let ((out (assoc-ref outputs "out")))
12497 (setenv "HOME" "/tmp")
12498 (invoke "jupyter" "kernelspec" "install"
12501 (string-append out "/site-library/IRkernel/kernelspec"))
12504 `(("jupyter" ,jupyter)))
12506 `(("r-crayon" ,r-crayon)
12507 ("r-digest" ,r-digest)
12508 ("r-evaluate" ,r-evaluate)
12509 ("r-irdisplay" ,r-irdisplay)
12510 ("r-jsonlite" ,r-jsonlite)
12511 ("r-pbdzmq" ,r-pbdzmq)
12513 ("r-uuid" ,r-uuid)))
12514 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
12515 (synopsis "Native R kernel for Jupyter")
12517 "The R kernel for the Jupyter environment executes R code which the
12518 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
12520 (license license:expat)))
12522 (define-public r-gmodels
12529 (uri (cran-uri "gmodels" version))
12532 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
12533 (build-system r-build-system)
12535 `(("r-gdata" ,r-gdata)
12536 ("r-mass" ,r-mass)))
12537 (home-page "https://cran.r-project.org/web/packages/gmodels/")
12538 (synopsis "Various R programming tools for model fitting")
12540 "This package provides various R programming tools for model fitting.")
12541 (license license:gpl2)))
12543 (define-public r-apcluster
12545 (name "r-apcluster")
12550 (uri (cran-uri "apcluster" version))
12553 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
12554 (build-system r-build-system)
12556 `(("r-matrix" ,r-matrix)
12557 ("r-rcpp" ,r-rcpp)))
12558 (home-page "https://cran.r-project.org/web/packages/apcluster/")
12559 (synopsis "Affinity propagation clustering")
12561 "This package implements affinity propagation clustering introduced by
12562 Frey and Dueck (2007). The package further provides leveraged affinity
12563 propagation and an algorithm for exemplar-based agglomerative clustering that
12564 can also be used to join clusters obtained from affinity propagation. Various
12565 plotting functions are available for analyzing clustering results.")
12566 (license license:gpl2+)))
12568 (define-public r-valr
12575 (uri (cran-uri "valr" version))
12578 "14jhrwkiwmha3vlmm7b50n2xxyizj6ddmy89gb20mpzq7qhz1ika"))))
12579 (build-system r-build-system)
12581 `(("r-broom" ,r-broom)
12582 ("r-dplyr" ,r-dplyr)
12583 ("r-ggplot2" ,r-ggplot2)
12585 ("r-readr" ,r-readr)
12586 ("r-rlang" ,r-rlang)
12587 ("r-stringr" ,r-stringr)
12588 ("r-tibble" ,r-tibble)))
12589 (home-page "http://github.com/rnabioco/valr")
12590 (synopsis "Genome interval arithmetic in R")
12592 "This package enables you to read and manipulate genome intervals and
12593 signals. It provides functionality similar to command-line tool suites within
12594 R, enabling interactive analysis and visualization of genome-scale data.")
12595 (license license:expat)))
12597 (define-public r-rematch2
12599 (name "r-rematch2")
12604 (uri (cran-uri "rematch2" version))
12607 "00cznm6rk33b53w7zybkz7549bnydc66znpi5mb0xd24pmqp0rvq"))))
12608 (build-system r-build-system)
12610 `(("r-tibble" ,r-tibble)))
12611 (home-page "https://github.com/r-lib/rematch2")
12612 (synopsis "Tidy output from regular expression matching")
12614 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
12615 return the match results in tidy data frames.")
12616 (license license:expat)))
12618 (define-public r-picante
12625 (uri (cran-uri "picante" version))
12628 "1bcq2j7fs89c2jib68qq6la67rxyg9raryf162mwvjakpf6k19l1"))))
12629 (build-system r-build-system)
12633 ("r-vegan" ,r-vegan)))
12634 (home-page "https://cran.r-project.org/web/packages/picante/")
12635 (synopsis "Integrating phylogenies and ecology")
12637 "This package provides functions for phylocom integration, community
12638 analyses, null-models, traits and evolution. It implements numerous
12639 ecophylogenetic approaches including measures of community phylogenetic and
12640 trait diversity, phylogenetic signal, estimation of trait values for
12641 unobserved taxa, null models for community and phylogeny randomizations, and
12642 utility functions for data input/output and phylogeny plotting. A full
12643 description of package functionality and methods are provided by Kembel et
12645 (license license:gpl2)))
12647 (define-public r-reinforcelearn
12649 (name "r-reinforcelearn")
12654 (uri (cran-uri "reinforcelearn" version))
12657 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
12658 (build-system r-build-system)
12660 `(("r-checkmate" ,r-checkmate)
12662 ("r-purrr" ,r-purrr)
12664 (home-page "https://markusdumke.github.io/reinforcelearn")
12665 (synopsis "Reinforcement learning")
12667 "This package implements reinforcement learning environments and
12668 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
12669 can be used with function approximation, eligibility traces (Singh & Sutton,
12670 1996) and experience replay (Mnih et al., 2013).")
12671 (license license:expat)))
12673 (define-public r-lemon
12680 (uri (cran-uri "lemon" version))
12683 "0wsn5bfg10wq4dnrgpyraz2bzx9p19c7hf1pwj3h4zmpqfgsdbpw"))))
12684 (build-system r-build-system)
12686 `(("r-ggplot2" ,r-ggplot2)
12687 ("r-gridextra" ,r-gridextra)
12688 ("r-gtable" ,r-gtable)
12689 ("r-knitr" ,r-knitr)
12690 ("r-lattice" ,r-lattice)
12692 ("r-scales" ,r-scales)))
12693 (home-page "https://github.com/stefanedwards/lemon")
12694 (synopsis "Freshen up your ggplot2 plots")
12696 "This package provides functions for working with legends and axis lines
12697 of ggplot2, facets that repeat axis lines on all panels, and some knitr
12699 (license license:gpl3)))
12701 (define-public r-wgaim
12708 (uri (cran-uri "wgaim" version))
12710 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
12711 (build-system r-build-system)
12713 `(("r-ggplot2" ,r-ggplot2)
12715 (home-page "https://cran.r-project.org/web/packages/wgaim")
12716 (synopsis "Whole genome average interval mapping for QTL detection")
12718 "This package integrates sophisticated mixed modelling methods with a
12719 whole genome approach to detecting significant QTL in linkage maps.")
12720 (license license:gpl2+)))
12722 (define-public r-bedr
12729 (uri (cran-uri "bedr" version))
12732 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
12733 (build-system r-build-system)
12735 `(("r-data-table" ,r-data-table)
12736 ("r-r-utils" ,r-r-utils)
12737 ("r-testthat" ,r-testthat)
12738 ("r-venndiagram" ,r-venndiagram)
12741 ("bedtools" ,bedtools)
12742 ("htslib" ,htslib))) ; for tabix
12744 `(("r-knitr" ,r-knitr))) ; for vignettes
12745 (home-page "https://cran.r-project.org/web/packages/bedr")
12746 (synopsis "Genomic region processing")
12748 "This package is for genomic regions processing using command line tools
12749 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
12750 utilities to perform genome arithmetic e.g indexing, formatting and merging.
12751 The bedr package's API enhances access to these tools as well as offers
12752 additional utilities for genomic regions processing.")
12753 (license license:gpl2)))
12755 (define-public r-sets
12762 (uri (cran-uri "sets" version))
12765 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
12766 (properties `((upstream-name . "sets")))
12767 (build-system r-build-system)
12768 (home-page "https://cran.r-project.org/web/packages/sets")
12769 (synopsis "Sets, generalized sets, customizable sets and intervals")
12771 "This package provides data structures and basic operations for ordinary
12772 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
12773 customizable sets, and intervals.")
12774 (license license:gpl2)))
12776 (define-public r-partitions
12778 (name "r-partitions")
12783 (uri (cran-uri "partitions" version))
12786 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
12787 (build-system r-build-system)
12790 ("r-polynom" ,r-polynom)
12791 ("r-sets" ,r-sets)))
12792 (home-page "https://cran.r-project.org/web/packages/partitions")
12793 (synopsis "Additive partitions of integers")
12795 "This package provides tools to enumerates the partitions, unequal
12796 partitions, and restricted partitions of an integer; the three corresponding
12797 partition functions are also given.")
12798 ;; Any version of the GPL
12799 (license license:gpl2+)))
12801 (define-public r-brobdingnag
12803 (name "r-brobdingnag")
12808 (uri (cran-uri "Brobdingnag" version))
12811 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
12812 (properties `((upstream-name . "Brobdingnag")))
12813 (build-system r-build-system)
12814 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
12815 (synopsis "Very large numbers in R")
12817 "This package handles very large numbers in R. Real numbers are held
12818 using their natural logarithms, plus a logical flag indicating sign. The
12819 package includes a vignette that gives a step-by-step introduction to using S4
12821 ;; Any version of the GPL
12822 (license license:gpl2+)))
12824 (define-public r-untb
12831 (uri (cran-uri "untb" version))
12834 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
12835 (build-system r-build-system)
12837 `(("r-brobdingnag" ,r-brobdingnag)
12838 ("r-partitions" ,r-partitions)
12839 ("r-polynom" ,r-polynom)))
12840 (home-page "https://github.com/RobinHankin/untb.git")
12841 (synopsis "Ecological drift under the UNTB")
12843 "This package provides numerical simulations, and visualizations, of
12844 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
12845 (license license:gpl2+)))
12847 (define-public r-stepwise
12849 (name "r-stepwise")
12854 (uri (cran-uri "stepwise" version))
12857 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
12858 (build-system r-build-system)
12859 (home-page "http://stat.sfu.ca/statgen/research/stepwise.html")
12860 (synopsis "Stepwise detection of recombination breakpoints")
12862 "This package provides a stepwise approach to identifying recombination
12863 breakpoints in a genomic sequence alignment.")
12864 (license license:gpl2+)))
12866 (define-public r-snpmaxsel
12868 (name "r-snpmaxsel")
12873 (uri (cran-uri "SNPmaxsel" version))
12876 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
12877 (properties `((upstream-name . "SNPmaxsel")))
12878 (build-system r-build-system)
12880 `(("r-combinat" ,r-combinat)
12881 ("r-mvtnorm" ,r-mvtnorm)))
12882 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
12883 (synopsis "Maximally selected statistics for SNP data")
12885 "This package implements asymptotic methods related to maximally selected
12886 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
12888 (license license:gpl2+)))
12890 (define-public r-acsnminer
12892 (name "r-acsnminer")
12893 (version "0.16.8.25")
12896 (uri (cran-uri "ACSNMineR" version))
12899 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
12900 (properties `((upstream-name . "ACSNMineR")))
12901 (build-system r-build-system)
12903 `(("r-ggplot2" ,r-ggplot2)
12904 ("r-gridextra" ,r-gridextra)))
12905 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
12906 (synopsis "Gene enrichment analysis")
12908 "This package provides tools to compute and represent gene set enrichment
12909 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
12910 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
12911 enrichment can be run with hypergeometric test or Fisher exact test, and can
12912 use multiple corrections. Visualization of data can be done either by
12913 barplots or heatmaps.")
12914 (license license:gpl2+)))
12916 (define-public r-seqinr
12923 (uri (cran-uri "seqinr" version))
12926 "0j30za6kji6y3v09cvcydiacnp65pv6ig8aw7cydl47l5s9chky4"))))
12927 (build-system r-build-system)
12929 `(("r-ade4" ,r-ade4)
12930 ("r-segmented" ,r-segmented)))
12933 (home-page "http://seqinr.r-forge.r-project.org/")
12934 (synopsis "Biological sequences retrieval and analysis")
12936 "This package provides tools for exploratory data analysis and data
12937 visualization of biological sequence (DNA and protein) data. It also includes
12938 utilities for sequence data management under the ACNUC system.")
12939 (license license:gpl2+)))
12941 (define-public r-units
12948 (uri (cran-uri "units" version))
12951 "02nls8m0r1r7kljs4x35naz3szq62hyqyd5vracf1xwi1kz5kdsh"))))
12952 (build-system r-build-system)
12954 `(("udunits" ,udunits)))
12956 `(("r-rcpp" ,r-rcpp)))
12957 (home-page "https://github.com/r-quantities/units/")
12958 (synopsis "Measurement Units for R Vectors")
12960 "This package provides support for measurement units in R vectors,
12961 matrices and arrays: automatic propagation, conversion, derivation and
12962 simplification of units; raising errors in case of unit incompatibility. It
12963 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
12965 (license license:gpl2)))
12967 (define-public r-classint
12969 (name "r-classint")
12974 (uri (cran-uri "classInt" version))
12977 "0w980hrw8sgfdfyd5dsimalq7gwhvqm7507abk7k363pvgks23dv"))))
12978 (properties `((upstream-name . "classInt")))
12979 (build-system r-build-system)
12981 `(("r-class" ,r-class)
12982 ("r-e1071" ,r-e1071)
12983 ("r-kernsmooth" ,r-kernsmooth)))
12984 (native-inputs `(("gfortran" ,gfortran)))
12985 (home-page "https://github.com/r-spatial/classInt/")
12986 (synopsis "Choose univariate class intervals")
12988 "This package provides selected commonly used methods for choosing
12989 univariate class intervals for mapping or other graphics purposes.")
12990 (license license:gpl2+)))
12992 (define-public r-spdata
12999 (uri (cran-uri "spData" version))
13002 "190msrrpn226x27pcnck4ac34f9k4xcn26cyz2apdri2nzkr6zbw"))))
13003 (properties `((upstream-name . "spData")))
13004 (build-system r-build-system)
13005 (home-page "https://github.com/Nowosad/spData")
13006 (synopsis "Datasets for spatial analysis")
13008 "This a package containing diverse spatial datasets for demonstrating,
13009 benchmarking and teaching spatial data analysis. It includes R data of class
13010 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
13011 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
13012 of the datasets are designed to illustrate specific analysis techniques.
13013 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
13014 illustrate point pattern analysis techniques.")
13015 (license license:cc0)))
13017 (define-public r-learnbayes
13019 (name "r-learnbayes")
13024 (uri (cran-uri "LearnBayes" version))
13027 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
13028 (properties `((upstream-name . "LearnBayes")))
13029 (build-system r-build-system)
13030 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
13031 (synopsis "Functions for learning Bayesian inference")
13033 "This package provides a collection of functions helpful in learning the
13034 basic tenets of Bayesian statistical inference. It contains functions for
13035 summarizing basic one and two parameter posterior distributions and predictive
13036 distributions. It contains MCMC algorithms for summarizing posterior
13037 distributions defined by the user. It also contains functions for regression
13038 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
13040 (license license:gpl2+)))
13042 (define-public r-deldir
13049 (uri (cran-uri "deldir" version))
13052 "0790dwxb2mz1ffz8gd5vwdr0if2q76dzy3vab5rsykf9kz72n4g0"))))
13053 (build-system r-build-system)
13054 (native-inputs `(("gfortran" ,gfortran)))
13055 (home-page "https://cran.r-project.org/web/packages/deldir")
13056 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
13058 "This package provides tools for calculating the Delaunay triangulation
13059 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
13060 of a planar point set. It plots triangulations and tessellations in various
13061 ways, clips tessellations to sub-windows, calculates perimeters of
13062 tessellations, and summarizes information about the tiles of the
13064 (license license:gpl2+)))
13066 (define-public r-sf
13073 (uri (cran-uri "sf" version))
13076 "05dyq0vcz2f1fl03hk3v1a4nz4s84yyqw4rc9w9cwfq71gvm9qwf"))))
13077 (build-system r-build-system)
13084 `(("r-classint" ,r-classint)
13086 ("r-magrittr" ,r-magrittr)
13088 ("r-units" ,r-units)))
13089 (native-inputs `(("pkg-config" ,pkg-config)))
13090 (home-page "https://github.com/r-spatial/sf/")
13091 (synopsis "Simple features for R")
13093 "This package provides support for simple features, a standardized way to
13094 encode spatial vector data. It binds to GDAL for reading and writing data, to
13095 GEOS for geometrical operations, and to PROJ for projection conversions and
13096 datum transformations.")
13097 ;; Either of these licenses
13098 (license (list license:gpl2 license:expat))))
13100 (define-public r-spdep
13107 (uri (cran-uri "spdep" version))
13110 "1f8cjffqqc6rnb3n4qym70ca6nz2kvrsd3g587wrqdr79nnbwnrk"))))
13111 (build-system r-build-system)
13113 `(("r-boot" ,r-boot)
13115 ("r-deldir" ,r-deldir)
13117 ("r-gmodels" ,r-gmodels)
13118 ("r-learnbayes" ,r-learnbayes)
13120 ("r-matrix" ,r-matrix)
13124 ("r-spdata" ,r-spdata)))
13125 (home-page "https://github.com/r-spatial/spdep/")
13126 (synopsis "Spatial dependence: weighting schemes, statistics and models")
13128 "This package provides a collection of functions to create spatial
13129 weights matrix objects from polygon contiguities, from point patterns by
13130 distance and tessellations, for summarizing these objects, and for permitting
13131 their use in spatial data analysis, including regional aggregation by minimum
13133 (license license:gpl2+)))
13135 (define-public r-adegenet
13137 (name "r-adegenet")
13142 (uri (cran-uri "adegenet" version))
13145 "0ynfblp0hbd3dp3k86fn1wyhqr28lk6hs2bg4q7gyf0sfdfzwhrh"))))
13146 (build-system r-build-system)
13148 `(("r-ade4" ,r-ade4)
13151 ("r-dplyr" ,r-dplyr)
13152 ("r-ggplot2" ,r-ggplot2)
13153 ("r-igraph" ,r-igraph)
13155 ("r-reshape2" ,r-reshape2)
13156 ("r-seqinr" ,r-seqinr)
13157 ("r-shiny" ,r-shiny)
13158 ("r-spdep" ,r-spdep)
13159 ("r-vegan" ,r-vegan)))
13160 (home-page "https://github.com/thibautjombart/adegenet")
13161 (synopsis "Exploratory analysis of genetic and genomic data")
13163 "This package provides a toolset for the exploration of genetic and
13164 genomic data. Adegenet provides formal (S4) classes for storing and handling
13165 various genetic data, including genetic markers with varying ploidy and
13166 hierarchical population structure (@code{genind} class), alleles counts by
13167 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
13168 also implements original multivariate methods (DAPC, sPCA), graphics,
13169 statistical tests, simulation tools, distance and similarity measures, and
13170 several spatial methods. A range of both empirical and simulated datasets is
13171 also provided to illustrate various methods.")
13172 (license license:gpl2+)))
13174 (define-public r-pegas
13181 (uri (cran-uri "pegas" version))
13183 (base32 "0sb8cmz4d238mcb56hv9fa0cagm00k82r7aj4cj4lxa1flxlpy8p"))))
13184 (build-system r-build-system)
13186 `(("r-adegenet" ,r-adegenet)
13188 (home-page "http://ape-package.ird.fr/pegas.html")
13189 (synopsis "Population and evolutionary genetics analysis system")
13191 "This package provides functions for reading, writing, plotting,
13192 analysing, and manipulating allelic and haplotypic data, including from VCF
13193 files, and for the analysis of population nucleotide sequences and
13194 micro-satellites including coalescent analyses, linkage disequilibrium,
13195 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
13196 minimum spanning tree and network, and median-joining networks.")
13197 (license license:gpl2+)))
13199 (define-public r-rmetasim
13201 (name "r-rmetasim")
13206 (uri (cran-uri "rmetasim" version))
13209 "0sz4mdprdi6sgkfwfdvh2hr9nxiwq17sw0vggq3cvs7lzb0i6m9r"))))
13210 (build-system r-build-system)
13212 `(("r-ade4" ,r-ade4)
13213 ("r-adegenet" ,r-adegenet)
13214 ("r-gtools" ,r-gtools)
13215 ("r-pegas" ,r-pegas)))
13216 (home-page "https://cran.r-project.org/web/packages/rmetasim")
13217 (synopsis "Individual-based population genetic simulation environment")
13219 "This package provides an interface between R and the metasim simulation
13220 engine. The simulation environment is documented in: Strand, A.(2002),
13221 Metasim 1.0: an individual-based environment for simulating population
13222 genetics of complex population dynamics.")
13224 (license license:gpl2+)))
13226 (define-public r-genetics
13228 (name "r-genetics")
13229 (version "1.3.8.1.2")
13233 (uri (cran-uri "genetics" version))
13236 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
13237 (build-system r-build-system)
13239 `(("r-combinat" ,r-combinat)
13240 ("r-gdata" ,r-gdata)
13241 ("r-gtools" ,r-gtools)
13243 ("r-mvtnorm" ,r-mvtnorm)))
13244 (home-page "https://cran.r-project.org/web/packages/genetics/")
13245 (synopsis "Population genetics")
13247 "This package provides classes and methods for handling genetic data.
13248 It includes classes to represent genotypes and haplotypes at single markers up
13249 to multiple markers on multiple chromosomes. Function include allele
13250 frequencies, flagging homo/heterozygotes, flagging carriers of certain
13251 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
13252 and testing for linkage disequilibrium, ...")
13253 ;; Any GPL version.
13254 (license license:gpl2+)))
13256 (define-public r-snp-plotter
13258 (name "r-snp-plotter")
13263 (uri (cran-uri "snp.plotter" version))
13266 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
13267 (properties `((upstream-name . "snp.plotter")))
13268 (build-system r-build-system)
13269 (propagated-inputs `(("r-genetics" ,r-genetics)))
13270 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
13271 (synopsis "Plot p-values using single SNP and/or haplotype data")
13273 "This package helps you create plots of p-values using single SNP and/or
13274 haplotype data. Main features of the package include options to display a
13275 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
13276 datasets simultaneously. Plots can be created using global and/or individual
13277 haplotype p-values along with single SNP p-values. Images are created as
13278 either PDF/EPS files.")
13279 (license license:gpl2+)))
13281 (define-public r-polspline
13283 (name "r-polspline")
13288 (uri (cran-uri "polspline" version))
13290 (base32 "0c7fnxpqpy3hibiim4yib6l6bq363s97wwvllxp4lp8h06fjcyyn"))))
13291 (build-system r-build-system)
13292 (native-inputs `(("gfortran" ,gfortran)))
13293 (home-page "https://cran.r-project.org/web/packages/polspline/")
13294 (synopsis "Polynomial spline routines")
13296 "This package provides routines for the polynomial spline fitting
13297 routines hazard regression, hazard estimation with flexible tails, logspline,
13298 lspec, polyclass, and polymars.")
13299 (license license:gpl2+)))
13301 (define-public r-rms
13308 (uri (cran-uri "rms" version))
13310 (base32 "19knh1sw0icw6jh9wfb2hq5jf49i2qfvp9myvqm5paa495689x9q"))))
13311 (build-system r-build-system)
13313 `(("r-ggplot2" ,r-ggplot2)
13314 ("r-hmisc" ,r-hmisc)
13315 ("r-htmltable" ,r-htmltable)
13316 ("r-htmltools" ,r-htmltools)
13317 ("r-lattice" ,r-lattice)
13318 ("r-multcomp" ,r-multcomp)
13320 ("r-polspline" ,r-polspline)
13321 ("r-quantreg" ,r-quantreg)
13322 ("r-rpart" ,r-rpart)
13323 ("r-sparsem" ,r-sparsem)
13324 ("r-survival" ,r-survival)))
13325 (native-inputs `(("gfortran" ,gfortran)))
13326 (home-page "http://biostat.mc.vanderbilt.edu/rms")
13327 (synopsis "Regression modeling strategies")
13329 "This is a package for regression modeling, testing, estimation,
13330 validation, graphics, prediction, and typesetting by storing enhanced model
13331 design attributes in the fit. The rms package is a collection of functions
13332 that assist with and streamline modeling. It also contains functions for
13333 binary and ordinal logistic regression models, ordinal models for continuous Y
13334 with a variety of distribution families, and the Buckley-James multiple
13335 regression model for right-censored responses, and implements penalized
13336 maximum likelihood estimation for logistic and ordinary linear models. The
13337 package works with almost any regression model, but it was especially written
13338 to work with binary or ordinal regression models, Cox regression, accelerated
13339 failure time models, ordinary linear models, the Buckley-James model,
13340 generalized least squares for serially or spatially correlated observations,
13341 generalized linear models, and quantile regression.")
13342 (license license:gpl2+)))
13344 (define-public r-haplo-stats
13346 (name "r-haplo-stats")
13351 (uri (cran-uri "haplo.stats" version))
13354 "19kxascqq5qz0zdxx0w837ji207y1z2ggxkl4vmlbay03k2dw2mx"))))
13355 (properties `((upstream-name . "haplo.stats")))
13356 (build-system r-build-system)
13358 `(("r-rms" ,r-rms)))
13360 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
13361 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
13362 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
13364 "This package provides routines for the analysis of indirectly measured
13365 haplotypes. The statistical methods assume that all subjects are unrelated
13366 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
13367 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
13368 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
13369 examples in the vignette.")
13370 (license license:gpl2+)))
13372 (define-public r-bqtl
13379 (uri (cran-uri "bqtl" version))
13382 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
13383 (build-system r-build-system)
13384 (native-inputs `(("gfortran" ,gfortran)))
13385 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
13386 (synopsis "Bayesian QTL mapping toolkit")
13388 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
13389 lines. It includes maximum likelihood and Bayesian tools.")
13390 (license license:gpl2+)))
13392 (define-public r-ibdreg
13399 (uri (cran-uri "ibdreg" version))
13402 "1kaa5q1byi30wzr0mw4w2cv1ssxprzcwf91wrpqwkgcsdy7dkh2g"))))
13403 (build-system r-build-system)
13404 (home-page "https://www.mayo.edu/research/labs/\
13405 statistical-genetics-genetic-epidemiology/software")
13406 (synopsis "Regression methods for IBD linkage with covariates")
13408 "This package provides a method to test genetic linkage with covariates
13409 by regression methods with response IBD sharing for relative pairs. Account
13410 for correlations of IBD statistics and covariates for relative pairs within
13411 the same pedigree.")
13412 (license license:gpl2+)))
13414 (define-public r-dlmap
13421 (uri (cran-uri "dlmap" version))
13424 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
13425 (build-system r-build-system)
13427 `(("r-ibdreg" ,r-ibdreg)
13431 ("r-wgaim" ,r-wgaim)))
13432 (home-page "https://cran.r-project.org/web/packages/dlmap/")
13433 (synopsis "Detection localization mapping for QTL")
13435 "This is package for QTL mapping in a mixed model framework with separate
13436 detection and localization stages. The first stage detects the number of QTL
13437 on each chromosome based on the genetic variation due to grouped markers on
13438 the chromosome; the second stage uses this information to determine the most
13439 likely QTL positions. The mixed model can accommodate general fixed and
13440 random effects, including spatial effects in field trials and pedigree
13441 effects. It is applicable to backcrosses, doubled haploids, recombinant
13442 inbred lines, F2 intercrosses, and association mapping populations.")
13443 (license license:gpl2)))
13445 (define-public r-ldheatmap
13447 (name "r-ldheatmap")
13452 (uri (cran-uri "LDheatmap" version))
13455 "1r0j8bihi5z1x0sgaf7dwzpsw9i0nc1vylvipvc0cia2ka1lr9dc"))))
13456 (properties `((upstream-name . "LDheatmap")))
13457 (build-system r-build-system)
13459 `(("r-genetics" ,r-genetics)
13461 ("r-snpstats" ,r-snpstats)))
13462 (home-page "http://stat.sfu.ca/statgen/research/ldheatmap.html")
13463 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
13465 "This package provides tools to produce a graphical display, as a heat
13466 map, of measures of pairwise linkage disequilibria between SNPs. Users may
13467 optionally include the physical locations or genetic map distances of each SNP
13469 (license license:gpl3)))
13471 (define-public r-hwde
13478 (uri (cran-uri "hwde" version))
13481 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
13482 (build-system r-build-system)
13483 (home-page "https://cran.r-project.org/web/packages/hwde/")
13484 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
13486 "This package fits models for genotypic disequilibria, as described in
13487 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
13488 terms are available that account for first order interactions between loci.
13489 It also implements, for a single locus in a single population, a conditional
13490 exact test for Hardy-Weinberg equilibrium.")
13491 (license license:gpl2+)))
13493 (define-public r-tdthap
13500 (uri (cran-uri "tdthap" version))
13503 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
13504 (build-system r-build-system)
13505 (home-page "https://cran.r-project.org/web/packages/tdthap/")
13506 (synopsis "TDT tests for extended haplotypes")
13508 "Functions and examples are provided for transmission/disequilibrium
13509 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
13510 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
13511 (license license:artistic2.0)))
13513 (define-public r-sparql
13519 (uri (cran-uri "SPARQL" version))
13522 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
13523 (properties `((upstream-name . "SPARQL")))
13524 (build-system r-build-system)
13526 `(("r-rcurl" ,r-rcurl)
13528 (home-page "https://cran.r-project.org/web/packages/SPARQL")
13529 (synopsis "SPARQL client for R")
13530 (description "This package provides an interface to use SPARQL to pose
13531 SELECT or UPDATE queries to an end-point.")
13532 ;; The only license indication is found in the DESCRIPTION file,
13533 ;; which states GPL-3. So we cannot assume GPLv3+.
13534 (license license:gpl3)))
13536 (define-public r-bookdown
13538 (name "r-bookdown")
13542 (uri (cran-uri "bookdown" version))
13545 "1gwgvx1yg6q3wccnhidr3gshdvlgr42i4pvlg4h29kpsa7smjiv1"))))
13546 (build-system r-build-system)
13548 `(("r-htmltools" ,r-htmltools)
13549 ("r-knitr" ,r-knitr)
13550 ("r-rmarkdown" ,r-rmarkdown)
13551 ("r-tinytex" ,r-tinytex)
13553 ("pandoc" ,ghc-pandoc)))
13554 (home-page "https://github.com/rstudio/bookdown")
13555 (synopsis "Authoring books and technical documents with R markdown")
13556 (description "This package provides output formats and utilities for
13557 authoring books and technical documents with R Markdown.")
13558 (license license:gpl3)))
13560 (define-public r-optparse
13562 (name "r-optparse")
13567 (uri (cran-uri "optparse" version))
13570 "0wyrc42ja3ab5szx46zmz8lm7vzfqxkjca0m0sms8g9hqbmmay6d"))))
13571 (build-system r-build-system)
13573 `(("r-getopt" ,r-getopt)))
13574 (home-page "https://github.com/trevorld/optparse")
13575 (synopsis "Command line option parser")
13577 "This package provides a command line parser inspired by Python's
13578 @code{optparse} library to be used with Rscript to write shebang scripts
13579 that accept short and long options.")
13580 (license license:gpl2+)))
13582 (define-public r-wgcna
13589 (uri (cran-uri "WGCNA" version))
13592 "1s7gy5vd7x67hpgli8r7ba2z99w3psiyv5hqmrh94zw141dg210a"))))
13593 (properties `((upstream-name . "WGCNA")))
13594 (build-system r-build-system)
13596 `(("r-annotationdbi" ,r-annotationdbi)
13597 ("r-doparallel" ,r-doparallel)
13598 ("r-dynamictreecut" ,r-dynamictreecut)
13599 ("r-fastcluster" ,r-fastcluster)
13600 ("r-foreach" ,r-foreach)
13601 ("r-go-db" ,r-go-db)
13602 ("r-hmisc" ,r-hmisc)
13603 ("r-impute" ,r-impute)
13605 ("r-robust" ,r-robust)
13606 ("r-survival" ,r-survival)
13607 ("r-matrixstats" ,r-matrixstats)
13608 ("r-preprocesscore" ,r-preprocesscore)))
13610 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
13611 (synopsis "Weighted correlation network analysis")
13613 "This package provides functions necessary to perform Weighted
13614 Correlation Network Analysis on high-dimensional data. It includes functions
13615 for rudimentary data cleaning, construction and summarization of correlation
13616 networks, module identification and functions for relating both variables and
13617 modules to sample traits. It also includes a number of utility functions for
13618 data manipulation and visualization.")
13619 (license license:gpl2+)))
13621 (define-public r-kernlab
13628 (uri (cran-uri "kernlab" version))
13630 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
13631 (build-system r-build-system)
13632 (home-page "https://cran.r-project.org/web/packages/kernlab")
13633 (synopsis "Kernel-based machine learning tools")
13635 "This package provides kernel-based machine learning methods for
13636 classification, regression, clustering, novelty detection, quantile regression
13637 and dimensionality reduction. Among other methods @code{kernlab} includes
13638 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
13640 (license license:gpl2)))
13642 (define-public r-hierfstat
13644 (name "r-hierfstat")
13645 (version "0.04-22")
13649 (uri (cran-uri "hierfstat" version))
13652 "1fav2v2996v5kb1ffa6v5wxfm921syxg6as034vd3j4jfhdibyfx"))))
13653 (build-system r-build-system)
13655 `(("r-ade4" ,r-ade4)
13656 ("r-adegenet" ,r-adegenet)
13657 ("r-gtools" ,r-gtools)))
13658 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
13659 (synopsis "Estimation and tests of hierarchical F-statistics")
13661 "This package allows the estimation of hierarchical F-statistics from
13662 haploid or diploid genetic data with any numbers of levels in the hierarchy,
13663 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
13664 are also given to test via randomisations the significance of each F and
13665 variance components, using the likelihood-ratio statistics G.")
13666 (license license:gpl2+)))
13668 (define-public r-hapassoc
13670 (name "r-hapassoc")
13675 (uri (cran-uri "hapassoc" version))
13678 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
13679 (build-system r-build-system)
13680 (home-page "http://stat.sfu.ca/statgen/research/hapassoc.html")
13681 (synopsis "Inference of trait associations with SNP haplotypes")
13683 "Hapassoc performs likelihood inference of trait associations with
13684 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
13685 functions are developed primarily for data collected in cohort or
13686 cross-sectional studies. They can accommodate uncertain haplotype phase and
13687 handle missing genotypes at some SNPs.")
13688 (license license:gpl2)))
13690 (define-public r-sampling
13692 (name "r-sampling")
13697 (uri (cran-uri "sampling" version))
13700 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
13701 (build-system r-build-system)
13703 `(("r-lpsolve" ,r-lpsolve)
13704 ("r-mass" ,r-mass)))
13705 (home-page "https://cran.r-project.org/web/packages/sampling/")
13706 (synopsis "Survey sampling")
13708 "This package provides functions for drawing and calibrating samples.")
13709 (license license:gpl2+)))
13711 (define-public r-r2html
13718 (uri (cran-uri "R2HTML" version))
13721 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
13722 (properties `((upstream-name . "R2HTML")))
13723 (build-system r-build-system)
13724 (home-page "https://github.com/nalimilan/R2HTML")
13725 (synopsis "HTML export for R objects")
13727 "This package includes HTML functions and methods to write in an HTML
13728 file. Thus, making HTML reports is easy. It includes a function that allows
13729 redirection on the fly, which appears to be very useful for teaching purposes,
13730 as the student can keep a copy of the produced output to keep all that they
13731 did during the course. The package comes with a vignette describing how to
13732 write HTML reports for statistical analysis. Finally, a driver for Sweave
13733 allows to parse HTML flat files containing R code and to automatically write
13734 the corresponding outputs (tables and graphs).")
13735 (license license:gpl2+)))
13737 (define-public r-rjava
13744 (uri (cran-uri "rJava" version))
13747 "0s9cjy1wh7snmbqwznh8f1r4ipylr7mgda4a979z963a8lqy32n2"))))
13748 (properties `((upstream-name . "rJava")))
13749 (build-system r-build-system)
13751 `(#:modules ((guix build utils)
13752 (guix build r-build-system)
13755 (modify-phases %standard-phases
13756 (add-after 'unpack 'set-JAVA_HOME
13757 (lambda* (#:key inputs #:allow-other-keys)
13758 (let ((jdk (assoc-ref inputs "jdk")))
13759 (setenv "JAVA_HOME" jdk)
13760 (setenv "JAVA" (which "java"))
13761 (setenv "JAR" (which "jar"))
13762 (setenv "JAVAC" (which "javac"))
13763 (setenv "JAVAH" (which "javah"))
13764 (setenv "JAVA_CPPFLAGS"
13765 (string-append "-I" jdk "/include "
13766 "-I" jdk "/include/linux"))
13767 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
13768 ((lib) (setenv "JAVA_LIBS" lib))
13769 (_ (error "Could not find libjvm.so"))))
13773 ("jdk" ,icedtea-8 "jdk")
13776 (home-page "http://www.rforge.net/rJava/")
13777 (synopsis "Low-Level R to Java interface")
13779 "This package provides a low-level interface to the Java VM very much
13780 like .C/.Call and friends. It allows the creation of objects, calling methods
13781 and accessing fields.")
13782 (license license:gpl2)))
13784 (define-public r-svmisc
13791 (uri (cran-uri "svMisc" version))
13794 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
13795 (properties `((upstream-name . "svMisc")))
13796 (build-system r-build-system)
13797 (home-page "https://github.com/SciViews/svMisc")
13798 (synopsis "Miscellaneous functions for SciViews")
13800 "This package provides miscellaneous functions for SciViews or general
13801 use, including tools to manage a temporary environment attached to the search
13802 path for temporary variables you do not want to @code{save()} or
13803 @code{load()}; test the current platform; showing progress bars, etc.")
13804 (license license:gpl2)))
13806 (define-public r-xyz
13813 (uri (cran-uri "xyz" version))
13816 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
13817 (build-system r-build-system)
13819 `(("r-rcpp" ,r-rcpp)))
13820 (home-page "https://cran.r-project.org/web/packages/xyz/")
13821 (synopsis "Algorithm for fast interaction search in high-dimensional data")
13823 "High dimensional interaction search by brute force requires a quadratic
13824 computational cost in the number of variables. The xyz algorithm provably
13825 finds strong interactions in almost linear time. For details of the algorithm
13826 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
13827 interaction search in high-dimensional data.")
13828 ;; Any version of the GPL.
13829 (license license:gpl2+)))
13831 (define-public r-rttf2pt1
13833 (name "r-rttf2pt1")
13838 (uri (cran-uri "Rttf2pt1" version))
13841 "12hf9r3mhjr9sawdvf7qhjf1zph2q64f77i81jwvy7awidbm0kja"))))
13842 (properties `((upstream-name . "Rttf2pt1")))
13843 (build-system r-build-system)
13844 (home-page "https://github.com/wch/Rttf2pt1")
13845 (synopsis "Font conversion utility")
13847 "This package contains the program @code{ttf2pt1}, for use with the
13848 @code{extrafont} package.")
13849 ;; Most of the files are covered under the Expat license. Some files are
13850 ;; covered under BSD-3. Deviations for individual files are recorded in
13851 ;; the LICENSE file.
13852 (license (list license:bsd-3 license:expat
13853 (license:non-copyleft "file://LICENSE")))))
13855 (define-public r-extrafontdb
13857 (name "r-extrafontdb")
13862 (uri (cran-uri "extrafontdb" version))
13865 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
13866 (build-system r-build-system)
13867 (home-page "https://github.com/wch/extrafontdb")
13868 (synopsis "Database for the extrafont package")
13870 "This package holds the database for the @code{extrafont} package.")
13871 (license license:gpl2)))
13873 (define-public r-extrafont
13875 (name "r-extrafont")
13880 (uri (cran-uri "extrafont" version))
13883 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
13884 (build-system r-build-system)
13886 `(("r-extrafontdb" ,r-extrafontdb)
13887 ("r-rttf2pt1" ,r-rttf2pt1)))
13888 (home-page "https://github.com/wch/extrafont")
13889 (synopsis "Tools for using fonts in R")
13891 "The extrafont package makes it easier to use fonts other than the basic
13892 PostScript fonts that R uses. Fonts that are imported into extrafont can be
13893 used with PDF or PostScript output files. There are two hurdles for using
13894 fonts in PDF (or Postscript) output files:
13897 @item Making R aware of the font and the dimensions of the characters.
13898 @item Embedding the fonts in the PDF file so that the PDF can be displayed
13899 properly on a device that doesn't have the font. This is usually needed if
13900 you want to print the PDF file or share it with others.
13903 The extrafont package makes both of these things easier.")
13904 (license license:gpl2)))
13906 (define-public r-xkcd
13913 (uri (cran-uri "xkcd" version))
13916 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
13917 (build-system r-build-system)
13919 `(("r-extrafont" ,r-extrafont)
13920 ("r-ggplot2" ,r-ggplot2)
13921 ("r-hmisc" ,r-hmisc)))
13922 (home-page "https://cran.r-project.org/web/packages/xkcd/")
13923 (synopsis "Plot ggplot2 graphics in the XKCD style")
13925 "This package provides the means to plot ggplot2 graphs in the style of
13926 the XKCD web comic.")
13927 (license license:gpl3)))
13929 (define-public r-msigdbr
13936 (uri (cran-uri "msigdbr" version))
13939 "19p8z617m3my8la7n1qgb1s2msf940r372im3q30qkbcx3qxg3sd"))))
13940 (build-system r-build-system)
13942 `(("r-dplyr" ,r-dplyr)
13943 ("r-magrittr" ,r-magrittr)
13944 ("r-rlang" ,r-rlang)
13945 ("r-tibble" ,r-tibble)))
13946 (home-page "https://github.com/igordot/msigdbr")
13947 (synopsis "MSigDB gene sets for multiple organisms")
13949 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
13950 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
13951 software in a standard R data frame with key-value pairs. Included are the
13952 original human gene symbols and Entrez IDs as well as the equivalents for
13953 various frequently studied model organisms such as mouse, rat, pig, fly, and
13955 ;; The package is covered under the Expat license, but the upstream MSigDB
13956 ;; files are made available under the Creative Commons Attribution 4.0
13957 ;; International license.
13958 (license (list license:expat license:cc-by4.0))))
13960 (define-public r-gridgraphics
13962 (name "r-gridgraphics")
13967 (uri (cran-uri "gridGraphics" version))
13970 "1kr3p54bkv2q7agxrva30y9bkwkiq1k2cfl5z1kvyjv6f5xi4w5p"))))
13971 (properties `((upstream-name . "gridGraphics")))
13972 (build-system r-build-system)
13973 (home-page "https://github.com/pmur002/gridgraphics")
13974 (synopsis "Redraw base graphics using @code{grid} graphics")
13976 "This package provides functions to convert a page of plots drawn with
13977 the @code{graphics} package into identical output drawn with the @code{grid}
13978 package. The result looks like the original @code{graphics}-based plot, but
13979 consists of @code{grid} grobs and viewports that can then be manipulated with
13980 @code{grid} functions (e.g., edit grobs and revisit viewports).")
13981 (license license:gpl2+)))
13983 (define-public r-farver
13990 (uri (cran-uri "farver" version))
13993 "0aq1hk561pz3s3lpay1adwsihha6mxp7zbj4n1m6307g34awlhhn"))))
13994 (build-system r-build-system)
13995 (home-page "https://github.com/thomasp85/farver")
13996 (synopsis "Vectorized color conversion and comparison")
13998 "The encoding of color can be handled in many different ways, using
13999 different color spaces. As different color spaces have different uses,
14000 efficient conversion between these representations are important. This
14001 package provides a set of functions that gives access to very fast color space
14002 conversion and comparisons implemented in C++, and offers 100-fold speed
14003 improvements over the @code{convertColor} function in the @code{grDevices}
14005 (license license:expat)))
14007 (define-public r-ggplotify
14009 (name "r-ggplotify")
14014 (uri (cran-uri "ggplotify" version))
14017 "0nv3wdmxnc5ww9m3xlgnb0jp30j45dg33nqc6gg3y36svg8anjcg"))))
14018 (build-system r-build-system)
14020 `(("r-ggplot2" ,r-ggplot2)
14021 ("r-gridgraphics" ,r-gridgraphics)
14022 ("r-rvcheck" ,r-rvcheck)))
14023 (home-page "https://github.com/GuangchuangYu/ggplotify")
14024 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
14026 "This package provides tools to convert plot function calls (using
14027 expression or formula) to @code{grob} or @code{ggplot} objects that are
14028 compatible with the @code{grid} and @code{ggplot2} environment. With this
14029 package, we are able to e.g. use @code{cowplot} to align plots produced by
14030 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
14031 converting them to @code{ggplot} objects.")
14032 (license license:artistic2.0)))
14034 (define-public r-triebeard
14036 (name "r-triebeard")
14041 (uri (cran-uri "triebeard" version))
14044 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
14045 (build-system r-build-system)
14046 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
14047 (home-page "https://github.com/Ironholds/triebeard/")
14048 (synopsis "Radix trees in Rcpp")
14050 "Radix trees, or tries, are key-value data structures optimized for
14051 efficient lookups, similar in purpose to hash tables. This package provides
14052 an implementation of radix trees for use in R programming and in developing
14053 packages with Rcpp.")
14054 (license license:expat)))
14056 (define-public r-tweenr
14063 (uri (cran-uri "tweenr" version))
14066 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
14067 (build-system r-build-system)
14069 `(("r-farver" ,r-farver)
14070 ("r-magrittr" ,r-magrittr)
14072 ("r-rlang" ,r-rlang)))
14073 (home-page "https://github.com/thomasp85/tweenr")
14074 (synopsis "Interpolate data for smooth animations")
14076 "In order to create smooth animation between states of data, tweening is
14077 necessary. This package provides a range of functions for creating tweened
14078 data that can be used as basis for animation. Furthermore it adds a number of
14079 vectorized interpolaters for common R data types such as numeric, date and
14081 (license license:expat)))
14083 (define-public r-polyclip
14085 (name "r-polyclip")
14090 (uri (cran-uri "polyclip" version))
14093 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
14094 (build-system r-build-system)
14095 (native-inputs `(("pkg-config" ,pkg-config)))
14096 (home-page "http://www.angusj.com/delphi/clipper.php")
14097 (synopsis "Polygon clipping")
14099 "This package provides an R port of the library Clipper. It performs
14100 polygon clipping operations (intersection, union, set minus, set difference)
14101 for polygonal regions of arbitrary complexity, including holes. It computes
14102 offset polygons (spatial buffer zones, morphological dilations, Minkowski
14103 dilations) for polygonal regions and polygonal lines. It computes the
14104 Minkowski Sum of general polygons. There is a function for removing
14105 self-intersections from polygon data.")
14106 (license license:boost1.0)))
14108 (define-public r-urltools
14110 (name "r-urltools")
14115 (uri (cran-uri "urltools" version))
14118 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
14119 (build-system r-build-system)
14121 `(("r-rcpp" ,r-rcpp)
14122 ("r-triebeard" ,r-triebeard)))
14123 (home-page "https://github.com/Ironholds/urltools/")
14124 (synopsis "Vectorized tools for URL handling and parsing")
14126 "This package provides a toolkit for all URL-handling needs, including
14127 encoding and decoding, parsing, parameter extraction and modification. All
14128 functions are designed to be both fast and entirely vectorized. It is
14129 intended to be useful for people dealing with web-related datasets, such as
14130 server-side logs, although may be useful for other situations involving large
14132 (license license:expat)))
14134 (define-public r-ggforce
14141 (uri (cran-uri "ggforce" version))
14144 "04926cqrda6psvy2nzkkw4czwyxdp7fnxg76byp14v12kgd72lm0"))))
14145 (build-system r-build-system)
14147 `(("r-ggplot2" ,r-ggplot2)
14148 ("r-gtable" ,r-gtable)
14150 ("r-polyclip" ,r-polyclip)
14152 ("r-rcppeigen" ,r-rcppeigen)
14153 ("r-rlang" ,r-rlang)
14154 ("r-scales" ,r-scales)
14155 ("r-tidyselect" ,r-tidyselect)
14156 ("r-tweenr" ,r-tweenr)
14157 ("r-withr" ,r-withr)))
14158 (home-page "https://ggforce.data-imaginist.com")
14159 (synopsis "Accelerating ggplot2")
14161 "The aim of the ggplot2 package is to aid in visual data investigations.
14162 This focus has led to a lack of facilities for composing specialized plots.
14163 Thi package aims to be a collection of mainly new statistics and geometries
14164 that fills this gap.")
14165 (license license:expat)))
14167 (define-public r-europepmc
14169 (name "r-europepmc")
14174 (uri (cran-uri "europepmc" version))
14177 "1ngqs1sqzkbwv98dd5z4cxj8bnz41wyd0g060a2vpqi3s99s4i2h"))))
14178 (build-system r-build-system)
14180 `(("r-dplyr" ,r-dplyr)
14182 ("r-jsonlite" ,r-jsonlite)
14184 ("r-progress" ,r-progress)
14185 ("r-purrr" ,r-purrr)
14186 ("r-urltools" ,r-urltools)
14187 ("r-xml2" ,r-xml2)))
14188 (home-page "https://github.com/ropensci/europepmc/")
14189 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
14191 "This package provides an R Client for the
14192 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
14193 Service}. It gives access to both metadata on life science literature and
14194 open access full texts. Europe PMC indexes all PubMed content and other
14195 literature sources including Agricola, a bibliographic database of citations
14196 to the agricultural literature, or Biological Patents. In addition to
14197 bibliographic metadata, the client allows users to fetch citations and
14198 reference lists. Links between life-science literature and other EBI
14199 databases, including ENA, PDB or ChEMBL are also accessible.")
14200 (license license:gpl3)))
14202 (define-public r-ggraph
14209 (uri (cran-uri "ggraph" version))
14212 "0qj7w3af0pgmd9mil6y571jikfkln7b8csvzg6b08spwbglfy1s3"))))
14213 (build-system r-build-system)
14215 `(("r-digest" ,r-digest)
14216 ("r-dplyr" ,r-dplyr)
14217 ("r-ggforce" ,r-ggforce)
14218 ("r-ggplot2" ,r-ggplot2)
14219 ("r-ggrepel" ,r-ggrepel)
14220 ("r-graphlayouts" ,r-graphlayouts)
14221 ("r-gtable" ,r-gtable)
14222 ("r-igraph" ,r-igraph)
14225 ("r-rlang" ,r-rlang)
14226 ("r-scales" ,r-scales)
14227 ("r-tidygraph" ,r-tidygraph)
14228 ("r-viridis" ,r-viridis)))
14229 (home-page "https://cran.r-project.org/web/packages/ggraph/")
14230 (synopsis "Implementation of grammar of graphics for graphs and networks")
14232 "The grammar of graphics as implemented in ggplot2 is a poor fit for
14233 graph and network visualizations due to its reliance on tabular data input.
14234 The ggraph package is an extension of the ggplot2 API tailored to graph
14235 visualizations and provides the same flexible approach to building up plots
14237 (license license:gpl3)))
14239 (define-public r-varselrf
14241 (name "r-varselrf")
14246 (uri (cran-uri "varSelRF" version))
14249 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
14250 (properties `((upstream-name . "varSelRF")))
14251 (build-system r-build-system)
14253 `(("r-randomforest" ,r-randomforest)))
14254 (home-page "http://ligarto.org/rdiaz/Software/Software.html")
14255 (synopsis "Variable selection using random forests")
14257 "This package provides tools for the variable selection from random
14258 forests using both backwards variable elimination (for the selection of small
14259 sets of non-redundant variables) and selection based on the importance
14260 spectrum (somewhat similar to scree plots; for the selection of large,
14261 potentially highly-correlated variables). The main applications are in
14262 high-dimensional data (e.g., microarray data, and other genomics and
14263 proteomics applications).")
14264 (license license:gpl2+)))
14266 (define-public r-pamr
14273 (uri (cran-uri "pamr" version))
14276 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
14277 (build-system r-build-system)
14279 `(("r-cluster" ,r-cluster)
14280 ("r-survival" ,r-survival)))
14281 (native-inputs `(("gfortran" ,gfortran)))
14282 (home-page "https://cran.r-project.org/web/packages/pamr/")
14283 (synopsis "Prediction Analysis for Microarrays")
14285 "This package provides some functions for sample classification in
14287 (license license:gpl2)))
14289 (define-public r-rda
14292 (version "1.0.2-2.1")
14296 (uri (cran-uri "rda" version))
14299 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
14300 (build-system r-build-system)
14301 (home-page "https://cran.r-project.org/web/packages/rda/")
14302 (synopsis "Shrunken centroids regularized discriminant analysis")
14304 "This package provides tools for shrunken centroids regularized
14305 discriminant analysis for the purpose of classifying high dimensional data.")
14306 (license license:gpl2+)))
14308 (define-public r-ggvis
14315 (uri (cran-uri "ggvis" version))
14318 "091i9f17912j8qcyxppjgwzjnyqj7769ixs9d2gjg6f2clskqdw2"))))
14319 (build-system r-build-system)
14321 `(("r-assertthat" ,r-assertthat)
14322 ("r-dplyr" ,r-dplyr)
14323 ("r-htmltools" ,r-htmltools)
14324 ("r-jsonlite" ,r-jsonlite)
14325 ("r-lazyeval" ,r-lazyeval)
14326 ("r-magrittr" ,r-magrittr)
14327 ("r-shiny" ,r-shiny)))
14328 (home-page "https://ggvis.rstudio.com/")
14329 (synopsis "Interactive grammar of graphics")
14331 "This package is a data visualization package for R providing an
14332 implementation of an interactive grammar of graphics, taking the best parts of
14333 ggplot2, combining them with the reactive framework of Shiny and drawing web
14334 graphics using Vega.")
14335 (license license:gpl2)))
14337 (define-public r-gbm
14344 (uri (cran-uri "gbm" version))
14347 "0vs6ljaqhwwpgr8wlbhmm4v147rd82kl16rpaijqiylxcc8dxyq6"))))
14348 (build-system r-build-system)
14350 `(("r-gridextra" ,r-gridextra)
14351 ("r-lattice" ,r-lattice)
14352 ("r-survival" ,r-survival)))
14353 (home-page "https://github.com/gbm-developers/gbm")
14354 (synopsis "Generalized boosted regression models")
14356 "This package is an implementation of extensions to Freund and Schapire's
14357 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
14358 regression methods for least squares, absolute loss, t-distribution loss,
14359 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
14360 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
14361 and Learning to Rank measures (LambdaMart).")
14362 (license license:gpl2+)))
14364 (define-public r-threejs
14371 (uri (cran-uri "threejs" version))
14374 "1s3rdlzy7man6177ycayg6xsh6k8y1r9rdj9yzn3b93j2rs0nxbi"))))
14375 (build-system r-build-system)
14377 `(#:modules ((guix build utils)
14378 (guix build r-build-system)
14382 (modify-phases %standard-phases
14383 (add-after 'unpack 'process-javascript
14384 (lambda* (#:key inputs #:allow-other-keys)
14385 (with-directory-excursion "inst"
14389 `((,(assoc-ref inputs "js-jquery")
14390 "htmlwidgets/lib/jquery/jquery.min.js")
14391 (,(assoc-ref inputs "js-threejs-85")
14392 "htmlwidgets/lib/threejs-85/three.min.js"))))
14393 (lambda (sources targets)
14394 (for-each (lambda (source target)
14395 (format #t "Processing ~a --> ~a~%"
14397 (delete-file target)
14398 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14399 (call-with-output-file target
14401 (dump-port minified port)))))
14402 sources targets))))
14405 `(("r-base64enc" ,r-base64enc)
14406 ("r-crosstalk" ,r-crosstalk)
14407 ("r-htmlwidgets" ,r-htmlwidgets)
14408 ("r-igraph" ,r-igraph)))
14410 `(("uglify-js" ,uglify-js)
14414 (uri "https://code.jquery.com/jquery-3.3.1.js")
14417 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
14421 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r85/build/three.js")
14424 "17khh3dmijdjw4qb9qih1rqhxgrmm3pc6w8lzdx6rf6a3mrc9xnl"))))))
14425 (home-page "https://bwlewis.github.io/rthreejs")
14426 (synopsis "Interactive 3D scatter plots, networks and globes")
14428 "Create interactive 3D scatter plots, network plots, and globes in R
14429 using the three.js visualization library.")
14430 (license license:expat)))
14432 (define-public r-mlbench
14439 (uri (cran-uri "mlbench" version))
14442 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
14443 (build-system r-build-system)
14444 (home-page "https://cran.r-project.org/web/packages/mlbench/")
14445 (synopsis "Machine learning benchmark problems")
14447 "This package provides a collection of artificial and real-world machine
14448 learning benchmark problems, including, e.g., several data sets from the UCI
14450 (license license:gpl2)))
14452 (define-public r-mpm
14459 (uri (cran-uri "mpm" version))
14462 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
14463 (build-system r-build-system)
14465 `(("r-kernsmooth" ,r-kernsmooth)
14466 ("r-mass" ,r-mass)))
14467 (home-page "http://mpm.r-forge.r-project.org")
14468 (synopsis "Multivariate projection methods")
14470 "This is a package for exploratory graphical analysis of multivariate
14471 data, specifically gene expression data with different projection methods:
14472 principal component analysis, correspondence analysis, spectral map
14474 (license license:gpl2+)))
14476 (define-public r-png
14482 (uri (cran-uri "png" version))
14485 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
14486 (build-system r-build-system)
14488 `(("libpng" ,libpng)
14490 (home-page "http://www.rforge.net/png/")
14491 (synopsis "Read and write PNG images")
14493 "This package provides an easy and simple way to read, write and display
14494 bitmap images stored in the PNG format. It can read and write both files and
14495 in-memory raw vectors.")
14496 ;; Any of these GPL versions.
14497 (license (list license:gpl2 license:gpl3))))
14499 (define-public r-ggcorrplot
14501 (name "r-ggcorrplot")
14506 (uri (cran-uri "ggcorrplot" version))
14509 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
14510 (build-system r-build-system)
14512 `(("r-ggplot2" ,r-ggplot2)
14513 ("r-reshape2" ,r-reshape2)))
14514 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
14515 (synopsis "Visualization of a correlation matrix using ggplot2")
14517 "The ggcorrplot package can be used to visualize easily a correlation
14518 matrix using ggplot2. It provides a solution for reordering the correlation
14519 matrix and displays the significance level on the plot. It also includes a
14520 function for computing a matrix of correlation p-values.")
14521 (license license:gpl2)))
14523 (define-public r-flexdashboard
14525 (name "r-flexdashboard")
14526 (version "0.5.1.1")
14530 (uri (cran-uri "flexdashboard" version))
14533 "0fy3nbrr67zqgd44r2mc850s5sp0hzfcw3zqs15m8kxzj1aw067x"))))
14534 (build-system r-build-system)
14536 `(#:modules ((guix build utils)
14537 (guix build r-build-system)
14541 (ice-9 textual-ports))
14543 (modify-phases %standard-phases
14544 (add-after 'unpack 'process-javascript
14545 (lambda* (#:key inputs #:allow-other-keys)
14546 (with-directory-excursion "inst"
14547 ;; Concatenate all components of prism.js
14548 (let ((contents (string-join
14549 (map (lambda (name)
14550 (call-with-input-file
14551 (assoc-ref inputs name)
14555 "js-prism-line-numbers"))
14557 (call-with-output-file "prism-src.js"
14558 (cut display contents <>)))
14562 `(("www/stickytableheaders/jquery.stickytableheaders.js"
14563 "www/stickytableheaders/jquery.stickytableheaders.min.js")
14565 "www/sly/sly.min.js")
14567 "www/prism/prism.js")
14568 (,(assoc-ref inputs "js-raphael")
14569 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
14570 (,(assoc-ref inputs "js-featherlight")
14571 "www/featherlight/featherlight.min.js"))))
14572 (lambda (sources targets)
14573 (for-each (lambda (source target)
14574 (format #t "Processing ~a --> ~a~%"
14576 (delete-file target)
14577 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14578 (call-with-output-file target
14580 (dump-port minified port)))))
14581 sources targets))))
14584 `(("r-htmltools" ,r-htmltools)
14585 ("r-htmlwidgets" ,r-htmlwidgets)
14586 ("r-jsonlite" ,r-jsonlite)
14587 ("r-knitr" ,r-knitr)
14588 ("r-rmarkdown" ,r-rmarkdown)
14589 ("r-shiny" ,r-shiny)))
14591 `(("uglify-js" ,uglify-js)
14595 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
14598 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
14602 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
14605 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
14609 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
14612 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
14613 ("js-prism-line-numbers"
14616 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
14619 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
14623 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
14626 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
14627 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
14628 (synopsis "R Markdown format for flexible dashboards")
14630 "This package provides an R Markdown format for converting an R Markdown
14631 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
14632 of its components to the containing web page.")
14633 (license license:expat)))
14635 (define-public r-preseqr
14642 (uri (cran-uri "preseqR" version))
14645 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
14646 (properties `((upstream-name . "preseqR")))
14647 (build-system r-build-system)
14649 `(("r-polynom" ,r-polynom)))
14650 (home-page "https://cran.r-project.org/web/packages/preseqR/")
14651 (synopsis "Predicting species accumulation curves")
14653 "This package can be used to predict the r-species accumulation
14654 curve (r-SAC), which is the number of species represented at least r times as
14655 a function of the sampling effort. When r = 1, the curve is known as the
14656 species accumulation curve, or the library complexity curve in high-throughput
14657 genomic sequencing. The package includes both parametric and nonparametric
14658 methods, as described by Deng C, et al. (2018).")
14659 (license license:gpl3)))
14661 (define-public r-mapplots
14663 (name "r-mapplots")
14668 (uri (cran-uri "mapplots" version))
14671 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
14672 (build-system r-build-system)
14673 (home-page "https://cran.r-project.org/web/packages/mapplots/")
14674 (synopsis "Data visualization on maps")
14676 "This package helps you create simple maps; add sub-plots like pie plots
14677 to a map or any other plot; format, plot and export gridded data. The package
14678 was developed for displaying fisheries data but most functions can be used for
14679 more generic data visualisation.")
14680 (license license:gpl2+)))
14682 (define-public r-pmcmr
14689 (uri (cran-uri "PMCMR" version))
14692 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
14693 (properties `((upstream-name . "PMCMR")))
14694 (build-system r-build-system)
14695 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
14696 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
14698 "This is a deprecated package for calculating pairwise multiple
14699 comparisons of mean rank sums. This package is superseded by the novel
14700 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
14701 compatibility of dependent packages for some time.")
14702 (license license:gpl3+)))
14704 (define-public r-downloader
14706 (name "r-downloader")
14711 (uri (cran-uri "downloader" version))
14714 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
14715 (build-system r-build-system)
14717 `(("r-digest" ,r-digest)))
14718 (home-page "https://github.com/wch/downloader")
14719 (synopsis "Download files over HTTP and HTTPS")
14721 "This package provides a wrapper for the @code{download.file} function,
14722 making it possible to download files over HTTPS across platforms. The
14723 @code{RCurl} package provides this functionality (and much more) but has
14724 external dependencies. This package has is implemented purely in R.")
14725 (license license:gpl2)))
14727 (define-public r-rex
14734 (uri (cran-uri "rex" version))
14737 "0alsadgjgass3wr8y5d247j12qqzg454sc84vpskclrkmz778g5x"))))
14738 (build-system r-build-system)
14740 `(("r-lazyeval" ,r-lazyeval)
14741 ("r-magrittr" ,r-magrittr)))
14742 (home-page "https://github.com/kevinushey/rex")
14743 (synopsis "Friendly regular expressions")
14745 "This package provides a friendly interface for the construction of
14746 regular expressions. Regular expressions are a very powerful feature, however
14747 they are often difficult to interpret. Rex allows you to build complex
14748 regular expressions from human readable expressions")
14749 (license license:expat)))
14751 (define-public r-xmlparsedata
14753 (name "r-xmlparsedata")
14758 (uri (cran-uri "xmlparsedata" version))
14761 "0gjr3l5z5dp276lchr2649as1rkj56d2mlvbr66yg393zzw50lsh"))))
14762 (properties `((upstream-name . "xmlparsedata")))
14763 (build-system r-build-system)
14764 (home-page "https://github.com/r-lib/xmlparsedata#readme")
14765 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
14767 "This package provides tools to convert the output of
14768 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
14769 @code{XPath}, and is easier to manipulate in general.")
14770 (license license:expat)))
14772 (define-public r-cyclocomp
14774 (name "r-cyclocomp")
14779 (uri (cran-uri "cyclocomp" version))
14782 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
14783 (properties `((upstream-name . "cyclocomp")))
14784 (build-system r-build-system)
14786 `(("r-callr" ,r-callr)
14787 ("r-crayon" ,r-crayon)
14789 ("r-remotes" ,r-remotes)
14790 ("r-withr" ,r-withr)))
14791 (home-page "https://github.com/MangoTheCat/cyclocomp")
14792 (synopsis "Cyclomatic complexity of R code")
14794 "Cyclomatic complexity is a software metric, used to indicate the
14795 complexity of a program. It is a quantitative measure of the number of
14796 linearly independent paths through a program's source code. This package
14797 provides tools to compute this metric.")
14798 (license license:expat)))
14800 (define-public r-lintr
14807 (uri (cran-uri "lintr" version))
14810 "09gbci4v5n4gsfzminly8332fw7faxdi1kkyvpa10dydx02sjcwb"))))
14811 (properties `((upstream-name . "lintr")))
14812 (build-system r-build-system)
14814 `(("r-codetools" ,r-codetools)
14815 ("r-crayon" ,r-crayon)
14816 ("r-cyclocomp" ,r-cyclocomp)
14817 ("r-digest" ,r-digest)
14819 ("r-jsonlite" ,r-jsonlite)
14820 ("r-knitr" ,r-knitr)
14822 ("r-rstudioapi" ,r-rstudioapi)
14823 ("r-stringdist" ,r-stringdist)
14824 ("r-testthat" ,r-testthat)
14826 ("r-xmlparsedata" ,r-xmlparsedata)))
14827 (home-page "https://github.com/jimhester/lintr")
14828 (synopsis "Linter for R code")
14829 (description "This package checks adherence to a given style, syntax
14830 errors and possible semantic issues. It supports on the fly checking of R
14831 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
14832 (license license:expat)))
14834 (define-public r-sctransform
14836 (name "r-sctransform")
14841 (uri (cran-uri "sctransform" version))
14844 "1r5kiqqs318q59h2i8m7c6nhghp9w6q26ss2y5a390lkhsawgx6p"))))
14845 (build-system r-build-system)
14847 `(("r-future" ,r-future)
14848 ("r-future-apply" ,r-future-apply)
14849 ("r-ggplot2" ,r-ggplot2)
14850 ("r-gridextra" ,r-gridextra)
14852 ("r-matrix" ,r-matrix)
14854 ("r-rcppeigen" ,r-rcppeigen)
14855 ("r-reshape2" ,r-reshape2)))
14856 (home-page "https://github.com/ChristophH/sctransform")
14857 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
14859 "This package provides a normalization method for single-cell UMI count
14860 data using a variance stabilizing transformation. The transformation is based
14861 on a negative binomial regression model with regularized parameters. As part
14862 of the same regression framework, this package also provides functions for
14863 batch correction, and data correction.")
14864 (license license:gpl3)))
14866 (define-public r-styler
14873 (uri (cran-uri "styler" version))
14876 "0rdbz60x8bymis6r6188ia1y0ip3nhf5y363i4cmakr618irjab9"))))
14877 (build-system r-build-system)
14879 `(("r-backports" ,r-backports)
14881 ("r-magrittr" ,r-magrittr)
14882 ("r-purrr" ,r-purrr)
14883 ("r-rematch2" ,r-rematch2)
14884 ("r-rlang" ,r-rlang)
14885 ("r-rprojroot" ,r-rprojroot)
14886 ("r-tibble" ,r-tibble)
14887 ("r-withr" ,r-withr)
14888 ("r-xfun" ,r-xfun)))
14889 (home-page "https://github.com/r-lib/styler")
14890 (synopsis "Non-invasive pretty printing of R code")
14892 "This is a package for pretty-printing R code without changing the user's
14893 formatting intent.")
14894 (license license:gpl3)))
14896 (define-public r-scrime
14903 (uri (cran-uri "scrime" version))
14906 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
14907 (build-system r-build-system)
14908 (home-page "https://cran.r-project.org/web/packages/scrime/")
14909 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
14911 "This package provides tools for the analysis of high-dimensional data
14912 developed/implemented at the group \"Statistical Complexity Reduction In
14913 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
14914 the functions can also be applied to other types of categorical data.")
14915 (license license:gpl2)))
14917 (define-public r-pbmcapply
14919 (name "r-pbmcapply")
14924 (uri (cran-uri "pbmcapply" version))
14927 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
14928 (build-system r-build-system)
14929 (home-page "https://github.com/kvnkuang/pbmcapply")
14930 (synopsis "Track the progress of apply procedures with a progress bar")
14932 "This light-weight package helps you track and visualize the progress of
14933 parallel versions of vectorized R functions of the @code{mc*apply} family.")
14934 (license license:expat)))
14936 (define-public r-blme
14943 (uri (cran-uri "blme" version))
14946 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
14947 (build-system r-build-system)
14948 (propagated-inputs `(("r-lme4" ,r-lme4)))
14949 (home-page "https://github.com/vdorie/blme")
14950 (synopsis "Bayesian linear mixed-effects models")
14952 "This package provides tools for maximum a posteriori estimation for
14953 linear and generalized linear mixed-effects models in a Bayesian setting. It
14954 extends the lme4 package.")
14955 (license license:gpl2+)))
14957 (define-public r-batchtools
14959 (name "r-batchtools")
14964 (uri (cran-uri "batchtools" version))
14967 "02mj21ypcjv5fs7ajf63p6bq0cyvihdl55hlpqx6kmsfjin1cr0v"))))
14968 (build-system r-build-system)
14970 `(("r-backports" ,r-backports)
14971 ("r-base64url" ,r-base64url)
14973 ("r-checkmate" ,r-checkmate)
14974 ("r-data-table" ,r-data-table)
14975 ("r-digest" ,r-digest)
14977 ("r-progress" ,r-progress)
14979 ("r-rappdirs" ,r-rappdirs)
14980 ("r-stringi" ,r-stringi)
14981 ("r-withr" ,r-withr)))
14982 (home-page "https://github.com/mllg/batchtools")
14983 (synopsis "Tools for computation on batch systems")
14985 "As a successor of the packages BatchJobs and BatchExperiments, this
14986 package provides a parallel implementation of the Map function for high
14987 performance computing systems managed by various schedulers. A multicore and
14988 socket mode allow the parallelization on a local machines, and multiple
14989 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
14990 the package provides an abstraction mechanism to define large-scale computer
14991 experiments in a well-organized and reproducible way.")
14992 (license license:lgpl3)))
14994 (define-public r-clue
15001 (uri (cran-uri "clue" version))
15004 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
15005 (build-system r-build-system)
15006 (propagated-inputs `(("r-cluster" ,r-cluster)))
15007 (home-page "https://cran.r-project.org/web/packages/clue/")
15008 (synopsis "Tools for analyzing cluster ensembles")
15009 (description "Cluster ensembles are collections of individual solutions to
15010 a given clustering problem which are useful or necessary to consider in a wide
15011 range of applications. This R package provides an extensible computational
15012 environment for creating and analyzing cluster ensembles, with basic data
15013 structures for representing partitions and hierarchies, and facilities for
15014 computing on them, including methods for measuring proximity and obtaining
15015 consensus and secondary clusterings.")
15016 (license license:gpl2)))
15018 (define-public r-sitmo
15025 (uri (cran-uri "sitmo" version))
15028 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
15029 (build-system r-build-system)
15030 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
15031 (home-page "https://github.com/coatless/sitmo/")
15032 (synopsis "Parallel pseudo random number generator header files")
15034 "This package provides two high quality and fast PPRNGs that may be used
15035 in an OpenMP parallel environment. In addition, there is a generator for one
15036 dimensional low-discrepancy sequence.")
15037 (license license:expat)))
15039 (define-public r-dqrng
15046 (uri (cran-uri "dqrng" version))
15049 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
15050 (build-system r-build-system)
15054 ("r-sitmo" ,r-sitmo)))
15055 (home-page "https://www.daqana.org/dqrng")
15056 (synopsis "Fast pseudo random number generators")
15058 "Several fast random number generators are provided as C++ header-only
15059 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
15060 Additionally, fast functions for generating random numbers according to a
15061 uniform, normal and exponential distribution are included. The latter two use
15062 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
15063 functions are exported to R and as a C++ interface and are enabled for use
15064 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
15065 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
15066 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
15067 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
15068 ;; whole is distributed under the terms of the AGPL 3.
15069 (license license:agpl3)))
15071 (define-public r-dalex
15078 (uri (cran-uri "DALEX" version))
15081 "1zviaf7530v8w996lbma0vplabrapgwldi7h70pr0439sxaqd421"))))
15082 (properties `((upstream-name . "DALEX")))
15083 (build-system r-build-system)
15084 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
15085 (home-page "https://pbiecek.github.io/DALEX/")
15086 (synopsis "Descriptive machine learning explanations")
15088 "Machine Learning models are widely used and have various applications in
15089 classification or regression. Models created with boosting, bagging, stacking
15090 or similar techniques are often used due to their high performance, but such
15091 black-box models usually lack interpretability. The DALEX package contains
15092 various explainers that help to understand the link between input variables
15093 and model output.")
15094 ;; Any version of the GPL
15095 (license license:gpl3+)))
15097 (define-public r-enrichr
15104 (uri (cran-uri "enrichR" version))
15107 "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
15108 (properties `((upstream-name . "enrichR")))
15109 (build-system r-build-system)
15111 `(("r-httr" ,r-httr)
15112 ("r-rjson" ,r-rjson)))
15113 (home-page "https://cran.r-project.org/web/packages/enrichR/")
15114 (synopsis "R Interface to Enrichr database for analyzing gene sets")
15116 "This package provides an R interface to all Enrichr databases, a
15117 web-based tool for analyzing gene sets and returns any enrichment of common
15118 annotated biological functions.")
15119 (license license:gpl2+)))
15121 (define-public r-plot3d
15128 (uri (cran-uri "plot3D" version))
15131 "0chn70fqwyca8lbnjnpbcj08ni0dfbax2gjmzhk2c4w72c04mzpn"))))
15132 (properties `((upstream-name . "plot3D")))
15133 (build-system r-build-system)
15134 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
15135 (home-page "https://cran.r-project.org/web/packages/plot3D")
15136 (synopsis "Plot multi-dimensional data")
15138 "This package provides functions for viewing 2D and 3D data, including
15139 perspective plots, slice plots, surface plots, scatter plots, etc. It
15140 includes data sets from oceanography.")
15141 (license license:gpl3+)))
15143 (define-public r-ggfortify
15145 (name "r-ggfortify")
15150 (uri (cran-uri "ggfortify" version))
15153 "191q2z7w0l4v7swjlxs2hjgbjngw2838688s7ygnj0kigsm310f3"))))
15154 (build-system r-build-system)
15156 `(("r-dplyr" ,r-dplyr)
15157 ("r-ggplot2" ,r-ggplot2)
15158 ("r-gridextra" ,r-gridextra)
15159 ("r-scales" ,r-scales)
15160 ("r-stringr" ,r-stringr)
15161 ("r-tibble" ,r-tibble)
15162 ("r-tidyr" ,r-tidyr)))
15163 (home-page "https://github.com/sinhrks/ggfortify")
15164 (synopsis "Data visualization tools for statistical analysis results")
15166 "This package provides unified plotting tools for statistics commonly
15167 used, such as GLM, time series, PCA families, clustering and survival
15168 analysis. The package offers a single plotting interface for these analysis
15169 results and plots in a unified style using the @code{ggplot2} package.")
15170 (license license:gpl2)))
15172 (define-public r-refmanager
15174 (name "r-refmanager")
15179 (uri (cran-uri "RefManageR" version))
15182 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
15183 (properties `((upstream-name . "RefManageR")))
15184 (build-system r-build-system)
15186 `(("r-bibtex" ,r-bibtex)
15188 ("r-jsonlite" ,r-jsonlite)
15189 ("r-lubridate" ,r-lubridate)
15191 ("r-stringr" ,r-stringr)
15192 ("r-xml2" ,r-xml2)))
15193 (home-page "https://github.com/ropensci/RefManageR/")
15194 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
15196 "This package provides tools for importing and working with bibliographic
15197 references. It greatly enhances the @code{bibentry} class by providing a
15198 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
15199 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
15200 by various formats for name lists (author by last names, translator by full
15201 names, etc.). Entries can be updated, combined, sorted, printed in a number
15202 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
15203 into R and converted to @code{BibEntry} objects.")
15204 ;; Any of these licenses may be picked.
15205 (license (list license:gpl2 license:gpl3 license:bsd-3))))
15207 (define-public r-citr
15214 (uri (cran-uri "citr" version))
15217 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
15218 (build-system r-build-system)
15220 `(("r-assertthat" ,r-assertthat)
15223 ("r-miniui" ,r-miniui)
15224 ("r-refmanager" ,r-refmanager)
15225 ("r-rstudioapi" ,r-rstudioapi)
15226 ("r-shiny" ,r-shiny)
15227 ("r-shinyjs" ,r-shinyjs)
15228 ("r-yaml" ,r-yaml)))
15229 (home-page "https://github.com/crsh/citr")
15230 (synopsis "RStudio add-in to insert Markdown citations")
15232 "This package provides functions and an RStudio add-in that search a
15233 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
15234 the current document.")
15235 (license license:expat)))
15237 (define-public r-xgboost
15240 (version "0.90.0.2")
15244 (uri (cran-uri "xgboost" version))
15247 "1gy9rzg43mjpfis893vf15drmbigfn0481zrzss9ajnmnk0q8194"))))
15248 (build-system r-build-system)
15250 `(("r-data-table" ,r-data-table)
15251 ("r-magrittr" ,r-magrittr)
15252 ("r-matrix" ,r-matrix)
15253 ("r-stringi" ,r-stringi)))
15254 (home-page "https://github.com/dmlc/xgboost")
15255 (synopsis "Extreme gradient boosting")
15257 "This package provides an R interface to Extreme Gradient Boosting, which
15258 is an efficient implementation of the gradient boosting framework from Chen
15259 and Guestrin (2016). The package includes efficient linear model solver and
15260 tree learning algorithms. The package can automatically do parallel
15261 computation on a single machine. It supports various objective functions,
15262 including regression, classification and ranking. The package is made to be
15263 extensible, so that users are also allowed to define their own objectives
15265 (license license:asl2.0)))
15267 (define-public r-umap
15270 (version "0.2.4.0")
15274 (uri (cran-uri "umap" version))
15277 "1dzbwq96k5vqr64wk6s26ks4311h570xg6gf0prr4vnn033pqnch"))))
15278 (build-system r-build-system)
15280 `(("r-openssl" ,r-openssl)
15282 ("r-reticulate" ,r-reticulate)
15283 ("r-rspectra" ,r-rspectra)))
15284 (home-page "https://github.com/tkonopka/umap")
15285 (synopsis "Uniform manifold approximation and projection")
15287 "Uniform manifold approximation and projection is a technique for
15288 dimension reduction. This package provides an interface to the UMAP algorithm
15289 in R, including a translation of the original algorithm into R.")
15290 (license license:expat)))
15292 (define-public r-uwot
15299 (uri (cran-uri "uwot" version))
15302 "0pz9wa89xq4d119q86lskrznf979m0r1db8iaprcz7kxbi6b8lrj"))))
15303 (build-system r-build-system)
15305 `(("r-dqrng" ,r-dqrng)
15307 ("r-irlba" ,r-irlba)
15308 ("r-matrix" ,r-matrix)
15310 ("r-rcppannoy" ,r-rcppannoy)
15311 ("r-rcppparallel" ,r-rcppparallel)
15312 ("r-rcppprogress" ,r-rcppprogress)
15313 ("r-rspectra" ,r-rspectra)))
15314 (home-page "https://github.com/jlmelville/uwot")
15315 (synopsis "Uniform manifold approximation and projection")
15317 "This package provides an implementation of the Uniform Manifold
15318 Approximation and Projection dimensionality reduction by McInnes et
15319 al. (2018). It also provides means to transform new data and to carry out
15320 supervised dimensionality reduction. An implementation of the related
15321 LargeVis method of Tang et al. (2016) is also provided.")
15322 (license license:gpl3)))
15324 (define-public r-kableextra
15326 (name "r-kableextra")
15331 (uri (cran-uri "kableExtra" version))
15334 "1nicvw06xsf3a1f5c10mih07b76m2v5s5h165vmz0qx6n1a3492i"))))
15335 (properties `((upstream-name . "kableExtra")))
15336 (build-system r-build-system)
15338 `(("r-digest" ,r-digest)
15340 ("r-htmltools" ,r-htmltools)
15341 ("r-knitr" ,r-knitr)
15342 ("r-magrittr" ,r-magrittr)
15343 ("r-readr" ,r-readr)
15344 ("r-rmarkdown" ,r-rmarkdown)
15345 ("r-rstudioapi" ,r-rstudioapi)
15346 ("r-rvest" ,r-rvest)
15347 ("r-scales" ,r-scales)
15348 ("r-stringr" ,r-stringr)
15349 ("r-viridislite" ,r-viridislite)
15350 ("r-webshot" ,r-webshot)
15351 ("r-xml2" ,r-xml2)))
15352 (home-page "https://haozhu233.github.io/kableExtra/")
15353 (synopsis "Construct complex tables with pipe syntax")
15355 "Build complex HTML or LaTeX tables using @code{kable()} from
15356 @code{knitr} and the piping syntax from @code{magrittr}. The function
15357 @code{kable()} is a light weight table generator coming from @code{knitr}.
15358 This package simplifies the way to manipulate the HTML or LaTeX codes
15359 generated by @code{kable()} and allows users to construct complex tables and
15360 customize styles using a readable syntax.")
15361 (license license:expat)))
15363 (define-public r-glasso
15370 (uri (cran-uri "glasso" version))
15372 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
15373 (build-system r-build-system)
15374 (native-inputs `(("gfortran" ,gfortran)))
15375 (home-page "http://www-stat.stanford.edu/~tibs/glasso")
15376 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
15378 "This is a package for estimation of a sparse inverse covariance matrix
15379 using a lasso (L1) penalty. Facilities are provided for estimates along a
15380 path of values for the regularization parameter.")
15381 (license license:gpl2)))
15383 (define-public r-rhpcblasctl
15385 (name "r-rhpcblasctl")
15386 (version "0.18-205")
15390 (uri (cran-uri "RhpcBLASctl" version))
15393 "1ls2286fvrp1g7p8v4l6axznychh3qndranfpzqz806cm9ml1cdp"))))
15394 (properties `((upstream-name . "RhpcBLASctl")))
15395 (build-system r-build-system)
15396 (home-page "http://prs.ism.ac.jp/~nakama/Rhpc/")
15397 (synopsis "Control the number of threads on BLAS")
15399 "This package allows you to control the number of threads the BLAS
15400 library uses. It is also possible to control the number of threads in
15402 (license license:agpl3+)))
15404 (define-public r-lda
15411 (uri (cran-uri "lda" version))
15414 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
15415 (build-system r-build-system)
15416 (home-page "https://cran.r-project.org/web/packages/lda/")
15417 (synopsis "Collapsed Gibbs sampling methods for topic models")
15419 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
15420 related models. This includes (but is not limited to) sLDA, corrLDA, and the
15421 mixed-membership stochastic blockmodel. Inference for all of these models is
15422 implemented via a fast collapsed Gibbs sampler written in C. Utility
15423 functions for reading/writing data typically used in topic models, as well as
15424 tools for examining posterior distributions are also included.")
15425 ;; Any version of the LGPL
15426 (license license:lgpl3+)))
15428 (define-public r-rann-l1
15435 (uri (cran-uri "RANN.L1" version))
15438 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
15439 (properties `((upstream-name . "RANN.L1")))
15440 (build-system r-build-system)
15441 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
15442 (synopsis "Fast nearest neighbour search using L1 metric")
15444 "This package provides tools to find the k nearest neighbours for every
15445 point in a given dataset in O(N log N) time using Arya and Mount's ANN
15446 library. There is support for approximate as well as exact searches, fixed
15447 radius searches and @code{bd} as well as @code{kd} trees. The distance is
15448 computed using the L1 (Manhattan, taxicab) metric.")
15449 (license license:gpl3+)))
15451 (define-public r-leiden
15458 (uri (cran-uri "leiden" version))
15461 "19gq27zin4gf4sh7h24gyq3f8jjir20n2l36a7pk1pbzcr4ixyhp"))))
15462 (properties `((upstream-name . "leiden")))
15463 (build-system r-build-system)
15465 `(("r-igraph" ,r-igraph)
15466 ("r-matrix" ,r-matrix)
15467 ("r-reticulate" ,r-reticulate)))
15468 (home-page "https://github.com/TomKellyGenetics/leiden")
15469 (synopsis "R implementation of Leiden clustering algorithm")
15471 "This package implements the Python @code{leidenalg} module to be called
15472 in R. It enables clustering using the Leiden algorithm for partitioning a
15473 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
15474 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
15475 (license license:gpl3)))
15477 (define-public r-patchwork
15478 ;; There has been no public release yet.
15479 (let ((commit "fd7958bae3e7a1e30237c751952e412a0a1d1242")
15482 (name "r-patchwork")
15483 (version (git-version "0.0.1" revision commit))
15487 (uri (git-reference
15488 (url "https://github.com/thomasp85/patchwork.git")
15490 (file-name (git-file-name name version))
15493 "00fq520xwy1ysg4k8x48x9b0yy9wyi8y8zj6dvxjg4bwx0yyp6s4"))))
15494 (build-system r-build-system)
15496 `(("r-ggplot2" ,r-ggplot2)
15497 ("r-gtable" ,r-gtable)))
15498 (home-page "https://github.com/thomasp85/patchwork")
15499 (synopsis "Compose ggplot2 plots")
15501 "The @code{ggplot2} package provides a strong API for sequentially
15502 building up a plot, but does not concern itself with composition of multiple
15503 plots. Patchwork is a package that expands the API to allow for arbitrarily
15504 complex composition of plots by providing mathmatical operators for combining
15506 (license license:expat))))
15508 (define-public r-liger
15515 (uri (git-reference
15516 (url "https://github.com/MacoskoLab/liger.git")
15517 (commit (string-append "v" version))))
15518 (file-name (git-file-name name version))
15521 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
15522 (modules '((guix build utils)))
15525 (delete-file "inst/java/ModularityOptimizer.jar")
15527 (build-system r-build-system)
15530 (modify-phases %standard-phases
15531 (add-after 'unpack 'build-java-part
15532 (lambda* (#:key inputs #:allow-other-keys)
15533 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
15534 (for-each (lambda (file) (invoke "javac" file))
15535 (find-files "." "\\.java$"))
15536 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
15537 (find-files "." "\\.class$"))
15540 `(("r-cowplot" ,r-cowplot)
15541 ("r-dosnow" ,r-dosnow)
15542 ("r-dplyr" ,r-dplyr)
15544 ("r-foreach" ,r-foreach)
15545 ("r-ggplot2" ,r-ggplot2)
15546 ("r-ggrepel" ,r-ggrepel)
15547 ("r-hmisc" ,r-hmisc)
15549 ("r-irlba" ,r-irlba)
15550 ("r-matrix" ,r-matrix)
15551 ("r-mclust" ,r-mclust)
15552 ("r-patchwork" ,r-patchwork)
15554 ("r-rann-l1" ,r-rann-l1)
15556 ("r-rcpparmadillo" ,r-rcpparmadillo)
15557 ("r-riverplot" ,r-riverplot)
15558 ("r-rtsne" ,r-rtsne)
15559 ("r-snow" ,r-snow)))
15561 `(("jdk" ,icedtea "jdk")
15562 ;; See https://github.com/MacoskoLab/liger/issues/96
15563 ;; The optimizer is released under the Expat license.
15567 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
15570 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
15572 ("r-knitr" ,r-knitr))) ; for vignettes
15573 (home-page "https://github.com/MacoskoLab/liger")
15574 (synopsis "Integrate and analyze multiple single-cell datasets")
15576 "LIGER is a package for integrating and analyzing multiple single-cell
15577 datasets, developed and maintained by the Macosko lab. It relies on
15578 integrative non-negative matrix factorization to identify shared and
15579 dataset-specific factors.")
15580 (license license:gpl3)))
15582 (define-public r-harmony
15583 ;; There are no tagged commits
15584 (let ((commit "4d1653870d4dd70fff1807c182882db1fbf9af5a")
15588 (version (git-version "1.0" revision commit))
15592 (uri (git-reference
15593 (url "https://github.com/immunogenomics/harmony")
15595 (file-name (git-file-name name version))
15598 "1gasdldr4aalr9h2q9kmm3y4i7azkgnhdn4bmvsszs7lg9xacw85"))))
15599 (build-system r-build-system)
15601 `(("r-cowplot" ,r-cowplot)
15602 ("r-dplyr" ,r-dplyr)
15603 ("r-ggplot2" ,r-ggplot2)
15604 ("r-irlba" ,r-irlba)
15605 ("r-matrix" ,r-matrix)
15607 ("r-rcpparmadillo" ,r-rcpparmadillo)
15608 ("r-rcppprogress" ,r-rcppprogress)
15609 ("r-rlang" ,r-rlang)
15610 ("r-tibble" ,r-tibble)
15611 ("r-tidyr" ,r-tidyr)))
15612 (home-page "https://github.com/immunogenomics/harmony")
15613 (synopsis "Integration of single cell sequencing data")
15615 "This package provides an implementation of the Harmony algorithm for
15616 single cell integration, described in Korsunsky et al
15617 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
15618 function and interfaces to external frameworks.")
15619 (license license:gpl3))))
15621 (define-public r-covr
15628 (uri (cran-uri "covr" version))
15630 (base32 "0p44kr6yz5sqza5zvq6divqglzkpv0if9pjpjmzhmdaaddjrqzg5"))))
15631 (properties `((upstream-name . "covr")))
15632 (build-system r-build-system)
15634 `(("r-crayon" ,r-crayon)
15635 ("r-digest" ,r-digest)
15637 ("r-jsonlite" ,r-jsonlite)
15639 ("r-withr" ,r-withr)
15640 ("r-yaml" ,r-yaml)))
15641 (home-page "https://github.com/r-lib/covr")
15642 (synopsis "Test coverage for R packages")
15644 "Thisp package enables you to track and report code coverage for your
15645 package and (optionally) upload the results to a coverage service. Code
15646 coverage is a measure of the amount of code being exercised by a set of tests.
15647 It is an indirect measure of test quality and completeness. This package is
15648 compatible with any testing methodology or framework and tracks coverage of
15649 both R code and compiled C/C++/FORTRAN code.")
15650 (license license:gpl3)))
15652 (define-public r-systemfonts
15654 (name "r-systemfonts")
15659 (uri (cran-uri "systemfonts" version))
15662 "0m0ljid683xcam2f14x7k2zv1yx4npac38a3gfv11vhxfbnpgp0z"))))
15663 (properties `((upstream-name . "systemfonts")))
15664 (build-system r-build-system)
15666 `(("fontconfig" ,fontconfig)
15667 ("freetype" ,freetype)
15670 `(("pkg-config" ,pkg-config)))
15671 (home-page "https://github.com/r-lib/systemfonts")
15672 (synopsis "System native font finding")
15674 "This package provides system native access to the font catalogue. As
15675 font handling varies between systems it is difficult to correctly locate
15676 installed fonts across different operating systems. The 'systemfonts' package
15677 provides bindings to the native libraries for finding font files that can then
15678 be used further by e.g. graphic devices.")
15679 (license license:expat)))
15681 (define-public r-graphlayouts
15683 (name "r-graphlayouts")
15688 (uri (cran-uri "graphlayouts" version))
15691 "03dizbhhdhnzbj2i5zvqgs617kwcv4h2pha4f16adic0fph1rxl3"))))
15692 (properties `((upstream-name . "graphlayouts")))
15693 (build-system r-build-system)
15695 `(("r-igraph" ,r-igraph)
15697 ("r-rcpparmadillo" ,r-rcpparmadillo)))
15698 (home-page "https://github.com/schochastics/graphlayouts")
15699 (synopsis "Additional layout algorithms for network visualizations")
15701 "This package provides several layout algorithms to visualize networks
15702 which are not part of the igraph library. Most are based on the concept of
15703 stress majorization by Gansner et al. (2004)
15704 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms allow to
15705 emphasize hidden group structures in networks or focus on specific nodes.")
15706 (license license:expat)))
15708 (define-public r-tidygraph
15710 (name "r-tidygraph")
15715 (uri (cran-uri "tidygraph" version))
15718 "1zpsarm74afbc7p5dlyb0whc09670qdcddw1ckb25cfc9hfh0hjn"))))
15719 (properties `((upstream-name . "tidygraph")))
15720 (build-system r-build-system)
15722 `(("r-dplyr" ,r-dplyr)
15723 ("r-igraph" ,r-igraph)
15724 ("r-magrittr" ,r-magrittr)
15725 ("r-pillar" ,r-pillar)
15728 ("r-rlang" ,r-rlang)
15729 ("r-tibble" ,r-tibble)
15730 ("r-tidyr" ,r-tidyr)))
15731 (home-page "https://github.com/thomasp85/tidygraph")
15732 (synopsis "Tidy API for graph manipulation")
15734 "This package provides a graph implementation that can be thought of as
15735 two tidy data frames describing node and edge data respectively. It provides
15736 an approach to manipulate these two virtual data frames using the API defined
15737 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
15738 common graph algorithms.")
15739 (license license:expat)))
15741 (define-public r-soupx
15742 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
15746 (version (git-version "0.3.1" revision commit))
15750 (uri (git-reference
15751 (url "https://github.com/constantAmateur/SoupX")
15753 (file-name (git-file-name name version))
15756 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
15757 (properties `((upstream-name . "SoupX")))
15758 (build-system r-build-system)
15760 `(("r-ggplot2" ,r-ggplot2)
15761 ("r-matrix" ,r-matrix)
15762 ("r-seurat" ,r-seurat)))
15763 (home-page "https://github.com/constantAmateur/SoupX")
15764 (synopsis "Single cell mRNA Soup eXterminator")
15766 "This package provides a package for quantifying, profiling and
15767 removing cell free mRNA contamination (the \"soup\") from droplet based single
15768 cell RNA-seq experiments.")
15769 (license license:gpl2))))
15771 (define-public r-assertr
15778 (uri (cran-uri "assertr" version))
15781 "0g4ii6vhp0155a29ljhs64a09x0nzy5ybvwwchhk4mkcgsvnvfkj"))))
15782 (build-system r-build-system)
15784 `(("r-dplyr" ,r-dplyr)
15786 ("r-rlang" ,r-rlang)))
15788 `(("r-knitr" ,r-knitr))) ; needed for vignette
15789 (home-page "https://github.com/ropensci/assertr")
15790 (synopsis "Assertive programming for R analysis pipelines")
15792 "This package provides functionality to assert conditions that have to be
15793 met so that errors in data used in analysis pipelines can fail quickly. It is
15794 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
15796 (license license:expat)))
15798 (define-public r-parameters
15800 (name "r-parameters")
15805 (uri (cran-uri "parameters" version))
15808 "0ifb9g1h8sn661q7jf9d8glk58gxdcym5ywbmx7phwn0y3is5wdv"))))
15809 (properties `((upstream-name . "parameters")))
15810 (build-system r-build-system)
15812 `(("r-bayestestr" ,r-bayestestr)
15813 ("r-insight" ,r-insight)))
15814 (home-page "https://cran.r-project.org/web/packages/parameters")
15815 (synopsis "Processing of model parameters")
15817 "This package provides utilities for processing the parameters of various
15818 statistical models. Beyond computing p values, CIs, and other indices for a
15819 wide variety of models, this package implements features like standardization
15820 or bootstrapping of parameters and models, feature reduction (feature
15821 extraction and variable selection) as well as conversion between indices of
15823 (license license:gpl3)))
15825 (define-public r-rgdal
15832 (uri (cran-uri "rgdal" version))
15834 (base32 "1jd691amf3ghznq5im15gvhl6v6k25klpl75m4ngrqf9xlxaa3as"))))
15835 (properties `((upstream-name . "rgdal")))
15836 (build-system r-build-system)
15844 `(("pkg-config" ,pkg-config)))
15845 (home-page "http://rgdal.r-forge.r-project.org")
15846 (synopsis "Bindings for the Geospatial Data Abstraction Library")
15848 "This package provides bindings to the Geospatial Data Abstraction
15849 Library (GDAL) and access to projection/transformation operations from the
15851 (license license:gpl2+)))
15853 (define-public r-insol
15860 (uri (cran-uri "insol" version))
15863 "14ikz05375pjn9hby7kwkhcnykjilbnkdy5i8lsl7c5qdbhmqcm5"))))
15864 (properties `((upstream-name . "insol")))
15865 (build-system r-build-system)
15867 `(("r-raster" ,r-raster)
15868 ("r-rgdal" ,r-rgdal)))
15870 `(("gfortran" ,gfortran)))
15871 (home-page "https://meteoexploration.com/R/insol/index.html")
15872 (synopsis "Tools for calculating solar radiation")
15874 "This package provides functions to compute insolation on tilted
15875 surfaces, computes atmospheric transmittance and related parameters such as:
15876 Earth radius vector, declination, sunset and sunrise, daylength, equation of
15877 time, vector in the direction of the sun, vector normal to surface, and some
15878 atmospheric physics.")
15879 (license license:gpl2+)))
15881 (define-public r-lifecycle
15883 (name "r-lifecycle")
15888 (uri (cran-uri "lifecycle" version))
15891 "11rk7hkw63rfrf4aqmb4xrb88kg95xh8hajpjvjfwjym2v02h74n"))))
15892 (properties `((upstream-name . "lifecycle")))
15893 (build-system r-build-system)
15895 `(("r-glue" ,r-glue)
15896 ("r-rlang" ,r-rlang)))
15897 (home-page "https://github.com/r-lib/lifecycle")
15898 (synopsis "Manage the life cycle of your package functions")
15900 "Manage the life cycle of your exported functions with shared
15901 conventions, documentation badges, and non-invasive deprecation warnings. The
15902 lifecycle package defines four development stages (experimental, maturing,
15903 stable, and questioning) and three deprecation stages (soft-deprecated,
15904 deprecated, and defunct). It makes it easy to insert badges corresponding to
15905 these stages in your documentation. Usage of deprecated functions are
15906 signalled with increasing levels of non-invasive verbosity.")
15907 (license license:gpl3)))
15909 (define-public r-assertable
15911 (name "r-assertable")
15916 (uri (cran-uri "assertable" version))
15919 "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
15920 (build-system r-build-system)
15922 `(("r-data-table" ,r-data-table)))
15923 (home-page "https://cran.r-project.org/web/packages/assertable/")
15924 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
15925 (description "This package provides simple, flexible assertions on
15926 data.frame or data.table objects with verbose output for vetting. While other
15927 assertion packages apply towards more general use-cases, @code{assertable} is
15928 tailored towards tabular data. It includes functions to check variable names
15929 and values, whether the dataset contains all combinations of a given set of
15930 unique identifiers, and whether it is a certain length. In addition,
15931 @code{assertable} includes utility functions to check the existence of target
15932 files and to efficiently import multiple tabular data files into one
15934 (license license:gpl3)))
15936 (define-public r-quadprog
15938 (name "r-quadprog")
15943 (uri (cran-uri "quadprog" version))
15945 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
15946 (build-system r-build-system)
15948 `(("gfortran" ,gfortran)))
15949 (home-page "https://cran.r-project.org/web/packages/quadprog")
15950 (synopsis "Functions to solve quadratic programming problems")
15952 "This package contains routines and documentation for solving quadratic
15953 programming problems.")
15954 (license license:gpl3+)))
15956 (define-public r-desolve
15963 (uri (cran-uri "deSolve" version))
15965 (base32 "0735y3p5glhqx69rzrc8qgmvs7p7w0p98qxmvylb6bgqp6kp0cbp"))))
15966 (properties `((upstream-name . "deSolve")))
15967 (build-system r-build-system)
15969 `(("gfortran" ,gfortran)))
15970 (home-page "https://desolve.r-forge.r-project.org/")
15971 (synopsis "Solvers for initial value problems of differential equations")
15972 (description "This package provides functions that solve initial value
15973 problems of a system of first-order @dfn{ordinary differential
15974 equations} (ODE), of @dfn{partial differential equations} (PDE), of
15975 @dfn{differential algebraic equations} (DAE), and of delay differential
15976 equations. The functions provide an interface to the FORTRAN functions
15977 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
15978 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
15979 C-implementation of solvers of the Runge-Kutta family with fixed or variable
15980 time steps. The package contains routines designed for solving ODEs resulting
15981 from 1-D, 2-D and 3-D partial differential equations that have been converted
15982 to ODEs by numerical differencing.")
15983 (license license:gpl2+)))
15985 (define-public r-pracma
15991 (uri (cran-uri "pracma" version))
15993 (base32 "0isd3s0i4mzmva8lkh0j76hwjy1w50q7d1n9lhxsnnkgalx3xs1g"))))
15994 (build-system r-build-system)
15995 (home-page "https://cran.r-project.org/web/packages/pracma/")
15996 (synopsis "Practical numerical math functions")
15997 (description "This package provides functions for numerical analysis and
15998 linear algebra, numerical optimization, differential equations, plus some
15999 special functions. It uses Matlab function names where appropriate to simplify
16001 (license license:gpl3+)))
16003 (define-public r-subplex
16010 (uri (cran-uri "subplex" version))
16013 "10cbgbx1bgsax5z7gz6716g360xpq4mvq19cf4qqrxv02mmwz57z"))))
16014 (build-system r-build-system)
16016 `(("gfortran" ,gfortran)))
16017 (home-page "https://cran.r-project.org/web/packages/subplex")
16018 (synopsis "Unconstrained optimization using the subplex algorithm")
16020 "This package implements the Subplex optimization algorithm.
16021 It solves unconstrained optimization problems using a simplex method on
16022 subspaces. The method is well suited for optimizing objective functions that
16023 are noisy or are discontinuous at the solution.")
16024 (license license:gpl3+)))
16026 (define-public r-txtplot
16033 (uri (cran-uri "txtplot" version))
16036 "1949ab1bzvysdb79g8x1gaknj0ih3d6g63pv9512h5m5l3a6c31h"))))
16037 (build-system r-build-system)
16038 (home-page "https://cran.r-project.org/web/packages/txtplot/")
16039 (synopsis "Text-based plotting")
16040 (description "This package provides functions to produce rudimentary ASCII
16041 graphics directly in the terminal window. This package provides a basic
16042 plotting function (and equivalents of curve, density, acf and barplot) as well
16043 as a boxplot function.")
16044 (license license:lgpl3+)))
16046 (define-public r-bio3d
16053 (uri (cran-uri "bio3d" version))
16056 "0ikpk1ppdp50m9kd289z616i382j9i7ji1zchyd4xqfyk8lnxf4s"))))
16057 (properties `((upstream-name . "bio3d")))
16058 (build-system r-build-system)
16059 (inputs `(("zlib" ,zlib)))
16060 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
16061 (home-page "http://thegrantlab.org/bio3d/")
16062 (synopsis "Biological structure analysis")
16064 "This package provides utilities to process, organize and explore protein
16065 structure, sequence and dynamics data. Features include the ability to read
16066 and write structure, sequence and dynamic trajectory data, perform sequence
16067 and structure database searches, data summaries, atom selection, alignment,
16068 superposition, rigid core identification, clustering, torsion analysis,
16069 distance matrix analysis, structure and sequence conservation analysis, normal
16070 mode analysis, principal component analysis of heterogeneous structure data,
16071 and correlation network analysis from normal mode and molecular dynamics data.
16072 In addition, various utility functions are provided to enable the statistical
16073 and graphical power of the R environment to work with biological sequence and
16075 (license license:gpl2+)))
16077 (define-public r-bios2cor
16079 (name "r-bios2cor")
16084 (uri (cran-uri "Bios2cor" version))
16087 "1rrz0vs6wbkwys3l5jv1rdnlhyb4r1q9pv7jlnmsx6c1b4f4vz5n"))))
16088 (properties `((upstream-name . "Bios2cor")))
16089 (build-system r-build-system)
16091 `(("r-bigmemory" ,r-bigmemory)
16092 ("r-bio3d" ,r-bio3d)
16093 ("r-circular" ,r-circular)
16094 ("r-igraph" ,r-igraph)))
16095 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
16096 (synopsis "From biological sequences and simulations to correlation analysis")
16098 "This package provides utilities for computation and analysis of
16099 correlation/covariation in multiple sequence alignments and in side chain
16100 motions during molecular dynamics simulations. Features include the
16101 computation of correlation/covariation scores using a variety of scoring
16102 functions between either sequence positions in alignments or side chain
16103 dihedral angles in molecular dynamics simulations and utilities to analyze the
16104 correlation/covariation matrix through a variety of tools including network
16105 representation and principal components analysis. In addition, several
16106 utility functions are based on the R graphical environment to provide friendly
16107 tools for help in data interpretation.")
16108 (license license:gpl2+)))
16110 ;; This package includes minified JavaScript files. When upgrading please
16111 ;; check that there are no new minified JavaScript files.
16112 (define-public r-networkd3
16114 (name "r-networkd3")
16119 (uri (cran-uri "networkD3" version))
16122 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
16125 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
16127 (properties `((upstream-name . "networkD3")))
16128 (build-system r-build-system)
16130 `(#:modules ((guix build utils)
16131 (guix build r-build-system)
16135 (modify-phases %standard-phases
16136 (add-after 'unpack 'process-javascript
16137 (lambda* (#:key inputs #:allow-other-keys)
16138 (with-directory-excursion "inst/htmlwidgets/lib/"
16142 `((,(assoc-ref inputs "d3.v4.js")
16143 "d3-4.5.0/d3.min.js"))))
16144 (lambda (sources targets)
16145 (for-each (lambda (source target)
16146 (format #t "Processing ~a --> ~a~%"
16148 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16149 (call-with-output-file target
16151 (dump-port minified port)))))
16152 sources targets))))
16155 `(("uglify-js" ,uglify-js)
16156 ;; NOTE: Make sure that this version of d3 is still valid when
16157 ;; upgrading the package.
16161 (uri "https://d3js.org/d3.v4.js")
16164 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
16166 `(("r-htmlwidgets" ,r-htmlwidgets)
16167 ("r-igraph" ,r-igraph)
16168 ("r-magrittr" ,r-magrittr)))
16169 (home-page "https://cran.r-project.org/package=networkD3")
16170 (synopsis "D3 JavaScript network graphs from R")
16172 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
16174 (license license:gpl3+)))
16176 (define-public r-aasea
16183 (uri (cran-uri "aaSEA" version))
16186 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
16187 (properties `((upstream-name . "aaSEA")))
16188 (build-system r-build-system)
16190 `(("r-bios2cor" ,r-bios2cor)
16192 ("r-hmisc" ,r-hmisc)
16193 ("r-magrittr" ,r-magrittr)
16194 ("r-networkd3" ,r-networkd3)
16195 ("r-plotly" ,r-plotly)
16196 ("r-seqinr" ,r-seqinr)
16197 ("r-shiny" ,r-shiny)
16198 ("r-shinydashboard" ,r-shinydashboard)))
16199 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
16200 (synopsis "Amino acid substitution effect analyzer")
16202 "Given a protein multiple sequence alignment, it is a daunting task to
16203 assess the effects of substitutions along sequence length. The aaSEA package
16204 is intended to help researchers to rapidly analyze property changes caused by
16205 single, multiple and correlated amino acid substitutions in proteins.")
16206 (license license:gpl3)))
16208 (define-public r-abacus
16215 (uri (cran-uri "ABACUS" version))
16218 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
16219 (properties `((upstream-name . "ABACUS")))
16220 (build-system r-build-system)
16222 `(("r-ggplot2" ,r-ggplot2)
16223 ("r-shiny" ,r-shiny)))
16224 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
16225 (synopsis "Apps-based activities for communicating and understanding statistics")
16227 "This package provides a set of Shiny apps for effective communication
16228 and understanding in statistics. The current version includes properties of
16229 normal distribution, properties of sampling distribution, one-sample z and t
16230 tests, two samples independent (unpaired) t test and analysis of variance.")
16231 (license license:gpl3)))
16233 (define-public r-abc-rap
16240 (uri (cran-uri "ABC.RAP" version))
16243 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
16244 (properties `((upstream-name . "ABC.RAP")))
16245 (build-system r-build-system)
16246 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
16247 (synopsis "Array-based CpG region analysis pipeline")
16249 "This package aims to identify candidate genes that are differentially
16250 methylated between cases and controls. It applies Student's t-test and delta
16251 beta analysis to identify candidate genes containing multiple CpG sites.")
16252 (license license:gpl3)))
16254 (define-public r-abcadm
16261 (uri (cran-uri "abcADM" version))
16264 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
16265 (properties `((upstream-name . "abcADM")))
16266 (build-system r-build-system)
16269 ("r-rcpp" ,r-rcpp)))
16270 (home-page "https://cran.r-project.org/web/packages/abcADM/")
16271 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
16273 "This package provides tools to estimate parameters of accumulated
16274 damage (load duration) models based on failure time data under a Bayesian
16275 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
16276 long-term reliability under stochastic load profiles.")
16277 (license license:gpl3)))
16279 (define-public r-rglpk
16286 (uri (cran-uri "Rglpk" version))
16289 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
16290 (properties `((upstream-name . "Rglpk")))
16291 (build-system r-build-system)
16293 `(("r-slam" ,r-slam)))
16296 (home-page "http://R-Forge.R-project.org/projects/rglp/")
16297 (synopsis "R interface to the GNU Linear Programming Kit")
16299 "This package provides an R interface to the GNU Linear Programming Kit,
16300 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
16301 integer linear programming} (MILP) and other related problems.")
16303 (license (list license:gpl2 license:gpl3))))
16305 (define-public r-abcdefba
16307 (name "r-abcdefba")
16312 (uri (cran-uri "abcdeFBA" version))
16315 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
16316 (properties `((upstream-name . "abcdeFBA")))
16317 (build-system r-build-system)
16319 `(("r-corrplot" ,r-corrplot)
16320 ("r-lattice" ,r-lattice)
16322 ("r-rglpk" ,r-rglpk)))
16323 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
16324 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
16326 "This package provides functions for Constraint Based Simulation using
16327 Flux Balance Analysis and informative analysis of the data generated during
16329 (license license:gpl2)))
16331 (define-public r-abcrlda
16338 (uri (cran-uri "abcrlda" version))
16341 "0j29ifsvmxfx2g6v4bpbb4s6miwfpf4vlkpbgj6f2q078s4clc85"))))
16342 (properties `((upstream-name . "abcrlda")))
16343 (build-system r-build-system)
16344 (home-page "https://ieeexplore.ieee.org/document/8720003/")
16345 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
16347 "This package offers methods to perform @dfn{asymptotically
16348 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
16349 cost-sensitive binary classification. The bias-correction is an estimate of
16350 the bias term added to regularized discriminant analysis that minimizes the
16352 (license license:gpl3)))
16354 (define-public r-abemus
16361 (uri (cran-uri "abemus" version))
16364 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
16365 (properties `((upstream-name . "abemus")))
16366 (build-system r-build-system)
16368 `(("r-data-table" ,r-data-table)))
16369 (home-page "https://cran.r-project.org/web/packages/abemus/")
16370 (synopsis "Adaptive base error model in ultra-deep sequencing data")
16372 "This package provides an implementation of @dfn{Adaptive Base Error
16373 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
16374 platform-specific genetic knowledge and empirical signal to readily detect and
16375 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
16376 cell free DNA} (cfDNA).")
16377 (license license:gpl3)))
16379 ;; This package includes minified JavaScript files. When upgrading please
16380 ;; check that there are no new minified JavaScript files.
16381 (define-public r-rintrojs
16383 (name "r-rintrojs")
16388 (uri (cran-uri "rintrojs" version))
16391 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
16392 (properties `((upstream-name . "rintrojs")))
16393 (build-system r-build-system)
16395 `(#:modules ((guix build utils)
16396 (guix build r-build-system)
16400 (modify-phases %standard-phases
16401 (add-after 'unpack 'process-javascript
16402 (lambda* (#:key inputs #:allow-other-keys)
16403 (with-directory-excursion "inst/javascript/introjs/"
16407 `((,(assoc-ref inputs "intro.js")
16409 (lambda (sources targets)
16410 (for-each (lambda (source target)
16411 (format #t "Processing ~a --> ~a~%"
16413 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16414 (call-with-output-file target
16416 (dump-port minified port)))))
16417 sources targets))))
16420 `(("uglify-js" ,uglify-js)
16424 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
16427 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
16429 `(("r-jsonlite" ,r-jsonlite)
16430 ("r-shiny" ,r-shiny)))
16431 (home-page "https://github.com/carlganz/rintrojs")
16432 (synopsis "Wrapper for the Intro.js library")
16434 "This package provides a wrapper for the @url{http://www.introjs.com,
16435 Intro.js} library. This package makes it easy to include step-by-step
16436 introductions, and clickable hints in a Shiny application. It supports both
16437 static introductions in the UI, and programmatic introductions from the
16439 (license license:agpl3+)))
16441 (define-public r-sysfonts
16443 (name "r-sysfonts")
16448 (uri (cran-uri "sysfonts" version))
16451 "0wng902plryf2d8fc7k7m3jx11acz51kb2d91cqbyhq7xpk06z43"))))
16452 (properties `((upstream-name . "sysfonts")))
16453 (build-system r-build-system)
16455 `(("freetype" ,freetype)
16459 `(("pkg-config" ,pkg-config)))
16460 (home-page "https://github.com/yixuan/sysfonts")
16461 (synopsis "Loading fonts into R")
16463 "This is a package to simplify loading of system fonts and Google Fonts
16464 into R, in order to support other packages.")
16465 (license license:gpl2)))
16467 (define-public r-showtextdb
16469 (name "r-showtextdb")
16474 (uri (cran-uri "showtextdb" version))
16477 "1qwwj9x2jvadvwn60h75k99c9xi7yhqjsgaakahz5paxgj583bsh"))))
16478 (properties `((upstream-name . "showtextdb")))
16479 (build-system r-build-system)
16481 `(("r-sysfonts" ,r-sysfonts)))
16482 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
16483 (synopsis "Font files for the 'showtext' package")
16485 "This package provides font files that can be used by the @code{showtext}
16487 (license license:asl2.0)))
16489 (define-public r-showtext
16491 (name "r-showtext")
16496 (uri (cran-uri "showtext" version))
16499 "1ihgqzfia36b0n9aa41p1w98wxxvs1lxh1zz0570hbfqmph1sk73"))))
16500 (properties `((upstream-name . "showtext")))
16501 (build-system r-build-system)
16503 `(("freetype" ,freetype)
16507 `(("r-showtextdb" ,r-showtextdb)
16508 ("r-sysfonts" ,r-sysfonts)))
16509 (native-inputs `(("pkg-config" ,pkg-config)))
16510 (home-page "https://github.com/yixuan/showtext")
16511 (synopsis "Using fonts more easily in R graphs")
16513 "This package aims to make it easy to use various types of
16514 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
16515 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
16516 will be converted into polygons or raster images, hence after the plot has
16517 been created, it no longer relies on the font files. No external software
16518 such as Ghostscript is needed to use this package.")
16519 (license license:asl2.0)))
16521 (define-public r-emojifont
16523 (name "r-emojifont")
16528 (uri (cran-uri "emojifont" version))
16531 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
16532 (properties `((upstream-name . "emojifont")))
16533 (build-system r-build-system)
16535 `(("r-ggplot2" ,r-ggplot2)
16536 ("r-proto" ,r-proto)
16537 ("r-showtext" ,r-showtext)
16538 ("r-sysfonts" ,r-sysfonts)))
16539 (home-page "https://guangchuangyu.github.io/emojifont")
16540 (synopsis "Emoji and Font Awesome in R graphics")
16542 "This package enables the use of emoji and the Font Awesome glyphs in
16543 both base and ggplot2 graphics.")
16544 (license license:artistic2.0)))
16546 (define-public r-abstractr
16548 (name "r-abstractr")
16553 (uri (cran-uri "abstractr" version))
16556 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
16557 (properties `((upstream-name . "abstractr")))
16558 (build-system r-build-system)
16560 `(("r-colourpicker" ,r-colourpicker)
16561 ("r-emojifont" ,r-emojifont)
16562 ("r-ggplot2" ,r-ggplot2)
16563 ("r-gridextra" ,r-gridextra)
16564 ("r-rintrojs" ,r-rintrojs)
16565 ("r-shiny" ,r-shiny)
16566 ("r-shinythemes" ,r-shinythemes)))
16567 (home-page "https://matt-kumar.shinyapps.io/portfolio")
16568 (synopsis "R-Shiny application for creating visual abstracts")
16570 "This package provides an R Shiny application to create visual abstracts
16571 for original research. A variety of user defined options and formatting are
16573 (license license:gpl3)))
16575 (define-public r-abtest
16582 (uri (cran-uri "abtest" version))
16585 "1ky3cf827kj24bhcpk00v5zl5jdkii1gca0x81ay1cjkzfispgws"))))
16586 (properties `((upstream-name . "abtest")))
16587 (build-system r-build-system)
16589 `(("r-matrix" ,r-matrix)
16590 ("r-mvtnorm" ,r-mvtnorm)
16591 ("r-plotrix" ,r-plotrix)
16592 ("r-rcolorbrewer" ,r-rcolorbrewer)
16595 ("r-truncnorm" ,r-truncnorm)
16596 ("r-vgam" ,r-vgam)))
16597 (home-page "https://cran.r-project.org/web/packages/abtest/")
16598 (synopsis "Bayesian A/B testing")
16600 "This package provides functions for Bayesian A/B testing including prior
16601 elicitation options based on Kass and Vaidyanathan (1992)
16602 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
16603 (license license:gpl2+)))
16605 (define-public r-accept
16612 (uri (cran-uri "accept" version))
16615 "1r4mhy9g4wjcjgdd0gwdarmr09292il3vdkmx0hz7vh9mffyr9kx"))))
16616 (properties `((upstream-name . "accept")))
16617 (build-system r-build-system)
16619 `(("r-dplyr" ,r-dplyr)
16620 ("r-extrafont" ,r-extrafont)
16622 ("r-plotly" ,r-plotly)
16623 ("r-stringr" ,r-stringr)
16624 ("r-viridis" ,r-viridis)))
16625 (home-page "https://cran.r-project.org/web/packages/accept/")
16626 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
16628 "This package allows clinicians to predict the rate and severity of
16629 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
16630 Disease} (COPD) patients, based on the clinical prediction model published in
16631 Adibi et al. (2019) @url{doi:10.1101/651901}.")
16632 (license license:gpl3)))