1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
4 ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
5 ;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
6 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
7 ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
8 ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
9 ;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net>
10 ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
11 ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
12 ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
13 ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
14 ;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com>
15 ;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
16 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
17 ;;; Copyright © 2018 Eric Brown <brown@fastmail.com>
18 ;;; Copyright © 2018, 2019 Brett Gilio <brettg@gnu.org>
19 ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
20 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
22 ;;; This file is part of GNU Guix.
24 ;;; GNU Guix is free software; you can redistribute it and/or modify it
25 ;;; under the terms of the GNU General Public License as published by
26 ;;; the Free Software Foundation; either version 3 of the License, or (at
27 ;;; your option) any later version.
29 ;;; GNU Guix is distributed in the hope that it will be useful, but
30 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
31 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
32 ;;; GNU General Public License for more details.
34 ;;; You should have received a copy of the GNU General Public License
35 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
37 (define-module (gnu packages cran)
38 #:use-module ((guix licenses) #:prefix license:)
39 #:use-module (guix packages)
40 #:use-module (guix download)
41 #:use-module (guix git-download)
42 #:use-module (guix utils)
43 #:use-module (guix build-system r)
44 #:use-module (gnu packages algebra)
45 #:use-module (gnu packages base)
46 #:use-module (gnu packages bioinformatics)
47 #:use-module (gnu packages c)
48 #:use-module (gnu packages compression)
49 #:use-module (gnu packages curl)
50 #:use-module (gnu packages databases)
51 #:use-module (gnu packages fontutils)
52 #:use-module (gnu packages gcc)
53 #:use-module (gnu packages geo)
54 #:use-module (gnu packages ghostscript)
55 #:use-module (gnu packages gl)
56 #:use-module (gnu packages gnome)
57 #:use-module (gnu packages graph)
58 #:use-module (gnu packages gtk)
59 #:use-module (gnu packages haskell-xyz)
60 #:use-module (gnu packages icu4c)
61 #:use-module (gnu packages image)
62 #:use-module (gnu packages imagemagick)
63 #:use-module (gnu packages java)
64 #:use-module (gnu packages javascript)
65 #:use-module (gnu packages lisp-xyz)
66 #:use-module (gnu packages machine-learning)
67 #:use-module (gnu packages maths)
68 #:use-module (gnu packages mpi)
69 #:use-module (gnu packages multiprecision)
70 #:use-module (gnu packages networking)
71 #:use-module (gnu packages pcre)
72 #:use-module (gnu packages perl)
73 #:use-module (gnu packages pkg-config)
74 #:use-module (gnu packages python)
75 #:use-module (gnu packages python-xyz)
76 #:use-module (gnu packages statistics)
77 #:use-module (gnu packages tcl)
78 #:use-module (gnu packages tls)
79 #:use-module (gnu packages web)
80 #:use-module (gnu packages xorg))
82 (define-public r-clipr
89 (uri (cran-uri "clipr" version))
92 "1qn2p13d0c1bpqss6mv9hk60980rzhznfqpyaf5x0fy65svy9903"))))
93 (build-system r-build-system)
94 (home-page "https://github.com/mdlincoln/clipr")
95 (synopsis "Read and write from the system clipboard")
97 "This package provides simple utility functions to read from and write to
98 the system clipboards.")
99 (license license:gpl3)))
101 (define-public r-scales
108 (uri (cran-uri "scales" version))
110 (base32 "00rdbfj5mwc3kr8pskidn3n2zkp4ms6cx36xazz54pxw3pysdr0y"))))
111 (build-system r-build-system)
113 `(("r-farver" ,r-farver)
114 ("r-labeling" ,r-labeling)
115 ("r-lifecycle" ,r-lifecycle)
116 ("r-munsell" ,r-munsell)
117 ("r-rcolorbrewer" ,r-rcolorbrewer)
119 ("r-viridislite" ,r-viridislite)))
120 (home-page "https://github.com/hadley/scales")
121 (synopsis "Scale functions for visualization")
123 "This package provides graphical scales that map data to aesthetics, and
124 provides methods for automatically determining breaks and labels for axes and
126 (license license:expat)))
128 (define-public r-pheatmap
135 (uri (cran-uri "pheatmap" version))
138 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
139 (build-system r-build-system)
141 `(("r-gtable" ,r-gtable)
142 ("r-rcolorbrewer" ,r-rcolorbrewer)
143 ("r-scales" ,r-scales)))
144 (home-page "https://cran.r-project.org/web/packages/pheatmap")
145 (synopsis "Pretty heatmaps")
147 "This package provides an implementation of heatmaps that offers more
148 control over dimensions and appearance.")
149 (license license:gpl2+)))
151 (define-public r-ellipsis
158 (uri (cran-uri "ellipsis" version))
161 "01z9gq311nzwv3a0sa49jhm5ylqd59srip4vjkrf23hzgb5i9y0b"))))
162 (build-system r-build-system)
164 `(("r-rlang" ,r-rlang)))
165 (home-page "https://github.com/hadley/ellipsis")
166 (synopsis "Tools for working with additional arguments")
168 "In S3 generics, it's useful to take @code{...} so that methods can have
169 additional arguments. But this flexibility comes at a cost: misspelled
170 arguments will be silently ignored. The @code{ellipsis} package is an
171 experiment that allows a generic to warn if any arguments passed in @code{...}
173 (license license:gpl3)))
182 (uri (cran-uri "grr" version))
185 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
186 (build-system r-build-system)
187 (home-page "https://cran.r-project.org/web/packages/grr")
188 (synopsis "Alternative implementations of base R functions")
190 "This package provides alternative implementations of some base R
191 functions, including @code{sort}, @code{order}, and @code{match}. The
192 functions are simplified but can be faster or have other advantages.")
193 (license license:gpl3)))
195 (define-public r-matrix-utils
197 (name "r-matrix-utils")
202 (uri (cran-uri "Matrix.utils" version))
205 "0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb"))))
206 (properties `((upstream-name . "Matrix.utils")))
207 (build-system r-build-system)
210 ("r-matrix" ,r-matrix)))
211 (home-page "https://github.com/cvarrichio/Matrix.utils")
213 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
215 "This package implements data manipulation methods such as @code{cast},
216 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
218 (license license:gpl3)))
227 (uri (cran-uri "sys" version))
230 "14wvy46i2iz9jn7lj3cvifmps932s3395wq681hniva0f8m7q8d6"))))
231 (build-system r-build-system)
232 (home-page "https://github.com/jeroen/sys")
233 (synopsis "Powerful and reliable tools for running system commands in R")
235 "This package provides drop-in replacements for the base @code{system2()}
236 function with fine control and consistent behavior across platforms. It
237 supports clean interruption, timeout, background tasks, and streaming STDIN /
238 STDOUT / STDERR over binary or text connections. The package also provides
239 functions for evaluating expressions inside a temporary fork. Such
240 evaluations have no side effects on the main R process, and support reliable
241 interrupts and timeouts. This provides the basis for a sandboxing
243 (license license:expat)))
245 (define-public r-askpass
252 (uri (cran-uri "askpass" version))
255 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
256 (build-system r-build-system)
257 (propagated-inputs `(("r-sys" ,r-sys)))
258 (home-page "https://github.com/jeroen/askpass")
259 (synopsis "Safe password entry for R")
261 "This package provides cross-platform utilities for prompting the user
262 for credentials or a passphrase, for example to authenticate with a server or
263 read a protected key.")
264 (license license:expat)))
266 (define-public r-vegan
273 (uri (cran-uri "vegan" version))
276 "0g60rgn1i7wqf9pf5m1yki1m45gcp7i5hmjic0ci0f6vng70mh5k"))))
277 (build-system r-build-system)
279 `(("gfortran" ,gfortran)))
281 `(("r-cluster" ,r-cluster)
282 ("r-knitr" ,r-knitr) ; needed for vignettes
283 ("r-lattice" ,r-lattice)
286 ("r-permute" ,r-permute)))
287 (home-page "https://cran.r-project.org/web/packages/vegan")
288 (synopsis "Functions for community ecology")
290 "The vegan package provides tools for descriptive community ecology. It
291 has most basic functions of diversity analysis, community ordination and
292 dissimilarity analysis. Most of its multivariate tools can be used for other
293 data types as well.")
294 (license license:gpl2+)))
296 (define-public r-tidyverse
303 (uri (cran-uri "tidyverse" version))
306 "02gyys08qv2v4cl2d66gml4d31ipxay0iyfwwksvxyclx60wp2kd"))))
307 (build-system r-build-system)
309 `(("r-broom" ,r-broom)
311 ("r-crayon" ,r-crayon)
312 ("r-dbplyr" ,r-dbplyr)
314 ("r-forcats" ,r-forcats)
315 ("r-ggplot2" ,r-ggplot2)
319 ("r-jsonlite" ,r-jsonlite)
320 ("r-lubridate" ,r-lubridate)
321 ("r-magrittr" ,r-magrittr)
322 ("r-modelr" ,r-modelr)
323 ("r-pillar" ,r-pillar)
326 ("r-readxl" ,r-readxl)
327 ("r-reprex" ,r-reprex)
329 ("r-rstudioapi" ,r-rstudioapi)
331 ("r-stringr" ,r-stringr)
332 ("r-tibble" ,r-tibble)
335 (home-page "https://tidyverse.tidyverse.org")
336 (synopsis "Install and load packages from the \"Tidyverse\"")
338 "The @code{tidyverse} is a set of packages that work in harmony because
339 they share common data representations and API design. This package is
340 designed to make it easy to install and load multiple tidyverse packages in a
342 (license license:gpl3)))
344 (define-public r-rvest
351 (uri (cran-uri "rvest" version))
353 (base32 "0r0a5jic09xw5pk0x42pr99r3zab5m9s4x85ymx1sl769jz42zqf"))))
354 (build-system r-build-system)
357 ("r-magrittr" ,r-magrittr)
358 ("r-selectr" ,r-selectr)
360 (home-page "https://github.com/hadley/rvest")
361 (synopsis "Simple web scraping for R")
363 "@code{r-rvest} helps you scrape information from web pages. It is
364 designed to work with @code{magrittr} to make it easy to express common web
365 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
366 (license license:gpl3)))
368 (define-public r-selectr
375 (uri (cran-uri "selectr" version))
377 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
378 (build-system r-build-system)
380 `(("r-stringr" ,r-stringr)
382 (home-page "https://sjp.co.nz/projects/selectr/")
383 (synopsis "Translate CSS selectors to XPath expressions")
385 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
386 expression. This allows you to use CSS selectors when working with the XML
387 package as it can only evaluate XPath expressions. Also provided are
388 convenience functions useful for using CSS selectors on XML nodes. This
389 package is a port of the Python package @code{cssselect}.")
390 (license license:bsd-3)))
392 (define-public r-reprex
399 (uri (cran-uri "reprex" version))
402 "0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10"))))
403 (build-system r-build-system)
405 `(("r-callr" ,r-callr)
409 ("r-rmarkdown" ,r-rmarkdown)
410 ("r-whisker" ,r-whisker)
411 ("r-withr" ,r-withr)))
412 (home-page "https://github.com/tidyverse/reprex")
413 (synopsis "Prepare reproducible R code examples for sharing")
415 "This package provides a convenience wrapper that uses the
416 @code{rmarkdown} package to render small snippets of code to target formats
417 that include both code and output. The goal is to encourage the sharing of
418 small, reproducible, and runnable examples on code-oriented websites or email.
419 @code{reprex} also extracts clean, runnable R code from various common formats,
420 such as copy/paste from an R session.")
421 (license license:expat)))
423 (define-public r-callr
430 (uri (cran-uri "callr" version))
433 "0bdlp0labwyfl36jqslj2g7zmw7zwr58v9gam435kiblhjimb8fc"))))
434 (build-system r-build-system)
437 ("r-processx" ,r-processx)))
438 (home-page "https://github.com/r-lib/callr#readme")
439 (synopsis "Call R from R")
441 "It is sometimes useful to perform a computation in a separate R process,
442 without affecting the current R process at all. This package does exactly
444 (license license:expat)))
446 (define-public r-readxl
453 (uri (cran-uri "readxl" version))
456 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
457 (build-system r-build-system)
459 `(("r-cellranger" ,r-cellranger)
460 ("r-progress" ,r-progress)
462 ("r-tibble" ,r-tibble)))
463 (home-page "https://readxl.tidyverse.org")
464 (synopsis "Read Excel files")
466 "This package lets you import Excel files into R. It supports
467 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
468 the embedded @code{RapidXML} C++ library.")
469 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
470 ;; 'rapidxml' which is Boost.
471 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
473 (define-public r-modelr
480 (uri (cran-uri "modelr" version))
483 "1x2m34m4qirb401krmgc5wg3g7ndbcglfab2l0655rmky3fz7rfp"))))
484 (build-system r-build-system)
486 `(("r-broom" ,r-broom)
488 ("r-magrittr" ,r-magrittr)
491 ("r-tibble" ,r-tibble)
493 ("r-tidyselect" ,r-tidyselect)))
494 (home-page "https://github.com/tidyverse/modelr")
495 (synopsis "Helper functions for modelling in pipelines")
497 "Functions for modelling that help you seamlessly integrate modelling
498 into a pipeline of data manipulation and visualisation.")
499 (license license:gpl3)))
501 (define-public r-httpuv
507 (uri (cran-uri "httpuv" version))
510 "13ax0hs2lc39ilznh1zarwqdzahcbhb8adilrfik3xg0fkljpcwk"))))
511 (build-system r-build-system)
515 ("r-promises" ,r-promises)
518 (home-page "https://github.com/rstudio/httpuv")
519 (synopsis "HTTP and WebSocket server library for R")
521 "The httpuv package provides low-level socket and protocol support for
522 handling HTTP and WebSocket requests directly from within R. It is primarily
523 intended as a building block for other packages, rather than making it
524 particularly easy to create complete web applications using httpuv alone.")
525 ;; This package includes third-party code that was originally released
526 ;; under various non-copyleft licenses. Full licensing information can be
527 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
528 (license license:gpl3+)))
530 (define-public r-jsonlite
536 (uri (cran-uri "jsonlite" version))
539 "0xrki07wc17bkmhz0h7jay784j1sls2i9bf1mfpj6yl59791v4kl"))))
540 (build-system r-build-system)
541 (home-page "https://arxiv.org/abs/1403.2805")
542 (synopsis "Robust, high performance JSON parser and generator for R")
544 "The jsonlite package provides a fast JSON parser and generator optimized
545 for statistical data and the web. It offers flexible, robust, high
546 performance tools for working with JSON in R and is particularly powerful for
547 building pipelines and interacting with a web API. In addition to converting
548 JSON data from/to R objects, jsonlite contains functions to stream, validate,
549 and prettify JSON data. The unit tests included with the package verify that
550 all edge cases are encoded and decoded consistently for use with dynamic data
551 in systems and applications.")
552 (license license:expat)))
554 (define-public r-servr
560 (uri (cran-uri "servr" version))
563 "106skz04iq4dkblr17idxsxfcfqic6rcaz8mahydkwjjppnhp5fc"))))
564 (build-system r-build-system)
566 `(("r-httpuv" ,r-httpuv)
567 ("r-jsonlite" ,r-jsonlite)
570 (home-page "https://github.com/yihui/servr")
571 (synopsis "Simple HTTP server to serve static files or dynamic documents")
573 "Servr provides an HTTP server in R to serve static files, or dynamic
574 documents that can be converted to HTML files (e.g., R Markdown) under a given
576 (license license:expat)))
578 (define-public r-htmltools
584 (uri (cran-uri "htmltools" version))
587 "06l17d8jkf438yk2mchpsp4j90bynnapz3nabh5vkcc324p5a62v"))))
588 (build-system r-build-system)
590 `(("r-digest" ,r-digest)
592 ("r-rlang" ,r-rlang)))
593 (home-page "https://cran.r-project.org/web/packages/htmltools")
594 (synopsis "R tools for HTML")
596 "This package provides tools for HTML generation and output in R.")
597 (license license:expat)))
599 (define-public r-htmlwidgets
601 (name "r-htmlwidgets")
605 (uri (cran-uri "htmlwidgets" version))
608 "10fp306l1nybkah6jrlrqwwdb6zvklbddp8i3w9v9naj8la5jbnl"))))
609 (build-system r-build-system)
611 `(("r-htmltools" ,r-htmltools)
612 ("r-jsonlite" ,r-jsonlite)
614 (home-page "https://github.com/ramnathv/htmlwidgets")
615 (synopsis "HTML Widgets for R")
617 "HTML widgets is a framework for creating HTML widgets that render in
618 various contexts including the R console, R Markdown documents, and Shiny web
620 (license license:expat)))
622 (define-public r-htmltable
629 (uri (cran-uri "htmlTable" version))
632 "0g9r156k9yl1f092hfw3b9wjx11akf0shbi3x0d0mvpnflvc8nfl"))))
633 (properties `((upstream-name . "htmlTable")))
634 (build-system r-build-system)
636 `(("r-checkmate" ,r-checkmate)
637 ("r-htmltools" ,r-htmltools)
638 ("r-htmlwidgets" ,r-htmlwidgets)
640 ("r-magrittr" ,r-magrittr)
641 ("r-rstudioapi" ,r-rstudioapi)
642 ("r-stringr" ,r-stringr)))
643 (home-page "http://gforge.se/packages/")
644 (synopsis "Advanced tables for Markdown/HTML")
646 "This package provides functions to build tables with advanced layout
647 elements such as row spanners, column spanners, table spanners, zebra
648 striping, and more. While allowing advanced layout, the underlying
649 CSS-structure is simple in order to maximize compatibility with word
650 processors such as LibreOffice. The package also contains a few text
651 formatting functions that help outputting text compatible with HTML or
653 (license license:gpl3+)))
655 (define-public r-curl
661 (uri (cran-uri "curl" version))
664 "1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl"))))
665 (build-system r-build-system)
668 (modify-phases %standard-phases
669 ;; The environment variable CURL_CA_BUNDLE is only respected when
670 ;; running Windows, so we disable the platform checks.
671 ;; This can be removed once the libcurl has been patched.
672 (add-after 'unpack 'allow-CURL_CA_BUNDLE
674 (substitute* "R/onload.R"
675 (("if \\(!grepl\\(\"mingw\".*")
677 (substitute* "src/handle.c"
678 (("#ifdef _WIN32") "#if 1"))
684 `(("pkg-config" ,pkg-config)))
685 (home-page "https://github.com/jeroenooms/curl")
686 (synopsis "HTTP client for R")
688 "The @code{curl()} and @code{curl_download()} functions provide highly
689 configurable drop-in replacements for base @code{url()} and
690 @code{download.file()} with better performance, support for encryption, gzip
691 compression, authentication, and other @code{libcurl} goodies. The core of
692 the package implements a framework for performing fully customized requests
693 where data can be processed either in memory, on disk, or streaming via the
694 callback or connection interfaces.")
695 (license license:expat)))
697 (define-public r-hwriter
704 (uri (cran-uri "hwriter" version))
707 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
708 (build-system r-build-system)
709 (home-page "https://cran.r-project.org/web/packages/hwriter")
710 (synopsis "Output R objects in HTML format")
712 "This package provides easy-to-use and versatile functions to output R
713 objects in HTML format.")
714 (license license:lgpl2.1+)))
716 (define-public r-rjson
723 (uri (cran-uri "rjson" version))
726 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
727 (build-system r-build-system)
728 (home-page "https://cran.r-project.org/web/packages/rjson")
729 (synopsis "JSON library for R")
731 "This package provides functions to convert R objects into JSON objects
733 (license license:gpl2+)))
735 (define-public r-fastmap
742 (uri (cran-uri "fastmap" version))
745 "1v7sp56xiha0bh78g3w92k52p9vkp7ryzpw0z66nyddxzrfv0y27"))))
746 (properties `((upstream-name . "fastmap")))
747 (build-system r-build-system)
748 (home-page "https://r-lib.github.io/fastmap/")
749 (synopsis "Fast implementation of a key-value store")
751 "This package provides a fast implementation of a key-value store.
752 Environments are commonly used as key-value stores, but every time a new key
753 is used, it is added to R's global symbol table, causing a small amount of
754 memory leakage. This can be problematic in cases where many different keys
755 are used. Fastmap avoids this memory leak issue by implementing the map using
756 data structures in C++.")
757 (license license:expat)))
759 (define-public r-shiny
767 (url "https://github.com/rstudio/shiny.git")
768 (commit (string-append "v" version))))
769 (file-name (git-file-name name version))
772 "17ac48g414h9dhi0k4wrah4gyik0q5r0xw3kc01c02qfjwimqsx7"))))
773 (build-system r-build-system)
775 `(#:modules ((guix build r-build-system)
776 (guix build minify-build-system)
779 #:imported-modules (,@%r-build-system-modules
780 (guix build minify-build-system))
782 (modify-phases (@ (guix build r-build-system) %standard-phases)
783 (add-after 'unpack 'replace-bundled-minified-JavaScript
784 (lambda* (#:key inputs #:allow-other-keys)
785 (let ((replace-file (lambda (old new)
786 (format #t "replacing ~a with ~a\n" old new)
789 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
790 ;; contain just data. They are not minified code, so we don't
792 (with-directory-excursion "inst/www/shared"
793 (replace-file "bootstrap/shim/respond.min.js"
794 (string-append (assoc-ref inputs "js-respond")
795 "/share/javascript/respond.min.js"))
796 (replace-file "bootstrap/shim/html5shiv.min.js"
797 (string-append (assoc-ref inputs "js-html5shiv")
798 "/share/javascript/html5shiv.min.js"))
799 (replace-file "json2-min.js"
800 (string-append (assoc-ref inputs "js-json2")
801 "/share/javascript/json2-min.js"))
802 (replace-file "strftime/strftime-min.js"
803 (string-append (assoc-ref inputs "js-strftime")
804 "/share/javascript/strftime.min.js"))
805 (replace-file "highlight/highlight.pack.js"
806 (string-append (assoc-ref inputs "js-highlight")
807 "/share/javascript/highlight.min.js"))
808 (replace-file "datatables/js/jquery.dataTables.min.js"
809 (string-append (assoc-ref inputs "js-datatables")
810 "/share/javascript/jquery.dataTables.min.js"))
811 (replace-file "selectize/js/selectize.min.js"
812 (string-append (assoc-ref inputs "js-selectize")
813 "/share/javascript/selectize.min.js"))
814 (replace-file "selectize/js/es5-shim.min.js"
815 (string-append (assoc-ref inputs "js-es5-shim")
816 "/share/javascript/es5-shim.min.js"))
817 (for-each (match-lambda
820 (minify source #:target target)))
821 '(("jqueryui/jquery-ui.js" .
822 "jqueryui/jquery-ui.min.js")
823 ("datepicker/js/bootstrap-datepicker.js" .
824 "datepicker/js/bootstrap-datepicker.min.js")
825 ("ionrangeslider/js/ion.rangeSlider.js" .
826 "ionrangeslider/js/ion.rangeSlider.min.js")
827 ("bootstrap/js/bootstrap.js" .
828 "bootstrap/js/bootstrap.min.js")
833 ("legacy/jquery.js" .
834 "legacy/jquery.min.js")
835 ("showdown/src/showdown.js" .
836 "showdown/compressed/showdown.js")))))
839 `(("r-crayon" ,r-crayon)
840 ("r-fastmap" ,r-fastmap)
841 ("r-httpuv" ,r-httpuv)
843 ("r-jsonlite" ,r-jsonlite)
844 ("r-xtable" ,r-xtable)
845 ("r-digest" ,r-digest)
846 ("r-htmltools" ,r-htmltools)
848 ("r-sourcetools" ,r-sourcetools)))
850 `(("js-datatables" ,js-datatables)
851 ("js-html5shiv" ,js-html5shiv)
852 ("js-json2" ,js-json2)
853 ("js-respond" ,js-respond)
854 ("js-selectize" ,js-selectize)
855 ("js-strftime" ,js-strftime)
856 ("js-highlight" ,js-highlight)
857 ("js-es5-shim" ,js-es5-shim)))
859 `(("uglify-js" ,uglify-js)))
860 (home-page "http://shiny.rstudio.com")
861 (synopsis "Easy interactive web applications with R")
863 "Makes it incredibly easy to build interactive web applications
864 with R. Automatic \"reactive\" binding between inputs and outputs and
865 extensive prebuilt widgets make it possible to build beautiful,
866 responsive, and powerful applications with minimal effort.")
867 (license license:artistic2.0)))
869 ;; This package includes minified JavaScript files. When upgrading please
870 ;; check that there are no new minified JavaScript files.
871 (define-public r-shinytree
878 (uri (cran-uri "shinyTree" version))
881 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
882 (modules '((guix build utils)))
885 ;; Delete minified JavaScript
886 (for-each delete-file
887 '("inst/www/jsTree-3.3.7/libs/require.js"
888 "inst/www/jsTree-3.3.7/libs/jquery.js"
889 "inst/www/jsTree-3.3.7/jstree.min.js"))
891 (properties `((upstream-name . "shinyTree")))
892 (build-system r-build-system)
894 `(#:modules ((guix build utils)
895 (guix build r-build-system)
899 (modify-phases %standard-phases
900 (add-after 'unpack 'replace-minified-javascript
901 (lambda* (#:key inputs #:allow-other-keys)
902 (with-directory-excursion "inst/www/jsTree-3.3.7/"
903 (symlink (string-append (assoc-ref inputs "js-requirejs")
904 "/share/javascript/require.min.js")
909 `((,(assoc-ref inputs "js-jquery")
913 (lambda (sources targets)
914 (for-each (lambda (source target)
915 (format #t "Processing ~a --> ~a~%"
917 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
918 (call-with-output-file target
920 (dump-port minified port)))))
924 `(("r-htmlwidgets" ,r-htmlwidgets)
925 ("r-jsonlite" ,r-jsonlite)
926 ("r-promises" ,r-promises)
928 ("r-stringr" ,r-stringr)))
930 `(("js-requirejs" ,js-requirejs)))
932 `(("uglify-js" ,uglify-js)
936 (uri "https://code.jquery.com/jquery-3.3.1.js")
939 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
940 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
941 (synopsis "jsTree bindings for Shiny")
943 "This package exposes R bindings to jsTree, a JavaScript library that
944 supports interactive trees, to enable rich, editable trees in Shiny.")
945 (license license:expat)))
947 (define-public r-shinydashboard
949 (name "r-shinydashboard")
953 (uri (cran-uri "shinydashboard" version))
956 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
957 (build-system r-build-system)
958 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
959 ;; Regenerate it from the included sources.
961 `(#:modules ((guix build utils)
962 (guix build r-build-system)
965 (modify-phases %standard-phases
966 (add-after 'unpack 'generate-minified-javascript
968 (with-directory-excursion "inst/AdminLTE"
969 (delete-file "app.min.js")
970 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
971 (call-with-output-file "app.min.js"
973 (dump-port minified port))))))))))
975 `(("r-htmltools" ,r-htmltools)
976 ("r-promises" ,r-promises)
977 ("r-shiny" ,r-shiny)))
979 `(("uglify-js" ,uglify-js)))
980 (home-page "http://rstudio.github.io/shinydashboard/")
981 (synopsis "Create dashboards with shiny")
982 (description "This package provides an extension to the Shiny web
983 application framework for R, making it easy to create attractive dashboards.")
984 ;; This package includes software that was released under the Expat
985 ;; license, but the whole package is released under GPL version 2 or
987 (license license:gpl2+)))
989 (define-public r-shinyfiles
991 (name "r-shinyfiles")
996 (uri (cran-uri "shinyFiles" version))
998 (base32 "1143m941hma9hc77c3xcw26c0ygfhn9ii2sbp9wrydxv4gc7mr8a"))))
999 (properties `((upstream-name . "shinyFiles")))
1000 (build-system r-build-system)
1003 ("r-htmltools" ,r-htmltools)
1004 ("r-jsonlite" ,r-jsonlite)
1005 ("r-shiny" ,r-shiny)
1006 ("r-tibble" ,r-tibble)))
1007 (home-page "https://github.com/thomasp85/shinyFiles")
1008 (synopsis "Server-side file system viewer for Shiny")
1010 "This package provides functionality for client-side navigation of the
1011 server side file system in shiny apps. In case the app is running locally
1012 this gives the user direct access to the file system without the need to
1013 \"download\" files to a temporary location. Both file and folder selection as
1014 well as file saving is available.")
1015 (license license:gpl2+)))
1017 (define-public r-shinythemes
1019 (name "r-shinythemes")
1024 (uri (cran-uri "shinythemes" version))
1027 "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf"))))
1028 (properties `((upstream-name . "shinythemes")))
1029 (build-system r-build-system)
1030 (propagated-inputs `(("r-shiny" ,r-shiny)))
1031 (home-page "http://rstudio.github.io/shinythemes/")
1032 (synopsis "Themes for Shiny")
1034 "This package provides themes for use with Shiny. It includes several
1035 Bootstrap themes, which are packaged for use with Shiny applications.")
1036 ;; The package is released under version 3 of the GPL, but it includes
1037 ;; source files that are covered by the Expat license. It also includes
1038 ;; fonts under SIL or the ASL.
1039 (license (list license:gpl3 license:expat
1040 license:silofl1.1 license:asl2.0))))
1042 ;; The package sources include minified variants of d3.js and non-minified
1043 ;; source code of d3-jetpack.
1044 (define-public r-d3r
1051 (uri (cran-uri "d3r" version))
1054 "0xl3im76lp7pd5lhp8jfyqdm4j4zvjrx5a5fl81xv2cf7x3n4f2a"))))
1055 (build-system r-build-system)
1057 `(#:modules ((guix build utils)
1058 (guix build r-build-system)
1062 (modify-phases %standard-phases
1063 (add-after 'unpack 'process-javascript
1064 (lambda* (#:key inputs #:allow-other-keys)
1065 (with-directory-excursion "inst/www/d3/"
1069 `((,(assoc-ref inputs "d3.v3.js")
1070 "v3/dist/d3.min.js")
1071 (,(assoc-ref inputs "d3.v4.js")
1072 "v4/dist/d3.min.js")
1073 (,(assoc-ref inputs "d3.v5.js")
1074 "v5/dist/d3.min.js"))))
1075 (lambda (sources targets)
1076 (for-each (lambda (source target)
1077 (format #t "Processing ~a --> ~a~%"
1079 (delete-file target)
1080 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1081 (call-with-output-file target
1083 (dump-port minified port)))))
1087 `(("r-dplyr" ,r-dplyr)
1088 ("r-htmltools" ,r-htmltools)
1089 ("r-tidyr" ,r-tidyr)))
1091 `(("uglify-js" ,uglify-js)
1095 (uri "https://d3js.org/d3.v3.js")
1098 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
1102 (uri "https://d3js.org/d3.v4.js")
1105 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
1109 (uri "https://d3js.org/d3.v5.js")
1112 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))))
1113 (home-page "https://github.com/timelyportfolio/d3r")
1114 (synopsis "d3.js utilities for R")
1116 "This package provides a suite of functions to help ease the use of the
1117 d3.js visualization library in R. These helpers include
1118 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
1119 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
1120 R objects into the JSON format that the d3.js library expects.")
1121 (license license:bsd-3)))
1123 ;; We use the latest commit here because the last release was in 2016 while
1124 ;; the latest commit was in 2018.
1125 (define-public r-sankeyd3
1126 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
1130 (version (git-version "0.3.2" revision commit))
1135 (url "https://github.com/fbreitwieser/sankeyD3.git")
1137 (file-name (git-file-name name version))
1140 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
1141 (build-system r-build-system)
1144 ("r-htmlwidgets" ,r-htmlwidgets)
1145 ("r-shiny" ,r-shiny)
1146 ("r-magrittr" ,r-magrittr)))
1147 (home-page "https://github.com/fbreitwieser/sankeyD3")
1148 (synopsis "Sankey network graphs from R")
1150 "This package provides an R library to generate Sankey network graphs
1151 in R and Shiny via the D3 visualization library.")
1152 ;; The R code is licensed under GPLv3+. It includes the non-minified
1153 ;; JavaScript source code of d3-sankey, which is released under the
1154 ;; 3-clause BSD license.
1155 (license (list license:gpl3+ license:bsd-3)))))
1157 (define-public r-crosstalk
1159 (name "r-crosstalk")
1164 (uri (cran-uri "crosstalk" version))
1167 "0lfa89vhrzi7a1rghmygcjr8gzddw35sinb3jx6g49mc9jias7mk"))))
1168 (build-system r-build-system)
1170 `(("r-ggplot2" ,r-ggplot2)
1171 ("r-htmltools" ,r-htmltools)
1172 ("r-jsonlite" ,r-jsonlite)
1173 ("r-lazyeval" ,r-lazyeval)
1175 ("r-shiny" ,r-shiny)))
1176 (home-page "https://rstudio.github.io/crosstalk/")
1177 (synopsis "Inter-widget interactivity for HTML widgets")
1179 "This package provides building blocks for allowing HTML widgets to
1180 communicate with each other, with Shiny or without (i.e. static @code{.html}
1181 files). It currently supports linked brushing and filtering.")
1182 (license license:expat)))
1184 (define-public r-rook
1191 (uri (cran-uri "Rook" version))
1194 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
1195 (properties `((upstream-name . "Rook")))
1196 (build-system r-build-system)
1197 (propagated-inputs `(("r-brew" ,r-brew)))
1198 (home-page "https://cran.r-project.org/web/packages/Rook")
1199 (synopsis "Web server interface for R")
1201 "This package contains the Rook specification and convenience software
1202 for building and running Rook applications. A Rook application is an R
1203 reference class object that implements a @code{call} method or an R closure
1204 that takes exactly one argument, an environment, and returns a list with three
1205 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
1206 (license license:gpl2)))
1208 (define-public r-miniui
1215 (uri (cran-uri "miniUI" version))
1218 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
1219 (properties `((upstream-name . "miniUI")))
1220 (build-system r-build-system)
1222 `(("r-htmltools" ,r-htmltools)
1223 ("r-shiny" ,r-shiny)))
1224 (home-page "https://cran.r-project.org/web/packages/miniUI/")
1225 (synopsis "Shiny UI widgets for small screens")
1227 "This package provides UI widget and layout functions for writing Shiny apps that
1228 work well on small screens.")
1229 (license license:gpl3)))
1231 (define-public r-feather
1238 (uri (cran-uri "feather" version))
1241 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
1242 (build-system r-build-system)
1246 ("r-tibble" ,r-tibble)))
1247 (home-page "https://github.com/wesm/feather")
1248 (synopsis "R Bindings to the Feather API")
1249 (description "Read and write feather files, a lightweight binary columnar
1250 data store designed for maximum speed.")
1251 (license license:asl2.0)))
1253 (define-public r-maps
1260 (uri (cran-uri "maps" version))
1263 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
1264 (build-system r-build-system)
1265 (home-page "https://cran.r-project.org/web/packages/maps")
1266 (synopsis "Draw geographical maps")
1267 (description "This package provides an R module for display of maps.
1268 Projection code and larger maps are in separate packages (@code{mapproj} and
1270 (license license:gpl2)))
1272 (define-public r-mapproj
1279 (uri (cran-uri "mapproj" version))
1282 "0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h"))))
1283 (build-system r-build-system)
1284 (propagated-inputs `(("r-maps" ,r-maps)))
1285 (home-page "https://cran.r-project.org/web/packages/mapproj")
1286 (synopsis "Map projection in R")
1287 (description "This package converts latitude/longitude into projected
1289 (license (list license:gpl2 ; The R interface
1290 (license:non-copyleft ; The C code
1291 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
1292 "Lucent Public License Version 1.02")))))
1294 (define-public r-rgooglemaps
1296 (name "r-rgooglemaps")
1301 (uri (cran-uri "RgoogleMaps" version))
1304 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
1305 (properties `((upstream-name . "RgoogleMaps")))
1306 (build-system r-build-system)
1310 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
1311 (synopsis "Use Google Maps in R")
1312 (description "This package serves two purposes:
1314 @item Provide a comfortable R interface to query the Google server for static
1316 @item Use the map as a background image to overlay plots within R. This
1317 requires proper coordinate scaling.
1319 (license license:gpl2+)))
1321 (define-public r-geosphere
1323 (name "r-geosphere")
1328 (uri (cran-uri "geosphere" version))
1331 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
1332 (build-system r-build-system)
1333 (propagated-inputs `(("r-sp" ,r-sp)))
1334 (home-page "https://cran.r-project.org/web/packages/geosphere")
1335 (synopsis "Spherical trigonometry")
1336 (description "This package computes spherical trigonometry for geographic
1337 applications. That is, compute distances and related measures for angular
1338 (longitude/latitude) locations.")
1339 (license license:gpl3+)))
1341 (define-public r-jpeg
1348 (uri (cran-uri "jpeg" version))
1351 "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
1352 (build-system r-build-system)
1353 (inputs `(("libjpeg" ,libjpeg)))
1354 (home-page "http://www.rforge.net/jpeg/")
1355 (synopsis "Read and write JPEG images with R")
1356 (description "This package provides a way to read, write and display
1357 bitmap images stored in the JPEG format with R. It can read and write both
1358 files and in-memory raw vectors.")
1359 (license license:gpl2+)))
1361 (define-public r-ggmap
1368 (uri (cran-uri "ggmap" version))
1371 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
1372 (build-system r-build-system)
1374 `(("r-bitops" ,r-bitops)
1375 ("r-digest" ,r-digest)
1376 ("r-dplyr" ,r-dplyr)
1377 ("r-ggplot2" ,r-ggplot2)
1381 ("r-magrittr" ,r-magrittr)
1384 ("r-purrr" ,r-purrr)
1385 ("r-rgooglemaps" ,r-rgooglemaps)
1386 ("r-rjson" ,r-rjson)
1387 ("r-scales" ,r-scales)
1388 ("r-stringr" ,r-stringr)
1389 ("r-tibble" ,r-tibble)
1390 ("r-tidyr" ,r-tidyr)))
1391 (home-page "https://github.com/dkahle/ggmap")
1392 (synopsis "Spatial visualization with ggplot2")
1393 (description "This package provides a collection of functions to visualize
1394 spatial data and models on top of static maps from various online sources (e.g
1395 Google Maps and Stamen Maps). It includes tools common to those tasks,
1396 including functions for geolocation and routing.")
1397 (license license:gpl2)))
1399 (define-public r-haven
1406 (uri (cran-uri "haven" version))
1409 "0g9d6mxqmrw2zdms78jpx2sx73pczlyy771v1h5hmxqz9sqyk7hr"))))
1410 (build-system r-build-system)
1414 `(("r-forcats" ,r-forcats)
1417 ("r-rlang" ,r-rlang)
1418 ("r-readr" ,r-readr)
1419 ("r-tibble" ,r-tibble)
1420 ("r-tidyselect" ,r-tidyselect)))
1421 (home-page "https://haven.tidyverse.org")
1422 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
1424 "This package lets you mport foreign statistical formats into R via the
1425 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
1426 (license license:expat)))
1428 (define-public r-amap
1434 (uri (cran-uri "amap" version))
1437 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
1438 (build-system r-build-system)
1440 `(("gfortran" ,gfortran)))
1441 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
1442 (synopsis "Another multidimensional analysis package")
1443 (description "This package provides tools for clustering and principal
1444 component analysis (with robust methods, and parallelized functions).")
1445 (license license:gpl2+)))
1447 (define-public r-ape
1454 (uri (cran-uri "ape" version))
1457 "08wbk1kxhs32bmmvqlqanbdg1w235amd35k8m00fngsj9h9xzc08"))))
1458 (build-system r-build-system)
1460 `(("r-lattice" ,r-lattice)
1462 ("r-rcpp" ,r-rcpp)))
1463 (home-page "http://ape-package.ird.fr/")
1464 (synopsis "Analyses of phylogenetics and evolution")
1466 "This package provides functions for reading, writing, plotting, and
1467 manipulating phylogenetic trees, analyses of comparative data in a
1468 phylogenetic framework, ancestral character analyses, analyses of
1469 diversification and macroevolution, computing distances from DNA sequences,
1470 and several other tools.")
1471 (license license:gpl2+)))
1473 (define-public r-abbyyr
1480 (uri (cran-uri "abbyyR" version))
1483 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
1484 (properties `((upstream-name . "abbyyR")))
1485 (build-system r-build-system)
1487 `(("r-curl" ,r-curl)
1490 ("r-progress" ,r-progress)
1491 ("r-readr" ,r-readr)
1493 (home-page "https://github.com/soodoku/abbyyR")
1494 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
1496 "This package provides tools to get text from images of text using Abbyy
1497 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
1498 OCR images, barcodes, forms, documents with machine readable zones, e.g.
1499 passports and get the results in a variety of formats including plain text and
1500 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
1501 (license license:expat)))
1503 (define-public r-colorspace
1505 (name "r-colorspace")
1510 (uri (cran-uri "colorspace" version))
1512 (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9"))))
1513 (build-system r-build-system)
1514 (home-page "https://cran.r-project.org/web/packages/colorspace")
1515 (synopsis "Color space manipulation")
1517 "This package carries out a mapping between assorted color spaces
1518 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
1519 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
1520 colors are provided.")
1521 (license license:bsd-3)))
1523 (define-public r-glue
1530 (uri (cran-uri "glue" version))
1533 "1a1ycg9r3gd91visp49q49rsrdgyf8kr9dxdy3hk99kikn4z5hag"))))
1534 (build-system r-build-system)
1535 (home-page "https://github.com/tidyverse/glue")
1536 (synopsis "Interpreted string literals")
1538 "This package provides an implementation of interpreted string literals,
1539 inspired by Python's Literal String Interpolation (PEP-0498) and
1540 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
1541 (license license:expat)))
1543 (define-public r-pastecs
1549 (uri (cran-uri "pastecs" version))
1552 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
1553 (build-system r-build-system)
1555 `(("r-boot" ,r-boot)))
1556 (home-page "http://www.sciviews.org/pastecs")
1557 (synopsis "Analysis of space-time ecological series")
1559 "This package provides functions for regulation, decomposition and analysis
1560 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
1561 initiative to bring PASSTEC 2000 functionalities to R.")
1562 (license license:gpl2+)))
1564 (define-public r-plogr
1571 (uri (cran-uri "plogr" version))
1574 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
1575 (build-system r-build-system)
1576 (home-page "https://github.com/krlmlr/plogr")
1577 (synopsis "R bindings for the plog C++ logging library")
1579 "This package provides the header files for a stripped-down version of
1580 the plog header-only C++ logging library, and a method to log to R's standard
1582 (license license:expat)))
1584 (define-public r-pls
1591 (uri (cran-uri "pls" version))
1593 (base32 "121byimd6bg7jbrq5wz5fpi0vxq0vh8g724vkhnjzszbvcv1xsb7"))))
1594 (build-system r-build-system)
1595 (home-page "http://mevik.net/work/software/pls.html")
1596 (synopsis "Partial Least Squares and Principal Component Regression")
1598 "The pls package implements multivariate regression methods: Partial Least
1599 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
1600 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
1603 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
1604 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
1605 @item multi-response models (or @dfn{PLS2})
1606 @item flexible cross-validation
1607 @item Jackknife variance estimates of regression coefficients
1608 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
1609 (R)MSEP, R², and correlation loadings
1610 @item formula interface, modelled after @code{lm()}, with methods for predict,
1611 print, summary, plot, update, etc.
1612 @item extraction functions for coefficients, scores, and loadings
1613 @item MSEP, RMSEP, and R² estimates
1614 @item multiplicative scatter correction (@dfn{MSC})
1616 (license license:gpl2)))
1625 (uri (cran-uri "ps" version))
1627 (base32 "0127q6pw9iw8hhcfp231gmdh29nahh2n5jzc38avrzy7yrm4bwl9"))))
1628 (build-system r-build-system)
1629 (home-page "https://ps.r-lib.org")
1630 (synopsis "List, query, and manipulate system processes")
1632 "The ps package implements an API to list, query, and manipulate system
1633 processes. Most of its code is based on the @code{psutil} Python package.")
1634 (license license:bsd-3)))
1636 (define-public r-pkgbuild
1643 (uri (cran-uri "pkgbuild" version))
1645 (base32 "0xnlz6ivhkbmncg9hfw5p69lm4rjy3wn5lyxmygxyf4rrfnnqwxx"))))
1646 (build-system r-build-system)
1648 `(("r-callr" ,r-callr)
1650 ("r-crayon" ,r-crayon)
1652 ("r-prettyunits" ,r-prettyunits)
1654 ("r-rprojroot" ,r-rprojroot)
1655 ("r-withr" ,r-withr)))
1656 (home-page "https://github.com/r-pkgs/pkgbuild")
1657 (synopsis "Find tools needed to build R packages")
1659 "This package provides functions used to build R packages. It locates
1660 compilers needed to build R packages on various platforms and ensures the PATH
1661 is configured appropriately so R can use them.")
1662 (license license:gpl3)))
1664 (define-public r-pkgload
1671 (uri (cran-uri "pkgload" version))
1674 "0z7jvharafahi2gv5547mk1n499isjzw06kfwymmxc0gd575d1ii"))))
1675 (build-system r-build-system)
1677 `(("r-desc" ,r-desc)
1678 ("r-pkgbuild" ,r-pkgbuild)
1679 ("r-rlang" ,r-rlang)
1680 ("r-rprojroot" ,r-rprojroot)
1681 ("r-rstudioapi" ,r-rstudioapi)
1682 ("r-withr" ,r-withr)))
1683 (home-page "https://github.com/r-lib/pkgload")
1684 (synopsis "Simulate package installation and attach")
1686 "This package simulates the process of installing a package and then
1687 attaching it. This is a key part of the @code{devtools} package as it allows
1688 you to rapidly iterate while developing a package.")
1689 (license license:gpl3)))
1691 (define-public r-rcpp
1698 (uri (cran-uri "Rcpp" version))
1700 (base32 "03h3zyjq948y0hrrs95lfk4zgx6wfrg64hjlrfrzf5na7bfh0d9b"))))
1701 (build-system r-build-system)
1703 `(("r-knitr" ,r-knitr))) ; for vignettes
1704 (home-page "http://www.rcpp.org")
1705 (synopsis "Seamless R and C++ integration")
1707 "The Rcpp package provides R functions as well as C++ classes which offer
1708 a seamless integration of R and C++. Many R data types and objects can be
1709 mapped back and forth to C++ equivalents which facilitates both writing of new
1710 code as well as easier integration of third-party libraries. Documentation
1711 about Rcpp is provided by several vignettes included in this package, via the
1712 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
1713 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
1714 @code{citation(\"Rcpp\")} for details on these last two.")
1715 (license license:gpl2+)))
1717 (define-public r-bindr
1724 (uri (cran-uri "bindr" version))
1727 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
1728 (build-system r-build-system)
1729 (home-page "https://github.com/krlmlr/bindr")
1730 (synopsis "Parametrized active bindings")
1732 "This package provides a simple interface for creating active bindings
1733 where the bound function accepts additional arguments.")
1734 (license license:expat)))
1736 (define-public r-bindrcpp
1743 (uri (cran-uri "bindrcpp" version))
1746 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
1747 (build-system r-build-system)
1749 `(("r-bindr" ,r-bindr)
1750 ("r-plogr" ,r-plogr)
1751 ("r-rcpp" ,r-rcpp)))
1752 (home-page "https://github.com/krlmlr/bindrcpp")
1753 (synopsis "Rcpp interface to active bindings")
1755 "This package provides an easy way to fill an environment with active
1756 bindings that call a C++ function.")
1757 (license license:expat)))
1759 (define-public r-auc
1766 (uri (cran-uri "AUC" version))
1769 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
1770 (properties `((upstream-name . "AUC")))
1771 (build-system r-build-system)
1772 (home-page "https://cran.r-project.org/web/packages/AUC")
1773 (synopsis "Compute the area under the curve of selected measures")
1775 "This package includes functions to compute the area under the curve of
1776 selected measures: the area under the sensitivity curve (AUSEC), the area
1777 under the specificity curve (AUSPC), the area under the accuracy
1778 curve (AUACC), and the area under the receiver operating characteristic
1779 curve (AUROC). The curves can also be visualized. Support for partial areas
1781 (license license:gpl2+)))
1783 (define-public r-calibrate
1785 (name "r-calibrate")
1790 (uri (cran-uri "calibrate" version))
1792 (base32 "1s423nr176l2sc66wp7hzgqkv7c2bq8d2bjrrvrrm5qa9y3zdx1k"))))
1793 (build-system r-build-system)
1795 `(("r-mass" ,r-mass)))
1796 (home-page "https://cran.r-project.org/web/packages/calibrate")
1797 (synopsis "Calibration of scatterplot and biplot axes")
1799 "This is a package for drawing calibrated scales with tick marks
1800 on (non-orthogonal) variable vectors in scatterplots and biplots.")
1801 (license license:gpl2)))
1803 (define-public r-shape
1810 (uri (cran-uri "shape" version))
1813 "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
1814 (build-system r-build-system)
1815 (home-page "https://cran.r-project.org/web/packages/shape")
1816 (synopsis "Functions for plotting graphical shapes")
1818 "This package provides functions for plotting graphical shapes such as
1819 ellipses, circles, cylinders, arrows, ...")
1820 (license license:gpl3+)))
1822 (define-public r-globaloptions
1824 (name "r-globaloptions")
1829 (uri (cran-uri "GlobalOptions" version))
1831 (base32 "0x89hfz80avq4zcskxl71i4zi0mgniqqxfrvz050aa2189wfyja2"))))
1832 (properties `((upstream-name . "GlobalOptions")))
1833 (build-system r-build-system)
1834 (home-page "https://github.com/jokergoo/GlobalOptions")
1835 (synopsis "Generate functions to get or set global options")
1837 "This package provides more controls on the option values such as
1838 validation and filtering on the values, making options invisible or private.")
1839 (license license:gpl2+)))
1841 (define-public r-circlize
1848 (uri (cran-uri "circlize" version))
1851 "0jvr9hmxyhg0zx101iiqkrg8wfaj86kp62xpv42n2j9fkn5r1mi2"))))
1852 (build-system r-build-system)
1854 `(("r-colorspace" ,r-colorspace)
1855 ("r-globaloptions" ,r-globaloptions)
1856 ("r-shape" ,r-shape)))
1857 (home-page "https://github.com/jokergoo/circlize")
1858 (synopsis "Circular visualization")
1860 "Circular layout is an efficient way to visualise huge amounts of
1861 information. This package provides an implementation of circular layout
1862 generation in R as well as an enhancement of available software. Its
1863 flexibility is based on the usage of low-level graphics functions such that
1864 self-defined high-level graphics can be easily implemented by users for
1865 specific purposes. Together with the seamless connection between the powerful
1866 computational and visual environment in R, it gives users more convenience and
1867 freedom to design figures for better understanding complex patterns behind
1868 multi-dimensional data.")
1869 (license license:gpl2+)))
1871 (define-public r-powerlaw
1878 (uri (cran-uri "poweRlaw" version))
1881 "1asr6ikr7hmj78jyg8r1gwvcjg14addkxdiz92nh06lv71a183r4"))))
1882 (properties `((upstream-name . "poweRlaw")))
1883 (build-system r-build-system)
1885 `(("r-vgam" ,r-vgam)))
1886 (home-page "https://github.com/csgillespie/poweRlaw")
1887 (synopsis "Tools for the analysis of heavy tailed distributions")
1889 "This package provides an implementation of maximum likelihood estimators
1890 for a variety of heavy tailed distributions, including both the discrete and
1891 continuous power law distributions. Additionally, a goodness-of-fit based
1892 approach is used to estimate the lower cut-off for the scaling region.")
1893 ;; Any of these GPL versions.
1894 (license (list license:gpl2 license:gpl3))))
1896 (define-public r-compare
1903 (uri (cran-uri "compare" version))
1906 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
1907 (build-system r-build-system)
1908 (home-page "https://cran.r-project.org/web/packages/compare")
1909 (synopsis "Comparing objects for differences")
1911 "This package provides functions to compare a model object to a
1912 comparison object. If the objects are not identical, the functions can be
1913 instructed to explore various modifications of the objects (e.g., sorting
1914 rows, dropping names) to see if the modified versions are identical.")
1915 (license license:gpl2+)))
1917 (define-public r-dendextend
1919 (name "r-dendextend")
1924 (uri (cran-uri "dendextend" version))
1927 "1pjbz6sb4pgh3d5pm53vmf3q8y6lq3hrgjd6547xxs3m63sb8mn4"))))
1928 (build-system r-build-system)
1930 `(("r-ggplot2" ,r-ggplot2)
1931 ("r-magrittr" ,r-magrittr)
1932 ("r-viridis" ,r-viridis)))
1933 (home-page "https://cran.r-project.org/web/packages/dendextend")
1934 (synopsis "Extending 'dendrogram' functionality in R")
1936 "This package offers a set of functions for extending @code{dendrogram}
1937 objects in R, letting you visualize and compare trees of hierarchical
1938 clusterings. You can adjust a tree's graphical parameters (the color, size,
1939 type, etc of its branches, nodes and labels) and visually and statistically
1940 compare different dendrograms to one another.")
1941 ;; Any of these versions
1942 (license (list license:gpl2 license:gpl3))))
1944 (define-public r-getoptlong
1946 (name "r-getoptlong")
1951 (uri (cran-uri "GetoptLong" version))
1954 "1l8xkvyl152bsyvxazsvx2sm1vkygn75x0lsg3sbg7xp6drdn3kc"))))
1955 (properties `((upstream-name . "GetoptLong")))
1956 (build-system r-build-system)
1960 `(("r-globaloptions" ,r-globaloptions)
1961 ("r-rjson" ,r-rjson)))
1962 (home-page "https://github.com/jokergoo/GetoptLong")
1963 (synopsis "Parsing command-line arguments and variable interpolation")
1965 "This is yet another command-line argument parser which wraps the
1966 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
1967 use in R. It also provides a simple way for variable interpolation in R.")
1968 (license license:gpl2+)))
1970 (define-public r-fastmatch
1972 (name "r-fastmatch")
1977 (uri (cran-uri "fastmatch" version))
1980 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
1981 (build-system r-build-system)
1982 (home-page "http://www.rforge.net/fastmatch")
1983 (synopsis "Fast match function")
1985 "This package provides a fast @code{match} replacement for cases that
1986 require repeated look-ups. It is slightly faster that R's built-in
1987 @code{match} function on first match against a table, but extremely fast on
1988 any subsequent lookup as it keeps the hash table in memory.")
1989 (license license:gpl2)))
1998 (uri (cran-uri "ff" version))
2001 "1w724q4jpzbvzpilb2ifviaxkjgk9lzwxz9gksnvicbmfa20fqqw"))))
2002 (build-system r-build-system)
2003 (propagated-inputs `(("r-bit" ,r-bit)))
2004 (home-page "http://ff.r-forge.r-project.org/")
2005 (synopsis "Memory-efficient storage of large data on disk and access functions")
2007 "This package provides data structures that are stored on disk but
2008 behave (almost) as if they were in RAM by transparently mapping only a section
2010 ;; error Architecture not supported.
2011 (supported-systems (delete "aarch64-linux" %supported-systems))
2012 (license license:gpl2)))
2014 (define-public r-ffbase
2021 (uri (cran-uri "ffbase" version))
2024 "04kxx2f3f0743c5nvpb7x1x0pcd220dazpd5ag1pidxbz3xa85nw"))))
2025 (build-system r-build-system)
2028 ("r-fastmatch" ,r-fastmatch)
2030 (home-page "http://github.com/edwindj/ffbase")
2031 (synopsis "Basic statistical functions for package 'ff'")
2033 "This package extends the out of memory vectors of @code{ff} with
2034 statistical functions and other utilities to ease their usage.")
2035 (license license:gpl3)))
2037 (define-public r-prettyunits
2039 (name "r-prettyunits")
2044 (uri (cran-uri "prettyunits" version))
2047 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
2048 (build-system r-build-system)
2049 (home-page "https://github.com/gaborcsardi/prettyunits")
2050 (synopsis "Pretty, human readable formatting of quantities")
2052 "This package provides tools for pretty, human readable formatting of
2054 (license license:expat)))
2056 (define-public r-reshape
2063 (uri (cran-uri "reshape" version))
2066 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
2067 (build-system r-build-system)
2069 `(("r-plyr" ,r-plyr)
2070 ("r-rcpp" ,r-rcpp)))
2071 (home-page "http://had.co.nz/reshape")
2072 (synopsis "Flexibly reshape data")
2074 "Flexibly restructure and aggregate data using just two functions:
2075 @code{melt} and @code{cast}. This package provides them.")
2076 (license license:expat)))
2078 (define-public r-progress
2085 (uri (cran-uri "progress" version))
2088 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
2089 (build-system r-build-system)
2091 `(("r-crayon" ,r-crayon)
2093 ("r-prettyunits" ,r-prettyunits)
2095 (home-page "https://github.com/gaborcsardi/progress")
2096 (synopsis "Terminal progress bars")
2098 "This package provides configurable progress bars. They may include
2099 percentage, elapsed time, and/or the estimated completion time. They work in
2100 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
2101 package also provides a C++ API, that works with or without Rcpp.")
2102 (license license:expat)))
2104 (define-public r-ggally
2111 (uri (cran-uri "GGally" version))
2114 "1zjmcc5bzagvy7c5cmdcl39xmx07fwi98yrj4i05w7y40kqcsiws"))))
2115 (properties `((upstream-name . "GGally")))
2116 (build-system r-build-system)
2118 `(("libressl" ,libressl)))
2120 `(("r-ggplot2" ,r-ggplot2)
2121 ("r-gtable" ,r-gtable)
2123 ("r-progress" ,r-progress)
2124 ("r-rcolorbrewer" ,r-rcolorbrewer)
2125 ("r-reshape" ,r-reshape)
2126 ("r-rlang" ,r-rlang)))
2127 (home-page "https://ggobi.github.io/ggally")
2128 (synopsis "Extension to ggplot2")
2130 "The R package ggplot2 is a plotting system based on the grammar of
2131 graphics. GGally extends ggplot2 by adding several functions to reduce the
2132 complexity of combining geometric objects with transformed data. Some of
2133 these functions include a pairwise plot matrix, a two group pairwise plot
2134 matrix, a parallel coordinates plot, a survival plot, and several functions to
2136 (license license:gpl2+)))
2138 (define-public r-proxy
2145 (uri (cran-uri "proxy" version))
2148 "17b6qfllqrhzrxqgx7dccffgybnkcria5a68ap5ly3plg04ypm4x"))))
2149 (build-system r-build-system)
2150 (home-page "https://cran.r-project.org/web/packages/proxy")
2151 (synopsis "Distance and similarity measures")
2153 "This package provides an extensible framework for the efficient
2154 calculation of auto- and cross-proximities, along with implementations of the
2155 most popular ones.")
2156 (license license:gpl2)))
2165 (uri (cran-uri "sp" version))
2167 (base32 "0fbh865r4py89g6ln8bslig2vbxxwa642p5k5g02rskyhajg35lg"))))
2168 (build-system r-build-system)
2170 `(("r-lattice" ,r-lattice)))
2171 (home-page "https://cran.r-project.org/web/packages/sp")
2172 (synopsis "Classes and methods for spatial data")
2174 "This package provides classes and methods for spatial data; the classes
2175 document where the spatial location information resides, for 2D or 3D data.
2176 Utility functions are provided, e.g. for plotting data as maps, spatial
2177 selection, as well as methods for retrieving coordinates, for subsetting,
2178 print, summary, etc.")
2179 (license license:gpl2+)))
2181 (define-public r-rmtstat
2188 (uri (cran-uri "RMTstat" version))
2191 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
2192 (properties `((upstream-name . "RMTstat")))
2193 (build-system r-build-system)
2194 (home-page "https://cran.r-project.org/web/packages/RMTstat")
2195 (synopsis "Distributions, statistics and tests derived from random matrix theory")
2197 "This package provides functions for working with the Tracy-Widom laws
2198 and other distributions related to the eigenvalues of large Wishart
2200 (license license:bsd-3)))
2202 (define-public r-rmpi
2208 (uri (cran-uri "Rmpi" version))
2211 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
2212 (properties `((upstream-name . "Rmpi")))
2213 (build-system r-build-system)
2215 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
2216 #:phases (modify-phases %standard-phases
2217 (add-before 'install 'mpi-setup
2220 `(("openmpi" ,openmpi)))
2222 `(("pkg-config" ,pkg-config)))
2223 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
2224 (synopsis "R interface to message-passing interface (MPI)")
2226 "This package provides an interface (wrapper) to MPI APIs. It also
2227 provides an interactive R manager and worker environment.")
2228 (license license:gpl2+)))
2230 (define-public r-lmoments
2237 (uri (cran-uri "Lmoments" version))
2240 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
2241 (properties `((upstream-name . "Lmoments")))
2242 (build-system r-build-system)
2244 `(("r-rcpp" ,r-rcpp)
2245 ("r-rcpparmadillo" ,r-rcpparmadillo)))
2246 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
2247 (synopsis "L-moments and quantile mixtures")
2249 "This package contains functions to estimate L-moments and trimmed
2250 L-moments from the data. It also contains functions to estimate the
2251 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
2252 quantile mixture from L-moments and trimmed L-moments.")
2253 (license license:gpl2)))
2255 (define-public r-distillery
2257 (name "r-distillery")
2262 (uri (cran-uri "distillery" version))
2265 "1mi3ig9jq0kd7yrwc5m37lmrw04p1b4lirnbsxi10z3n5yay4429"))))
2266 (build-system r-build-system)
2267 (home-page "https://ral.ucar.edu/staff/ericg/")
2268 (synopsis "Functions for confidence intervals and object information")
2270 "This package provides some very simple method functions for confidence
2271 interval calculation and to distill pertinent information from a potentially
2272 complex object; primarily used in common with the packages extRemes and
2274 (license license:gpl2+)))
2276 (define-public r-extremes
2283 (uri (cran-uri "extRemes" version))
2286 "0hmgynxhzswqnhwb2sxrkczgam8c17s3vpxqc5bcz0bwczpxxyvm"))))
2287 (properties `((upstream-name . "extRemes")))
2288 (build-system r-build-system)
2290 `(("r-distillery" ,r-distillery)
2291 ("r-lmoments" ,r-lmoments)))
2292 (home-page "https://www.assessment.ucar.edu/toolkit/")
2293 (synopsis "Extreme value analysis")
2295 "ExtRemes is a suite of functions for carrying out analyses on the
2296 extreme values of a process of interest; be they block maxima over long blocks
2297 or excesses over a high threshold.")
2298 (license license:gpl2+)))
2300 (define-public r-lmtest
2307 (uri (cran-uri "lmtest" version))
2310 "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx"))))
2311 (build-system r-build-system)
2313 `(("r-zoo" ,r-zoo)))
2315 `(("gfortran" ,gfortran)))
2316 (home-page "https://cran.r-project.org/web/packages/lmtest")
2317 (synopsis "Testing linear regression models")
2319 "This package provides a collection of tests, data sets, and examples for
2320 diagnostic checking in linear regression models. Furthermore, some generic
2321 tools for inference in parametric models are provided.")
2322 ;; Either version is okay
2323 (license (list license:gpl2 license:gpl3))))
2325 (define-public r-idr
2331 (uri (cran-uri "idr" version))
2334 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
2335 (build-system r-build-system)
2336 (home-page "https://cran.r-project.org/web/packages/idr/")
2337 (synopsis "Irreproducible discovery rate")
2339 "This is a package for estimating the copula mixture model and plotting
2340 correspondence curves in \"Measuring reproducibility of high-throughput
2341 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
2342 by Li, Brown, Huang, and Bickel")
2343 (license license:gpl2+)))
2345 (define-public r-inline
2351 (uri (cran-uri "inline" version))
2354 "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
2355 (build-system r-build-system)
2356 (home-page "https://cran.r-project.org/web/packages/inline")
2357 (synopsis "Functions to inline C, C++, Fortran function calls from R")
2359 "This package provides functionality to dynamically define R functions
2360 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
2361 @code{.Call} calling conventions.")
2362 ;; Any version of the LGPL.
2363 (license license:lgpl3+)))
2365 (define-public r-bdsmatrix
2367 (name "r-bdsmatrix")
2372 (uri (cran-uri "bdsmatrix" version))
2375 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
2376 (properties `((upstream-name . "bdsmatrix")))
2377 (build-system r-build-system)
2378 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
2379 (synopsis "Routines for block diagonal symmetric matrices")
2381 "This package provides procedures to work with block diagonal symmetric
2382 matrices, a special case of sparse matrices.")
2383 (license license:lgpl2.0)))
2385 (define-public r-bbmle
2388 (version "1.0.23.1")
2392 (uri (cran-uri "bbmle" version))
2395 "0p3l9shbr2846qmw8n0fyzf4j7gmi08aypl82jml3dwh26q1whk0"))))
2396 (build-system r-build-system)
2398 `(("r-bdsmatrix" ,r-bdsmatrix)
2399 ("r-lattice" ,r-lattice)
2401 ("r-matrix" ,r-matrix)
2402 ("r-mvtnorm" ,r-mvtnorm)
2403 ("r-numderiv" ,r-numderiv)))
2404 (home-page "https://cran.r-project.org/web/packages/bbmle")
2405 (synopsis "Tools for General Maximum Likelihood Estimation")
2407 "This package provides methods and functions for fitting maximum
2408 likelihood models in R. This package modifies and extends the @code{mle}
2409 classes in the @code{stats4} package.")
2410 ;; Any version of the GPL
2411 (license license:gpl2+)))
2413 (define-public r-emdbook
2420 (uri (cran-uri "emdbook" version))
2423 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
2424 (build-system r-build-system)
2426 `(("r-bbmle" ,r-bbmle)
2428 ("r-lattice" ,r-lattice)
2430 ("r-plyr" ,r-plyr)))
2431 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
2432 (synopsis "Support functions and data for \"Ecological Models and Data\"")
2434 "This package provides auxiliary functions and data sets for \"Ecological
2435 Models and Data\", a book presenting maximum likelihood estimation and related
2436 topics for ecologists (ISBN 978-0-691-12522-0).")
2438 (license (list license:gpl2 license:gpl3))))
2440 (define-public r-lpsolve
2447 (uri (cran-uri "lpSolve" version))
2450 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
2451 (properties `((upstream-name . "lpSolve")))
2452 (build-system r-build-system)
2453 (home-page "https://cran.r-project.org/web/packages/lpSolve")
2454 (synopsis "R interface to Lp_solve to solve linear/integer programs")
2456 "Lp_solve is software for solving linear, integer and mixed integer
2457 programs. This implementation supplies a \"wrapper\" function in C and some R
2458 functions that solve general linear/integer problems, assignment problems, and
2459 transportation problems.")
2460 (license license:lgpl2.0)))
2462 (define-public r-limsolve
2469 (uri (cran-uri "limSolve" version))
2472 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
2473 (properties `((upstream-name . "limSolve")))
2474 (build-system r-build-system)
2476 `(("r-lpsolve" ,r-lpsolve)
2478 ("r-quadprog" ,r-quadprog)))
2479 (native-inputs `(("gfortran" ,gfortran)))
2480 (home-page "https://cran.r-project.org/web/packages/limSolve")
2481 (synopsis "Solving linear inverse models")
2483 "This package provides functions that:
2486 @item find the minimum/maximum of a linear or quadratic function,
2487 @item sample an underdetermined or overdetermined system,
2488 @item solve a linear system Ax=B for the unknown x.
2491 It includes banded and tridiagonal linear systems. The package calls Fortran
2492 functions from LINPACK.")
2494 (license (list license:gpl2+ license:gpl3+))))
2496 (define-public r-fitdistrplus
2498 (name "r-fitdistrplus")
2503 (uri (cran-uri "fitdistrplus" version))
2506 "10q08wsv8v3w7797jdvvv60bgrf1bi6438wf0jcqv81ays82a245"))))
2507 (build-system r-build-system)
2509 `(("r-mass" ,r-mass)
2510 ("r-npsurv" ,r-npsurv)
2511 ("r-survival" ,r-survival)))
2512 (home-page "http://riskassessment.r-forge.r-project.org")
2513 (synopsis "Fitting a parametric distribution from data")
2515 "This package extends the @code{fitdistr} function of the MASS package
2516 with several functions to help the fit of a parametric distribution to
2517 non-censored or censored data. Censored data may contain left-censored,
2518 right-censored and interval-censored values, with several lower and upper
2519 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
2520 provides moment matching (MME), quantile matching (QME) and maximum
2521 goodness-of-fit estimation (MGE) methods (available only for non-censored
2522 data). Weighted versions of MLE, MME and QME are available.")
2523 (license license:gpl2+)))
2525 (define-public r-energy
2532 (uri (cran-uri "energy" version))
2535 "13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37"))))
2536 (build-system r-build-system)
2538 `(("r-boot" ,r-boot)
2539 ("r-rcpp" ,r-rcpp)))
2540 (home-page "https://cran.r-project.org/web/packages/energy")
2541 (synopsis "Multivariate inference via the energy of data")
2543 "This package provides e-statistics (energy) tests and statistics for
2544 multivariate and univariate inference, including distance correlation,
2545 one-sample, two-sample, and multi-sample tests for comparing multivariate
2546 distributions, are implemented. Measuring and testing multivariate
2547 independence based on distance correlation, partial distance correlation,
2548 multivariate goodness-of-fit tests, clustering based on energy distance,
2549 testing for multivariate normality, distance components (disco) for
2550 non-parametric analysis of structured data, and other energy
2551 statistics/methods are implemented.")
2552 (license license:gpl2+)))
2554 (define-public r-suppdists
2556 (name "r-suppdists")
2561 (uri (cran-uri "SuppDists" version))
2564 "01j6p94m1g363nph2158fq2rmd6z3h5dvcv6aidh2d6syw131xak"))))
2565 (properties `((upstream-name . "SuppDists")))
2566 (build-system r-build-system)
2567 (home-page "https://cran.r-project.org/web/packages/SuppDists")
2568 (synopsis "Supplementary distributions")
2570 "This package provides ten distributions supplementing those built into
2571 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
2572 Spearman's rho, maximum F ratio, the Pearson product moment correlation
2573 coefficient, Johnson distributions, normal scores and generalized
2574 hypergeometric distributions. In addition two random number generators of
2575 George Marsaglia are included.")
2576 (license license:gpl2+)))
2578 (define-public r-ksamples
2585 (uri (cran-uri "kSamples" version))
2588 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
2589 (properties `((upstream-name . "kSamples")))
2590 (build-system r-build-system)
2592 `(("r-suppdists" ,r-suppdists)))
2593 (home-page "https://cran.r-project.org/web/packages/kSamples")
2594 (synopsis "K-Sample rank tests and their combinations")
2596 "This package provides tools to compares k samples using the
2597 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
2598 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
2599 test. It computes asymptotic, simulated or (limited) exact P-values, all
2600 valid under randomization, with or without ties, or conditionally under random
2601 sampling from populations, given the observed tie pattern. Except for Steel's
2602 test and the JT test it also combines these tests across several blocks of
2604 (license license:gpl2+)))
2606 (define-public r-cvst
2613 (uri (cran-uri "CVST" version))
2616 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
2617 (properties `((upstream-name . "CVST")))
2618 (build-system r-build-system)
2620 `(("r-kernlab" ,r-kernlab)
2621 ("r-matrix" ,r-matrix)))
2622 (home-page "https://cran.r-project.org/web/packages/CVST")
2623 (synopsis "Fast cross-validation via sequential testing")
2625 "This package implements the fast cross-validation via sequential
2626 testing (CVST) procedure. CVST is an improved cross-validation procedure
2627 which uses non-parametric testing coupled with sequential analysis to
2628 determine the best parameter set on linearly increasing subsets of the data.
2629 Additionally to the CVST the package contains an implementation of the
2630 ordinary k-fold cross-validation with a flexible and powerful set of helper
2631 objects and methods to handle the overall model selection process. The
2632 implementations of the Cochran's Q test with permutations and the sequential
2633 testing framework of Wald are generic and can therefore also be used in other
2635 (license license:gpl2+)))
2637 (define-public r-squarem
2644 (uri (cran-uri "SQUAREM" version))
2647 "1j6sa93xjvynnzx9jx79a3fysbykmbqyknknsqif5bcha6xp6cvf"))))
2648 (properties `((upstream-name . "SQUAREM")))
2649 (build-system r-build-system)
2650 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
2651 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
2653 "This package provides algorithms for accelerating the convergence of
2654 slow, monotone sequences from smooth, contraction mapping such as the EM
2655 algorithm. It can be used to accelerate any smooth, linearly convergent
2656 acceleration scheme. A tutorial style introduction to this package is
2657 available in a vignette.")
2658 (license license:gpl2+)))
2660 (define-public r-lava
2667 (uri (cran-uri "lava" version))
2670 "0ffzxbb8pvfh1m6j61az4ga37snyhylq2941fyc76w7w9i2sixv3"))))
2671 (build-system r-build-system)
2673 `(("r-numderiv" ,r-numderiv)
2674 ("r-squarem" ,r-squarem)
2675 ("r-survival" ,r-survival)))
2676 (home-page "https://github.com/kkholst/lava")
2677 (synopsis "Latent variable models")
2679 "This package provides tools for the estimation and simulation of latent
2681 (license license:gpl3)))
2683 (define-public r-drr
2690 (uri (cran-uri "DRR" version))
2693 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
2694 (properties `((upstream-name . "DRR")))
2695 (build-system r-build-system)
2697 `(("r-cvst" ,r-cvst)
2698 ("r-kernlab" ,r-kernlab)
2699 ("r-matrix" ,r-matrix)))
2700 (home-page "https://cran.r-project.org/web/packages/DRR")
2701 (synopsis "Dimensionality reduction via regression")
2703 "This package provides an implementation of dimensionality reduction via
2704 regression using Kernel Ridge Regression.")
2705 (license license:gpl3)))
2707 (define-public r-prodlim
2710 (version "2019.11.13")
2714 (uri (cran-uri "prodlim" version))
2717 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
2718 (build-system r-build-system)
2720 `(("r-kernsmooth" ,r-kernsmooth)
2723 ("r-survival" ,r-survival)))
2724 (home-page "https://cran.r-project.org/web/packages/prodlim")
2725 (synopsis "Product-limit estimation for censored event history analysis")
2727 "This package provides a fast and user-friendly implementation of
2728 nonparametric estimators for censored event history (survival) analysis with
2729 the Kaplan-Meier and Aalen-Johansen methods.")
2730 (license license:gpl2+)))
2732 (define-public r-dimred
2739 (uri (cran-uri "dimRed" version))
2742 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
2743 (properties `((upstream-name . "dimRed")))
2744 (build-system r-build-system)
2747 ("r-magrittr" ,r-magrittr)))
2748 (home-page "https://github.com/gdkrmr/dimRed")
2749 (synopsis "Framework for dimensionality reduction")
2751 "This package provides a collection of dimensionality reduction
2752 techniques from R packages and provides a common interface for calling the
2754 (license license:gpl3)))
2756 (define-public r-timedate
2759 (version "3043.102")
2763 (uri (cran-uri "timeDate" version))
2766 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
2767 (properties `((upstream-name . "timeDate")))
2768 (build-system r-build-system)
2769 (home-page "https://www.rmetrics.org")
2770 (synopsis "Chronological and calendar objects")
2772 "This package provides an environment for teaching \"Financial
2773 Engineering and Computational Finance\" and for managing chronological and
2775 (license license:gpl2+)))
2777 (define-public r-magic
2784 (uri (cran-uri "magic" version))
2787 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
2788 (build-system r-build-system)
2790 `(("r-abind" ,r-abind)))
2791 (home-page "https://github.com/RobinHankin/magic.git")
2792 (synopsis "Create and investigate magic squares")
2794 "This package provides a collection of efficient, vectorized algorithms
2795 for the creation and investigation of magic squares and hypercubes, including
2796 a variety of functions for the manipulation and analysis of arbitrarily
2797 dimensioned arrays.")
2798 (license license:gpl2)))
2800 (define-public r-rmysql
2807 (uri (cran-uri "RMySQL" version))
2810 "0269pfq791qvax69lrwvvzgllyzm3cy3sdp9sakwxzvw5pxk2vhv"))))
2811 (properties `((upstream-name . "RMySQL")))
2812 (build-system r-build-system)
2814 `(("mariadb" ,mariadb "lib")
2815 ("mariadb-dev" ,mariadb "dev")
2818 `(("r-dbi" ,r-dbi)))
2819 (home-page "https://github.com/r-dbi/RMySQL")
2820 (synopsis "Database interface and MySQL driver for R")
2822 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
2823 package contains an old implementation based on legacy code from S-PLUS which
2824 is being phased out. A modern MySQL client based on Rcpp is available from
2825 the RMariaDB package.")
2826 (license license:gpl2)))
2828 (define-public r-rpostgresql
2830 (name "r-rpostgresql")
2835 (uri (cran-uri "RPostgreSQL" version))
2838 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
2839 (properties `((upstream-name . "RPostgreSQL")))
2840 (build-system r-build-system)
2842 `(("postgresql" ,postgresql)))
2844 `(("r-dbi" ,r-dbi)))
2845 (home-page "https://github.com/tomoakin/RPostgreSQL")
2846 (synopsis "R interface to the PostgreSQL database system")
2848 "This package provides a Database Interface (DBI) compliant driver for R
2849 to access PostgreSQL database systems.")
2850 ;; The whole package is released under GPL version 2. It includes code
2851 ;; under the PostgreSQL license.
2852 (license license:gpl2)))
2854 (define-public r-linprog
2861 (uri (cran-uri "linprog" version))
2864 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
2865 (build-system r-build-system)
2866 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
2867 (home-page "http://linprog.r-forge.r-project.org/")
2868 (synopsis "Linear programming and optimization")
2870 "This package can be used to solve Linear Programming / Linear
2871 Optimization problems by using the simplex algorithm.")
2872 (license license:gpl2+)))
2874 (define-public r-geometry
2881 (uri (cran-uri "geometry" version))
2884 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
2885 (build-system r-build-system)
2887 `(("r-magic" ,r-magic)
2888 ("r-linprog" ,r-linprog)
2889 ("r-lpsolve" ,r-lpsolve)
2891 ("r-rcppprogress" ,r-rcppprogress)))
2892 (home-page "http://geometry.r-forge.r-project.org/")
2893 (synopsis "Mesh generation and surface tesselation")
2895 "This package makes the qhull library available in R, in a similar manner
2896 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
2897 intersections about a point, Voronoi diagrams, furthest-site Delaunay
2898 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
2899 and higher dimensions. It implements the Quickhull algorithm for computing
2900 the convex hull. Qhull does not support constrained Delaunay triangulations,
2901 or mesh generation of non-convex objects, but the package does include some R
2902 functions that allow for this. Currently the package only gives access to
2903 Delaunay triangulation and convex hull computation.")
2904 ;; The Qhull sources are included and are distributed under a custom
2905 ;; non-copyleft license. The R sources are released under GPL version 2.
2906 (license (list license:gpl2
2907 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
2909 (define-public r-ddalpha
2916 (uri (cran-uri "ddalpha" version))
2919 "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3"))))
2920 (build-system r-build-system)
2923 ("r-class" ,r-class)
2924 ("r-geometry" ,r-geometry)
2927 ("r-robustbase" ,r-robustbase)
2928 ("r-sfsmisc" ,r-sfsmisc)))
2930 `(("gfortran" ,gfortran)))
2931 (home-page "https://cran.r-project.org/web/packages/ddalpha")
2932 (synopsis "Depth-Based classification and calculation of data depth")
2934 "This package contains procedures for depth-based supervised learning,
2935 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
2936 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
2937 statistical depth function to a compact low-dimensional space, where the final
2938 classification is done. It also offers an extension to functional data and
2939 routines for calculating certain notions of statistical depth functions. 50
2940 multivariate and 5 functional classification problems are included.")
2941 (license license:gpl2)))
2943 (define-public r-gower
2950 (uri (cran-uri "gower" version))
2953 "007ivwn1nagpi26qq8iih1c2l61c53glvv60n90hi341ry8vwgxg"))))
2954 (build-system r-build-system)
2955 (home-page "https://github.com/markvanderloo/gower")
2956 (synopsis "Gower's distance")
2958 "This package provides tools to compute Gower's distance (or similarity)
2959 coefficient between records, and to compute the top-n matches between records.
2960 Core algorithms are executed in parallel on systems supporting OpenMP.")
2961 (license license:gpl3)))
2963 (define-public r-rcpproll
2970 (uri (cran-uri "RcppRoll" version))
2973 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
2974 (properties `((upstream-name . "RcppRoll")))
2975 (build-system r-build-system)
2977 `(("r-rcpp" ,r-rcpp)))
2978 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
2979 (synopsis "Efficient rolling and windowed operations")
2981 "This package provides fast and efficient routines for common rolling /
2982 windowed operations. Routines for the efficient computation of windowed mean,
2983 median, sum, product, minimum, maximum, standard deviation and variance are
2985 (license license:gpl2+)))
2987 (define-public r-ipred
2994 (uri (cran-uri "ipred" version))
2997 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
2998 (build-system r-build-system)
3000 `(("r-class" ,r-class)
3003 ("r-prodlim" ,r-prodlim)
3004 ("r-rpart" ,r-rpart)
3005 ("r-survival" ,r-survival)))
3006 (home-page "https://cran.r-project.org/web/packages/ipred")
3007 (synopsis "Improved predictors")
3009 "This package provides improved predictive models by indirect
3010 classification and bagging for classification, regression and survival
3011 problems as well as resampling based estimators of prediction error.")
3012 (license license:gpl2+)))
3014 (define-public r-psych
3017 (version "1.9.12.31")
3021 (uri (cran-uri "psych" version))
3024 "02i9p6appf15hjdsi58g39bzs9as40f9qhy8m7ki30hd1fz1vrr5"))))
3025 (build-system r-build-system)
3027 `(("r-lattice" ,r-lattice)
3028 ("r-mnormt" ,r-mnormt)
3029 ("r-nlme" ,r-nlme)))
3030 (home-page "https://cran.r-project.org/web/packages/psych/")
3031 (synopsis "Procedures for psychological, psychometric, and personality research")
3033 "This package provides a general purpose toolbox for personality,
3034 psychometric theory and experimental psychology. Functions are primarily for
3035 multivariate analysis and scale construction using factor analysis, principal
3036 component analysis, cluster analysis and reliability analysis, although others
3037 provide basic descriptive statistics. Item Response Theory is done using
3038 factor analysis of tetrachoric and polychoric correlations. Functions for
3039 analyzing data at multiple levels include within and between group statistics,
3040 including correlations and factor analysis. Functions for simulating and
3041 testing particular item and test structures are included. Several functions
3042 serve as a useful front end for structural equation modeling. Graphical
3043 displays of path diagrams, factor analysis and structural equation models are
3044 created using basic graphics.")
3045 (license license:gpl2+)))
3047 (define-public r-generics
3054 (uri (cran-uri "generics" version))
3057 "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi"))))
3058 (build-system r-build-system)
3059 (home-page "https://github.com/r-lib/generics")
3060 (synopsis "Common S3 generics not provided by base R methods")
3062 "In order to reduce potential package dependencies and conflicts,
3063 generics provides a number of commonly used S3 generics that are not provided
3064 by base R methods related to model fitting.")
3065 (license license:gpl2)))
3067 (define-public r-broom
3074 (uri (cran-uri "broom" version))
3077 "0n7zd64263kfavdi28rl2bxrsa00c3m4vjhhjdrfwvvmrcxj39fx"))))
3078 (build-system r-build-system)
3080 `(("r-backports" ,r-backports)
3081 ("r-dplyr" ,r-dplyr)
3082 ("r-generics" ,r-generics)
3084 ("r-purrr" ,r-purrr)
3085 ("r-reshape2" ,r-reshape2)
3086 ("r-stringr" ,r-stringr)
3087 ("r-tibble" ,r-tibble)
3088 ("r-tidyr" ,r-tidyr)))
3089 (home-page "https://github.com/tidyverse/broom")
3090 (synopsis "Convert statistical analysis objects into tidy data frames")
3092 "This package provides tools to convert statistical analysis objects from
3093 R into tidy data frames, so that they can more easily be combined, reshaped
3094 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
3095 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
3096 summarizes a model's statistical findings such as coefficients of a
3097 regression; @code{augment}, which adds columns to the original data such as
3098 predictions, residuals and cluster assignments; and @code{glance}, which
3099 provides a one-row summary of model-level statistics.")
3100 (license license:expat)))
3102 (define-public r-recipes
3109 (uri (cran-uri "recipes" version))
3112 "1fmnka583sqm6v5bhxbllb4cd5xfqbf268aij2xgxiwckv3c0ynm"))))
3113 (build-system r-build-system)
3115 `(("r-dplyr" ,r-dplyr)
3116 ("r-generics" ,r-generics)
3118 ("r-gower" ,r-gower)
3119 ("r-ipred" ,r-ipred)
3120 ("r-lubridate" ,r-lubridate)
3121 ("r-magrittr" ,r-magrittr)
3122 ("r-matrix" ,r-matrix)
3123 ("r-purrr" ,r-purrr)
3124 ("r-rlang" ,r-rlang)
3125 ("r-tibble" ,r-tibble)
3126 ("r-tidyr" ,r-tidyr)
3127 ("r-tidyselect" ,r-tidyselect)
3128 ("r-timedate" ,r-timedate)
3129 ("r-withr" ,r-withr)))
3130 (home-page "https://github.com/topepo/recipes")
3131 (synopsis "Preprocessing tools to create design matrices")
3133 "Recipes is an extensible framework to create and preprocess design
3134 matrices. Recipes consist of one or more data manipulation and analysis
3135 \"steps\". Statistical parameters for the steps can be estimated from an
3136 initial data set and then applied to other data sets. The resulting design
3137 matrices can then be used as inputs into statistical or machine learning
3139 (license license:gpl2)))
3141 (define-public r-pdist
3148 (uri (cran-uri "pdist" version))
3151 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
3152 (build-system r-build-system)
3153 (home-page "https://github.com/jeffwong/pdist")
3154 (synopsis "Partitioned distance function")
3156 "Pdist computes the euclidean distance between rows of a matrix X and
3157 rows of another matrix Y. Previously, this could be done by binding the two
3158 matrices together and calling @code{dist}, but this creates unnecessary
3159 computation by computing the distances between a row of X and another row of
3160 X, and likewise for Y. Pdist strictly computes distances across the two
3161 matrices, not within the same matrix, making computations significantly faster
3162 for certain use cases.")
3163 (license license:gpl3+)))
3165 (define-public r-ggrepel
3172 (uri (cran-uri "ggrepel" version))
3175 "1qaifn3dazdqbqlii210xhw7yf142iw7g9p2axmmxbz90p0by08d"))))
3176 (build-system r-build-system)
3178 `(("r-ggplot2" ,r-ggplot2)
3180 ("r-scales" ,r-scales)))
3182 `(("r-knitr" ,r-knitr))) ; for vignettes
3183 (home-page "http://github.com/slowkow/ggrepel")
3184 (synopsis "Repulsive text and label geometries for ggplot2")
3186 "This package provides text and label geometries for ggplot2 that help to
3187 avoid overlapping text labels. Labels repel away from each other and away
3188 from the data points.")
3189 (license license:gpl3)))
3191 (define-public r-corrplot
3198 (uri (cran-uri "corrplot" version))
3201 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
3202 (build-system r-build-system)
3203 (home-page "https://github.com/taiyun/corrplot")
3204 (synopsis "Visualization of a correlation matrix")
3206 "This package provides a graphical display of a correlation matrix or
3207 general matrix. It also contains some algorithms to do matrix reordering. In
3208 addition, corrplot is good at details, including choosing color, text labels,
3209 color labels, layout, etc.")
3210 ;; Any version of the GPL
3211 (license license:gpl2+)))
3213 (define-public r-stringdist
3215 (name "r-stringdist")
3220 (uri (cran-uri "stringdist" version))
3222 (base32 "1dqfakclzaf878x7mhwmqrcpcql2h9cv19fz5f3ygpajf3si5kqi"))))
3223 (build-system r-build-system)
3224 (home-page "https://github.com/markvanderloo/stringdist")
3225 (synopsis "Approximate string matching and string distance functions")
3227 "This package implements an approximate string matching version of R's
3228 native @code{match} function. It can calculate various string distances based
3229 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
3230 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
3231 Jaro-Winkler). An implementation of soundex is provided as well. Distances
3232 can be computed between character vectors while taking proper care of encoding
3233 or between integer vectors representing generic sequences.")
3234 (license license:gpl3+)))
3236 (define-public r-ucminf
3243 (uri (cran-uri "ucminf" version))
3246 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
3247 (build-system r-build-system)
3248 (native-inputs `(("gfortran" ,gfortran)))
3249 (home-page "https://cran.r-project.org/web/packages/ucminf/")
3250 (synopsis "General-purpose unconstrained non-linear optimization")
3252 "This package provides an implementation of an algorithm for
3253 general-purpose unconstrained non-linear optimization. The algorithm is of
3254 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
3255 search with a trust region type monitoring of the input to the line search
3256 algorithm. The interface of @code{ucminf} is designed for easy interchange
3257 with the package @code{optim}.")
3258 (license license:gpl2+)))
3260 (define-public r-ordinal
3263 (version "2019.12-10")
3267 (uri (cran-uri "ordinal" version))
3270 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
3271 (build-system r-build-system)
3273 `(("r-mass" ,r-mass)
3274 ("r-matrix" ,r-matrix)
3275 ("r-numderiv" ,r-numderiv)
3276 ("r-ucminf" ,r-ucminf)))
3277 (home-page "https://github.com/runehaubo/ordinal")
3278 (synopsis "Regression models for ordinal data")
3280 "This package provides an implementation of cumulative link (mixed)
3281 models also known as ordered regression models, proportional odds models,
3282 proportional hazards models for grouped survival times and ordered models.
3283 Estimation is via maximum likelihood and mixed models are fitted with the
3284 Laplace approximation and adaptive Gauss-Hermite quadrature.")
3285 (license license:gpl2+)))
3287 (define-public r-jomo
3294 (uri (cran-uri "jomo" version))
3297 "1k9l4290g350zbw1pjs871q9bxj3j2h1dilxpp06v4wy4n7d8qs0"))))
3298 (build-system r-build-system)
3300 `(("r-lme4" ,r-lme4)
3302 ("r-ordinal" ,r-ordinal)
3303 ("r-survival" ,r-survival)))
3304 (home-page "https://cran.r-project.org/web/packages/jomo/")
3305 (synopsis "Multilevel Joint Modelling Multiple Imputation")
3307 "Similarly to Schafer's package pan, jomo is a package for multilevel
3308 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
3309 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
3310 possibility of handling binary and categorical data through latent normal
3311 variables, the option to use cluster-specific covariance matrices and to
3312 impute compatibly with the substantive model.")
3313 (license license:gpl2)))
3315 (define-public r-pan
3322 (uri (cran-uri "pan" version))
3325 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
3326 (build-system r-build-system)
3327 (native-inputs `(("gfortran" ,gfortran)))
3328 (home-page "https://cran.r-project.org/web/packages/pan/")
3329 (synopsis "Multiple imputation for multivariate panel or clustered data")
3331 "This package implements multiple imputation for multivariate panel or
3333 (license license:gpl3)))
3335 (define-public r-mitml
3342 (uri (cran-uri "mitml" version))
3345 "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
3346 (build-system r-build-system)
3348 `(("r-haven" ,r-haven)
3351 (home-page "https://cran.r-project.org/web/packages/mitml/")
3352 (synopsis "Tools for multiple imputation in multilevel modeling")
3354 "This package provides tools for multiple imputation of missing data in
3355 multilevel modeling. It includes a user-friendly interface to the packages
3356 pan and jomo, and several functions for visualization, data management and the
3357 analysis of multiply imputed data sets.")
3358 (license license:gpl2+)))
3360 (define-public r-mice
3367 (uri (cran-uri "mice" version))
3370 "1ibybvigqkkla4xwhqs2w4m6c68alfcdsljx99nn4p92rzb1ig04"))))
3371 (build-system r-build-system)
3373 `(("r-broom" ,r-broom)
3374 ("r-dplyr" ,r-dplyr)
3375 ("r-lattice" ,r-lattice)
3377 ("r-tidyr" ,r-tidyr)))
3378 (home-page "https://cran.r-project.org/web/packages/mice/")
3379 (synopsis "Multivariate imputation by chained equations")
3381 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
3382 implemented by the MICE algorithm as described in @url{Van Buuren and
3383 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
3384 variable has its own imputation model. Built-in imputation models are
3385 provided for continuous data (predictive mean matching, normal), binary
3386 data (logistic regression), unordered categorical data (polytomous logistic
3387 regression) and ordered categorical data (proportional odds). MICE can also
3388 impute continuous two-level data (normal model, pan, second-level variables).
3389 Passive imputation can be used to maintain consistency between variables.
3390 Various diagnostic plots are available to inspect the quality of the
3392 ;; Any of these two versions.
3393 (license (list license:gpl2 license:gpl3))))
3395 (define-public r-truncnorm
3397 (name "r-truncnorm")
3402 (uri (cran-uri "truncnorm" version))
3405 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
3406 (build-system r-build-system)
3407 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
3408 (synopsis "Truncated normal distribution")
3409 (description "This package provides functions for the truncated normal
3410 distribution with mean equal to @code{mean} and standard deviation equal to
3411 @code{sd}. It includes density, distribution, quantile, and expected value
3412 functions, as well as a random generation function.")
3413 (license license:gpl2)))
3415 (define-public r-rsolnp
3422 (uri (cran-uri "Rsolnp" version))
3425 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
3426 (properties `((upstream-name . "Rsolnp")))
3427 (build-system r-build-system)
3429 `(("r-truncnorm" ,r-truncnorm)))
3430 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
3431 (synopsis "General non-linear optimization")
3432 (description "The Rsolnp package implements a general non-linear augmented
3433 Lagrange multiplier method solver, a @dfn{sequential quadratic
3434 programming} (SQP) based solver).")
3435 ;; Any version of the GPL.
3436 (license license:gpl2+)))
3438 (define-public r-hardyweinberg
3440 (name "r-hardyweinberg")
3445 (uri (cran-uri "HardyWeinberg" version))
3448 "1irz44q6nf95h37av868f47aakwv3jgwgw217xfsfw0afkm7s25f"))))
3449 (properties `((upstream-name . "HardyWeinberg")))
3450 (build-system r-build-system)
3452 `(("r-mice" ,r-mice)
3454 ("r-rsolnp" ,r-rsolnp)))
3455 (home-page "https://cran.r-project.org/package=HardyWeinberg")
3456 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
3458 "This package contains tools for exploring Hardy-Weinberg equilibrium for
3459 diallelic genetic marker data. All classical tests (chi-square, exact,
3460 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
3461 included in the package, as well as functions for power computation and for
3462 the simulation of marker data under equilibrium and disequilibrium. Routines
3463 for dealing with markers on the X-chromosome are included. Functions for
3464 testing equilibrium in the presence of missing data by using multiple
3465 imputation are also provided. Implements several graphics for exploring the
3466 equilibrium status of a large set of diallelic markers: ternary plots with
3467 acceptance regions, log-ratio plots and Q-Q plots.")
3468 (license license:gpl2+)))
3477 (uri (cran-uri "sm" version))
3480 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
3481 (build-system r-build-system)
3482 (native-inputs `(("gfortran" ,gfortran)))
3483 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
3484 (synopsis "Smoothing methods for nonparametric regression and density estimation")
3486 "This is software accompanying the book 'Applied Smoothing Techniques for
3487 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
3488 University Press. It provides smoothing methods for nonparametric regression
3489 and density estimation")
3490 (license license:gpl2+)))
3492 (define-public r-venndiagram
3494 (name "r-venndiagram")
3498 (uri (cran-uri "VennDiagram" version))
3501 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
3502 (properties `((upstream-name . "VennDiagram")))
3503 (build-system r-build-system)
3505 `(("r-futile-logger" ,r-futile-logger)))
3506 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
3507 (synopsis "Generate High-Resolution Venn and Euler Plots")
3509 "This package provides a set of functions to generate high-resolution
3510 Venn and Euler plots. It includes handling for several special cases,
3511 including two-case scaling, and extensive customization of plot shape and
3513 (license license:gpl2+)))
3515 (define-public r-vioplot
3522 (uri (cran-uri "vioplot" version))
3525 "1fsklymilspzz5fzlj7666x09aglaw0v4x0yfjjzy4vr5qpjc529"))))
3526 (build-system r-build-system)
3530 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
3531 (synopsis "Violin plot")
3533 "This package provides a violin plot, which is a combination of a box
3534 plot and a kernel density plot.")
3535 (license license:bsd-3)))
3537 (define-public r-rsofia
3543 ;; This package has been removed from CRAN, so we can
3544 ;; only fetch it from the archives.
3545 (uri (string-append "https://cran.r-project.org/src/"
3546 "contrib/Archive/RSofia/RSofia_"
3550 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
3551 (properties `((upstream-name . "RSofia")))
3552 (build-system r-build-system)
3554 `(("r-rcpp" ,r-rcpp)))
3555 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
3556 (synopsis "Port of sofia-ml to R")
3557 (description "This package is a port of sofia-ml to R. Sofia-ml is a
3558 suite of fast incremental algorithms for machine learning that can be used for
3559 training models for classification or ranking.")
3560 (license license:asl2.0)))
3562 (define-public r-xts
3569 (uri (cran-uri "xts" version))
3572 "0q4cc8ynp7ndmgll1jj3lxyl6wmgg89ad3wq09kjc2ngszdfc4fz"))))
3573 (build-system r-build-system)
3574 (propagated-inputs `(("r-zoo" ,r-zoo)))
3575 (home-page "https://github.com/joshuaulrich/xts")
3576 (synopsis "Extensible time series")
3578 "This package provides for uniform handling of R's different time-based
3579 data classes by extending @code{zoo}, maximizing native format information
3580 preservation and allowing for user-level customization and extension, while
3581 simplifying cross-class interoperability.")
3582 (license license:gpl2+)))
3584 (define-public r-performanceanalytics
3586 (name "r-performanceanalytics")
3591 (uri (cran-uri "PerformanceAnalytics" version))
3594 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
3596 `((upstream-name . "PerformanceAnalytics")))
3597 (build-system r-build-system)
3599 `(("r-quadprog" ,r-quadprog)
3602 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
3603 (synopsis "Econometric tools for performance and risk analysis")
3604 (description "This is a collection of econometric functions for
3605 performance and risk analysis. This package aims to aid practitioners and
3606 researchers in utilizing the latest research in analysis of non-normal return
3607 streams. In general, it is most tested on return (rather than price) data on
3608 a regular scale, but most functions will work with irregular return data as
3609 well, and increasing numbers of functions will work with P&L or price data
3611 ;; Either version may be picked.
3612 (license (list license:gpl2 license:gpl3))))
3614 (define-public r-laeken
3621 (uri (cran-uri "laeken" version))
3624 "199rjkhjjygpr6cjzab87as46acb5npi44m4yycvk7lnd0blma8s"))))
3625 (build-system r-build-system)
3627 `(("r-boot" ,r-boot)
3628 ("r-mass" ,r-mass)))
3629 (home-page "https://cran.r-project.org/web/packages/laeken/")
3630 (synopsis "Estimation of indicators on social exclusion and poverty")
3631 (description "This package provides tools for the estimation of indicators
3632 on social exclusion and poverty, as well as an implementation of Pareto tail
3633 modeling for empirical income distributions.")
3634 (license license:gpl2+)))
3636 (define-public r-vcd
3643 (uri (cran-uri "vcd" version))
3646 "0rjz49py5l6wnaimw6k8rcyzlvs8cyz5g2xwqj2qis92ly0l103z"))))
3647 (build-system r-build-system)
3649 `(("r-colorspace" ,r-colorspace)
3650 ("r-lmtest" ,r-lmtest)
3651 ("r-mass" ,r-mass)))
3652 (home-page "https://cran.r-project.org/web/packages/vcd/")
3653 (synopsis "Visualizing categorical data")
3654 (description "This package provides visualization techniques, data sets,
3655 summary and inference procedures aimed particularly at categorical data.
3656 Special emphasis is given to highly extensible grid graphics. The package was
3657 originally inspired by the book \"Visualizing Categorical Data\" by Michael
3658 Friendly and is now the main support package for a new book, \"Discrete Data
3659 Analysis with R\" by Michael Friendly and David Meyer (2015).")
3660 (license license:gpl2)))
3662 (define-public r-ica
3669 (uri (cran-uri "ica" version))
3672 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
3673 (build-system r-build-system)
3674 (home-page "https://cran.r-project.org/web/packages/ica/")
3675 (synopsis "Independent component analysis")
3676 (description "This package provides tools for @dfn{Independent Component
3677 Analysis} (ICA) using various algorithms: FastICA,
3678 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
3679 of Eigenmatrices} (JADE).")
3680 (license license:gpl2+)))
3682 (define-public r-dtw
3689 (uri (cran-uri "dtw" version))
3692 "02hyhx1sy5h3vzh9zixy18a7d47df4k5d0wyflcvlcbsbcl6p90s"))))
3693 (build-system r-build-system)
3694 (propagated-inputs `(("r-proxy" ,r-proxy)))
3695 (home-page "http://dtw.r-forge.r-project.org/")
3696 (synopsis "Dynamic Time Warping Algorithms")
3697 (description "This package provides a comprehensive implementation of
3698 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
3699 optimal (least cumulative distance) alignment between points of two time
3700 series. Common DTW variants covered include local (slope) and global (window)
3701 constraints, subsequence matches, arbitrary distance definitions,
3702 normalizations, minimum variance matching, and so on.")
3703 (license license:gpl2+)))
3705 (define-public r-sdmtools
3708 (version "1.1-221.2")
3712 (uri (cran-uri "SDMTools" version))
3715 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
3716 (properties `((upstream-name . "SDMTools")))
3717 (build-system r-build-system)
3718 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
3719 (home-page "https://www.rforge.net/SDMTools/")
3720 (synopsis "Species distribution modelling tools")
3721 (description "This package provides a set of tools for post processing
3722 the outcomes of species distribution modeling exercises. It includes novel
3723 methods for comparing models and tracking changes in distributions through
3724 time. It further includes methods for visualizing outcomes, selecting
3725 thresholds, calculating measures of accuracy and landscape fragmentation
3727 (license license:gpl3+)))
3729 (define-public r-scatterplot3d
3731 (name "r-scatterplot3d")
3736 (uri (cran-uri "scatterplot3d" version))
3739 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
3740 (build-system r-build-system)
3741 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
3742 (synopsis "3D scatter plot")
3743 (description "This package provides an implementation of scatter plots for
3744 plotting. a three dimensional point cloud.")
3745 (license license:gpl2)))
3747 (define-public r-ggridges
3754 (uri (cran-uri "ggridges" version))
3757 "03pz257aw0mkh5k75rby9givkc1ky3n5scvhjhjiz9vry9fpffmh"))))
3758 (build-system r-build-system)
3760 `(("r-ggplot2" ,r-ggplot2)
3762 ("r-scales" ,r-scales)
3763 ("r-withr" ,r-withr)))
3764 (home-page "https://github.com/clauswilke/ggridges")
3765 (synopsis "Ridgeline plots in ggplot2")
3767 "Ridgeline plots provide a convenient way of visualizing changes in
3768 distributions over time or space. This package enables the creation of such
3769 plots in @code{ggplot2}.")
3770 (license license:gpl2)))
3772 (define-public r-ggjoy
3779 (uri (cran-uri "ggjoy" version))
3782 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
3783 (build-system r-build-system)
3785 `(("r-ggplot2" ,r-ggplot2)
3786 ("r-ggridges" ,r-ggridges)))
3787 (home-page "https://github.com/clauswilke/ggjoy")
3788 (synopsis "Joyplots in ggplot2")
3789 (description "Joyplots provide a convenient way of visualizing changes in
3790 distributions over time or space. This package enables the creation of such
3791 plots in @code{ggplot2}.")
3792 (license license:gpl2)))
3794 (define-public r-cli
3801 (uri (cran-uri "cli" version))
3804 "1dhkah6jvr96k4h4agcc2rfls75bpjb0j58fzaz3dc0fp3jk8229"))))
3805 (build-system r-build-system)
3807 `(("r-assertthat" ,r-assertthat)
3808 ("r-crayon" ,r-crayon)
3809 ("r-fansi" ,r-fansi)
3810 ("r-glue" ,r-glue)))
3811 (home-page "https://github.com/r-lib/cli#readme")
3812 (synopsis "Helpers for developing command line interfaces")
3813 (description "This package provides a suite of tools designed to build
3814 attractive command line interfaces (CLIs). It includes tools for drawing
3815 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
3816 (license license:expat)))
3818 (define-public r-argparser
3820 (name "r-argparser")
3825 (uri (cran-uri "argparser" version))
3828 "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x"))))
3829 (build-system r-build-system)
3830 (home-page "https://bitbucket.org/djhshih/argparser")
3831 (synopsis "Command-line argument parser")
3833 "This package provides a cross-platform command-line argument parser
3834 written purely in R with no external dependencies. It is useful with the
3835 Rscript front-end and facilitates turning an R script into an executable
3837 (license license:gpl3+)))
3839 (define-public r-debugme
3846 (uri (cran-uri "debugme" version))
3849 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
3850 (build-system r-build-system)
3851 (propagated-inputs `(("r-crayon" ,r-crayon)))
3852 (home-page "https://github.com/r-lib/debugme#readme")
3853 (synopsis "Debug R packages")
3855 "This package allows the user to specify debug messages as special string
3856 constants, and control debugging of packages via environment variables.")
3857 (license license:expat)))
3859 (define-public r-processx
3866 (uri (cran-uri "processx" version))
3869 "02awswxq6wh3rl99dncw5n6c1xmd0v81xcdp2dfyi6vm6b3gz84l"))))
3870 (build-system r-build-system)
3874 (home-page "https://github.com/r-lib/processx3")
3875 (synopsis "Execute and control system processes")
3877 "This package provides portable tools to run system processes in the
3878 background. It can check if a background process is running; wait on a
3879 background process to finish; get the exit status of finished processes; kill
3880 background processes and their children; restart processes. It can read the
3881 standard output and error of the processes, using non-blocking connections.
3882 @code{processx} can poll a process for standard output or error, with a
3883 timeout. It can also poll several processes at once.")
3884 (license license:expat)))
3886 (define-public r-tsp
3893 (uri (cran-uri "TSP" version))
3896 "183m6crb0dv17llj86059n3hbgsahbhfcqlx0ijdzkssg11i1cy7"))))
3897 (properties `((upstream-name . "TSP")))
3898 (build-system r-build-system)
3899 (propagated-inputs `(("r-foreach" ,r-foreach)))
3900 (home-page "https://cran.r-project.org/web/packages/TSP/")
3901 (synopsis "Traveling salesperson problem (TSP)")
3902 (description "This package provides basic infrastructure and some
3903 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
3904 traveling salesman problem).")
3905 (license license:gpl3)))
3907 (define-public r-qap
3914 (uri (cran-uri "qap" version))
3917 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
3918 (build-system r-build-system)
3919 (native-inputs `(("gfortran" ,gfortran)))
3920 (home-page "https://cran.r-project.org/web/packages/qap/")
3921 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
3922 (description "This package implements heuristics for the @dfn{quadratic
3923 assignment problem} (QAP). Currently only a simulated annealing heuristic is
3925 (license license:gpl3)))
3927 (define-public r-gclus
3934 (uri (cran-uri "gclus" version))
3937 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
3938 (build-system r-build-system)
3939 (propagated-inputs `(("r-cluster" ,r-cluster)))
3940 (home-page "https://cran.r-project.org/web/packages/gclus/")
3941 (synopsis "Clustering graphics")
3942 (description "This package orders panels in scatterplot matrices and
3943 parallel coordinate displays by some merit index. It contains various indices
3944 of merit, ordering functions, and enhanced versions of @code{pairs} and
3945 @code{parcoord} which color panels according to their merit level.")
3946 (license license:gpl2+)))
3948 (define-public r-webshot
3955 (uri (cran-uri "webshot" version))
3958 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
3959 (build-system r-build-system)
3961 `(("r-callr" ,r-callr)
3962 ("r-jsonlite" ,r-jsonlite)
3963 ("r-magrittr" ,r-magrittr)))
3964 (home-page "https://github.com/wch/webshot/")
3965 (synopsis "Take screenshots of web pages")
3967 "Webshot makes it easy to take screenshots of web pages from within R.
3968 It can also run Shiny applications locally and take screenshots of the
3969 application; and it can render and screenshot static as well as interactive R
3970 Markdown documents.")
3971 (license license:gpl2)))
3973 (define-public r-seriation
3975 (name "r-seriation")
3980 (uri (cran-uri "seriation" version))
3983 "1zbdxq0s5rc5v307b69fw9k52m0654ls7pf22lh35ggirig6lwsk"))))
3984 (build-system r-build-system)
3986 `(("r-cluster" ,r-cluster)
3987 ("r-colorspace" ,r-colorspace)
3988 ("r-dendextend" ,r-dendextend)
3989 ("r-gclus" ,r-gclus)
3990 ("r-gplots" ,r-gplots)
3993 ("r-registry" ,r-registry)
3995 (native-inputs `(("gfortran" ,gfortran)))
3996 (home-page "https://s2.smu.edu/IDA/seriation/")
3997 (synopsis "Infrastructure for ordering objects using seriation")
3999 "This package provides infrastructure for seriation with an
4000 implementation of several seriation/sequencing techniques to reorder matrices,
4001 dissimilarity matrices, and dendrograms. It also provides (optimally)
4002 reordered heatmaps, color images and clustering visualizations like
4003 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
4005 (license license:gpl3)))
4007 (define-public r-xfun
4014 (uri (cran-uri "xfun" version))
4016 (base32 "0sgh8kafi9x1glmmcp1ly827pm8q7fsfngbplr41fbb4nc9363df"))))
4017 (build-system r-build-system)
4018 (home-page "https://github.com/yihui/xfun")
4019 (synopsis "Miscellaneous functions")
4021 "This package provides miscellaneous functions commonly used in other
4022 packages maintained by Yihui Xie.")
4023 (license license:expat)))
4025 (define-public r-utf8
4032 (uri (cran-uri "utf8" version))
4035 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
4036 (build-system r-build-system)
4037 (home-page "https://github.com/patperry/r-utf8")
4038 (synopsis "Unicode text processing")
4040 "This package provides tools to process and print UTF-8 encoded
4041 international text (Unicode). Input, validate, normalize, encode, format, and
4043 (license license:asl2.0)))
4045 (define-public r-zeallot
4052 (uri (cran-uri "zeallot" version))
4055 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
4056 (build-system r-build-system)
4057 (home-page "https://github.com/nteetor/zeallot")
4058 (synopsis "Multiple, unpacking, and destructuring assignment")
4060 "This package provides a @code{%<-%} operator to perform multiple,
4061 unpacking, and destructuring assignment in R. The operator unpacks the
4062 right-hand side of an assignment into multiple values and assigns these values
4063 to variables on the left-hand side of the assignment.")
4064 (license license:expat)))
4066 (define-public r-vctrs
4073 (uri (cran-uri "vctrs" version))
4076 "1pnjnxp1pwsr083qa6xp5akls6q0pnjz8pq2m9d7z3kc1886sw8w"))))
4077 (build-system r-build-system)
4079 `(("r-digest" ,r-digest)
4080 ("r-ellipsis" ,r-ellipsis)
4082 ("r-rlang" ,r-rlang)))
4083 (home-page "https://github.com/r-lib/vctrs")
4084 (synopsis "Vector helpers")
4086 "There are three main goals to the @code{vctrs} package:
4089 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
4090 @code{length()} and @code{class()}. These definitions are paired with a
4091 framework for type-coercion and size-recycling.
4092 @item To define type- and size-stability as desirable function properties, use
4093 them to analyse existing base function, and to propose better alternatives.
4094 This work has been particularly motivated by thinking about the ideal
4095 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
4096 @item To provide a new @code{vctr} base class that makes it easy to create new
4097 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
4098 a few new @code{vctrs} generics, making implementation considerably simpler
4101 (license license:gpl3)))
4103 (define-public r-pillar
4110 (uri (cran-uri "pillar" version))
4113 "02sn7zw80wq33jgxk2i6m5jb83sk7y72dfhgyy0apfinv05w92ss"))))
4114 (build-system r-build-system)
4117 ("r-crayon" ,r-crayon)
4118 ("r-fansi" ,r-fansi)
4119 ("r-rlang" ,r-rlang)
4121 ("r-vctrs" ,r-vctrs)))
4122 (home-page "https://github.com/r-lib/pillar")
4123 (synopsis "Coloured formatting for columns")
4125 "This package provides a @code{pillar} generic designed for formatting
4126 columns of data using the full range of colours provided by modern
4128 (license license:gpl3)))
4130 (define-public r-uuid
4137 (uri (cran-uri "uuid" version))
4140 "0gm9ii7ncvllxbvyk6srsiinjmqyj7lmh84w43x4nhqpvafj9q4q"))))
4141 (build-system r-build-system)
4142 (home-page "http://www.rforge.net/uuid")
4143 (synopsis "Tools for generating and handling of UUIDs")
4145 "This package provides tools for generating and handling of
4146 @dfn{Universally Unique Identifiers} (UUIDs).")
4147 (license license:expat)))
4149 (define-public r-tinytex
4156 (uri (cran-uri "tinytex" version))
4159 "0n8v8inpsc99r0snvqbjhqlc6nm9hxjsw120hrxc2mw03pa5fvkg"))))
4160 (build-system r-build-system)
4162 `(("r-xfun" ,r-xfun)))
4163 (home-page "https://github.com/yihui/tinytex")
4164 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
4166 "This package provides helper functions to install and maintain the LaTeX
4167 distribution named TinyTeX, a lightweight, cross-platform, portable, and
4168 easy-to-maintain version of TeX Live. This package also contains helper
4169 functions to compile LaTeX documents, and install missing LaTeX packages
4171 (license license:expat)))
4173 (define-public r-network
4180 (uri (cran-uri "network" version))
4183 "0dnf1wl3za2lhx2lwd8smhlijl1cfhckgr8zz9piiirrfi2m2kx2"))))
4184 (build-system r-build-system)
4186 `(("r-magrittr" ,r-magrittr)
4187 ("r-tibble" ,r-tibble)))
4188 (home-page "https://statnet.org/")
4189 (synopsis "Classes for relational data")
4191 "This package provides tools to create and modify network objects. The
4192 @code{network} class can represent a range of relational data types, and
4193 supports arbitrary vertex/edge/graph attributes.")
4194 (license license:gpl2+)))
4196 (define-public r-statnet-common
4198 (name "r-statnet-common")
4203 (uri (cran-uri "statnet.common" version))
4206 "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3"))))
4208 `((upstream-name . "statnet.common")))
4209 (build-system r-build-system)
4211 `(("r-coda" ,r-coda)))
4212 (home-page "https://statnet.org")
4213 (synopsis "R scripts and utilities used by the Statnet software")
4214 (description "This package provides non-statistical utilities used by the
4215 software developed by the Statnet Project.")
4216 (license license:gpl3)))
4218 (define-public r-statcheck
4220 (name "r-statcheck")
4225 (uri (cran-uri "statcheck" version))
4228 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
4229 (build-system r-build-system)
4231 `(("r-ggplot2" ,r-ggplot2)
4233 ("r-rmarkdown" ,r-rmarkdown)))
4234 (home-page "https://cran.r-project.org/web/packages/statcheck/")
4235 (synopsis "Extract statistics from articles and recompute p-values")
4236 (description "This package can automatically extract statistical
4237 null-hypothesis significant testing (NHST) results from articles and recompute
4238 the p-values based on the reported test statistic and degrees of freedom to
4239 detect possible inconsistencies.")
4240 (license license:gpl2)))
4242 (define-public r-sna
4249 (uri (cran-uri "sna" version))
4252 "1j3i6300m686qqfmyvadim377cd3mplzgj6mandygw8brg50id8k"))))
4253 (build-system r-build-system)
4255 `(("r-network" ,r-network)
4256 ("r-statnet-common" ,r-statnet-common)))
4257 (home-page "https://statnet.org")
4258 (synopsis "Tools for social network analysis")
4260 "This package provides a range of tools for social network analysis,
4261 including node and graph-level indices, structural distance and covariance
4262 methods, structural equivalence detection, network regression, random graph
4263 generation, and 2D/3D network visualization.")
4264 (license license:gpl2+)))
4266 (define-public r-tfisher
4273 (uri (cran-uri "TFisher" version))
4276 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
4277 (properties `((upstream-name . "TFisher")))
4278 (build-system r-build-system)
4280 `(("r-matrix" ,r-matrix)
4281 ("r-mvtnorm" ,r-mvtnorm)
4283 (home-page "https://cran.r-project.org/web/packages/TFisher/")
4284 (synopsis "Optimal thresholding Fisher's p-value combination method")
4286 "This package provides the @dfn{cumulative distribution function} (CDF),
4287 quantile, and statistical power calculator for a collection of thresholding
4288 Fisher's p-value combination methods, including Fisher's p-value combination
4289 method, truncated product method and, in particular, soft-thresholding
4290 Fisher's p-value combination method which is proven to be optimal in some
4291 context of signal detection. The p-value calculator for the omnibus version
4292 of these tests are also included.")
4293 (license license:gpl2)))
4295 (define-public r-ttr
4302 (uri (cran-uri "TTR" version))
4305 "0rg22ma3x07s9djlxscfw5jcq1gbir05cwhgvwfi53x1sf4hmhdg"))))
4306 (properties `((upstream-name . "TTR")))
4307 (build-system r-build-system)
4309 `(("r-curl" ,r-curl)
4312 (home-page "https://github.com/joshuaulrich/TTR")
4313 (synopsis "Technical trading rules")
4315 "This package provides functions and data to construct technical trading
4317 (license license:gpl2)))
4319 (define-public r-leaps
4326 (uri (cran-uri "leaps" version))
4329 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
4330 (build-system r-build-system)
4331 (native-inputs `(("gfortran" ,gfortran)))
4332 (home-page "https://cran.r-project.org/web/packages/leaps/")
4333 (synopsis "Regression subset selection")
4335 "This package provides tools for regression subset selection, including
4336 exhaustive search.")
4337 (license license:gpl2+)))
4339 (define-public r-splus2r
4346 (uri (cran-uri "splus2R" version))
4349 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
4350 (properties `((upstream-name . "splus2R")))
4351 (build-system r-build-system)
4352 (native-inputs `(("gfortran" ,gfortran)))
4353 (home-page "https://cran.r-project.org/web/packages/splus2R/")
4354 (synopsis "Supplemental S-PLUS functionality in R")
4356 "Currently there are many functions in S-PLUS that are missing in R. To
4357 facilitate the conversion of S-PLUS packages to R packages, this package
4358 provides some missing S-PLUS functionality in R.")
4359 (license license:gpl2)))
4361 (define-public r-ifultools
4363 (name "r-ifultools")
4368 (uri (cran-uri "ifultools" version))
4371 "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j"))))
4372 (build-system r-build-system)
4374 `(("r-mass" ,r-mass)
4375 ("r-splus2r" ,r-splus2r)))
4376 (home-page "https://cran.r-project.org/web/packages/ifultools/")
4377 (synopsis "Insightful research tools")
4378 (description "This package provides C code used by the wmtsa, fractal, and
4380 (license license:gpl2)))
4382 (define-public r-sapa
4389 (uri (cran-uri "sapa" version))
4392 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
4393 (build-system r-build-system)
4395 `(("r-ifultools" ,r-ifultools)
4396 ("r-splus2r" ,r-splus2r)))
4397 (home-page "https://cran.r-project.org/web/packages/sapa/")
4398 (synopsis "Spectral analysis for physical applications")
4399 (description "This package provides software for the book Spectral
4400 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
4401 Cambridge University Press, 1993.")
4402 (license license:gpl2)))
4404 (define-public r-aggregation
4406 (name "r-aggregation")
4411 (uri (cran-uri "aggregation" version))
4414 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
4415 (build-system r-build-system)
4416 (home-page "https://cran.r-project.org/web/packages/aggregation/")
4417 (synopsis "Methods for p-value aggregation")
4419 "This package contains functionality for performing the following methods
4420 of p-value aggregation: Fisher's method, the Lancaster method (weighted
4421 Fisher's method), and Sidak correction.")
4422 (license license:gpl3)))
4424 (define-public r-quantmod
4431 (uri (cran-uri "quantmod" version))
4434 "12l5br8abr1yagxqjnjvqzp79sqsv5vx56cxs37gk73r474f4vc2"))))
4435 (build-system r-build-system)
4437 `(("r-curl" ,r-curl)
4441 (home-page "https://cran.r-project.org/web/packages/quantmod/")
4442 (synopsis "Quantitative financial modelling framework")
4443 (description "This package provides a quantitative financial modelling
4444 framework to allow users to specify, build, trade, and analyse quantitative
4445 financial trading strategies.")
4446 (license license:gpl3)))
4448 (define-public r-tseries
4455 (uri (cran-uri "tseries" version))
4458 "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
4459 (build-system r-build-system)
4461 `(("r-quadprog" ,r-quadprog)
4462 ("r-quantmod" ,r-quantmod)
4465 `(("gfortran" ,gfortran)))
4466 (home-page "https://cran.r-project.org/web/packages/tseries/")
4467 (synopsis "Time series analysis and computational finance")
4469 "This package provides functions relating to time series analysis and
4470 computational finance.")
4471 (license license:gpl2)))
4473 (define-public r-wmtsa
4480 (uri (cran-uri "wmtsa" version))
4483 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
4484 (build-system r-build-system)
4486 `(("r-ifultools" ,r-ifultools)
4488 ("r-splus2r" ,r-splus2r)))
4489 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
4490 (synopsis "Wavelet methods for time series analysis")
4492 "This package provides software to accompany the book \"Wavelet Methods
4493 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
4494 University Press, 2000.")
4495 (license license:gpl2)))
4497 (define-public r-tsa
4504 (uri (cran-uri "TSA" version))
4507 "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q"))))
4508 (properties `((upstream-name . "TSA")))
4509 (build-system r-build-system)
4511 `(("r-leaps" ,r-leaps)
4512 ("r-locfit" ,r-locfit)
4513 ("r-mgcv" ,r-mgcv)))
4514 (home-page "http://www.stat.uiowa.edu/~kchan/TSA.htm")
4515 (synopsis "Time series analysis")
4517 "This package contains R functions and datasets detailed in the book
4518 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
4519 Cryer and Kung-Sik Chan.")
4520 (license license:gpl2+)))
4522 (define-public r-extradistr
4524 (name "r-extradistr")
4529 (uri (cran-uri "extraDistr" version))
4532 "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3"))))
4533 (properties `((upstream-name . "extraDistr")))
4534 (build-system r-build-system)
4536 `(("r-rcpp" ,r-rcpp)))
4537 (home-page "https://github.com/twolodzko/extraDistr")
4538 (synopsis "Additional univariate and multivariate distributions")
4540 "This package implements density, distribution functions, quantile
4541 functions and random generation functions for a large number of univariate and
4542 multivariate distributions.")
4543 (license license:gpl2)))
4545 (define-public r-fractal
4552 (uri (cran-uri "fractal" version))
4555 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
4556 (build-system r-build-system)
4558 `(("r-ifultools" ,r-ifultools)
4561 ("r-scatterplot3d" ,r-scatterplot3d)
4562 ("r-splus2r" ,r-splus2r)
4563 ("r-wmtsa" ,r-wmtsa)))
4564 (home-page "https://cran.r-project.org/web/packages/fractal/")
4565 (synopsis "Fractal time series modeling and analysis")
4567 "This package provides tools for stochastic fractal and deterministic
4568 chaotic time series analysis.")
4569 (license license:gpl2)))
4571 (define-public r-urca
4578 (uri (cran-uri "urca" version))
4581 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
4582 (build-system r-build-system)
4583 (propagated-inputs `(("r-nlme" ,r-nlme)))
4584 (native-inputs `(("gfortran" ,gfortran)))
4585 (home-page "https://cran.r-project.org/web/packages/urca/")
4586 (synopsis "Unit root and cointegration tests for time series data")
4588 "This package provides unit root and cointegration tests encountered in
4589 applied econometric analysis.")
4590 (license license:gpl2+)))
4592 (define-public r-cubature
4599 (uri (cran-uri "cubature" version))
4602 "0jpyq8j7x06dpiz29w48av879ygldzgls9z810192hsymkmfaz6r"))))
4603 (build-system r-build-system)
4605 `(("r-rcpp" ,r-rcpp)))
4606 (home-page "https://github.com/bnaras/cubature")
4607 (synopsis "Adaptive multivariate integration over hypercubes")
4609 "This package is an R wrapper around the cubature C library for adaptive
4610 multivariate integration over hypercubes. This version provides both
4611 @code{hcubature} and @code{pcubature} routines in addition to a vector
4613 ;; The included cubature C library is released under GPLv2+, but the
4614 ;; wrapper declares the license to be GPLv3+.
4615 (license (list license:gpl2+ license:gpl3+))))
4617 (define-public r-trend
4624 (uri (cran-uri "trend" version))
4627 "09b6ycyfgs4xlhx6kn6qm5rl2acp58hzhv8qclzn3kb1wjjyvxy5"))))
4628 (build-system r-build-system)
4630 `(("r-extradistr" ,r-extradistr)))
4632 `(("gfortran" ,gfortran)))
4633 (home-page "https://cran.r-project.org/web/packages/trend/")
4634 (synopsis "Non-parametric trend tests and change-point detection")
4636 "The analysis of environmental data often requires the detection of
4637 trends and change-points. This package includes tests for trend
4638 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
4639 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
4640 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
4641 correlation trend test), change-point detection (Lanzante's test procedures,
4642 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
4643 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
4644 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
4645 sample Robust Rank-Order Distributional Test.")
4646 (license license:gpl3)))
4648 (define-public r-expm
4655 (uri (cran-uri "expm" version))
4658 "15k0acg2aqb2ajhwal6l7vhhp03m4lg579805d34554cl0kn9l2q"))))
4659 (build-system r-build-system)
4660 (propagated-inputs `(("r-matrix" ,r-matrix)))
4661 (native-inputs `(("gfortran" ,gfortran)))
4662 (home-page "https://r-forge.r-project.org/projects/expm/")
4663 (synopsis "Tools for matrix exponentials and related quantities")
4665 "This package provides tools for the computation of the matrix
4666 exponential, logarithm, square root, and related quantities.")
4667 (license license:gpl2+)))
4669 (define-public r-complexplus
4671 (name "r-complexplus")
4676 (uri (cran-uri "complexplus" version))
4679 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
4680 (build-system r-build-system)
4682 `(("r-expm" ,r-expm)
4683 ("r-matrix" ,r-matrix)))
4684 (home-page "https://cran.r-project.org/web/packages/complexplus/")
4685 (synopsis "Functions of complex or real variables")
4687 "This package extends several functions to the complex domain, including
4688 the matrix exponential and logarithm, and the determinant.")
4689 (license license:gpl2)))
4691 (define-public r-phontools
4693 (name "r-phontools")
4698 (uri (cran-uri "phonTools" version))
4701 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
4702 (properties `((upstream-name . "phonTools")))
4703 (build-system r-build-system)
4704 (home-page "http://www.santiagobarreda.com/rscripts.html")
4705 (synopsis "Tools for phonetic and acoustic analyses")
4707 "This package contains tools for the organization, display, and analysis
4708 of the sorts of data frequently encountered in phonetics research and
4709 experimentation, including the easy creation of IPA vowel plots, and the
4710 creation and manipulation of WAVE audio files.")
4711 (license license:bsd-2)))
4720 (uri (cran-uri "np" version))
4723 "06h8k0kdv5s258jr6s08fabvlycrbs7iq34jk2f2hfmqm2y4nyx2"))))
4724 (build-system r-build-system)
4726 `(("r-boot" ,r-boot)
4727 ("r-cubature" ,r-cubature)
4728 ("r-quadprog" ,r-quadprog)
4729 ("r-quantreg" ,r-quantreg)))
4730 (home-page "https://github.com/JeffreyRacine/R-Package-np")
4731 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
4732 (description "This package provides non-parametric (and semi-parametric)
4733 kernel methods that seamlessly handle a mix of continuous, unordered, and
4734 ordered factor data types.")
4735 ;; Any version of the GPL.
4736 (license license:gpl3+)))
4738 (define-public r-powerplus
4740 (name "r-powerplus")
4745 (uri (cran-uri "powerplus" version))
4748 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
4749 (build-system r-build-system)
4751 `(("r-complexplus" ,r-complexplus)
4754 ("r-matrix" ,r-matrix)
4755 ("r-phontools" ,r-phontools)))
4756 (home-page "https://cran.r-project.org/web/packages/powerplus/")
4757 (synopsis "Exponentiation operations")
4759 "This package provides tools for the computation of matrix and scalar
4761 (license license:gpl2)))
4763 (define-public r-egg
4770 (uri (cran-uri "egg" version))
4773 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
4774 (properties `((upstream-name . "egg")))
4775 (build-system r-build-system)
4777 `(("r-ggplot2" ,r-ggplot2)
4778 ("r-gridextra" ,r-gridextra)
4779 ("r-gtable" ,r-gtable)))
4780 (home-page "https://cran.r-project.org/web/packages/egg")
4781 (synopsis "Extensions for ggplot2")
4783 "This package provides miscellaneous functions to help customize ggplot2
4784 objects. High-level functions are provided to post-process ggplot2 layouts
4785 and allow alignment between plot panels, as well as setting panel sizes to
4786 fixed values. Other functions include a custom @code{geom}, and helper
4787 functions to enforce symmetric scales or add tags to facetted plots.")
4788 (license license:gpl3)))
4790 (define-public r-heatmaply
4792 (name "r-heatmaply")
4797 (uri (cran-uri "heatmaply" version))
4800 "0576gml3bcl7r1biigzj1rag2xzz422knbw7arc8d2gsakjj757g"))))
4801 (build-system r-build-system)
4803 `(("r-assertthat" ,r-assertthat)
4804 ("r-colorspace" ,r-colorspace)
4805 ("r-dendextend" ,r-dendextend)
4807 ("r-ggplot2" ,r-ggplot2)
4808 ("r-htmlwidgets" ,r-htmlwidgets)
4809 ("r-magrittr" ,r-magrittr)
4810 ("r-plotly" ,r-plotly)
4811 ("r-rcolorbrewer" ,r-rcolorbrewer)
4812 ("r-reshape2" ,r-reshape2)
4813 ("r-scales" ,r-scales)
4814 ("r-seriation" ,r-seriation)
4815 ("r-viridis" ,r-viridis)
4816 ("r-webshot" ,r-webshot)))
4818 `(("r-knitr" ,r-knitr)))
4819 (home-page "https://cran.r-project.org/package=heatmaply")
4820 (synopsis "Interactive cluster heat maps using plotly")
4822 "This package enables you to create interactive cluster heatmaps that can
4823 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
4824 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
4825 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
4826 a popular graphical method for visualizing high-dimensional data, in which a
4827 table of numbers is encoded as a grid of colored cells. The rows and columns
4828 of the matrix are ordered to highlight patterns and are often accompanied by
4830 ;; Either version of the license.
4831 (license (list license:gpl2 license:gpl3))))
4840 (uri (cran-uri "h5" version))
4843 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
4844 (build-system r-build-system)
4849 `(("which" ,which)))
4851 `(("r-rcpp" ,r-rcpp)))
4852 (home-page "https://github.com/mannau/h5")
4853 (synopsis "Interface to the HDF5 Library")
4855 "This package provides an S4 interface to the HDF5 library supporting
4856 fast storage and retrieval of R-objects like vectors, matrices and arrays to
4857 binary files in a language independent format. The HDF5 format can therefore
4858 be used as an alternative to R's save/load mechanism. Since h5 is able to
4859 access only subsets of stored data it can also handle data sets which do not
4861 (license license:bsd-2)))
4863 (define-public r-cgdsr
4870 (uri (cran-uri "cgdsr" version))
4873 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
4874 (build-system r-build-system)
4876 `(("r-httr" ,r-httr)
4877 ("r-r-methodss3" ,r-r-methodss3)
4878 ("r-r-oo" ,r-r-oo)))
4879 (home-page "https://github.com/cBioPortal/cgdsr")
4880 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
4882 "This package provides a basic set of R functions for querying the Cancer
4883 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
4884 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
4885 (license license:lgpl3)))
4887 (define-public r-import
4894 (uri (cran-uri "import" version))
4897 "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
4898 (build-system r-build-system)
4899 (home-page "https://github.com/smbache/import")
4900 (synopsis "Import mechanism for R")
4902 "This is an alternative mechanism for importing objects from packages.
4903 The syntax allows for importing multiple objects from a package with a single
4904 command in an expressive way. The import package bridges some of the gap
4905 between using @code{library} (or @code{require}) and direct (single-object)
4906 imports. Furthermore the imported objects are not placed in the current
4907 environment. It is also possible to import objects from stand-alone @code{.R}
4909 (license license:expat)))
4911 (define-public r-shinyace
4918 (uri (cran-uri "shinyAce" version))
4921 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
4922 (properties `((upstream-name . "shinyAce")))
4923 (build-system r-build-system)
4925 `(("r-shiny" ,r-shiny)
4926 ("r-jsonlite" ,r-jsonlite)))
4927 (home-page "http://cran.r-project.org/web/packages/shinyAce")
4928 (synopsis "Ace editor bindings for Shiny")
4930 "This package provides Ace editor bindings to enable a rich text editing
4931 environment within Shiny.")
4932 (license license:expat)))
4934 (define-public r-base64url
4936 (name "r-base64url")
4941 (uri (cran-uri "base64url" version))
4944 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
4945 (build-system r-build-system)
4947 `(("r-backports" ,r-backports)))
4948 (home-page "https://github.com/mllg/base64url")
4949 (synopsis "Fast and URL-safe base64 encoder and decoder")
4951 "This package provides a URL-safe base64 encoder and decoder. In
4952 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
4953 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
4954 encoder does not fill the string with trailing @code{=}. The resulting
4955 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
4956 and thus are safe to use in URLs or for file names. The package also comes
4957 with a simple base32 encoder/decoder suited for case insensitive file
4959 (license license:gpl3)))
4961 (define-public r-radiant-data
4963 (name "r-radiant-data")
4968 (uri (cran-uri "radiant.data" version))
4971 "08x7zasxf429m021482p86lx3zc6dqz2mih0id8s34isg4gafapg"))
4972 (modules '((guix build utils)))
4975 ;; Delete files that are under CC-NC-SA.
4976 (delete-file-recursively "inst/app/tools/help")
4978 (properties `((upstream-name . "radiant.data")))
4979 (build-system r-build-system)
4981 `(("r-base64enc" ,r-base64enc)
4982 ("r-broom" ,r-broom)
4985 ("r-dplyr" ,r-dplyr)
4988 ("r-ggplot2" ,r-ggplot2)
4989 ("r-gridextra" ,r-gridextra)
4990 ("r-import" ,r-import)
4991 ("r-jsonlite" ,r-jsonlite)
4992 ("r-knitr" ,r-knitr)
4993 ("r-lubridate" ,r-lubridate)
4994 ("r-magrittr" ,r-magrittr)
4995 ("r-markdown" ,r-markdown)
4996 ("r-plotly" ,r-plotly)
4997 ("r-psych" ,r-psych)
4998 ("r-readr" ,r-readr)
4999 ("r-readxl" ,r-readxl)
5000 ("r-rlang" ,r-rlang)
5001 ("r-rmarkdown" ,r-rmarkdown)
5002 ("r-rstudioapi" ,r-rstudioapi)
5003 ("r-scales" ,r-scales)
5004 ("r-shiny" ,r-shiny)
5005 ("r-shinyfiles" ,r-shinyfiles)
5006 ("r-shinyace" ,r-shinyace)
5007 ("r-stringi" ,r-stringi)
5008 ("r-tibble" ,r-tibble)
5009 ("r-tidyr" ,r-tidyr)
5010 ("r-writexl" ,r-writexl)))
5011 (home-page "https://github.com/radiant-rstats/radiant.data")
5012 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
5014 "The Radiant Data menu includes interfaces for loading, saving, viewing,
5015 visualizing, summarizing, transforming, and combining data. It also contains
5016 functionality to generate reproducible reports of the analyses conducted in
5018 (license license:agpl3)))
5020 (define-public r-algdesign
5022 (name "r-algdesign")
5027 (uri (cran-uri "AlgDesign" version))
5029 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
5030 (properties `((upstream-name . "AlgDesign")))
5031 (build-system r-build-system)
5032 (home-page "https://github.com/jvbraun/AlgDesign")
5033 (synopsis "Algorithmic experimental design")
5035 "This package provides tools to calculate exact and approximate theory
5036 experimental designs for D, A, and I criteria. Very large designs may be
5037 created. Experimental designs may be blocked or blocked designs created from
5038 a candidate list, using several criteria. The blocking can be done when whole
5039 and within plot factors interact.")
5040 (license license:gpl2+)))
5042 (define-public r-signal
5049 (uri (cran-uri "signal" version))
5052 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
5053 (build-system r-build-system)
5054 (propagated-inputs `(("r-mass" ,r-mass)))
5055 (native-inputs `(("gfortran" ,gfortran)))
5056 (home-page "https://cran.r-project.org/web/packages/signal/")
5057 (synopsis "Signal processing")
5059 "This package provides a set of signal processing functions originally
5060 written for Matlab and GNU Octave. It includes filter generation utilities,
5061 filtering functions, resampling routines, and visualization of filter models.
5062 It also includes interpolation functions.")
5063 (license license:gpl2)))
5065 (define-public r-gsubfn
5072 (uri (cran-uri "gsubfn" version))
5075 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
5076 (build-system r-build-system)
5077 (propagated-inputs `(("r-proto" ,r-proto)))
5078 (home-page "http://gsubfn.googlecode.com")
5079 (synopsis "Utilities for strings and function arguments.")
5081 "This package provides @code{gsubfn} which is like @code{gsub} but can
5082 take a replacement function or certain other objects instead of the
5083 replacement string. Matches and back references are input to the replacement
5084 function and replaced by the function output. @code{gsubfn} can be used to
5085 split strings based on content rather than delimiters and for quasi-perl-style
5086 string interpolation. The package also has facilities for translating
5087 formulas to functions and allowing such formulas in function calls instead of
5089 (license license:gpl2+)))
5091 (define-public r-sqldf
5098 (uri (cran-uri "sqldf" version))
5101 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
5102 (build-system r-build-system)
5104 `(("r-chron" ,r-chron)
5106 ("r-gsubfn" ,r-gsubfn)
5107 ("r-proto" ,r-proto)
5108 ("r-rsqlite" ,r-rsqlite)))
5109 (home-page "https://github.com/ggrothendieck/sqldf")
5110 (synopsis "Manipulate R data frames using SQL")
5112 "The @code{sqldf} function is typically passed a single argument which is
5113 an SQL select statement where the table names are ordinary R data frame names.
5114 @code{sqldf} transparently sets up a database, imports the data frames into
5115 that database, performs the SQL statement and returns the result using a
5116 heuristic to determine which class to assign to each column of the returned
5117 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
5118 used to read filtered files into R even if the original files are larger than
5119 R itself can handle.")
5120 (license license:gpl2)))
5122 (define-public r-abind
5129 (uri (cran-uri "abind" version))
5132 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
5133 (build-system r-build-system)
5134 (home-page "https://cran.r-project.org/web/packages/abind/")
5135 (synopsis "Combine multidimensional arrays")
5137 "This package provides tools to combine multidimensional arrays into a
5138 single array. This is a generalization of @code{cbind} and @code{rbind}. It
5139 works with vectors, matrices, and higher-dimensional arrays. It also provides
5140 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
5141 extracting and replacing data in arrays.")
5142 (license license:lgpl2.0+)))
5144 (define-public r-prroc
5151 (uri (cran-uri "PRROC" version))
5154 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
5155 (properties `((upstream-name . "PRROC")))
5156 (build-system r-build-system)
5157 (home-page "https://cran.r-project.org/web/packages/PRROC/")
5158 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
5160 "This package computes the areas under the @dfn{precision-recall} (PR)
5161 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
5162 contrast to other implementations, the interpolation between points of the PR
5163 curve is done by a non-linear piecewise function. In addition to the areas
5164 under the curves, the curves themselves can also be computed and plotted by a
5165 specific S3-method.")
5166 (license license:gpl3)))
5168 (define-public r-vim
5175 (uri (cran-uri "VIM" version))
5178 "09600piny3qrxrmh8844iwrvgrhwan1c3nlh6irqy1vjha2w4gb3"))))
5179 (properties `((upstream-name . "VIM")))
5180 (build-system r-build-system)
5183 ("r-colorspace" ,r-colorspace)
5184 ("r-data-table" ,r-data-table)
5185 ("r-e1071" ,r-e1071)
5186 ("r-laeken" ,r-laeken)
5187 ("r-magrittr" ,r-magrittr)
5190 ("r-ranger" ,r-ranger)
5192 ("r-robustbase" ,r-robustbase)
5195 (home-page "https://github.com/alexkowa/VIM")
5196 (synopsis "Visualization and imputation of missing values")
5198 "This package provides tools for the visualization of missing and/or
5199 imputed values are introduced, which can be used for exploring the data and
5200 the structure of the missing and/or imputed values. Depending on this
5201 structure of the missing values, the corresponding methods may help to
5202 identify the mechanism generating the missing values and allows to explore the
5203 data including missing values. In addition, the quality of imputation can be
5204 visually explored using various univariate, bivariate, multiple and
5205 multivariate plot methods.")
5206 (license license:gpl2+)))
5208 (define-public r-fnn
5215 (uri (cran-uri "FNN" version))
5218 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
5219 (properties `((upstream-name . "FNN")))
5220 (build-system r-build-system)
5221 (home-page "https://cran.r-project.org/web/packages/FNN")
5222 (synopsis "Fast nearest neighbor search algorithms and applications")
5224 "This package provides cover-tree and kd-tree fast k-nearest neighbor
5225 search algorithms. Related applications including KNN classification,
5226 regression and information measures are implemented.")
5227 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
5228 ;; later can be used.
5229 (license license:gpl2+)))
5231 (define-public r-smoother
5238 (uri (cran-uri "smoother" version))
5241 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
5242 (build-system r-build-system)
5244 `(("r-ttr" ,r-ttr)))
5245 (home-page "https://cran.r-project.org/web/packages/smoother")
5246 (synopsis "Functions relating to the smoothing of numerical data")
5248 "This package provides a collection of methods for smoothing numerical
5249 data, commencing with a port of the Matlab gaussian window smoothing function.
5250 In addition, several functions typically used in smoothing of financial data
5252 (license license:gpl2)))
5254 (define-public r-riverplot
5256 (name "r-riverplot")
5261 (uri (cran-uri "riverplot" version))
5264 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
5265 (build-system r-build-system)
5266 (home-page "https://logfc.wordpress.com")
5267 (synopsis "Sankey or ribbon plots")
5269 "Sankey plots are a type of diagram that is convenient to illustrate how
5270 flow of information, resources etc. separates and joins, much like observing
5271 how rivers split and merge. For example, they can be used to compare
5272 different clusterings. This package provides an implementation of Sankey
5274 (license license:gpl2+)))
5276 (define-public r-dyn
5283 (uri (cran-uri "dyn" version))
5286 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
5287 (build-system r-build-system)
5289 `(("r-zoo" ,r-zoo)))
5290 (home-page "https://cran.r-project.org/web/packages/dyn")
5291 (synopsis "Time series regression")
5293 "This package provides the dyn class interfaces @code{ts}, @code{irts},
5294 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
5295 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
5296 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
5297 @code{randomForest::randomForest()} and other regression functions, allowing
5298 those functions to be used with time series including specifications that may
5299 contain lags, diffs and missing values.")
5301 (license license:gpl2+)))
5303 (define-public r-catdap
5310 (uri (cran-uri "catdap" version))
5313 "0i877l61f6c75pczi235rzci67w29zv1d7z5zn5p5ymndclvlpl2"))))
5314 (build-system r-build-system)
5316 `(("gfortran" ,gfortran)))
5317 (home-page "https://cran.r-project.org/web/packages/catdap/")
5318 (synopsis "Tools for categorical data analysis")
5320 "This package provides functions for analyzing multivariate data.
5321 Dependencies of the distribution of the specified variable (response
5322 variable) to other variables (explanatory variables) are derived and
5323 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
5324 (license license:gpl2+)))
5326 (define-public r-arules
5333 (uri (cran-uri "arules" version))
5336 "003c5cd3xzq39h7c19px077ygm0n1v7k83icy5zzrnkagyds2p8n"))))
5337 (build-system r-build-system)
5339 `(("r-matrix" ,r-matrix)))
5340 (home-page "https://github.com/mhahsler/arules")
5341 (synopsis "Mining association rules and frequent itemsets")
5343 "This package provides an infrastructure for representing, manipulating
5344 and analyzing transaction data and patterns (frequent itemsets and association rules).
5345 It also provides C implementations of the association mining algorithms Apriori
5347 (license license:gpl3)))
5349 (define-public r-parsedate
5351 (name "r-parsedate")
5356 (uri (cran-uri "parsedate" version))
5359 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
5360 (build-system r-build-system)
5362 `(("r-rematch2" ,r-rematch2)))
5363 (home-page "https://github.com/gaborcsardi/parsedate")
5365 "Recognize and parse dates in various formats")
5367 "This package provides three functions for dealing with dates:
5368 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
5369 time formats, @code{parse_date} parses dates in unspecified formats,
5370 and @code{format_iso_8601} formats a date in ISO 8601 format.")
5371 (license license:gpl2)))
5373 (define-public r-abc-data
5380 (uri (cran-uri "abc.data" version))
5383 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
5384 (properties `((upstream-name . "abc.data")))
5385 (build-system r-build-system)
5386 (home-page "https://cran.r-project.org/web/packages/abc.data/")
5387 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
5389 "This package contains data which are used by functions of the abc
5390 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
5391 algorithms for performing parameter estimation, model selection, and
5393 (license license:gpl3+)))
5395 (define-public r-abc
5402 (uri (cran-uri "abc" version))
5405 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
5406 (build-system r-build-system)
5408 `(("r-abc-data" ,r-abc-data)
5409 ("r-locfit" ,r-locfit)
5412 ("r-quantreg" ,r-quantreg)))
5413 (home-page "https://cran.r-project.org/web/packages/abc/")
5414 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
5416 "This package implements several @dfn{Approximate Bayesian
5417 Computation} (ABC) algorithms for performing parameter estimation, model
5418 selection, and goodness-of-fit. Cross-validation tools are also available for
5419 measuring the accuracy of ABC estimates, and to calculate the
5420 misclassification probabilities of different models.")
5421 (license license:gpl3+)))
5423 (define-public r-zip
5430 (uri (cran-uri "zip" version))
5433 "1c02amk3pl6xir5jnbfiwiv2wvpkpbkkb1w71y6lf2yk7g3d0pdb"))))
5434 (build-system r-build-system)
5435 (home-page "https://github.com/gaborcsardi/zip")
5436 (synopsis "Cross-platform Zip compression")
5438 "This package provides a cross-platform Zip compression library for R.
5439 It is a replacement for the @code{zip} function, that does not require any
5440 additional external tools on any platform.")
5441 (license license:cc0)))
5443 (define-public r-openxlsx
5450 (uri (cran-uri "openxlsx" version))
5453 "1mwxldw9i9nfksx1i6h1kfs7vmsz9fgyllbsipar4vnfyqhqp8q7"))))
5454 (build-system r-build-system)
5456 `(("r-rcpp" ,r-rcpp)
5457 ("r-stringi" ,r-stringi)
5459 (home-page "https://github.com/awalker89/openxlsx")
5460 (synopsis "Read, write and edit XLSX files")
5462 "This package simplifies the creation of Excel @code{.xlsx} files by
5463 providing a high level interface to writing, styling and editing worksheets.
5464 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
5465 and @code{XLConnect} packages with the added benefit of removing the
5466 dependency on Java.")
5467 (license license:gpl3)))
5469 (define-public r-rio
5476 (uri (cran-uri "rio" version))
5479 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
5480 (build-system r-build-system)
5482 `(("r-curl" ,r-curl)
5483 ("r-data-table" ,r-data-table)
5484 ("r-foreign" ,r-foreign)
5485 ("r-haven" ,r-haven)
5486 ("r-openxlsx" ,r-openxlsx)
5487 ("r-readxl" ,r-readxl)
5488 ("r-tibble" ,r-tibble)))
5489 (home-page "https://github.com/leeper/rio")
5490 (synopsis "Swiss-army knife for data I/O")
5492 "This package provides streamlined data import and export infrastructure
5493 by making assumptions that the user is probably willing to make: @code{import}
5494 and @code{export} determine the data structure from the file extension,
5495 reasonable defaults are used for data import and export (e.g.,
5496 @code{stringsAsFactors=FALSE}), web-based import is natively
5497 supported (including from SSL/HTTPS), compressed files can be read directly
5498 without explicit decompression, and fast import packages are used where
5499 appropriate. An additional convenience function, @code{convert}, provides a
5500 simple method for converting between file types.")
5501 (license license:gpl2)))
5503 (define-public r-maptools
5510 (uri (cran-uri "maptools" version))
5513 "0v4llkxk8qs61vq4ykvaim4k23aagdaz0p62ns7zfq02sln3pfk9"))))
5514 (build-system r-build-system)
5516 `(("r-foreign" ,r-foreign)
5517 ("r-lattice" ,r-lattice)
5519 (home-page "http://r-forge.r-project.org/projects/maptools/")
5520 (synopsis "Tools for reading and handling spatial objects")
5522 "This package provides a set of tools for manipulating and reading
5523 geographic data, in particular ESRI Shapefiles. It includes binary access to
5524 GSHHG shoreline files. The package also provides interface wrappers for
5525 exchanging spatial objects with other R packages.")
5526 ;; The C source files from shapelib are released under the Expat license.
5527 ;; The R code is released under GPL version 2 or later.
5528 (license (list license:gpl2+
5531 (define-public r-later
5538 (uri (cran-uri "later" version))
5541 "11xjavj7siz0xv2ffq1ld4bwl35jyrcfpvvs4p3ilpifxx49hyr7"))))
5542 (build-system r-build-system)
5546 ("r-rlang" ,r-rlang)))
5547 (home-page "https://github.com/r-lib/later")
5548 (synopsis "Utilities for delaying function execution")
5550 "This package provides tools to execute arbitrary R or C functions some
5551 time after the current time, after the R execution stack has emptied.")
5552 (license license:gpl2+)))
5554 (define-public r-promises
5561 (uri (cran-uri "promises" version))
5564 "01l0ydjvvy6afcg5d6pzvk1ikd3djq8n2flv8c831ksn68z0zsn8"))))
5565 (build-system r-build-system)
5567 `(("r-later" ,r-later)
5568 ("r-magrittr" ,r-magrittr)
5571 ("r-rlang" ,r-rlang)))
5572 (home-page "https://rstudio.github.io/promises")
5573 (synopsis "Abstractions for promise-based asynchronous programming")
5575 "This package provides fundamental abstractions for doing asynchronous
5576 programming in R using promises. Asynchronous programming is useful for
5577 allowing a single R process to orchestrate multiple tasks in the background
5578 while also attending to something else. Semantics are similar to JavaScript
5579 promises, but with a syntax that is idiomatic R.")
5580 (license license:expat)))
5582 (define-public r-dosnow
5589 (uri (cran-uri "doSNOW" version))
5592 "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh"))))
5593 (properties `((upstream-name . "doSNOW")))
5594 (build-system r-build-system)
5596 `(("r-foreach" ,r-foreach)
5597 ("r-iterators" ,r-iterators)
5598 ("r-snow" ,r-snow)))
5599 (home-page "https://cran.r-project.org/web/packages/doSNOW")
5600 (synopsis "Foreach parallel adaptor for the snow package")
5602 "This package provides a parallel backend for the @code{%dopar%} function
5603 using the @code{snow} package.")
5604 (license license:gpl2)))
5606 (define-public r-snowfall
5609 (version "1.84-6.1")
5612 (uri (cran-uri "snowfall" version))
5614 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
5615 (build-system r-build-system)
5617 `(("r-snow" ,r-snow)))
5618 (home-page "http://cran.r-project.org/web/packages/snowfall/")
5619 (synopsis "Easier cluster computing")
5620 (description "This package is a usability wrapper around snow for easier
5621 development of parallel R programs. This package offers e.g. extended error
5622 checks, and additional functions. All functions work in sequential mode, too,
5623 if no cluster is present or wished. The package is also designed as connector
5624 to the cluster management tool @code{sfCluster}, but can also used without
5626 (license license:gpl2+)))
5628 (define-public r-rappdirs
5635 (uri (cran-uri "rappdirs" version))
5638 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
5639 (build-system r-build-system)
5640 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
5641 (synopsis "Determine where to save data, caches, and logs")
5643 "This package provides an easy way to determine which directories on the
5644 user's computer should be used to save data, caches and logs. It is a port of
5645 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
5646 (license license:expat)))
5648 (define-public r-renv
5655 (uri (cran-uri "renv" version))
5658 "02ayfgbpw4b58148dcxz31anaxncwczmxs1zzkskwj0rzhb2x60r"))))
5659 (properties `((upstream-name . "renv")))
5660 (build-system r-build-system)
5661 (home-page "https://rstudio.github.io/renv")
5662 (synopsis "Project environments")
5664 "This package provides a dependency management toolkit for R. Using
5665 renv, you can create and manage project-local R libraries, save the state of
5666 these libraries to a lockfile, and later restore your library as required.
5667 Together, these tools can help make your projects more isolated, portable, and
5669 (license license:expat)))
5671 (define-public r-learnr
5678 (uri (cran-uri "learnr" version))
5681 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
5682 (build-system r-build-system)
5684 `(("r-checkmate" ,r-checkmate)
5685 ("r-ellipsis" ,r-ellipsis)
5686 ("r-evaluate" ,r-evaluate)
5687 ("r-htmltools" ,r-htmltools)
5688 ("r-htmlwidgets" ,r-htmlwidgets)
5689 ("r-jsonlite" ,r-jsonlite)
5690 ("r-knitr" ,r-knitr)
5691 ("r-markdown" ,r-markdown)
5692 ("r-rappdirs" ,r-rappdirs)
5694 ("r-rmarkdown" ,r-rmarkdown)
5695 ("r-rprojroot" ,r-rprojroot)
5696 ("r-shiny" ,r-shiny)
5697 ("r-withr" ,r-withr)))
5698 (home-page "https://rstudio.github.io/learnr/")
5699 (synopsis "Interactive tutorials for R")
5701 "This package provides tools to create interactive tutorials using R
5702 Markdown. Use a combination of narrative, figures, videos, exercises, and
5703 quizzes to create self-paced tutorials for learning about R and R packages.")
5704 (license license:asl2.0)))
5706 (define-public r-analytics
5708 (name "r-analytics")
5713 (uri (cran-uri "analytics" version))
5716 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
5717 (build-system r-build-system)
5720 ("r-cluster" ,r-cluster)
5721 ("r-fractal" ,r-fractal)
5722 ("r-lmtest" ,r-lmtest)
5725 ("r-powerplus" ,r-powerplus)
5726 ("r-robust" ,r-robust)
5727 ("r-trend" ,r-trend)
5731 (home-page "https://cran.r-project.org/web/packages/analytics/")
5732 (synopsis "Collection of data analysis tools")
5734 "This package is a collection of data analysis tools. It includes tools
5735 for regression outlier detection in a fitted linear model, stationary
5736 bootstrap using a truncated geometric distribution, a comprehensive test for
5737 weak stationarity, column means by group, weighted biplots, and a heuristic to
5738 obtain a better initial configuration in non-metric MDS.")
5739 (license license:gpl2)))
5741 (define-public r-reticulate
5743 (name "r-reticulate")
5748 (uri (cran-uri "reticulate" version))
5751 "0icb9zl9zlx75njv7y1dr450k0yw2n3q2jkr4nicnphdyfn69gkn"))))
5752 (build-system r-build-system)
5753 (inputs `(("python" ,python)))
5755 `(("r-rappdirs" ,r-rappdirs)
5756 ("r-jsonlite" ,r-jsonlite)
5757 ("r-matrix" ,r-matrix)
5758 ("r-rcpp" ,r-rcpp)))
5759 (home-page "https://github.com/rstudio/reticulate")
5760 (synopsis "R interface to Python")
5762 "This package provides an interface from R to Python modules, classes,
5763 and functions. When calling into Python, R data types are automatically
5764 converted to their equivalent Python types. When values are returned from
5765 Python to R they are converted back to R types.")
5766 (license license:asl2.0)))
5768 (define-public r-bibtex
5775 (uri (cran-uri "bibtex" version))
5778 "140hkjzdp3033cvji861rd06z1ixgpnn4n5amygqsmhnixk8ff07"))))
5779 (build-system r-build-system)
5780 (propagated-inputs `(("r-stringr" ,r-stringr)))
5781 (home-page "https://github.com/romainfrancois/bibtex")
5782 (synopsis "Bibtex parser")
5783 (description "This package provides a utility for R to parse a bibtex
5785 (license license:gpl2+)))
5787 (define-public r-ggseqlogo
5789 (name "r-ggseqlogo")
5794 (uri (cran-uri "ggseqlogo" version))
5797 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
5798 (build-system r-build-system)
5799 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
5800 (home-page "https://github.com/omarwagih/ggseqlogo")
5801 (synopsis "ggplot2 extension for drawing genetic sequence logos")
5803 "The range of functions provided by this package makes it possible to
5804 draw highly versatile genomic sequence logos. Features include, but are not
5805 limited to, modifying colour schemes and fonts used to draw the logo,
5806 generating multiple logo plots, and aiding the visualisation with annotations.
5807 Sequence logos can easily be combined with other ggplot2 plots.")
5808 ;; Unspecified version of the LGPL.
5809 (license license:lgpl3+)))
5811 (define-public r-ggsci
5818 (uri (cran-uri "ggsci" version))
5821 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
5822 (build-system r-build-system)
5824 `(("r-ggplot2" ,r-ggplot2)
5825 ("r-scales" ,r-scales)))
5826 (home-page "https://nanx.me/ggsci/")
5827 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
5829 "This package provides a collection of ggplot2 color palettes inspired by
5830 plots in scientific journals, data visualization libraries, science fiction
5831 movies, and TV shows.")
5832 (license license:gpl3)))
5834 (define-public r-ggsignif
5841 (uri (cran-uri "ggsignif" version))
5844 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
5845 (build-system r-build-system)
5847 `(("r-ggplot2" ,r-ggplot2)))
5848 (home-page "https://github.com/const-ae/ggsignif")
5849 (synopsis "Significance brackets for ggplot2")
5851 "Enrich your ggplots with group-wise comparisons. This package provides
5852 an easy way to indicate if two groups are significantly different. Commonly
5853 this is shown by a bracket on top connecting the groups of interest which
5854 itself is annotated with the level of significance. The package provides a
5855 single layer that takes the groups for comparison and the test as arguments
5856 and adds the annotation to the plot.")
5857 (license license:gpl3)))
5859 (define-public r-ggpubr
5866 (uri (cran-uri "ggpubr" version))
5869 "0kb3hpmnhj4mkbx1kx0kv5y22himr8dijqx7ra0h8hi0pf2l2ha7"))))
5870 (build-system r-build-system)
5872 `(("r-cowplot" ,r-cowplot)
5873 ("r-dplyr" ,r-dplyr)
5874 ("r-ggplot2" ,r-ggplot2)
5875 ("r-ggrepel" ,r-ggrepel)
5876 ("r-ggsci" ,r-ggsci)
5877 ("r-ggsignif" ,r-ggsignif)
5879 ("r-gridextra" ,r-gridextra)
5880 ("r-magrittr" ,r-magrittr)
5881 ("r-polynom" ,r-polynom)
5882 ("r-purrr" ,r-purrr)
5883 ("r-rlang" ,r-rlang)
5884 ("r-scales" ,r-scales)
5885 ("r-tidyr" ,r-tidyr)))
5886 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
5887 (synopsis "ggplot2-based publication-ready plots")
5889 "The ggplot2 package is an excellent and flexible package for elegant
5890 data visualization in R. However the default generated plots require some
5891 formatting before we can send them for publication. The ggpubr package
5892 provides some easy-to-use functions for creating and customizing ggplot2-based
5893 publication-ready plots.")
5894 (license license:gpl2)))
5896 (define-public r-ellipse
5903 (uri (cran-uri "ellipse" version))
5906 "0g82vc51m3c1k0hnpp2zla6amxxgk2mmkl8ssnsc49jv3599r6hs"))))
5907 (build-system r-build-system)
5908 (home-page "https://cran.r-project.org/web/packages/ellipse/")
5909 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
5911 "This package contains various routines for drawing ellipses and
5912 ellipse-like confidence regions, implementing the plots described in Murdoch
5913 and Chow (1996), A graphical display of large correlation matrices, The
5914 American Statistician 50, 178-180. There are also routines implementing the
5915 profile plots described in Bates and Watts (1988), Nonlinear Regression
5916 Analysis and its Applications.")
5917 (license license:gpl2+)))
5919 (define-public r-flashclust
5921 (name "r-flashclust")
5926 (uri (cran-uri "flashClust" version))
5929 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
5930 (properties `((upstream-name . "flashClust")))
5931 (build-system r-build-system)
5932 (native-inputs `(("gfortran" ,gfortran)))
5933 (home-page "https://cran.r-project.org/web/packages/flashClust/")
5934 (synopsis "Implementation of optimal hierarchical clustering")
5936 "This package provides a fast implementation of hierarchical
5938 (license license:gpl2+)))
5940 (define-public r-factominer
5942 (name "r-factominer")
5947 (uri (cran-uri "FactoMineR" version))
5950 "0ldgf3daksh6lpblhqys67m4mxqx3q9s9n5plfam6dwshfik0ky6"))))
5951 (properties `((upstream-name . "FactoMineR")))
5952 (build-system r-build-system)
5955 ("r-cluster" ,r-cluster)
5956 ("r-ellipse" ,r-ellipse)
5957 ("r-flashclust" ,r-flashclust)
5958 ("r-ggplot2" ,r-ggplot2)
5959 ("r-ggrepel" ,r-ggrepel)
5960 ("r-lattice" ,r-lattice)
5961 ("r-leaps" ,r-leaps)
5963 ("r-scatterplot3d" ,r-scatterplot3d)))
5964 (home-page "http://factominer.free.fr")
5965 (synopsis "Multivariate exploratory data analysis and data mining")
5967 "This package provides exploratory data analysis methods to summarize,
5968 visualize and describe datasets. The main principal component methods are
5969 available, those with the largest potential in terms of applications:
5970 principal component analysis (PCA) when variables are quantitative,
5971 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
5972 variables are categorical, Multiple Factor Analysis when variables are
5973 structured in groups, etc. and hierarchical cluster analysis.")
5974 (license license:gpl2+)))
5976 (define-public r-factoextra
5978 (name "r-factoextra")
5983 (uri (cran-uri "factoextra" version))
5986 "0bpsbcmp6jpa9qk53dhfzghrz98dh0h0n68brl7rjz724yjbvhn8"))))
5987 (build-system r-build-system)
5989 `(("r-abind" ,r-abind)
5990 ("r-cluster" ,r-cluster)
5991 ("r-dendextend" ,r-dendextend)
5992 ("r-factominer" ,r-factominer)
5993 ("r-ggplot2" ,r-ggplot2)
5994 ("r-ggpubr" ,r-ggpubr)
5995 ("r-ggrepel" ,r-ggrepel)
5996 ("r-reshape2" ,r-reshape2)
5997 ("r-tidyr" ,r-tidyr)))
5998 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
5999 (synopsis "Extract and visualize the results of multivariate data analyses")
6001 "This package provides some easy-to-use functions to extract and
6002 visualize the output of multivariate data analyses, including
6003 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
6004 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
6005 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
6006 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
6007 packages. It contains also functions for simplifying some clustering analysis
6008 steps and provides ggplot2-based elegant data visualization.")
6009 (license license:gpl2)))
6011 (define-public r-fansi
6018 (uri (cran-uri "fansi" version))
6021 "028ywjy538psnmdnddvy5jr3idzffr4hikzr4x97x0m30g4fws9w"))))
6022 (build-system r-build-system)
6024 `(("r-knitr" ,r-knitr))) ; for vignettes
6025 (home-page "https://github.com/brodieG/fansi")
6026 (synopsis "ANSI control sequence aware string functions")
6028 "This package provides counterparts to R string manipulation functions
6029 that account for the effects of ANSI text formatting control sequences.")
6030 (license license:gpl2+)))
6032 (define-public r-nbclust
6039 (uri (cran-uri "NbClust" version))
6042 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
6043 (properties `((upstream-name . "NbClust")))
6044 (build-system r-build-system)
6045 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
6046 (synopsis "Determine the best number of clusters in a data set")
6048 "NbClust provides 30 indexes for determining the optimal number of
6049 clusters in a data set and offers the best clustering scheme from different
6050 results to the user.")
6051 (license license:gpl2)))
6053 (define-public r-hdf5r
6060 (uri (cran-uri "hdf5r" version))
6063 "0hvi2cvyv6zlxgpawnmsihxclp2ln88slbrnmaxagmjswskxsrpx"))))
6064 (build-system r-build-system)
6069 `(("r-bit64" ,r-bit64)
6071 (home-page "https://hhoeflin.github.io/hdf5r")
6072 (synopsis "Interface to the HDF5 binary data format")
6074 "HDF5 is a data model, library and file format for storing and managing
6075 large amounts of data. This package provides a nearly feature complete,
6076 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
6077 functionality is added so that HDF5 objects behave very similar to their
6078 corresponding R counterparts.")
6079 (license license:asl2.0)))
6081 (define-public r-itertools
6083 (name "r-itertools")
6088 (uri (cran-uri "itertools" version))
6091 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
6092 (build-system r-build-system)
6094 `(("r-iterators" ,r-iterators)))
6095 (home-page "https://cran.r-project.org/web/packages/itertools/")
6096 (synopsis "Iterator tools")
6098 "This package provides various tools for creating iterators, many
6099 patterned after functions in the Python @code{itertools} module, and others
6100 patterned after functions in the snow package.")
6101 (license license:gpl2)))
6103 (define-public r-polynom
6110 (uri (cran-uri "polynom" version))
6113 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
6114 (build-system r-build-system)
6115 (home-page "https://cran.r-project.org/web/packages/polynom/")
6116 (synopsis "Functions for univariate polynomial manipulations")
6118 "This package provides a collection of functions to implement a class for
6119 univariate polynomial manipulations.")
6120 (license license:gpl2)))
6122 (define-public r-gbrd
6129 (uri (cran-uri "gbRd" version))
6132 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
6133 (properties `((upstream-name . "gbRd")))
6134 (build-system r-build-system)
6135 (home-page "https://cran.r-project.org/web/packages/gbRd/")
6136 (synopsis "Utilities for processing Rd objects and files")
6138 "This package provides utilities for processing Rd objects and files.
6139 Extract argument descriptions and other parts of the help pages of
6141 (license license:gpl2+)))
6143 (define-public r-rjags
6150 (uri (cran-uri "rjags" version))
6153 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
6154 (build-system r-build-system)
6156 `(("r-coda" ,r-coda)))
6160 `(("pkg-config" ,pkg-config)))
6161 (home-page "http://mcmc-jags.sourceforge.net")
6162 (synopsis "Bayesian graphical models using MCMC")
6164 "This package provides an R interface to the JAGS MCMC library. JAGS is
6165 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
6166 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
6167 (license license:gpl2)))
6169 (define-public r-rdpack
6176 (uri (cran-uri "Rdpack" version))
6179 "080y15p2hl4jsq91ak2f1y2kx1iqq5c5wzyx3zyhjwp01cahy0jq"))))
6180 (properties `((upstream-name . "Rdpack")))
6181 (build-system r-build-system)
6183 `(("r-bibtex" ,r-bibtex)
6184 ("r-gbrd" ,r-gbrd)))
6185 (home-page "https://github.com/GeoBosh/Rdpack")
6186 (synopsis "Update and manipulate Rd documentation objects")
6188 "This package provides functions for manipulation of R documentation
6189 objects, including functions @code{reprompt()} and @code{ereprompt()} for
6190 updating Rd documentation for functions, methods and classes; it also includes
6191 Rd macros for citations and import of references from bibtex files for use in
6192 Rd files and roxygen2 comments, as well as many functions for manipulation of
6193 references and Rd files.")
6194 (license license:gpl2+)))
6196 (define-public r-officer
6203 (uri (cran-uri "officer" version))
6206 "1zyrcf0xxm67bskynjac8dhil2as7rb0mmqaq30zp9lrgfwiycpz"))))
6207 (build-system r-build-system)
6209 `(("r-digest" ,r-digest)
6210 ("r-magrittr" ,r-magrittr)
6215 (home-page "https://davidgohel.github.io/officer")
6216 (synopsis "Manipulation of Word and PowerPoint documents")
6218 "This package provides tools to access and manipulate Word and PowerPoint
6219 documents from R. The package focuses on tabular and graphical reporting from
6220 R; it also provides two functions that let users get document content into
6221 data objects. A set of functions lets add and remove images, tables and
6222 paragraphs of text in new or existing documents. When working with PowerPoint
6223 presentations, slides can be added or removed; shapes inside slides can also
6224 be added or removed. When working with Word documents, a cursor can be used
6225 to help insert or delete content at a specific location in the document.")
6226 (license license:gpl3)))
6228 (define-public r-abn
6235 (uri (cran-uri "abn" version))
6238 "19w6bdjyp4zwqs6p0flry4qxqynf9rh8ykdrfrp61wrdf7kysw0d"))))
6239 (build-system r-build-system)
6243 `(("r-lme4" ,r-lme4)
6247 ("r-rcpparmadillo" ,r-rcpparmadillo)
6248 ("r-rjags" ,r-rjags)))
6249 (home-page "https://r-bayesian-networks.org/")
6250 (synopsis "Modelling multivariate data with additive bayesian networks")
6252 "Bayesian network analysis is a form of probabilistic graphical models
6253 which derives from empirical data a directed acyclic graph, DAG, describing
6254 the dependency structure between random variables. An additive Bayesian
6255 network model consists of a form of a DAG where each node comprises a
6256 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
6257 equivalent to Bayesian multivariate regression using graphical modelling, they
6258 generalises the usual multivariable regression, GLM, to multiple dependent
6259 variables. This package provides routines to help determine optimal Bayesian
6260 network models for a given data set, where these models are used to identify
6261 statistical dependencies in messy, complex data.")
6262 (license license:gpl2+)))
6264 (define-public r-acd
6271 (uri (cran-uri "ACD" version))
6274 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
6275 (properties `((upstream-name . "ACD")))
6276 (build-system r-build-system)
6277 (home-page "https://cran.r-project.org/web/packages/ACD/")
6278 (synopsis "Categorical data analysis with complete or missing responses")
6280 "This package provides tools for categorical data analysis with complete
6281 or missing responses.")
6282 (license license:gpl2+)))
6284 (define-public r-acdm
6291 (uri (cran-uri "ACDm" version))
6294 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
6295 (properties `((upstream-name . "ACDm")))
6296 (build-system r-build-system)
6298 `(("r-dplyr" ,r-dplyr)
6299 ("r-ggplot2" ,r-ggplot2)
6301 ("r-rsolnp" ,r-rsolnp)
6303 (home-page "https://cran.r-project.org/web/packages/ACDm/")
6304 (synopsis "Tools for Autoregressive Conditional Duration Models")
6306 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
6307 and Russell, 1998) models. It creates trade, price or volume durations from
6308 transactions (tic) data, performs diurnal adjustments, fits various ACD models
6310 (license license:gpl2+)))
6312 (define-public r-overlap
6319 (uri (cran-uri "overlap" version))
6322 "1j3m6ir1chdz0si2fhcw6gs7c9h09bv0chz18rpzxsywww6d4rzy"))))
6323 (build-system r-build-system)
6324 (home-page "https://cran.r-project.org/web/packages/overlap/")
6325 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
6327 "This package provides functions to fit kernel density functions to data
6328 on temporal activity patterns of animals; estimate coefficients of overlapping
6329 of densities for two species; and calculate bootstrap estimates of confidence
6331 (license license:gpl3+)))
6333 (define-public r-snakecase
6335 (name "r-snakecase")
6340 (uri (cran-uri "snakecase" version))
6343 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
6344 (build-system r-build-system)
6346 `(("r-stringi" ,r-stringi)
6347 ("r-stringr" ,r-stringr)))
6348 (home-page "https://github.com/Tazinho/snakecase")
6349 (synopsis "Convert strings into any case")
6351 "This package provides a consistent, flexible and easy to use tool to
6352 parse and convert strings into cases like snake or camel among others.")
6353 (license license:gpl3)))
6355 (define-public r-prediction
6357 (name "r-prediction")
6362 (uri (cran-uri "prediction" version))
6365 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
6366 (build-system r-build-system)
6368 `(("r-data-table" ,r-data-table)))
6369 (home-page "https://github.com/leeper/prediction")
6370 (synopsis "Tidy, type-safe prediction methods")
6372 "This package provides the @code{prediction()} function, a type-safe
6373 alternative to @code{predict()} that always returns a data frame. The package
6374 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
6375 from the @code{stats} package, as well as numerous other model classes from
6376 other add-on packages.")
6377 (license license:expat)))
6379 (define-public r-insight
6386 (uri (cran-uri "insight" version))
6389 "0fjf7dwpv1a7qfbzixppg348z1ksq19kdjm08vcb2am7w0k3plcj"))))
6390 (build-system r-build-system)
6392 `(("r-knitr" ,r-knitr)))
6393 (home-page "https://easystats.github.io/insight/")
6394 (synopsis "Easy access to model information for various model objects")
6396 "This package provides a tool to provide an easy, intuitive and
6397 consistent access to information contained in various R models, like model
6398 formulas, model terms, information about random effects, data that was used to
6399 fit the model or data from response variables. The package mainly revolves
6400 around two types of functions: Functions that find (the names of) information,
6401 starting with @code{find_}, and functions that get the underlying data,
6402 starting with @code{get_}. The package has a consistent syntax and works with
6403 many different model objects, where otherwise functions to access these
6404 information are missing.")
6405 (license license:gpl3)))
6407 (define-public r-sjlabelled
6409 (name "r-sjlabelled")
6414 (uri (cran-uri "sjlabelled" version))
6417 "1amq7i9sxf0pkxhskqc53xq5wvc9rdxm7cxyb4b6xh6qsskjnlsj"))))
6418 (build-system r-build-system)
6420 `(("r-haven" ,r-haven)
6421 ("r-insight" ,r-insight)))
6422 (home-page "https://github.com/strengejacke/sjlabelled")
6423 (synopsis "Labelled data utility functions")
6425 "This package provides a collection of functions dealing with labelled
6426 data, like reading and writing data between R and other statistical software
6427 packages. This includes easy ways to get, set or change value and variable
6428 label attributes, to convert labelled vectors into factors or numeric (and
6429 vice versa), or to deal with multiple declared missing values.")
6430 (license license:gpl3)))
6432 (define-public r-sjmisc
6439 (uri (cran-uri "sjmisc" version))
6442 "0w8l9grmp4q775jrf4q6rxx36ld5daz9b0gdxyyh42xfihk6m62h"))))
6443 (build-system r-build-system)
6445 `(("r-dplyr" ,r-dplyr)
6446 ("r-insight" ,r-insight)
6447 ("r-magrittr" ,r-magrittr)
6448 ("r-purrr" ,r-purrr)
6449 ("r-rlang" ,r-rlang)
6450 ("r-sjlabelled" ,r-sjlabelled)
6451 ("r-tidyselect" ,r-tidyselect)))
6452 (home-page "https://github.com/strengejacke/sjmisc")
6453 (synopsis "Data and variable transformation functions")
6455 "This package is a collection of miscellaneous utility functions,
6456 supporting data transformation tasks like recoding, dichotomizing or grouping
6457 variables, setting and replacing missing values. The data transformation
6458 functions also support labelled data, and all integrate seamlessly into a
6459 tidyverse workflow.")
6460 (license license:gpl3)))
6462 (define-public r-nortest
6469 (uri (cran-uri "nortest" version))
6472 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
6473 (build-system r-build-system)
6474 (home-page "https://cran.r-project.org/web/packages/nortest/")
6475 (synopsis "Tests for normality")
6477 "This package provides five omnibus tests for testing the composite
6478 hypothesis of normality.")
6479 (license license:gpl2+)))
6481 (define-public r-moonbook
6488 (uri (cran-uri "moonBook" version))
6491 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
6492 (properties `((upstream-name . "moonBook")))
6493 (build-system r-build-system)
6495 `(("r-magrittr" ,r-magrittr)
6496 ("r-nortest" ,r-nortest)
6497 ("r-purrr" ,r-purrr)
6498 ("r-sjmisc" ,r-sjmisc)
6499 ("r-stringr" ,r-stringr)
6500 ("r-survival" ,r-survival)))
6501 (home-page "https://github.com/cardiomoon/moonBook")
6502 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
6504 "This package provides several analysis-related functions for the book
6505 entitled \"R statistics and graph for medical articles\" (written in Korean),
6506 version 1, by Keon-Woong Moon with Korean demographic data with several plot
6508 (license license:gpl2)))
6510 (define-public r-flextable
6512 (name "r-flextable")
6517 (uri (cran-uri "flextable" version))
6520 "1rkz0nhwjy1l8sb0kmna5v492n2ydnk7gydswnmf88r8vfyjczhw"))))
6521 (build-system r-build-system)
6523 `(("r-base64enc" ,r-base64enc)
6524 ("r-data-table" ,r-data-table)
6525 ("r-gdtools" ,r-gdtools)
6526 ("r-htmltools" ,r-htmltools)
6527 ("r-knitr" ,r-knitr)
6528 ("r-officer" ,r-officer)
6529 ("r-rlang" ,r-rlang)
6530 ("r-rmarkdown" ,r-rmarkdown)
6531 ("r-xml2" ,r-xml2)))
6532 (home-page "https://davidgohel.github.io/flextable")
6533 (synopsis "Functions for tabular reporting")
6535 "This package provides tools to create pretty tables for HTML documents
6536 and other formats. Functions are provided to let users create tables, modify
6537 and format their content. It extends the @code{officer} package and can be
6538 used within R markdown documents when rendering to HTML and to Word
6540 (license license:gpl3)))
6542 (define-public r-writexl
6549 (uri (cran-uri "writexl" version))
6552 "09fhdip6igcg97fjx4c7727cx2lb49l4d74l4i8rg2bag2s5lrj3"))))
6553 (build-system r-build-system)
6554 (inputs `(("zlib" ,zlib)))
6555 (home-page "https://github.com/ropensci/writexl")
6556 (synopsis "Export data frames to xlsx format")
6558 "This package provides a data frame to xlsx exporter based on
6560 (license license:bsd-2)))
6562 (define-public r-biasedurn
6564 (name "r-biasedurn")
6569 (uri (cran-uri "BiasedUrn" version))
6572 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
6573 (properties `((upstream-name . "BiasedUrn")))
6574 (build-system r-build-system)
6575 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
6576 (synopsis "Biased Urn model distributions")
6578 "This package provides statistical models of biased sampling in the form
6579 of univariate and multivariate noncentral hypergeometric distributions,
6580 including Wallenius' noncentral hypergeometric distribution and Fisher's
6581 noncentral hypergeometric distribution (also called extended hypergeometric
6583 (license license:gpl3)))
6585 (define-public r-goplot
6592 (uri (cran-uri "GOplot" version))
6595 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
6596 (properties `((upstream-name . "GOplot")))
6597 (build-system r-build-system)
6599 `(("r-ggdendro" ,r-ggdendro)
6600 ("r-ggplot2" ,r-ggplot2)
6601 ("r-gridextra" ,r-gridextra)
6602 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6603 (home-page "https://github.com/wencke/wencke.github.io")
6604 (synopsis "Visualization of functional analysis data")
6606 "This package provides an implementation of multilayered visualizations
6607 for enhanced graphical representation of functional analysis data. It
6608 combines and integrates omics data derived from expression and functional
6609 annotation enrichment analyses. Its plotting functions have been developed
6610 with an hierarchical structure in mind: starting from a general overview to
6611 identify the most enriched categories (modified bar plot, bubble plot) to a
6612 more detailed one displaying different types of relevant information for the
6613 molecules in a given set of categories (circle plot, chord plot, cluster plot,
6614 Venn diagram, heatmap).")
6615 (license license:gpl2)))
6617 (define-public r-getopt
6624 (uri (cran-uri "getopt" version))
6627 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
6628 (build-system r-build-system)
6629 (home-page "https://github.com/trevorld/getopt")
6630 (synopsis "Command-line option processor for R")
6632 "This package is designed to be used with Rscript to write shebang
6633 scripts that accept short and long options. Many users will prefer to
6634 use the packages @code{optparse} or @code{argparse} which add extra
6635 features like automatically generated help options and usage texts,
6636 support for default values, positional argument support, etc.")
6637 (license license:gpl2+)))
6639 (define-public r-findpython
6641 (name "r-findpython")
6646 (uri (cran-uri "findpython" version))
6649 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
6650 (build-system r-build-system)
6651 (home-page "https://github.com/trevorld/findpython")
6652 (synopsis "Functions to find an acceptable Python binary")
6654 "This package was designed to find an acceptable Python binary that
6655 matches version and feature constraints.")
6656 (license license:expat)))
6658 ;; This in not the same as "r-argparser"
6659 (define-public r-argparse
6666 (uri (cran-uri "argparse" version))
6669 "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l"))))
6670 (build-system r-build-system)
6671 (inputs `(("python" ,python)))
6673 `(("r-findpython" ,r-findpython)
6674 ("r-jsonlite" ,r-jsonlite)
6676 (home-page "https://github.com/trevorld/argparse")
6677 (synopsis "Command line optional and positional argument parser")
6679 "This package provides a command line parser to be used with Rscript to
6680 write shebang scripts that gracefully accept positional and optional arguments
6681 and automatically generate usage notices.")
6682 (license license:gpl2+)))
6684 (define-public r-hash
6691 (uri (cran-uri "hash" version))
6694 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
6695 (build-system r-build-system)
6696 (home-page "https://cran.r-project.org/web/packages/hash/")
6697 (synopsis "Implementation of hash/associated arrays/dictionaries")
6699 "This package implements a data structure similar to hashes in Perl and
6700 dictionaries in Python but with a purposefully R flavor. For objects of
6701 appreciable size, access using hashes outperforms native named lists and
6703 (license license:gpl2+)))
6705 (define-public r-orddom
6712 (uri (cran-uri "orddom" version))
6715 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
6716 (build-system r-build-system)
6717 (propagated-inputs `(("r-psych" ,r-psych)))
6718 (home-page "https://cran.r-project.org/web/packages/orddom/")
6719 (synopsis "Ordinal dominance statistics")
6721 "This package provides tools to compute ordinal, statistics and effect
6722 sizes as an alternative to mean comparison: Cliff's delta or success rate
6723 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
6724 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
6725 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
6726 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
6727 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
6728 Group (Non-)Overlap considerations.")
6729 (license license:gpl2)))
6731 (define-public r-deriv
6738 (uri (cran-uri "Deriv" version))
6741 "03mlfy8jzzzbh2l18gnmw0a71n9savx4cw72yhkxq93v2xj8fy3n"))))
6742 (properties `((upstream-name . "Deriv")))
6743 (build-system r-build-system)
6744 (home-page "https://cran.r-project.org/web/packages/Deriv")
6745 (synopsis "Symbolic differentiation")
6747 "This package provides an R-based solution for symbolic differentiation.
6748 It admits user-defined functions as well as function substitution in arguments
6749 of functions to be differentiated. Some symbolic simplification is part of
6751 (license license:gpl3+)))
6753 (define-public r-doby
6760 (uri (cran-uri "doBy" version))
6763 "1ckazh701b4ilg8bj17ji903538jmb49d997gm49ah5j5jc1x0g7"))))
6764 (properties `((upstream-name . "doBy")))
6765 (build-system r-build-system)
6767 `(("r-broom" ,r-broom)
6768 ("r-deriv" ,r-deriv)
6769 ("r-dplyr" ,r-dplyr)
6770 ("r-magrittr" ,r-magrittr)
6772 ("r-matrix" ,r-matrix)
6774 ("r-pbkrtest" ,r-pbkrtest)
6775 ("r-tibble" ,r-tibble)))
6776 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
6777 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
6779 "This package contains:
6782 @item facilities for working with grouped data: @code{do}
6783 something to data stratified @code{by} some variables.
6784 @item implementations of least-squares means, general linear contrasts, and
6785 @item miscellaneous other utilities.
6787 (license license:gpl2+)))
6789 (define-public r-refgenome
6791 (name "r-refgenome")
6796 (uri (cran-uri "refGenome" version))
6799 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
6800 (properties `((upstream-name . "refGenome")))
6801 (build-system r-build-system)
6805 ("r-rsqlite" ,r-rsqlite)))
6806 (home-page "https://cran.r-project.org/web/packages/refGenome/")
6808 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
6810 "This package contains functionality for importing and managing of
6811 downloaded genome annotation data from the Ensembl genome browser (European
6812 Bioinformatics Institute) and from the UCSC genome browser (University of
6813 California, Santa Cruz) and annotation routines for genomic positions and
6814 splice site positions.")
6815 (license license:gpl2)))
6817 (define-public r-basix
6824 (uri (cran-uri "BASIX" version))
6827 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
6828 (properties `((upstream-name . "BASIX")))
6829 (build-system r-build-system)
6830 (home-page "https://cran.r-project.org/web/packages/BASIX/")
6831 (synopsis "Efficient C/C++ toolset for R")
6833 "BASIX provides some efficient C/C++ implementations of native R
6834 procedures to speed up calculations in R.")
6835 (license license:gpl2)))
6837 (define-public r-blockfest
6839 (name "r-blockfest")
6844 (uri (cran-uri "BlockFeST" version))
6847 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
6848 (properties `((upstream-name . "BlockFeST")))
6849 (build-system r-build-system)
6850 (propagated-inputs `(("r-basix" ,r-basix)))
6851 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
6852 (synopsis "Bayesian calculation of region-specific fixation index")
6854 "This package provides an R implementation of an extension of the
6855 BayeScan software for codominant markers, adding the option to group
6856 individual SNPs into pre-defined blocks. A typical application of this new
6857 approach is the identification of genomic regions, genes, or gene sets
6858 containing one or more SNPs that evolved under directional selection.")
6859 (license license:gpl2)))
6861 (define-public r-proc
6868 (uri (cran-uri "pROC" version))
6871 "0qkp1byl2xspxaaf0by6mvvrhg7wlz6fxmynz2hkh0ds24w7ig9m"))))
6872 (properties `((upstream-name . "pROC")))
6873 (build-system r-build-system)
6875 `(("r-plyr" ,r-plyr)
6876 ("r-rcpp" ,r-rcpp)))
6877 (home-page "http://expasy.org/tools/pROC/")
6878 (synopsis "Display and analyze ROC curves")
6880 "This package provides tools for visualizing, smoothing and comparing
6881 receiver operating characteristic (ROC curves). The area under the
6882 curve (AUC) can be compared with statistical tests based on U-statistics or
6883 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
6884 (license license:gpl3+)))
6886 (define-public r-rootsolve
6888 (name "r-rootsolve")
6893 (uri (cran-uri "rootSolve" version))
6896 "0rj7c4zcrzgz7sb0vgvh7swpfafnw4040cxp7ypas3s8fnihn54l"))))
6897 (properties `((upstream-name . "rootSolve")))
6898 (build-system r-build-system)
6899 (native-inputs `(("gfortran" ,gfortran)))
6900 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
6901 (synopsis "Tools for the analysis of ordinary differential equations")
6903 "This package provides routines to find the root of nonlinear functions,
6904 and to perform steady-state and equilibrium analysis of @dfn{ordinary
6905 differential equations} (ODE). It includes routines that:
6908 @item generate gradient and jacobian matrices (full and banded),
6909 @item find roots of non-linear equations by the Newton-Raphson method,
6910 @item estimate steady-state conditions of a system of (differential) equations
6911 in full, banded or sparse form, using the Newton-Raphson method, or by
6912 dynamically running,
6913 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
6914 and 3-D partial differential equations, that have been converted to ordinary
6915 differential equations by numerical differencing (using the method-of-lines
6918 (license license:gpl2+)))
6920 (define-public r-abcanalysis
6922 (name "r-abcanalysis")
6927 (uri (cran-uri "ABCanalysis" version))
6929 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
6930 (properties `((upstream-name . "ABCanalysis")))
6931 (build-system r-build-system)
6932 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
6933 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
6934 (synopsis "Computed ABC Analysis")
6936 "Multivariate data sets often differ in several factors or derived statistical
6937 parameters, which have to be selected for a valid interpretation. Basing this
6938 selection on traditional statistical limits leads occasionally to the perception
6939 of losing information from a data set. This package provides tools to calculate
6940 these limits on the basis of the mathematical properties of the distribution of
6941 the analyzed items.")
6942 (license license:gpl3)))
6944 (define-public r-slam
6951 (uri (cran-uri "slam" version))
6953 (base32 "12fggw2c7hz3bpvsaqm24g3r6lbpq6jgli24g7x5j859iak5cqv9"))))
6954 (build-system r-build-system)
6955 (home-page "https://cran.r-project.org/web/packages/slam/")
6956 (synopsis "Sparse lightweight arrays and matrices")
6958 "This package contains data structures and algorithms for sparse arrays and matrices,
6959 based on index arrays and simple triplet representations, respectively.")
6960 (license license:gpl2)))
6962 (define-public r-manipulatewidget
6964 (name "r-manipulatewidget")
6969 (uri (cran-uri "manipulateWidget" version))
6971 (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx"))))
6973 `((upstream-name . "manipulateWidget")))
6974 (build-system r-build-system)
6976 `(("r-base64enc" ,r-base64enc)
6977 ("r-codetools" ,r-codetools)
6978 ("r-htmltools" ,r-htmltools)
6979 ("r-htmlwidgets" ,r-htmlwidgets)
6980 ("r-knitr" ,r-knitr)
6981 ("r-miniui" ,r-miniui)
6982 ("r-shiny" ,r-shiny)
6983 ("r-webshot" ,r-webshot)))
6984 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
6985 (synopsis "Add even more interactivity to interactive charts")
6987 "This package lets you create in just a few lines of R code a nice user interface to
6988 modify the data or the graphical parameters of one or multiple interactive
6989 charts. It is useful to quickly explore visually some data or for package
6990 developers to generate user interfaces easy to maintain.")
6991 (license license:gpl2+)))
7000 (uri (cran-uri "A3" version))
7002 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
7003 (properties `((upstream-name . "A3")))
7004 (build-system r-build-system)
7006 `(("r-pbapply" ,r-pbapply)
7007 ("r-xtable" ,r-xtable)))
7008 (home-page "https://cran.r-project.org/web/packages/A3/")
7009 (synopsis "Error metrics for predictive models")
7011 "This package supplies tools for tabulating and analyzing the results of predictive
7012 models. The methods employed are applicable to virtually any predictive model
7013 and make comparisons between different methodologies straightforward.")
7014 (license license:gpl2+)))
7016 (define-public r-infotheo
7023 (uri (cran-uri "infotheo" version))
7026 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
7027 (build-system r-build-system)
7028 (home-page "http://homepage.meyerp.com/software")
7029 (synopsis "Information-theoretic measures")
7031 "This package implements various measures of information theory based on
7032 several entropy estimators.")
7033 (license license:gpl3+)))
7035 (define-public r-abcoptim
7042 (uri (cran-uri "ABCoptim" version))
7044 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
7045 (properties `((upstream-name . "ABCoptim")))
7046 (build-system r-build-system)
7047 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
7048 (home-page "https://github.com/gvegayon/ABCoptim/")
7049 (synopsis "Optimization of Artificial Bee Colony algorithm")
7051 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
7052 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
7053 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
7054 algorithms, and uses only common control parameters such as colony size and
7055 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
7056 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
7057 This version is a work-in-progress and is written in R code.")
7058 (license license:expat)))
7060 (define-public r-abcp2
7067 (uri (cran-uri "ABCp2" version))
7069 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
7070 (properties `((upstream-name . "ABCp2")))
7071 (build-system r-build-system)
7072 (propagated-inputs `(("r-mass" ,r-mass)))
7073 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
7074 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
7076 "This package tests the goodness of fit of a distribution of offspring to the Normal,
7077 Poisson, and Gamma distribution and estimates the proportional paternity of the
7078 second male (P2) based on the best fit distribution.")
7079 (license license:gpl2)))
7081 (define-public r-abcrf
7088 (uri (cran-uri "abcrf" version))
7090 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
7091 (build-system r-build-system)
7093 `(("r-doparallel" ,r-doparallel)
7094 ("r-foreach" ,r-foreach)
7096 ("r-matrixstats" ,r-matrixstats)
7097 ("r-ranger" ,r-ranger)
7099 ("r-rcpparmadillo" ,r-rcpparmadillo)
7100 ("r-readr" ,r-readr)
7101 ("r-stringr" ,r-stringr)))
7102 (home-page "https://cran.r-project.org/web/packages/abcrf/")
7103 (synopsis "Approximate bayesian computation via random forests")
7105 "This package performs approximate bayesian computation (ABC) model choice and
7106 parameter inference via random forests. This machine learning tool named random
7107 forests (RF) can conduct selection among the highly complex models covered by
7109 (license license:gpl2+)))
7111 (define-public r-abctools
7118 (uri (cran-uri "abctools" version))
7120 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
7121 (build-system r-build-system)
7124 ("r-abind" ,r-abind)
7125 ("r-hmisc" ,r-hmisc)
7126 ("r-plyr" ,r-plyr)))
7127 (home-page "https://github.com/dennisprangle/abctools/")
7128 (synopsis "Tools for ABC analyses")
7130 "This @code{r-abctools} package provides tools for approximate Bayesian computation
7131 including summary statistic selection and assessing coverage. This includes
7132 recent dimension reduction algorithms to tune the choice of summary statistics,
7133 and coverage methods to tune the choice of threshold.")
7134 (license license:gpl2+)))
7136 (define-public r-ggstance
7143 (uri (cran-uri "ggstance" version))
7145 (base32 "0kdksay61hyb6612b07r84chh7a9aibjyclk3qcypvr9aang8hkh"))))
7146 (build-system r-build-system)
7148 `(("r-ggplot2" ,r-ggplot2)
7150 ("r-rlang" ,r-rlang)
7151 ("r-withr" ,r-withr)))
7152 (home-page "https://cran.r-project.org/web/packages/ggstance/")
7153 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
7155 "This package is a @code{r-ggplot2} extension that provides flipped components:
7157 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
7158 @item vertical versions of @code{r-ggplot2} positions.
7160 (license license:gpl3)))
7162 (define-public r-mosaiccore
7164 (name "r-mosaiccore")
7169 (uri (cran-uri "mosaicCore" version))
7171 (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
7172 (properties `((upstream-name . "mosaicCore")))
7173 (build-system r-build-system)
7175 `(("r-dplyr" ,r-dplyr)
7176 ("r-lazyeval" ,r-lazyeval)
7178 ("r-rlang" ,r-rlang)
7179 ("r-tidyr" ,r-tidyr)))
7180 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
7181 (synopsis "Common utilities for mosaic family packages")
7183 "Common utilities used in other Mosaic family packages are collected here.")
7184 (license license:gpl2+)))
7186 (define-public r-ggformula
7188 (name "r-ggformula")
7193 (uri (cran-uri "ggformula" version))
7195 (base32 "04vdhg1bbc1psrx9ggaphz7cx4fw5xsmhkqpqfcg2w4ba2bjy46f"))))
7196 (build-system r-build-system)
7198 `(("r-ggforce" ,r-ggforce)
7199 ("r-ggplot2" ,r-ggplot2)
7200 ("r-ggstance" ,r-ggstance)
7201 ("r-magrittr" ,r-magrittr)
7202 ("r-mosaiccore" ,r-mosaiccore)
7203 ("r-rlang" ,r-rlang)
7204 ("r-stringr" ,r-stringr)
7205 ("r-tibble" ,r-tibble)))
7206 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
7207 (synopsis "Formula interface for the @code{r-ggplot2}")
7209 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
7210 gf_density(), and so on, bring the formula interface to ggplot(). This captures
7211 and extends the excellent simplicity of the lattice-graphics formula interface,
7212 while providing the intuitive capabilities of @code{r-ggplot2}.")
7213 (license license:expat)))
7215 (define-public r-mosaicdata
7217 (name "r-mosaicdata")
7222 (uri (cran-uri "mosaicData" version))
7224 (base32 "04z0mdm52mykqsxsinhmsihn181zf6cw321gayk2rjp7lj7mwdq9"))))
7225 (properties `((upstream-name . "mosaicData")))
7226 (build-system r-build-system)
7227 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
7228 (synopsis "Data sets for project Mosaic")
7230 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
7231 used to teach mathematics, statistics, computation and modeling.")
7232 (license license:gpl2+)))
7234 (define-public r-raster
7241 (uri (cran-uri "raster" version))
7244 "0rrbsigkqxsdic8fly6nrsc79zsliwvr1x2b4xqpl9d34vr50dvg"))))
7245 (build-system r-build-system)
7247 `(("r-rcpp" ,r-rcpp)
7249 (home-page "https://www.rspatial.org/")
7250 (synopsis "Geographic data analysis and modeling")
7252 "The package implements basic and high-level functions for reading,
7253 writing, manipulating, analyzing and modeling of gridded spatial data.
7254 Processing of very large files is supported.")
7255 (license license:gpl3+)))
7257 (define-public r-mosaic
7264 (uri (cran-uri "mosaic" version))
7266 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
7267 (build-system r-build-system)
7269 `(("r-broom" ,r-broom)
7270 ("r-dplyr" ,r-dplyr)
7271 ("r-ggdendro" ,r-ggdendro)
7272 ("r-ggformula" ,r-ggformula)
7273 ("r-ggplot2" ,r-ggplot2)
7274 ("r-ggrepel" ,r-ggrepel)
7276 ("r-gridextra" ,r-gridextra)
7277 ("r-lattice" ,r-lattice)
7278 ("r-latticeextra" ,r-latticeextra)
7279 ("r-lazyeval" ,r-lazyeval)
7281 ("r-matrix" ,r-matrix)
7282 ("r-mosaiccore" ,r-mosaiccore)
7283 ("r-mosaicdata" ,r-mosaicdata)
7284 ("r-readr" ,r-readr)
7285 ("r-tidyr" ,r-tidyr)))
7287 `(("r-knitr" ,r-knitr)))
7288 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
7289 (synopsis "Mathematics, statistics, and computation teaching utilities")
7291 "This package contain data sets and utilities from
7292 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
7293 statistics, computation and modeling. Project MOSAIC is a community of
7294 educators working to tie together aspects of quantitative work that students
7295 in science, technology, engineering and mathematics will need in their
7296 professional lives, but which are usually taught in isolation, if at all.")
7297 (license license:gpl2+)))
7299 (define-public r-abd
7306 (uri (cran-uri "abd" version))
7308 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
7309 (build-system r-build-system)
7311 `(("r-lattice" ,r-lattice)
7312 ("r-mosaic" ,r-mosaic)
7313 ("r-nlme" ,r-nlme)))
7314 (home-page "https://cran.r-project.org/web/packages/abd/")
7315 (synopsis "Analysis of biological data")
7317 "The @code{r-abd} package contains data sets and sample code for the Analysis of
7318 biological data by Michael Whitlock and Dolph Schluter.")
7319 (license license:gpl2)))
7321 (define-public r-svgui
7328 (uri (cran-uri "svGUI" version))
7330 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
7331 (properties `((upstream-name . "svGUI")))
7332 (build-system r-build-system)
7333 (home-page "https://github.com/SciViews/svGUI/")
7334 (synopsis "Functions for managing GUI clients in R")
7336 "The SciViews @code{svGUI} package eases the management of Graphical User
7337 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
7338 centralizes info about GUI elements currently used, and it dispatches GUI
7339 calls to the particular toolkits in use in function of the context.")
7340 (license license:gpl2)))
7342 (define-public r-svdialogs
7344 (name "r-svdialogs")
7349 (uri (cran-uri "svDialogs" version))
7351 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
7352 (properties `((upstream-name . "svDialogs")))
7353 (build-system r-build-system)
7356 ("zenity" ,zenity)))
7358 `(("r-rstudioapi" ,r-rstudioapi)
7359 ("r-svgui" ,r-svgui)))
7360 (home-page "https://github.com/SciViews/svDialogs/")
7361 (synopsis "Portable dialog boxes")
7363 "This package helps to construct standard dialog boxes for your GUI, including
7364 message boxes, input boxes, list, file or directory selection, and others. In
7365 case R cannot display GUI dialog boxes, a simpler command line version of these
7366 interactive elements is also provided as a fallback solution.")
7367 (license license:gpl2)))
7369 (define-public r-abe
7376 (uri (cran-uri "abe" version))
7379 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
7380 (build-system r-build-system)
7381 (home-page "https://cran.r-project.org/web/packages/abe/")
7382 (synopsis "Augmented backward elimination")
7384 "This package performs augmented backward elimination and checks the
7385 stability of the obtained model. Augmented backward elimination combines
7386 significance or information based criteria with the change in estimate to
7387 either select the optimal model for prediction purposes or to serve as a tool
7388 to obtain a practically sound, highly interpretable model.")
7389 (license license:gpl2+)))
7391 (define-public r-abf2
7398 (uri (cran-uri "abf2" version))
7400 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
7401 (build-system r-build-system)
7402 (home-page "https://cran.r-project.org/web/packages/abf2/")
7403 (synopsis "Load gap-free axon @code{r-abf2} files")
7405 "This package loads electrophysiology data from ABF2 files, as created by
7406 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
7407 mode are currently supported.")
7408 (license license:artistic2.0)))
7410 (define-public r-abhgenotyper
7412 (name "r-abhgenotyper")
7417 (uri (cran-uri "ABHgenotypeR" version))
7419 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
7420 (properties `((upstream-name . "ABHgenotypeR")))
7421 (build-system r-build-system)
7423 `(("r-ggplot2" ,r-ggplot2)
7424 ("r-reshape2" ,r-reshape2)))
7425 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
7426 (synopsis "Visualize and manipulate ABH genotypes")
7428 "The @code{r-abhgenotyper} package provides simple imputation,
7429 error-correction and plotting capacities for genotype data. The package is
7430 supposed to serve as an intermediate but independent analysis tool between the
7431 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
7432 not found in either TASSEL or @code{r-qtl} in addition to visualization of
7433 genotypes as \"graphical genotypes\".")
7434 (license license:gpl3)))
7436 (define-public r-furrr
7443 (uri (cran-uri "furrr" version))
7446 "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx"))))
7447 (build-system r-build-system)
7449 `(("r-future" ,r-future)
7450 ("r-globals" ,r-globals)
7451 ("r-purrr" ,r-purrr)
7452 ("r-rlang" ,r-rlang)))
7453 (home-page "https://github.com/DavisVaughan/furrr")
7454 (synopsis "Apply mapping functions in parallel using futures")
7456 "This package provides implementations of the family of @code{map()}
7457 functions from the @code{purrr} package that can be resolved using any
7458 @code{future}-supported backend, e.g. parallel on the local machine or
7459 distributed on a compute cluster.")
7460 (license license:lgpl2.1+)))
7462 (define-public r-abjutils
7469 (uri (cran-uri "abjutils" version))
7471 (base32 "0n4zps65y3zg0gfzlv97w91si52a9izkncirskbkj5x9hk0nhxcv"))))
7472 (build-system r-build-system)
7474 `(("r-devtools" ,r-devtools)
7475 ("r-dplyr" ,r-dplyr)
7476 ("r-furrr" ,r-furrr)
7477 ("r-future" ,r-future)
7480 ("r-magrittr" ,r-magrittr)
7481 ("r-progress" ,r-progress)
7482 ("r-purrr" ,r-purrr)
7483 ("r-readr" ,r-readr)
7484 ("r-rlang" ,r-rlang)
7485 ("r-rstudioapi" ,r-rstudioapi)
7486 ("r-scales" ,r-scales)
7487 ("r-stringi" ,r-stringi)
7488 ("r-stringr" ,r-stringr)
7489 ("r-tibble" ,r-tibble)
7490 ("r-tidyr" ,r-tidyr)))
7491 (home-page "https://github.com/abjur/abjutils/")
7492 (synopsis "Collection of tools for jurimetrical analysis")
7494 "This package implements general purpose tools, such as functions for
7495 sampling and basic manipulation of Brazilian lawsuits identification number.
7496 It also implements functions for text cleaning, such as accentuation
7498 (license license:expat)))
7500 (define-public r-abnormality
7502 (name "r-abnormality")
7507 (uri (cran-uri "abnormality" version))
7509 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
7510 (build-system r-build-system)
7512 `(("r-mass" ,r-mass)
7513 ("r-matrix" ,r-matrix)))
7514 (home-page "https://cran.r-project.org/web/packages/abnormality/")
7515 (synopsis "Measure a subject's abnormality with respect to a reference population")
7517 "This package contains functions to implement the methodology and
7518 considerations laid out by Marks et al. in the article \"Measuring abnormality
7519 in high dimensional spaces: applications in biomechanical gait analysis\".
7520 Using high-dimensional datasets to measure a subject's overall level of
7521 abnormality as compared to a reference population is often needed in outcomes
7523 (license license:expat)))
7525 (define-public r-abodoutlier
7527 (name "r-abodoutlier")
7532 (uri (cran-uri "abodOutlier" version))
7534 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
7535 (properties `((upstream-name . "abodOutlier")))
7536 (build-system r-build-system)
7538 `(("r-cluster" ,r-cluster)))
7539 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
7540 (synopsis "Angle-based outlier detection")
7542 "This package performs angle-based outlier detection on a given data
7543 frame. It offers three methods to process data:
7545 @item full but slow implementation using all the data that has cubic
7547 @item a fully randomized method;
7548 @item a method using k-nearest neighbours.
7550 These algorithms are well suited for high dimensional data outlier
7552 (license license:expat)))
7554 (define-public r-abps
7561 (uri (cran-uri "ABPS" version))
7563 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
7564 (properties `((upstream-name . "ABPS")))
7565 (build-system r-build-system)
7566 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
7567 (home-page "https://cran.r-project.org/web/packages/ABPS/")
7568 (synopsis "Abnormal blood profile score to detect blood doping")
7570 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
7571 The ABPS is a part of the Athlete biological passport program of the World
7572 anti-doping agency, which combines several blood parameters into a single
7573 score in order to detect blood doping. The package also contains functions to
7574 calculate other scores used in anti-doping programs, such as the ratio of
7575 hemoglobin to reticulocytes (OFF-score), as well as example data.")
7576 (license license:gpl2+)))
7578 (define-public r-parmigene
7580 (name "r-parmigene")
7585 (uri (cran-uri "parmigene" version))
7588 "1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d"))))
7589 (build-system r-build-system)
7590 (home-page "https://cran.r-project.org/web/packages/parmigene/")
7591 (synopsis "Mutual information estimation for gene network reconstruction")
7593 "This package provides a parallel estimation of the mutual information
7594 based on entropy estimates from k-nearest neighbors distances and algorithms
7595 for the reconstruction of gene regulatory networks.")
7596 (license license:agpl3+)))
7598 (define-public r-pscl
7605 (uri (cran-uri "pscl" version))
7607 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
7608 (build-system r-build-system)
7610 `(("r-mass" ,r-mass)))
7611 (home-page "https://github.com/atahk/pscl/")
7612 (synopsis "Political science computational laboratory")
7614 "The @code{pscl} is an R package providing classes and methods for:
7616 @item Bayesian analysis of roll call data (item-response models);
7617 @item elementary Bayesian statistics;
7618 @item maximum likelihood estimation of zero-inflated and hurdle models for count
7620 @item utility functions.
7622 (license license:gpl2)))
7624 (define-public r-accelmissing
7626 (name "r-accelmissing")
7631 (uri (cran-uri "accelmissing" version))
7633 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
7634 (build-system r-build-system)
7636 `(("r-mice" ,r-mice)
7637 ("r-pscl" ,r-pscl)))
7638 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
7639 (synopsis "Missing value imputation for accelerometer data")
7641 "This package provides a statistical method to impute the missing values in
7642 accelerometer data. The methodology includes both parametric and
7643 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
7644 model. It also provides multiple functions to preprocess the accelerometer data
7645 previous to the missing data imputation. These include detecting the wearing
7646 and the non-wearing time, selecting valid days and subjects, and creating plots.")
7647 (license license:gpl2+)))
7649 (define-public r-mhsmm
7656 (uri (cran-uri "mhsmm" version))
7658 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
7659 (build-system r-build-system)
7660 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
7661 (home-page "https://github.com/jaredo/mhsmm/")
7662 (synopsis "Inference for hidden Markov and semi-Markov models")
7664 "The @code{r-mhsmm} package implements estimation and prediction methods for
7665 hidden Markov and semi-Markov models for multiple observation sequences. Such
7666 techniques are of interest when observed data is thought to be dependent on some
7667 unobserved (or hidden) state. Also, this package is suitable for equidistant
7668 time series data, with multivariate and/or missing data. Allows user defined
7669 emission distributions.")
7670 (license license:gpl2+)))
7672 (define-public r-nleqslv
7679 (uri (cran-uri "nleqslv" version))
7681 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
7682 (build-system r-build-system)
7683 (native-inputs `(("gfortran" ,gfortran)))
7684 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
7685 (synopsis "Solve systems of nonlinear equations")
7687 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
7688 Broyden or a Newton method with a choice of global strategies such as line
7689 search and trust region. There are options for using a numerical or user
7690 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
7691 singular or ill-conditioned Jacobian.")
7692 (license license:gpl2+)))
7694 (define-public r-physicalactivity
7696 (name "r-physicalactivity")
7701 (uri (cran-uri "PhysicalActivity" version))
7703 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
7705 `((upstream-name . "PhysicalActivity")))
7706 (build-system r-build-system)
7707 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
7708 (synopsis "Procesing accelerometer data for physical activity measurement")
7710 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
7711 for classification of monitor wear and nonwear time intervals in accelerometer
7712 data collected to assess physical activity. The package also contains functions
7713 for making plots of accelerometer data and obtaining the summary of various
7714 information including daily monitor wear time and the mean monitor wear time
7715 during valid days. The revised package version 0.2-1 improved the functions
7716 regarding speed, robustness and add better support for time zones and daylight
7717 saving. In addition, several functions were added:
7719 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
7720 @item the @code{markPAI} can categorize physical activity intensity level based
7721 on user-defined cut-points of accelerometer counts.
7723 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
7724 @code{queryActigraph} functions.")
7725 (license license:gpl3+)))
7727 (define-public r-acc
7734 (uri (cran-uri "acc" version))
7736 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
7737 (build-system r-build-system)
7739 `(("r-circlize" ,r-circlize)
7741 ("r-ggplot2" ,r-ggplot2)
7742 ("r-iterators" ,r-iterators)
7743 ("r-mhsmm" ,r-mhsmm)
7744 ("r-nleqslv" ,r-nleqslv)
7745 ("r-physicalactivity" ,r-physicalactivity)
7747 ("r-r-utils" ,r-r-utils)
7749 ("r-rcpparmadillo" ,r-rcpparmadillo)
7750 ("r-rsqlite" ,r-rsqlite)
7752 (home-page "https://cran.r-project.org/web/packages/acc/")
7753 (synopsis "Exploring accelerometer data")
7755 "This package processes accelerometer data from uni-axial and tri-axial devices
7756 and generates data summaries. Also, includes functions to plot, analyze, and
7757 simulate accelerometer data.")
7758 (license license:gpl2+)))
7760 (define-public r-rbenchmark
7762 (name "r-rbenchmark")
7767 (uri (cran-uri "rbenchmark" version))
7769 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
7770 (build-system r-build-system)
7771 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
7772 (synopsis "Benchmarking routine for R")
7774 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
7775 and is intended to facilitate benchmarking of arbitrary R code. The library
7776 consists of just one function, benchmark, which is a simple wrapper around
7777 system.time. Given a specification of the benchmarking process (counts of
7778 replications, evaluation environment) and an arbitrary number of expressions,
7779 benchmark evaluates each of the expressions in the specified environment,
7780 replicating the evaluation as many times as specified, and returning the results
7781 conveniently wrapped into a data frame.")
7782 (license license:gpl2+)))
7784 (define-public r-mitools
7791 (uri (cran-uri "mitools" version))
7794 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
7795 (build-system r-build-system)
7796 (propagated-inputs `(("r-dbi" ,r-dbi)))
7797 (home-page "https://cran.r-project.org/web/packages/mitools/")
7798 (synopsis "Tools for multiple imputation of missing data")
7800 "This package provides tools to perform analyses and combine results from
7801 multiple-imputation datasets.")
7802 (license license:gpl2)))
7804 (define-public r-magick
7811 (uri (cran-uri "magick" version))
7814 "182b4wahkq9q0scn99mql4vm9fp92nja0r5yizc4x9rjl492ahd8"))))
7815 (build-system r-build-system)
7817 `(("imagemagick" ,imagemagick)
7820 `(("r-curl" ,r-curl)
7821 ("r-magrittr" ,r-magrittr)
7822 ("r-rcpp" ,r-rcpp)))
7824 `(("pkg-config" ,pkg-config)))
7825 (home-page "https://github.com/ropensci/magick")
7826 (synopsis "Advanced graphics and image-processing in R")
7828 "This package provides bindings to ImageMagick, a comprehensive image
7829 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
7830 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
7831 operations are vectorized via the Magick++ STL meaning they operate either on
7832 a single frame or a series of frames for working with layers, collages, or
7833 animation. In RStudio, images are automatically previewed when printed to the
7834 console, resulting in an interactive editing environment.")
7835 (license license:expat)))
7837 (define-public r-survey
7844 (uri (cran-uri "survey" version))
7847 "1f31dvh48gzzan13pdrwh84ls35x9116095i7mdrcbrhz809r8dy"))))
7848 (build-system r-build-system)
7850 `(("r-lattice" ,r-lattice)
7851 ("r-matrix" ,r-matrix)
7852 ("r-minqa" ,r-minqa)
7853 ("r-mitools" ,r-mitools)
7854 ("r-numderiv" ,r-numderiv)
7855 ("r-survival" ,r-survival)))
7856 (home-page "http://r-survey.r-forge.r-project.org/survey/")
7857 (synopsis "Analysis of complex survey samples")
7859 "This package provides tools for the analysis of complex survey samples.
7860 The provided features include: summary statistics, two-sample tests, rank
7861 tests, generalised linear models, cumulative link models, Cox models,
7862 loglinear models, and general maximum pseudolikelihood estimation for
7863 multistage stratified, cluster-sampled, unequally weighted survey samples;
7864 variances by Taylor series linearisation or replicate weights;
7865 post-stratification, calibration, and raking; two-phase subsampling designs;
7866 graphics; PPS sampling without replacement; principal components, and factor
7868 ;; Either version of the GPL.
7869 (license (list license:gpl2 license:gpl3))))
7871 (define-public r-gee
7878 (uri (cran-uri "gee" version))
7881 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
7882 (properties `((upstream-name . "gee")))
7883 (build-system r-build-system)
7885 `(("gfortran" ,gfortran)))
7886 (home-page "https://cran.r-project.org/web/packages/gee/")
7887 (synopsis "Generalized estimation equation solver")
7889 "This package provides a solver for generalized estimation equations.")
7890 (license license:gpl2)))
7892 (define-public r-tab
7899 (uri (cran-uri "tab" version))
7902 "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
7903 (properties `((upstream-name . "tab")))
7904 (build-system r-build-system)
7906 `(("r-dplyr" ,r-dplyr)
7908 ("r-knitr" ,r-knitr)
7910 ("r-survey" ,r-survey)
7911 ("r-survival" ,r-survival)
7912 ("r-xtable" ,r-xtable)))
7913 (home-page "https://cran.r-project.org/web/packages/tab/")
7914 (synopsis "Create summary tables for statistical reports")
7916 "This package contains functions for creating various types of summary
7917 tables, e.g. comparing characteristics across levels of a categorical variable
7918 and summarizing fitted generalized linear models, generalized estimating
7919 equations, and Cox proportional hazards models. Functions are available to
7920 handle data from simple random samples as well as complex surveys.")
7921 (license license:gpl3+)))
7923 (define-public r-dvmisc
7930 (uri (cran-uri "dvmisc" version))
7932 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
7933 (build-system r-build-system)
7935 `(("r-cubature" ,r-cubature)
7936 ("r-data-table" ,r-data-table)
7937 ("r-dplyr" ,r-dplyr)
7938 ("r-ggplot2" ,r-ggplot2)
7940 ("r-mvtnorm" ,r-mvtnorm)
7941 ("r-pracma" ,r-pracma)
7942 ("r-rbenchmark" ,r-rbenchmark)
7944 ("r-survey" ,r-survey)
7946 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
7947 (synopsis "Faster computation of common statistics and miscellaneous functions")
7949 "This package implements faster versions of base R functions (e.g. mean, standard
7950 deviation, covariance, weighted mean), mostly written in C++, along with
7951 miscellaneous functions for various purposes (e.g. create the histogram with
7952 fitted probability density function or probability mass function curve, create
7953 the body mass index groups, assess the linearity assumption in logistic
7955 (license license:gpl2)))
7957 (define-public r-accelerometry
7959 (name "r-accelerometry")
7964 (uri (cran-uri "accelerometry" version))
7966 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
7967 (build-system r-build-system)
7969 `(("r-dvmisc" ,r-dvmisc)
7970 ("r-rcpp" ,r-rcpp)))
7971 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
7972 (synopsis "Functions for processing accelerometer data")
7974 "This package provides a collection of functions that perform operations on
7975 time-series accelerometer data, such as identify the non-wear time, flag minutes
7976 that are part of an activity bout, and find the maximum 10-minute average count
7977 value. The functions are generally very flexible, allowing for a variety of
7978 algorithms to be implemented.")
7979 (license license:gpl3)))
7981 (define-public r-absim
7988 (uri (cran-uri "AbSim" version))
7990 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
7991 (properties `((upstream-name . "AbSim")))
7992 (build-system r-build-system)
7995 ("r-powerlaw" ,r-powerlaw)))
7996 (home-page "https://cran.r-project.org/web/packages/AbSim/")
7997 (synopsis "Time resolved simulations of antibody repertoires")
7999 "This package provides simulation methods for the evolution of antibody repertoires.
8000 The heavy and light chain variable region of both human and C57BL/6 mice can
8001 be simulated in a time-dependent fashion. Both single lineages using one set of
8002 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
8003 with an initial V-D-J recombination event, starting the first phylogenetic tree.
8004 Upon completion, the main loop of the algorithm begins, with each iteration
8005 representing one simulated time step. Various mutation events are possible at
8006 each time step, contributing to a diverse final repertoire.")
8007 (license license:gpl2)))
8009 (define-public r-quic
8016 (uri (cran-uri "QUIC" version))
8018 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
8019 (properties `((upstream-name . "QUIC")))
8020 (build-system r-build-system)
8021 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
8022 (synopsis "Regularized sparse inverse covariance matrix estimation")
8024 "This package implements the regularized Gaussian maximum likelihood
8025 estimation of the inverse of a covariance matrix. It uses Newton's method and
8026 coordinate descent to solve the regularized inverse covariance matrix
8027 estimation problem.")
8028 ;; The project home page states that the release is under GPLv3 or later.
8029 ;; The CRAN page only says GPL-3.
8030 (license license:gpl3+)))
8032 (define-public r-abundant
8039 (uri (cran-uri "abundant" version))
8041 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
8042 (build-system r-build-system)
8044 `(("r-quic" ,r-quic)))
8045 (home-page "https://cran.r-project.org/web/packages/abundant/")
8046 (synopsis "Abundant regression and high-dimensional principal fitted components")
8048 "This package provides tools to fit and predict with the high-dimensional
8049 principal fitted components model. This model is described by Cook, Forzani,
8050 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
8051 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
8052 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
8053 (license license:gpl2+)))
8055 (define-public r-ac3net
8062 (uri (cran-uri "Ac3net" version))
8064 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
8065 (properties `((upstream-name . "Ac3net")))
8066 (build-system r-build-system)
8068 `(("r-data-table" ,r-data-table)))
8069 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
8070 (synopsis "Inferring directional conservative causal core gene networks")
8071 (description "This package infers directional Conservative causal core
8072 (gene) networks (C3NET). This is a version of the algorithm C3NET with
8073 directional network.")
8074 (license license:gpl3+)))
8076 (define-public r-aca
8083 (uri (cran-uri "ACA" version))
8085 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
8086 (properties `((upstream-name . "ACA")))
8087 (build-system r-build-system)
8088 (home-page "https://cran.r-project.org/web/packages/ACA/")
8089 (synopsis "Abrupt change-point or aberration detection in point series")
8091 "This package offers an interactive function for the detection of breakpoints in
8093 ;; Any version of the GPL
8094 (license (list license:gpl2+ license:gpl3+))))
8096 (define-public r-acceptancesampling
8098 (name "r-acceptancesampling")
8103 (uri (cran-uri "AcceptanceSampling" version))
8105 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
8107 `((upstream-name . "AcceptanceSampling")))
8108 (build-system r-build-system)
8109 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
8110 (synopsis "Creation and evaluation of acceptance sampling plans")
8112 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
8113 acceptance sampling plans. Acceptance sampling is a methodology commonly used
8114 in quality control and improvement. International standards of acceptance
8115 sampling provide sampling plans for specific circumstances. The aim of this
8116 package is to provide an easy-to-use interface to visualize single, double or
8117 multiple sampling plans. In addition, methods have been provided to enable the
8118 user to assess sampling plans against pre-specified levels of performance, as
8119 measured by the probability of acceptance for a given level of quality in the
8121 (license license:gpl3+)))
8123 (define-public r-acclma
8130 (uri (cran-uri "ACCLMA" version))
8132 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
8133 (properties `((upstream-name . "ACCLMA")))
8134 (build-system r-build-system)
8135 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
8136 (synopsis "ACC & LMA graph plotting")
8138 "This package contains a function that imports data from a @acronym{CSV,
8139 Comma-Separated Values} file, or uses manually entered data from the format (x,
8140 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
8141 Curve} vs @acronym{LOI, Line of Independence} graph and
8142 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
8143 function is @code{plotLMA} (source file, header) that takes a data set and plots the
8144 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
8145 string) was passed, a manual data entry window is opened. The header parameter
8146 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
8147 a header row or not. The dataset should contain only one independent variable
8148 (x) and one dependent variable (y) and can contain a weight for each
8150 (license license:gpl2)))
8152 (define-public r-aspi
8159 (uri (cran-uri "aspi" version))
8161 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
8162 (build-system r-build-system)
8164 "https://cran.r-project.org/web/packages/aspi/")
8166 "Analysis of symmetry of parasitic infections")
8168 "This package provides tools for the analysis and visualization of bilateral
8169 asymmetry in parasitic infections.")
8170 (license license:gpl3+)))
8172 (define-public r-sandwich
8179 (uri (cran-uri "sandwich" version))
8182 "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv"))))
8183 (build-system r-build-system)
8185 `(("r-zoo" ,r-zoo)))
8186 (home-page "https://cran.r-project.org/web/packages/sandwich/")
8187 (synopsis "Robust Covariance Matrix Estimators")
8189 "This package provides model-robust standard error estimators for
8190 cross-sectional, time series, clustered, panel, and longitudinal data.")
8191 ;; Either version of the license.
8192 (license (list license:gpl2 license:gpl3))))
8194 (define-public r-th-data
8201 (uri (cran-uri "TH.data" version))
8204 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
8205 (properties `((upstream-name . "TH.data")))
8206 (build-system r-build-system)
8208 `(("r-mass" ,r-mass)
8209 ("r-survival" ,r-survival)))
8210 (home-page "https://cran.r-project.org/web/packages/TH.data/")
8211 (synopsis "Shared data sets")
8213 "This package contains supporting data sets that are used in other
8214 packages maintained by Torsten Hothorn.")
8215 (license license:gpl3)))
8217 (define-public r-multcomp
8224 (uri (cran-uri "multcomp" version))
8227 "14c2f10rz546w7ly5f4r6wnd07yj5gic38an17gxny1vf2nsff0b"))))
8228 (build-system r-build-system)
8230 `(("r-codetools" ,r-codetools)
8231 ("r-mvtnorm" ,r-mvtnorm)
8232 ("r-sandwich" ,r-sandwich)
8233 ("r-survival" ,r-survival)
8234 ("r-th-data" ,r-th-data)))
8235 (home-page "https://cran.r-project.org/web/packages/multcomp/")
8236 (synopsis "Simultaneous inference in general parametric models")
8238 "Simultaneous tests and confidence intervals for general linear
8239 hypotheses in parametric models, including linear, generalized linear, linear
8240 mixed effects, and survival models. The package includes demos reproducing
8241 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
8242 Hothorn, Westfall, 2010, CRC Press).")
8243 (license license:gpl2)))
8245 (define-public r-emmeans
8252 (uri (cran-uri "emmeans" version))
8255 "10fmvmd6q4zjr6b18hhc85mwrzv778qzj6lwl9kbs2fsfvsgw7mm"))))
8256 (build-system r-build-system)
8258 `(("r-estimability" ,r-estimability)
8259 ("r-mvtnorm" ,r-mvtnorm)
8260 ("r-numderiv" ,r-numderiv)
8262 ("r-xtable" ,r-xtable)))
8263 (home-page "https://github.com/rvlenth/emmeans")
8264 (synopsis "Estimated marginal means, aka least-squares means")
8266 "This package provides tools to obtain @dfn{estimated marginal
8267 means} (EMMs) for many linear, generalized linear, and mixed models. It can
8268 be used to compute contrasts or linear functions of EMMs, trends, and
8269 comparisons of slopes.")
8270 ;; Either version of the license.
8271 (license (list license:gpl2 license:gpl3))))
8273 (define-public r-pwr
8280 (uri (cran-uri "pwr" version))
8283 "0r5g781lr677vp3zyhgmi7r68c87l8gd05l1s3ffnxgn5wf043sm"))))
8284 (build-system r-build-system)
8286 `(("r-knitr" ,r-knitr)))
8287 (home-page "https://github.com/heliosdrm/pwr")
8288 (synopsis "Basic functions for power analysis")
8290 "This package provides power analysis functions along the lines of
8292 (license license:gpl3+)))
8294 (define-public r-libcoin
8301 (uri (cran-uri "libcoin" version))
8304 "1cm9x1dlg9f7fh7n5nw3x4a7rl88c7ylrlc8x3rx4mq5w1j42x0a"))))
8305 (build-system r-build-system)
8306 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8307 (home-page "https://cran.r-project.org/web/packages/libcoin")
8308 (synopsis "Linear test statistics for permutation inference")
8310 "This package provides basic infrastructure for linear test statistics
8311 and permutation inference in the framework of Strasser and Weber (1999).")
8312 (license license:gpl2)))
8314 (define-public r-coin
8321 (uri (cran-uri "coin" version))
8324 "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx"))))
8325 (build-system r-build-system)
8327 `(("r-libcoin" ,r-libcoin)
8328 ("r-matrixstats" ,r-matrixstats)
8329 ("r-modeltools" ,r-modeltools)
8330 ("r-multcomp" ,r-multcomp)
8331 ("r-mvtnorm" ,r-mvtnorm)
8332 ("r-survival" ,r-survival)))
8333 (home-page "http://coin.r-forge.r-project.org")
8334 (synopsis "Conditional inference procedures in a permutation test framework")
8336 "This package provides conditional inference procedures for the general
8337 independence problem including two-sample, K-sample (non-parametric ANOVA),
8338 correlation, censored, ordered and multivariate problems.")
8339 (license license:gpl2)))
8341 (define-public r-bayesplot
8343 (name "r-bayesplot")
8348 (uri (cran-uri "bayesplot" version))
8351 "0sq0ajnm96hmlqf1cv5n2gshh3qdij4n1zbm7qrniz2q6b5aj342"))))
8352 (build-system r-build-system)
8354 `(("pandoc" ,ghc-pandoc)
8355 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
8357 `(("r-dplyr" ,r-dplyr)
8358 ("r-ggplot2" ,r-ggplot2)
8359 ("r-ggridges" ,r-ggridges)
8361 ("r-reshape2" ,r-reshape2)
8362 ("r-rlang" ,r-rlang)
8363 ("r-tibble" ,r-tibble)
8364 ("r-tidyselect" ,r-tidyselect)))
8365 (home-page "https://mc-stan.org/bayesplot")
8366 (synopsis "Plotting for Bayesian models")
8368 "This package provides plotting functions for posterior analysis, model
8369 checking, and MCMC diagnostics. The package is designed not only to provide
8370 convenient functionality for users, but also a common set of functions that
8371 can be easily used by developers working on a variety of R packages for
8372 Bayesian modeling.")
8373 (license license:gpl3+)))
8375 (define-public r-tmb
8382 (uri (cran-uri "TMB" version))
8385 "0lly12hdi99iklwr0vg9xkyhi038w4gncbf895qcwbndmqp0lx44"))))
8386 (properties `((upstream-name . "TMB")))
8387 (build-system r-build-system)
8389 `(("r-matrix" ,r-matrix)
8390 ("r-rcppeigen" ,r-rcppeigen)))
8391 (home-page "http://tmb-project.org")
8392 (synopsis "Template model builder: a general random effect tool")
8394 "With this tool, a user should be able to quickly implement complex
8395 random effect models through simple C++ templates. The package combines
8396 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
8397 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
8398 from R) to obtain an efficient implementation of the applied Laplace
8399 approximation with exact derivatives. Key features are: Automatic sparseness
8400 detection, parallelism through BLAS and parallel user templates.")
8401 (license license:gpl2)))
8403 (define-public r-sjstats
8410 (uri (cran-uri "sjstats" version))
8412 (base32 "0938ac6ixvkif07azd2msa8g3qnn9rabj6jg17almbysl83kg4nm"))))
8413 (build-system r-build-system)
8415 `(("r-bayestestr" ,r-bayestestr)
8416 ("r-broom" ,r-broom)
8417 ("r-dplyr" ,r-dplyr)
8418 ("r-effectsize" ,r-effectsize)
8419 ("r-emmeans" ,r-emmeans)
8420 ("r-insight" ,r-insight)
8422 ("r-magrittr" ,r-magrittr)
8424 ("r-modelr" ,r-modelr)
8425 ("r-parameters" ,r-parameters)
8426 ("r-performance" ,r-performance)
8427 ("r-purrr" ,r-purrr)
8428 ("r-rlang" ,r-rlang)
8429 ("r-sjlabelled" ,r-sjlabelled)
8430 ("r-sjmisc" ,r-sjmisc)
8431 ("r-tidyr" ,r-tidyr)))
8432 (home-page "https://github.com/strengejacke/sjstats")
8433 (synopsis "Functions for common statistical computations")
8435 "This package provides a collection of convenient functions for common
8436 statistical computations, which are not directly provided by R's @code{base}
8437 or @code{stats} packages. This package aims at providing, first, shortcuts
8438 for statistical measures, which otherwise could only be calculated with
8439 additional effort. Second, these shortcut functions are generic, and can be
8440 applied not only to vectors, but also to other objects as well. The focus of
8441 most functions lies on summary statistics or fit measures for regression
8442 models, including generalized linear models, mixed effects models and Bayesian
8444 (license license:gpl3)))
8446 (define-public r-glmmtmb
8453 (uri (cran-uri "glmmTMB" version))
8456 "1md4yw4kbng953rz1n9g1v2xffk3cxx1qmp0kvbdayg1s82l1rgx"))))
8457 (properties `((upstream-name . "glmmTMB")))
8458 (build-system r-build-system)
8460 `(("r-lme4" ,r-lme4)
8461 ("r-matrix" ,r-matrix)
8463 ("r-rcppeigen" ,r-rcppeigen)
8466 `(("r-knitr" ,r-knitr))) ; for vignettes
8467 (home-page "https://github.com/glmmTMB")
8468 (synopsis "Generalized linear mixed models")
8470 "Fit linear and generalized linear mixed models with various extensions,
8471 including zero-inflation. The models are fitted using maximum likelihood
8472 estimation via the Template Model Builder. Random effects are assumed to be
8473 Gaussian on the scale of the linear predictor and are integrated out using the
8474 Laplace approximation. Gradients are calculated using automatic
8476 (license license:agpl3+)))
8478 (define-public r-bayestestr
8480 (name "r-bayestestr")
8485 (uri (cran-uri "bayestestR" version))
8488 "1l0kqw793d8fnk0745fllmqwjwnj9srvqzv4baq5s05ls1gbi2mw"))))
8489 (properties `((upstream-name . "bayestestR")))
8490 (build-system r-build-system)
8492 `(("r-insight" ,r-insight)))
8493 (home-page "https://github.com/easystats/bayestestR")
8494 (synopsis "Describe Bayesian models and posterior distributions")
8496 "This package provides utilities to understand and describe posterior
8497 distributions and Bayesian models. It includes point-estimates such as
8498 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
8499 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
8500 ROPE percentage and pd).")
8501 (license license:gpl3)))
8503 (define-public r-performance
8505 (name "r-performance")
8510 (uri (cran-uri "performance" version))
8513 "18h9y66cpsb3k6xnaya87vnpv2s3chf4bzsc4ym3n5sxhh41j7la"))))
8514 (build-system r-build-system)
8516 `(("r-bayestestr" ,r-bayestestr)
8517 ("r-insight" ,r-insight)))
8518 (home-page "https://easystats.github.io/performance/")
8519 (synopsis "Assessment of regression models performance")
8521 "This package provides utilities for computing measures to assess model
8522 quality, which are not directly provided by R's @code{base} or @code{stats}
8523 packages. These include e.g. measures like r-squared, intraclass correlation
8524 coefficient, root mean squared error or functions to check models for
8525 overdispersion, singularity or zero-inflation and more. Functions apply to a
8526 large variety of regression models, including generalized linear models, mixed
8527 effects models and Bayesian models.")
8528 (license license:gpl3)))
8530 (define-public r-ggeffects
8532 (name "r-ggeffects")
8537 (uri (cran-uri "ggeffects" version))
8540 "07pvs18vlybp96zz1wjr7cwiwi1cvjwkb9ahxzq0vd6adnd6ya59"))))
8541 (build-system r-build-system)
8543 `(("r-insight" ,r-insight)
8545 ("r-sjlabelled" ,r-sjlabelled)))
8546 (home-page "https://github.com/strengejacke/ggeffects")
8547 (synopsis "Create tidy data frames of marginal effects for ggplot")
8549 "This package provides tools to compute marginal effects from statistical
8550 models and return the result as tidy data frames. These data frames are ready
8551 to use with the @code{ggplot2} package. Marginal effects can be calculated
8552 for many different models. Interaction terms, splines and polynomial terms
8553 are also supported. The two main functions are @code{ggpredict()} and
8554 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
8555 results using @code{ggplot2}.")
8556 (license license:gpl3)))
8558 (define-public r-effectsize
8560 (name "r-effectsize")
8565 (uri (cran-uri "effectsize" version))
8568 "1liix8rf8xq3hzi7684bl0s20iflsq6g5mxr5k59wp2qwn1i6aww"))))
8569 (properties `((upstream-name . "effectsize")))
8570 (build-system r-build-system)
8572 `(("r-bayestestr" ,r-bayestestr)
8573 ("r-insight" ,r-insight)
8574 ("r-parameters" ,r-parameters)))
8575 (home-page "https://github.com/easystats/effectsize")
8576 (synopsis "Indices of effect size and standardized parameters")
8578 "This package provides utilities to work with indices of effect size and
8579 standardized parameters for a wide variety of models, allowing computation and
8580 conversion of indices such as Cohen's d, r, odds, etc.")
8581 (license license:gpl3)))
8583 (define-public r-sjplot
8590 (uri (cran-uri "sjPlot" version))
8592 (base32 "16721a5006q0gv45zjcwnkykxhjkzpq5n35vhik0g0ixgm3a2vci"))))
8593 (properties `((upstream-name . "sjPlot")))
8594 (build-system r-build-system)
8596 `(("r-bayestestr" ,r-bayestestr)
8597 ("r-dplyr" ,r-dplyr)
8598 ("r-effectsize" ,r-effectsize)
8599 ("r-forcats" ,r-forcats)
8600 ("r-ggeffects" ,r-ggeffects)
8601 ("r-ggplot2" ,r-ggplot2)
8602 ("r-insight" ,r-insight)
8603 ("r-knitr" ,r-knitr)
8605 ("r-parameters" ,r-parameters)
8606 ("r-performance" ,r-performance)
8607 ("r-purrr" ,r-purrr)
8608 ("r-rlang" ,r-rlang)
8609 ("r-scales" ,r-scales)
8610 ("r-sjlabelled" ,r-sjlabelled)
8611 ("r-sjmisc" ,r-sjmisc)
8612 ("r-sjstats" ,r-sjstats)
8613 ("r-tidyr" ,r-tidyr)))
8614 (home-page "https://strengejacke.github.io/sjPlot/")
8615 (synopsis "Data visualization for statistics in social science")
8617 "This package represents a collection of plotting and table output
8618 functions for data visualization. Results of various statistical
8619 analyses (that are commonly used in social sciences) can be visualized using
8620 this package, including simple and cross tabulated frequencies, histograms,
8621 box plots, (generalized) linear models, mixed effects models, principal
8622 component analysis and correlation matrices, cluster analyses, scatter plots,
8623 stacked scales, effects plots of regression models (including interaction
8624 terms) and much more. This package supports labelled data.")
8625 (license license:gpl3)))
8627 (define-public r-ini
8634 (uri (cran-uri "ini" version))
8637 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
8638 (build-system r-build-system)
8639 (home-page "https://github.com/dvdscripter/ini")
8640 (synopsis "Read and write configuration files")
8642 "This package provides tools to parse simple @code{.ini} configuration
8643 files to an structured list. Users can manipulate this resulting list with
8644 @code{lapply()} functions. This same structured list can be used to write
8645 back to file after modifications.")
8646 (license license:gpl3)))
8655 (uri (cran-uri "gh" version))
8658 "1bc9bn1078s664hc806dh0y1ncxif77q479rfmxfir9z7hwaz7yy"))))
8659 (build-system r-build-system)
8664 ("r-jsonlite" ,r-jsonlite)))
8665 (home-page "https://github.com/r-lib/gh#readme")
8666 (synopsis "Access the GitHub API via R")
8668 "This package provides a minimal R client to access the GitHub API.")
8669 (license license:expat)))
8678 (uri (cran-uri "fs" version))
8681 "1w30bflx4d7a6f3dn96bf7s7v6aqpvz2yzzxal6qz9jyhb16bxaz"))))
8682 (build-system r-build-system)
8684 `(("r-rcpp" ,r-rcpp)))
8686 `(("pkg-config" ,pkg-config)))
8687 (home-page "https://fs.r-lib.org")
8688 (synopsis "Cross-platform file system operations based on libuv")
8690 "This package provides a cross-platform interface to file system
8691 operations, built on top of the libuv C library.")
8692 (license license:gpl3)))
8694 (define-public r-clisymbols
8696 (name "r-clisymbols")
8701 (uri (cran-uri "clisymbols" version))
8704 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
8705 (build-system r-build-system)
8706 (home-page "https://github.com/gaborcsardi/clisymbols")
8707 (synopsis "Unicode symbols at the R prompt")
8709 "This package provides a small subset of Unicode symbols, that are useful
8710 when building command line applications. They fall back to alternatives on
8711 terminals that do not support Unicode.")
8712 (license license:expat)))
8714 (define-public r-usethis
8721 (uri (cran-uri "usethis" version))
8724 "07an5wbikilg7cb3q6x5aykw8dfqnjrc3wpfb7gjmy0d9fh20fcy"))))
8725 (build-system r-build-system)
8727 `(("r-clipr" ,r-clipr)
8728 ("r-clisymbols" ,r-clisymbols)
8729 ("r-crayon" ,r-crayon)
8734 ("r-git2r" ,r-git2r)
8736 ("r-purrr" ,r-purrr)
8737 ("r-rlang" ,r-rlang)
8738 ("r-rprojroot" ,r-rprojroot)
8739 ("r-rstudioapi" ,r-rstudioapi)
8740 ("r-whisker" ,r-whisker)
8741 ("r-withr" ,r-withr)
8742 ("r-yaml" ,r-yaml)))
8743 (home-page "https://github.com/r-lib/usethis")
8744 (synopsis "Automate R package and project setup")
8746 "This package helps you to automate R package and project setup tasks
8747 that are otherwise performed manually. This includes setting up unit testing,
8748 test coverage, continuous integration, Git, GitHub integration, licenses,
8749 Rcpp, RStudio projects, and more.")
8750 (license license:gpl3)))
8752 (define-public r-sessioninfo
8754 (name "r-sessioninfo")
8759 (uri (cran-uri "sessioninfo" version))
8762 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
8763 (build-system r-build-system)
8766 ("r-withr" ,r-withr)))
8767 (home-page "https://github.com/r-lib/sessioninfo#readme")
8768 (synopsis "R session information")
8770 "This package provides tools to query and print information about the
8771 current R session. It is similar to @code{utils::sessionInfo()}, but includes
8772 more information about packages, and where they were installed from.")
8773 (license license:gpl2)))
8775 (define-public r-remotes
8782 (uri (cran-uri "remotes" version))
8785 "12qinl7jv54f2524ri13gcrv6d523rg1harpi500j676zi30fnaf"))))
8786 (build-system r-build-system)
8787 (home-page "https://github.com/r-lib/remotes#readme")
8788 (synopsis "R package installation from remote repositories")
8790 "Download and install R packages stored in GitHub, BitBucket, or plain
8791 subversion or git repositories. This package is a lightweight replacement of
8792 the @code{install_*} functions in the @code{devtools} package. Indeed most of
8793 the code was copied over from @code{devtools}.")
8794 (license license:gpl2+)))
8796 (define-public r-xopen
8803 (uri (cran-uri "xopen" version))
8806 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
8807 (build-system r-build-system)
8809 `(("r-processx" ,r-processx)))
8810 (home-page "https://github.com/r-lib/xopen#readme")
8811 (synopsis "Open system files, URLs, anything")
8813 "This package provides a cross-platform solution to open files,
8814 directories or URLs with their associated programs.")
8815 (license license:expat)))
8817 (define-public r-rcmdcheck
8819 (name "r-rcmdcheck")
8824 (uri (cran-uri "rcmdcheck" version))
8827 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
8828 (build-system r-build-system)
8830 `(("r-callr" ,r-callr)
8832 ("r-crayon" ,r-crayon)
8834 ("r-digest" ,r-digest)
8835 ("r-pkgbuild" ,r-pkgbuild)
8836 ("r-prettyunits" ,r-prettyunits)
8838 ("r-rprojroot" ,r-rprojroot)
8839 ("r-sessioninfo" ,r-sessioninfo)
8840 ("r-withr" ,r-withr)
8841 ("r-xopen" ,r-xopen)))
8842 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
8843 (synopsis "Run R CMD check from R and capture results")
8845 "Run @code{R CMD check} from R programmatically, and capture the results
8846 of the individual checks.")
8847 (license license:expat)))
8849 (define-public r-rapportools
8851 (name "r-rapportools")
8856 (uri (cran-uri "rapportools" version))
8859 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
8860 (build-system r-build-system)
8862 `(("r-pander" ,r-pander)
8864 ("r-reshape" ,r-reshape)))
8865 (home-page "https://cran.r-project.org/web/packages/rapportools/")
8866 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
8868 "This package provides helper functions that act as wrappers to more
8869 advanced statistical methods with the advantage of having sane defaults for
8871 (license license:agpl3+)))
8873 (define-public r-pander
8880 (uri (cran-uri "pander" version))
8883 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
8884 (build-system r-build-system)
8886 `(("r-digest" ,r-digest)
8887 ("r-rcpp" ,r-rcpp)))
8888 (home-page "https://rapporter.github.io/pander")
8889 (synopsis "Render R objects into Pandoc's markdown")
8891 "The main aim of the pander R package is to provide a minimal and easy
8892 tool for rendering R objects into Pandoc's markdown. The package is also
8893 capable of exporting/converting complex Pandoc documents (reports) in various
8895 ;; This package is licensed under either the AGPLv3+ or the very rarely
8897 (license license:agpl3+)))
8899 (define-public r-summarytools
8901 (name "r-summarytools")
8906 (uri (cran-uri "summarytools" version))
8909 "03pcb2ild1rb9f15yq8b68p9bg10z5wk2x7ahgyzkwdh5f81vbq2"))))
8910 (build-system r-build-system)
8912 `(("r-base64enc" ,r-base64enc)
8913 ("r-checkmate" ,r-checkmate)
8914 ("r-dplyr" ,r-dplyr)
8915 ("r-htmltools" ,r-htmltools)
8916 ("r-lubridate" ,r-lubridate)
8917 ("r-magick" ,r-magick)
8918 ("r-matrixstats" ,r-matrixstats)
8919 ("r-pander" ,r-pander)
8921 ("r-rapportools" ,r-rapportools)
8922 ("r-tibble" ,r-tibble)
8923 ("r-tidyr" ,r-tidyr)))
8924 (home-page "https://github.com/dcomtois/summarytools")
8925 (synopsis "Tools to quickly and neatly summarize data")
8927 "This package provides tools for data frame summaries, cross-tabulations,
8928 weight-enabled frequency tables and common univariate statistics in concise
8929 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
8930 good point-of-entry for exploring data, both for experienced and new R
8932 (license license:gpl2)))
8934 (define-public r-lsei
8941 (uri (cran-uri "lsei" version))
8944 "1xl06fb3is744pxlh42wx5hn1h0ab1k31wnmsmh0524kxzcyp0a7"))))
8945 (build-system r-build-system)
8947 `(("gfortran" ,gfortran)))
8948 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
8949 (synopsis "Solve regression problems under equality/inequality constraints")
8951 "It contains functions that solve least squares linear regression
8952 problems under linear equality/inequality constraints. Functions for solving
8953 quadratic programming problems are also available, which transform such
8954 problems into least squares ones first.")
8955 (license license:gpl2+)))
8957 (define-public r-npsurv
8964 (uri (cran-uri "npsurv" version))
8967 "1wq4c9yfha5azjhrn40iiqkshmvh611sa90jp3lh82n4bl9zfk20"))))
8968 (build-system r-build-system)
8970 `(("r-lsei" ,r-lsei)))
8971 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
8972 (synopsis "Nonparametric survival analysis")
8974 "This package contains functions for non-parametric survival analysis of
8975 exact and interval-censored observations.")
8976 (license license:gpl2+)))
8978 (define-public r-clusteval
8980 (name "r-clusteval")
8985 (uri (cran-uri "clusteval" version))
8988 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
8989 (build-system r-build-system)
8991 `(("r-mvtnorm" ,r-mvtnorm)
8992 ("r-rcpp" ,r-rcpp)))
8993 (home-page "https://cran.r-project.org/web/packages/clusteval/")
8994 (synopsis "Evaluation of clustering algorithms")
8996 "This R package provides a suite of tools to evaluate clustering
8997 algorithms, clusterings, and individual clusters.")
8998 (license license:expat)))
9000 (define-public r-tweedie
9007 (uri (cran-uri "tweedie" version))
9010 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
9011 (build-system r-build-system)
9012 (native-inputs `(("gfortran" ,gfortran)))
9013 (home-page "https://cran.r-project.org/web/packages/tweedie/")
9014 (synopsis "Evaluation of Tweedie exponential family models")
9016 "Maximum likelihood computations for Tweedie families, including the
9017 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
9018 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
9019 and related methods.")
9020 (license license:gpl2+)))
9022 (define-public r-rcppgsl
9029 (uri (cran-uri "RcppGSL" version))
9031 (base32 "0cnw2k7cfqrm79r6j283aybflxig80x4n4rjkfp2317wf10mrsa5"))))
9032 (properties `((upstream-name . "RcppGSL")))
9033 (build-system r-build-system)
9035 `(("r-rcpp" ,r-rcpp)
9038 `(("r-knitr" ,r-knitr))) ; for vignettes
9039 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
9040 (synopsis "Rcpp integration for GSL vectors and matrices")
9042 "The GNU Scientific Library (or GSL) is a collection of numerical
9043 routines for scientific computing. It is particularly useful for C and C++
9044 programs as it provides a standard C interface to a wide range of mathematical
9045 routines. There are over 1000 functions in total with an extensive test
9046 suite. The RcppGSL package provides an easy-to-use interface between GSL data
9047 structures and R using concepts from Rcpp which is itself a package that eases
9048 the interfaces between R and C++.")
9049 (license license:gpl2+)))
9051 (define-public r-mvabund
9058 (uri (cran-uri "mvabund" version))
9061 "1z58h4dk3mc2hfnfvc7pghk471cbp7ah2s1z2ria5igw4s80962b"))))
9062 (build-system r-build-system)
9064 `(("r-mass" ,r-mass)
9066 ("r-rcppgsl" ,r-rcppgsl)
9067 ("r-statmod" ,r-statmod)
9068 ("r-tweedie" ,r-tweedie)))
9069 (home-page "https://cran.r-project.org/web/packages/mvabund/")
9070 (synopsis "Statistical methods for analysing multivariate abundance data")
9072 "This package provides a set of tools for displaying, modeling and
9073 analysing multivariate abundance data in community ecology.")
9074 (license license:lgpl2.1+)))
9076 (define-public r-afex
9083 (uri (cran-uri "afex" version))
9086 "0h3p1svgk1ap3lj08fi8nzdb3710h99bv150krf1x8wci1a0r1if"))))
9087 (build-system r-build-system)
9091 ("r-lmertest" ,r-lmertest)
9092 ("r-pbkrtest" ,r-pbkrtest)
9093 ("r-reshape2" ,r-reshape2)))
9094 (home-page "https://afex.singmann.science/")
9095 (synopsis "Analysis of factorial experiments")
9097 "This package provides convenience functions for analyzing factorial
9098 experiments using ANOVA or mixed models.")
9099 (license license:gpl2+)))
9101 (define-public r-lmertest
9108 (uri (cran-uri "lmerTest" version))
9111 "0r2vvs3nl6p8xla3gd943khb4ixp0alvspqpnz2y6n3wk8zgh3jj"))))
9112 (properties `((upstream-name . "lmerTest")))
9113 (build-system r-build-system)
9115 `(("r-ggplot2" ,r-ggplot2)
9118 ("r-numderiv" ,r-numderiv)))
9119 (home-page "https://github.com/runehaubo/lmerTestR")
9120 (synopsis "Tests in linear mixed effects models")
9122 "This package provides p-values in type I, II or III anova and summary
9123 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
9124 method. A Kenward-Roger method is also available via the @code{pbkrtest}
9125 package. Model selection methods include step, drop1 and anova-like tables
9126 for random effects (ranova). Methods for Least-Square means (LS-means) and
9127 tests of linear contrasts of fixed effects are also available.")
9128 (license license:gpl2+)))
9130 (define-public r-r2glmm
9137 (uri (cran-uri "r2glmm" version))
9140 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
9141 (build-system r-build-system)
9143 `(("r-afex" ,r-afex)
9144 ("r-data-table" ,r-data-table)
9145 ("r-dplyr" ,r-dplyr)
9146 ("r-ggplot2" ,r-ggplot2)
9147 ("r-gridextra" ,r-gridextra)
9148 ("r-lmertest" ,r-lmertest)
9150 ("r-matrix" ,r-matrix)
9152 ("r-pbkrtest" ,r-pbkrtest)))
9153 (home-page "https://github.com/bcjaeger/r2glmm")
9154 (synopsis "Compute R squared for mixed (multilevel) models")
9156 "This package computes model and semi partial R squared with confidence
9157 limits for the linear and generalized linear mixed model (LMM and GLMM). The
9158 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
9159 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
9161 (license license:gpl2)))
9163 (define-public r-weights
9170 (uri (cran-uri "weights" version))
9173 "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5"))))
9174 (build-system r-build-system)
9176 `(("r-gdata" ,r-gdata)
9177 ("r-hmisc" ,r-hmisc)
9178 ("r-mice" ,r-mice)))
9180 "https://cran.r-project.org/web/packages/weights/")
9181 (synopsis "Weighting and weighted statistics")
9182 (description "This package Provides a variety of functions for producing
9183 simple weighted statistics, such as weighted Pearson's correlations, partial
9184 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
9185 includes some software for quickly recoding survey data and plotting point
9186 estimates from interaction terms in regressions (and multiply imputed
9187 regressions). NOTE: Weighted partial correlation calculations pulled to
9189 (license license:gpl2+)))
9191 (define-public r-rcppannoy
9193 (name "r-rcppannoy")
9198 (uri (cran-uri "RcppAnnoy" version))
9201 "1rlw6npwwcp066midvkhnzf0xmmfkkdf6f581j3j1s2naqss3fvl"))))
9202 (properties `((upstream-name . "RcppAnnoy")))
9203 (build-system r-build-system)
9205 `(("r-rcpp" ,r-rcpp)))
9207 `(("r-knitr" ,r-knitr))) ; for vignettes
9208 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
9209 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
9211 "Annoy is a small C++ library for Approximate Nearest Neighbors written
9212 for efficient memory usage as well an ability to load from and save to disk.
9213 This package provides an R interface.")
9214 ;; Annoy is released under ASL 2.0, but this wrapper is released under
9216 (license (list license:gpl2+ license:asl2.0))))
9218 (define-public r-rcpphnsw
9225 (uri (cran-uri "RcppHNSW" version))
9228 "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv"))))
9229 (properties `((upstream-name . "RcppHNSW")))
9230 (build-system r-build-system)
9231 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9232 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
9233 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
9235 "Hnswlib is a C++ library for approximate nearest neighbors. This
9236 package provides a minimal R interface by relying on the Rcpp package.")
9237 ;; hnswlib is released under Version 2.0 of the Apache License.
9238 (license (list license:gpl3 license:asl2.0))))
9240 (define-public r-rcppparallel
9242 (name "r-rcppparallel")
9247 (uri (cran-uri "RcppParallel" version))
9250 "0p13f2mywjr7gmskf8ri4y8p5yr1bvr4xrpw2w11vdvafwz1vcia"))))
9251 (properties `((upstream-name . "RcppParallel")))
9252 (build-system r-build-system)
9253 (home-page "http://rcppcore.github.io/RcppParallel")
9254 (synopsis "Parallel programming tools for Rcpp")
9256 "This package provides high level functions for parallel programming with
9257 Rcpp. For example, the @code{parallelFor()} function can be used to convert
9258 the work of a standard serial @code{for} loop into a parallel one and the
9259 @code{parallelReduce()} function can be used for accumulating aggregates or
9261 (license license:gpl2)))
9263 (define-public r-ncdf4
9270 (uri (cran-uri "ncdf4" version))
9273 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
9274 (build-system r-build-system)
9276 `(("netcdf" ,netcdf)
9278 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
9279 (synopsis "R interface to Unidata netCDF format data files")
9281 "This package provides a high-level R interface to data files written
9282 using Unidata's netCDF library (version 4 or earlier), which are binary data
9283 files that are portable across platforms and include metadata information in
9284 addition to the data sets. Using this package, netCDF files can be opened and
9285 data sets read in easily. It is also easy to create new netCDF dimensions,
9286 variables, and files, in either version 3 or 4 format, and manipulate existing
9288 (license license:gpl3+)))
9290 (define-public r-biocmanager
9292 (name "r-biocmanager")
9297 (uri (cran-uri "BiocManager" version))
9299 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
9300 (properties `((upstream-name . "BiocManager")))
9301 (build-system r-build-system)
9302 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
9303 (synopsis "Access the Bioconductor project package repository")
9305 "This package provides a convenient tool to install and update
9306 Bioconductor packages.")
9307 (license license:artistic2.0)))
9309 (define-public r-rgl
9312 (version "0.100.50")
9316 (uri (cran-uri "rgl" version))
9319 "165p932ml7dpjkm41zc47p5cdxar69il0m5yvg0avi8q01vr17ay"))))
9320 (build-system r-build-system)
9322 `(("pkg-config" ,pkg-config)))
9324 `(("freetype" ,freetype)
9328 ("ghc-pandoc" ,ghc-pandoc)
9331 `(("r-crosstalk" ,r-crosstalk)
9332 ("r-htmltools" ,r-htmltools)
9333 ("r-htmlwidgets" ,r-htmlwidgets)
9334 ("r-jsonlite" ,r-jsonlite)
9335 ("r-knitr" ,r-knitr)
9336 ("r-magrittr" ,r-magrittr)
9337 ("r-manipulatewidget" ,r-manipulatewidget)
9338 ("r-shiny" ,r-shiny)))
9339 (home-page "https://r-forge.r-project.org/projects/rgl/")
9340 (synopsis "3D visualization using OpenGL")
9342 "This package provides medium to high level functions for 3D interactive graphics,
9343 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
9344 as functions for constructing representations of geometric
9345 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
9346 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
9347 image formats, including PNG, Postscript, SVG, PGF.")
9348 ;; Any version of the GPL.
9349 (license (list license:gpl2+ license:gpl3+))))
9351 (define-public r-multicool
9353 (name "r-multicool")
9358 (uri (cran-uri "multicool" version))
9361 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
9362 (build-system r-build-system)
9363 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9364 (home-page "https://cran.r-project.org/web/packages/multicool/")
9365 (synopsis "Permutations of multisets in cool-lex order")
9367 "This package provides a set of tools to permute multisets without loops
9368 or hash tables and to generate integer partitions. Cool-lex order is similar
9369 to colexicographical order.")
9370 (license license:gpl2)))
9372 (define-public r-misc3d
9379 (uri (cran-uri "misc3d" version))
9382 "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
9383 (build-system r-build-system)
9384 (home-page "https://cran.r-project.org/web/packages/misc3d/")
9385 (synopsis "Miscellaneous 3D Plots")
9387 "This package provides a collection of miscellaneous 3d plots, including
9389 ;; Any version of the GPL.
9390 (license (list license:gpl2+ license:gpl3+))))
9399 (uri (cran-uri "ks" version))
9401 (base32 "1f6jvxy0hmngyvnvrknzbmhl42njk0vqyycvydm4qnp8cqirqvba"))))
9402 (build-system r-build-system)
9405 ("r-kernlab" ,r-kernlab)
9406 ("r-kernsmooth" ,r-kernsmooth)
9407 ("r-matrix" ,r-matrix)
9408 ("r-mclust" ,r-mclust)
9410 ("r-multicool" ,r-multicool)
9411 ("r-mvtnorm" ,r-mvtnorm)))
9412 (home-page "http://www.mvstat.net/tduong/")
9413 (synopsis "Kernel smoothing")
9415 "This package provides kernel smoothers for univariate and multivariate
9416 data, including density functions, density derivatives, cumulative
9417 distributions, modal clustering, discriminant analysis, and two-sample
9418 hypothesis testing.")
9419 ;; Either version of the GPL.
9420 (license (list license:gpl2 license:gpl3))))
9422 (define-public r-feature
9429 (uri (cran-uri "feature" version))
9432 "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
9433 (build-system r-build-system)
9436 ("r-misc3d" ,r-misc3d)
9438 (home-page "http://www.mvstat.net/tduong/")
9439 (synopsis "Inferential feature significance for kernel density estimation")
9441 "The feature package contains functions to display and compute kernel
9442 density estimates, significant gradient and significant curvature regions.
9443 Significant gradient and/or curvature regions often correspond to significant
9444 features (e.g. local modes).")
9445 ;; Either version of the GPL.
9446 (license (list license:gpl2 license:gpl3))))
9448 (define-public r-arm
9455 (uri (cran-uri "arm" version))
9458 "0vvp90jygajd6ydky57z66wqjq9msfbl88irj5jbsray574mh4bg"))))
9459 (build-system r-build-system)
9461 `(("r-abind" ,r-abind)
9465 ("r-matrix" ,r-matrix)
9466 ("r-nlme" ,r-nlme)))
9467 (home-page "https://cran.r-project.org/web/packages/arm/")
9468 (synopsis "Data analysis using regression and multilevel/hierarchical models")
9470 "This package provides functions to accompany A. Gelman and J. Hill,
9471 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
9472 University Press, 2007.")
9473 (license license:gpl3+)))
9475 (define-public r-circular
9482 (uri (cran-uri "circular" version))
9485 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
9486 (build-system r-build-system)
9488 `(("r-boot" ,r-boot)
9489 ("r-mvtnorm" ,r-mvtnorm)))
9491 `(("gfortran" ,gfortran)))
9492 (home-page "https://cran.r-project.org/web/packages/circular/")
9493 (synopsis "Circular statistics")
9495 "This package provides tools for circular statistics, from \"Topics in
9496 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
9498 (license license:gpl2+)))
9500 (define-public r-activity
9507 (uri (cran-uri "activity" version))
9510 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
9511 (build-system r-build-system)
9513 `(("r-circular" ,r-circular)
9514 ("r-insol" ,r-insol)
9515 ("r-pbapply" ,r-pbapply)))
9516 (home-page "https://cran.r-project.org/web/packages/activity/")
9517 (synopsis "Animal activity statistics")
9519 "This package provides functions to fit kernel density functions to
9520 animal activity time data; plot activity distributions; quantify overall
9521 levels of activity; statistically compare activity metrics through
9522 bootstrapping; and evaluate variation in linear variables with time (or other
9523 circular variables).")
9524 (license license:gpl3)))
9526 (define-public r-ouch
9533 (uri (cran-uri "ouch" version))
9536 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
9537 (build-system r-build-system)
9538 (propagated-inputs `(("r-subplex" ,r-subplex)))
9539 (home-page "http://kingaa.github.io/ouch/")
9540 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
9542 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
9543 for evolution along a phylogenetic tree.")
9544 (license license:gpl2+)))
9546 (define-public r-fmsb
9553 (uri (cran-uri "fmsb" version))
9556 "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
9557 (build-system r-build-system)
9558 (home-page "http://minato.sip21c.org/msb/")
9559 (synopsis "Functions for medical statistics book with demographic data")
9561 "This package provides several utility functions for the book entitled
9562 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
9563 Japan, 2007) with Japanese demographic data and some demographic analysis
9564 related functions.")
9565 (license license:gpl2+)))
9567 (define-public r-stabledist
9569 (name "r-stabledist")
9574 (uri (cran-uri "stabledist" version))
9577 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
9578 (build-system r-build-system)
9579 (home-page "http://www.rmetrics.org")
9580 (synopsis "Stable distribution functions")
9582 "This package provides density, probability and quantile functions, and
9583 random number generation for (skew) stable distributions, using the
9584 parametrizations of Nolan.")
9585 (license license:gpl2+)))
9587 (define-public r-gsl
9594 (uri (cran-uri "gsl" version))
9597 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
9598 (build-system r-build-system)
9601 (home-page "https://cran.r-project.org/web/packages/gsl")
9602 (synopsis "Wrapper for the GNU Scientific Library")
9604 "This package provides an R wrapper for the special functions and quasi
9605 random number generators of the GNU Scientific Library.")
9606 (license license:gpl2+)))
9608 (define-public r-adgoftest
9610 (name "r-adgoftest")
9615 (uri (cran-uri "ADGofTest" version))
9618 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
9619 (properties `((upstream-name . "ADGofTest")))
9620 (build-system r-build-system)
9621 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
9622 (synopsis "Anderson-Darling GoF test")
9624 "This package provides an implementation of the Anderson-Darling GoF test
9625 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
9626 Anderson-Darling Distribution\".")
9627 ;; Any version of the GPL.
9628 (license license:gpl3+)))
9630 (define-public r-softimpute
9632 (name "r-softimpute")
9637 (uri (cran-uri "softImpute" version))
9640 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
9641 (properties `((upstream-name . "softImpute")))
9642 (build-system r-build-system)
9644 `(("r-matrix" ,r-matrix)))
9646 `(("gfortran" ,gfortran)))
9647 (home-page "https://cran.r-project.org/web/packages/softImpute")
9648 (synopsis "Matrix completion via iterative soft-thresholded SVD")
9650 "This package provides iterative methods for matrix completion that use
9651 nuclear-norm regularization. The package includes procedures for centering
9652 and scaling rows, columns or both, and for computing low-rank @dfn{single
9653 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
9655 (license license:gpl2)))
9657 (define-public r-fftwtools
9659 (name "r-fftwtools")
9664 (uri (cran-uri "fftwtools" version))
9667 "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6"))))
9668 (build-system r-build-system)
9669 (inputs `(("fftw" ,fftw)))
9670 (home-page "https://github.com/krahim/fftwtools")
9671 (synopsis "Wrapper for FFTW3")
9673 "This package provides a wrapper for several FFTW functions. It provides
9674 access to the two-dimensional FFT, the multivariate FFT, and the
9675 one-dimensional real to complex FFT using the FFTW3 library. The package
9676 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
9677 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
9678 The FFT functions have a parameter that allows them to not return the
9679 redundant complex conjugate when the input is real data.")
9680 (license license:gpl2+)))
9682 (define-public r-tiff
9689 (uri (cran-uri "tiff" version))
9692 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
9693 (build-system r-build-system)
9695 `(("libtiff" ,libtiff)
9696 ("libjpeg" ,libjpeg)
9698 (home-page "http://www.rforge.net/tiff/")
9699 (synopsis "Read and write TIFF images")
9701 "This package provides an easy and simple way to read, write and display
9702 bitmap images stored in the TIFF format. It can read and write both files and
9703 in-memory raw vectors.")
9704 ;; Either of these two license versions.
9705 (license (list license:gpl2 license:gpl3))))
9707 (define-public r-nlp
9714 (uri (cran-uri "NLP" version))
9717 "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w"))))
9718 (properties `((upstream-name . "NLP")))
9719 (build-system r-build-system)
9720 (home-page "https://cran.r-project.org/web/packages/NLP/")
9721 (synopsis "Natural language processing infrastructure")
9723 "This package provides basic classes and methods for Natural Language
9725 (license license:gpl3)))
9734 (uri (cran-uri "tm" version))
9737 "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh"))))
9738 (properties `((upstream-name . "tm")))
9739 (build-system r-build-system)
9745 ("r-xml2" ,r-xml2)))
9746 (home-page "http://tm.r-forge.r-project.org/")
9747 (synopsis "Text mining package")
9749 "This package provides a framework for text mining applications within R.")
9750 (license license:gpl3)))
9752 (define-public r-waveslim
9759 (uri (cran-uri "waveslim" version))
9762 "166ai4q3mlh3v338si952z7fbgph80h0l4ws6bna8ig5jx81rnmz"))))
9763 (build-system r-build-system)
9765 `(("gfortran" ,gfortran)))
9766 (home-page "http://waveslim.blogspot.com")
9767 (synopsis "Basic wavelet routines for signal processing")
9769 "This package provides basic wavelet routines for time series (1D),
9770 image (2D) and array (3D) analysis. The code provided here is based on
9771 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
9772 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
9773 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
9774 pairs (Selesnick 2001, 2002).")
9775 (license license:bsd-3)))
9777 (define-public r-wordcloud
9779 (name "r-wordcloud")
9784 (uri (cran-uri "wordcloud" version))
9787 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
9788 (build-system r-build-system)
9790 `(("r-rcolorbrewer" ,r-rcolorbrewer)
9792 ;; The "tm" package is only "suggested" according to CRAN, but the
9793 ;; wordcloud package cannot be loaded without it.
9795 (home-page "https://cran.r-project.org/web/packages/wordcloud")
9796 (synopsis "Word clouds")
9798 "This package provides functionality to create pretty word clouds,
9799 visualize differences and similarity between documents, and avoid
9800 over-plotting in scatter plots with text.")
9801 (license license:lgpl2.1)))
9803 (define-public r-colorramps
9805 (name "r-colorramps")
9810 (uri (cran-uri "colorRamps" version))
9813 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
9814 (properties `((upstream-name . "colorRamps")))
9815 (build-system r-build-system)
9816 (home-page "https://cran.r-project.org/web/packages/colorRamps")
9817 (synopsis "Build color tables")
9818 (description "This package provides features to build gradient color
9820 ;; Any version of the GPL
9821 (license license:gpl3+)))
9823 (define-public r-tidytree
9830 (uri (cran-uri "tidytree" version))
9832 (base32 "1bnzs62z2l8ck2h9gabmxvayizv4nfn8dmyzry83fv0cspjbyiv7"))))
9833 (build-system r-build-system)
9836 ("r-dplyr" ,r-dplyr)
9837 ("r-lazyeval" ,r-lazyeval)
9838 ("r-magrittr" ,r-magrittr)
9839 ("r-rlang" ,r-rlang)
9840 ("r-tibble" ,r-tibble)))
9841 (home-page "https://github.com/GuangchuangYu/tidytree")
9842 (synopsis "Tidy tool for phylogenetic tree data manipulation")
9844 "Phylogenetic trees generally contain multiple components including nodes,
9845 edges, branches and associated data. This package provides an approach to
9846 convert tree objects to tidy data frames. It also provides tidy interfaces to
9847 manipulate tree data.")
9848 (license license:artistic2.0)))
9850 (define-public r-rvcheck
9857 (uri (cran-uri "rvcheck" version))
9859 (base32 "0627bc8qmhxmd63yh6f90qni3qw1zwdpxjln2qbychzmzd4am9ac"))))
9860 (build-system r-build-system)
9862 `(("r-biocmanager" ,r-biocmanager)
9863 ("r-rlang" ,r-rlang)))
9864 (home-page "https://cran.r-project.org/web/packages/rvcheck")
9865 (synopsis "R package version check")
9867 "This package provides tools to check the latest release version of R and
9868 R packages (on CRAN, Bioconductor or Github).")
9869 (license license:artistic2.0)))
9871 (define-public r-docopt
9878 (uri (cran-uri "docopt" version))
9881 "06zknnd0c5s2y0hbddzdlr3m63ib783izpck6pgz7sjbab5pd068"))))
9882 (build-system r-build-system)
9883 (home-page "https://github.com/docopt/docopt.R")
9884 (synopsis "Command-line interface specification language")
9886 "This package enables you to define a command-line interface by just
9887 giving it a description in the specific format.")
9888 (license license:expat)))
9890 (define-public r-sparsesvd
9892 (name "r-sparsesvd")
9897 (uri (cran-uri "sparsesvd" version))
9900 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
9901 (build-system r-build-system)
9902 (propagated-inputs `(("r-matrix" ,r-matrix)))
9903 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
9904 (synopsis "Sparse truncated singular value decomposition")
9906 "This package provides a Wrapper around the SVDLIBC library
9907 for (truncated) singular value decomposition of a sparse matrix. Currently,
9908 only sparse real matrices in Matrix package format are supported.")
9909 ;; SVDLIBC is released under BSD-2. The R interface is released under
9911 (license (list license:bsd-3 license:bsd-2))))
9913 (define-public r-speedglm
9920 (uri (cran-uri "speedglm" version))
9923 "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz"))))
9924 (build-system r-build-system)
9926 `(("r-mass" ,r-mass)
9927 ("r-matrix" ,r-matrix)))
9928 (home-page "https://cran.r-project.org/web/packages/speedglm")
9929 (synopsis "Fit linear and generalized linear models to large data sets")
9931 "This package provides tools for fitting linear models and generalized
9932 linear models to large data sets by updating algorithms.")
9933 ;; Any version of the GPL
9934 (license license:gpl2+)))
9936 (define-public r-densityclust
9938 (name "r-densityclust")
9943 (uri (cran-uri "densityClust" version))
9946 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
9947 (properties `((upstream-name . "densityClust")))
9948 (build-system r-build-system)
9951 ("r-ggplot2" ,r-ggplot2)
9952 ("r-ggrepel" ,r-ggrepel)
9953 ("r-gridextra" ,r-gridextra)
9954 ("r-rcolorbrewer" ,r-rcolorbrewer)
9956 ("r-rtsne" ,r-rtsne)))
9957 (home-page "https://cran.r-project.org/web/packages/densityClust")
9958 (synopsis "Clustering by fast search and find of density peaks")
9960 "This package provides an improved implementation (based on k-nearest
9961 neighbors) of the density peak clustering algorithm, originally described by
9962 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
9963 large datasets (> 100,000 samples) very efficiently.")
9964 (license license:gpl2+)))
9966 (define-public r-combinat
9973 (uri (cran-uri "combinat" version))
9976 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
9977 (build-system r-build-system)
9978 (home-page "https://cran.r-project.org/web/packages/combinat")
9979 (synopsis "Combinatorics utilities")
9980 (description "This package provides assorted routines for combinatorics.")
9981 (license license:gpl2)))
9983 (define-public r-qlcmatrix
9985 (name "r-qlcmatrix")
9990 (uri (cran-uri "qlcMatrix" version))
9993 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
9994 (properties `((upstream-name . "qlcMatrix")))
9995 (build-system r-build-system)
9997 `(("r-docopt" ,r-docopt)
9998 ("r-matrix" ,r-matrix)
10000 ("r-sparsesvd" ,r-sparsesvd)))
10001 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
10002 (synopsis "Sparse matrix functions for quantitative language comparison")
10004 "This package provides an extension of the functionality of the Matrix
10005 package for using sparse matrices. Some of the functions are very general,
10006 while other are highly specific for the special data format used for
10007 @dfn{quantitative language comparison} (QLC).")
10008 (license license:gpl3)))
10010 (define-public r-ddrtree
10017 (uri (cran-uri "DDRTree" version))
10020 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
10021 (properties `((upstream-name . "DDRTree")))
10022 (build-system r-build-system)
10025 ("r-irlba" ,r-irlba)
10027 ("r-rcppeigen" ,r-rcppeigen)))
10028 (home-page "https://cran.r-project.org/web/packages/DDRTree")
10029 (synopsis "Learning principal graphs with DDRTree")
10031 "This package provides an implementation of the framework of
10032 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
10033 dimensional space while constructs a principal tree which passes through the
10034 middle of the data simultaneously. DDRTree shows superiority to
10035 alternatives (Wishbone, DPT) for inferring the ordering as well as the
10036 intrinsic structure of single cell genomics data. In general, it could be
10037 used to reconstruct the temporal progression as well as the bifurcation
10038 structure of any data type.")
10039 (license license:asl2.0)))
10041 (define-public r-corpcor
10048 (uri (cran-uri "corpcor" version))
10051 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
10052 (build-system r-build-system)
10053 (home-page "http://strimmerlab.org/software/corpcor/")
10054 (synopsis "Efficient estimation of covariance and (partial) correlation")
10056 "This package implements a James-Stein-type shrinkage estimator for the
10057 covariance matrix, with separate shrinkage for variances and correlations.
10058 Furthermore, functions are available for fast singular value decomposition,
10059 for computing the pseudoinverse, and for checking the rank and positive
10060 definiteness of a matrix.")
10061 (license license:gpl3+)))
10063 (define-public r-rspectra
10065 (name "r-rspectra")
10070 (uri (cran-uri "RSpectra" version))
10073 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
10074 (properties `((upstream-name . "RSpectra")))
10075 (build-system r-build-system)
10077 `(("r-matrix" ,r-matrix)
10079 ("r-rcppeigen" ,r-rcppeigen)))
10080 (home-page "https://github.com/yixuan/RSpectra")
10081 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
10083 "This package provides an R interface to the Spectra library for
10084 large-scale eigenvalue and SVD problems. It is typically used to compute a
10085 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
10086 which is usually more efficient than @code{eigen()} if k << n.")
10088 (license license:mpl2.0)))
10090 (define-public r-vbsr
10097 (uri (cran-uri "vbsr" version))
10100 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
10101 (build-system r-build-system)
10102 (home-page "https://cran.r-project.org/web/packages/vbsr")
10103 (synopsis "Variational Bayes spike regression regularized linear models")
10105 "This package provides an efficient algorithm for solving ultra-sparse
10106 regularized regression models using a variational Bayes algorithm with a spike
10107 prior. The algorithm is solved on a path, with coordinate updates, and is
10108 capable of generating very sparse models. Very general model
10109 diagnostics for controlling type-1 errors are also provided.")
10110 (license license:gpl2)))
10112 (define-public r-flare
10115 (version "1.6.0.2")
10119 (uri (cran-uri "flare" version))
10122 "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
10123 (build-system r-build-system)
10125 `(("r-igraph" ,r-igraph)
10126 ("r-lattice" ,r-lattice)
10128 ("r-matrix" ,r-matrix)))
10129 (home-page "https://cran.r-project.org/web/packages/flare")
10130 (synopsis "Family of Lasso regression implementations")
10132 "This package provides implementations of a family of Lasso variants
10133 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
10134 high dimensional sparse linear models.")
10135 (license license:gpl2)))
10137 (define-public r-lassopv
10144 (uri (cran-uri "lassopv" version))
10147 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
10148 (build-system r-build-system)
10149 (propagated-inputs `(("r-lars" ,r-lars)))
10150 (home-page "https://github.com/lingfeiwang/lassopv")
10151 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
10153 "This package enables you to estimate the p-values for predictors x
10154 against target variable y in Lasso regression, using the regularization
10155 strength when each predictor enters the active set of regularization path for
10156 the first time as the statistic.")
10157 (license license:gpl3)))
10159 (define-public r-splitstackshape
10161 (name "r-splitstackshape")
10166 (uri (cran-uri "splitstackshape" version))
10169 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
10170 (build-system r-build-system)
10172 `(("r-data-table" ,r-data-table)))
10173 (home-page "https://github.com/mrdwab/splitstackshape")
10174 (synopsis "Stack and reshape datasets after splitting concatenated values")
10176 "Online data collection tools like Google Forms often export
10177 multiple-response questions with data concatenated in cells. The
10178 @code{concat.split} (cSplit) family of functions provided by this package
10179 splits such data into separate cells. This package also includes functions to
10180 stack groups of columns and to reshape wide data, even when the data are
10181 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
10182 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
10184 (license license:gpl3)))
10186 (define-public r-tfmpvalue
10188 (name "r-tfmpvalue")
10193 (uri (cran-uri "TFMPvalue" version))
10196 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
10197 (properties `((upstream-name . "TFMPvalue")))
10198 (build-system r-build-system)
10199 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10200 (home-page "https://github.com/ge11232002/TFMPvalue")
10201 (synopsis "P-value computation for position weight matrices")
10203 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
10204 identification from sequence/alignments, we are interested in the significance
10205 of certain match scores. TFMPvalue provides the accurate calculation of a
10206 p-value with a score threshold for position weight matrices, or the score with
10207 a given p-value. It is an interface to code originally made available by
10208 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
10209 Touzet and Varre (2007).")
10210 (license license:gpl2)))
10212 (define-public r-rnifti
10219 (uri (cran-uri "RNifti" version))
10222 "1z8ninp3aq18w0slcfn8r2fp48cdz8l0k0namsrnvgyp8lzcpqpn"))))
10223 (properties `((upstream-name . "RNifti")))
10224 (build-system r-build-system)
10225 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10226 (home-page "https://github.com/jonclayden/RNifti")
10227 (synopsis "Fast R and C++ access to NIfTI images")
10229 "This package provides very fast read and write access to images stored
10230 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
10231 compiled C and interpreted R code. It also provides a C/C++ API that can be
10232 used by other packages.")
10233 (license license:gpl2)))
10235 (define-public r-shades
10242 (uri (cran-uri "shades" version))
10245 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
10246 (build-system r-build-system)
10247 (home-page "https://github.com/jonclayden/shades")
10248 (synopsis "Simple color manipulation")
10250 "This package provides functions for easily manipulating colors,
10251 creating color scales and calculating color distances.")
10252 (license license:bsd-3)))
10254 (define-public r-ore
10261 (uri (cran-uri "ore" version))
10263 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
10264 (build-system r-build-system)
10265 (home-page "https://github.com/jonclayden/ore")
10266 (synopsis "R interface to the Onigmo regular expression library")
10268 "This package provides an alternative to R's built-in functionality for
10269 handling regular expressions, based on the Onigmo library. It offers
10270 first-class compiled regex objects, partial matching and function-based
10271 substitutions, amongst other features.")
10272 (license license:bsd-3)))
10274 (define-public r-reportr
10281 (uri (cran-uri "reportr" version))
10284 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
10285 (build-system r-build-system)
10286 (propagated-inputs `(("r-ore" ,r-ore)))
10287 (home-page "https://github.com/jonclayden/reportr")
10288 (synopsis "General message and error reporting system")
10290 "This package provides a system for reporting messages, which offers
10291 certain useful features over the standard R system, such as the incorporation
10292 of output consolidation, message filtering, assertions, expression
10293 substitution, automatic generation of stack traces for debugging, and
10294 conditional reporting based on the current \"output level\".")
10295 (license license:gpl2)))
10297 (define-public r-tractor-base
10299 (name "r-tractor-base")
10304 (uri (cran-uri "tractor.base" version))
10307 "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i"))))
10308 (properties `((upstream-name . "tractor.base")))
10309 (build-system r-build-system)
10312 ("r-reportr" ,r-reportr)
10313 ("r-rnifti" ,r-rnifti)
10314 ("r-shades" ,r-shades)))
10315 (home-page "http://www.tractor-mri.org.uk")
10316 (synopsis "Read, manipulate and visualize magnetic resonance images")
10318 "This package provides functions for working with magnetic resonance
10319 images. It supports reading and writing of popular file formats (DICOM,
10320 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
10321 visualization; flexible image manipulation; metadata and sparse image
10323 (license license:gpl2)))
10325 (define-public r-grimport
10327 (name "r-grimport")
10332 (uri (cran-uri "grImport" version))
10335 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
10336 (properties `((upstream-name . "grImport")))
10337 (build-system r-build-system)
10339 `(("ghostscript" ,ghostscript)))
10341 `(("r-xml" ,r-xml)))
10342 (home-page "https://cran.r-project.org/web/packages/grImport")
10343 (synopsis "Convert, import, and draw PostScript pictures")
10345 "This package provides functions for converting, importing, and drawing
10346 PostScript pictures in R plots.")
10347 (license license:gpl2+)))
10349 (define-public r-grimport2
10351 (name "r-grimport2")
10356 (uri (cran-uri "grImport2" version))
10359 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
10360 (properties `((upstream-name . "grImport2")))
10361 (build-system r-build-system)
10363 `(("r-base64enc" ,r-base64enc)
10367 (home-page "https://cran.r-project.org/web/packages/grImport2/")
10368 (synopsis "Import SVG graphics")
10370 "This package provides functions for importing external vector images and
10371 drawing them as part of R plots. This package is different from the
10372 @code{grImport} package because, where that package imports PostScript format
10373 images, this package imports SVG format images. Furthermore, this package
10374 imports a specific subset of SVG, so external images must be preprocessed
10375 using a package like @code{rsvg} to produce SVG that this package can import.
10376 SVG features that are not supported by R graphics, such as gradient fills, can
10377 be imported and then exported via the @code{gridSVG} package.")
10378 (license license:gpl2+)))
10380 (define-public r-kohonen
10387 (uri (cran-uri "kohonen" version))
10390 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
10391 (build-system r-build-system)
10393 `(("r-rcpp" ,r-rcpp)))
10394 (home-page "https://cran.r-project.org/web/packages/kohonen")
10395 (synopsis "Supervised and unsupervised self-organising maps")
10397 "This package provides functions to train @dfn{self-organising
10398 maps} (SOMs). Also interrogation of the maps and prediction using trained
10399 maps are supported. The name of the package refers to Teuvo Kohonen, the
10400 inventor of the SOM.")
10401 (license license:gpl2+)))
10403 (define-public r-nnls
10410 (uri (cran-uri "nnls" version))
10413 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
10414 (build-system r-build-system)
10415 (native-inputs `(("gfortran" ,gfortran)))
10416 (home-page "https://cran.r-project.org/web/packages/nnls")
10417 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
10419 "This package provides an R interface to the Lawson-Hanson implementation
10420 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
10421 the combination of non-negative and non-positive constraints.")
10422 (license license:gpl2+)))
10424 (define-public r-iso
10431 (uri (cran-uri "Iso" version))
10434 "014mm5b1f7i6nwlz3kyg1biph0y542kcx5bd13p68cv5a928qzid"))))
10435 (properties `((upstream-name . "Iso")))
10436 (build-system r-build-system)
10437 (native-inputs `(("gfortran" ,gfortran)))
10438 (home-page "http://www.stat.auckland.ac.nz/~rolf/")
10439 (synopsis "Functions to perform isotonic regression")
10441 "This package provides support for linear order and unimodal
10442 order (univariate) isotonic regression and bivariate isotonic regression with
10443 linear order on both variables.")
10444 (license license:gpl2+)))
10446 (define-public r-chemometricswithr
10448 (name "r-chemometricswithr")
10453 (uri (cran-uri "ChemometricsWithR" version))
10456 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
10458 `((upstream-name . "ChemometricsWithR")))
10459 (build-system r-build-system)
10461 `(("r-devtools" ,r-devtools)
10462 ("r-kohonen" ,r-kohonen)
10465 (home-page "https://github.com/rwehrens/CWR")
10466 (synopsis "Chemometrics with R")
10468 "This package provides functions and scripts used in the book
10469 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
10470 Life Sciences\" by Ron Wehrens, Springer (2011).")
10471 (license license:gpl2+)))
10473 (define-public r-als
10480 (uri (cran-uri "ALS" version))
10483 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
10484 (properties `((upstream-name . "ALS")))
10485 (build-system r-build-system)
10488 ("r-nnls" ,r-nnls)))
10489 (home-page "https://cran.r-project.org/web/packages/ALS")
10490 (synopsis "Multivariate curve resolution alternating least squares")
10492 "Alternating least squares is often used to resolve components
10493 contributing to data with a bilinear structure; the basic technique may be
10494 extended to alternating constrained least squares. This package provides an
10495 implementation of @dfn{multivariate curve resolution alternating least
10496 squares} (MCR-ALS).
10498 Commonly applied constraints include unimodality, non-negativity, and
10499 normalization of components. Several data matrices may be decomposed
10500 simultaneously by assuming that one of the two matrices in the bilinear
10501 decomposition is shared between datasets.")
10502 (license license:gpl2+)))
10504 (define-public r-strucchange
10506 (name "r-strucchange")
10511 (uri (cran-uri "strucchange" version))
10514 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
10515 (build-system r-build-system)
10517 `(("r-sandwich" ,r-sandwich)
10519 (home-page "https://cran.r-project.org/web/packages/strucchange")
10520 (synopsis "Testing, monitoring, and dating structural changes")
10522 "This package provides tools for testing, monitoring and dating
10523 structural changes in (linear) regression models. It features tests/methods
10524 from the generalized fluctuation test framework as well as from the F
10525 test (Chow test) framework. This includes methods to fit, plot and test
10526 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
10527 statistics, respectively. It is possible to monitor incoming data online
10528 using fluctuation processes. Finally, the breakpoints in regression models
10529 with structural changes can be estimated together with confidence intervals.
10530 Emphasis is always given to methods for visualizing the data.")
10531 ;; Either of these two GPL versions
10532 (license (list license:gpl2 license:gpl3))))
10534 (define-public r-pixmap
10541 (uri (cran-uri "pixmap" version))
10544 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
10545 (build-system r-build-system)
10546 (home-page "https://cran.r-project.org/web/packages/pixmap")
10547 (synopsis "Tools for bitmap images")
10549 "This package provides functions for importing, exporting, plotting and
10550 other manipulations of bitmapped images.")
10551 (license license:gpl2)))
10553 (define-public r-rapidjsonr
10555 (name "r-rapidjsonr")
10560 (uri (cran-uri "rapidjsonr" version))
10563 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
10564 (build-system r-build-system)
10565 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
10566 (synopsis "JSON parser")
10568 "This package provides JSON parsing capability through the Rapidjson
10570 (license license:expat)))
10572 (define-public r-ontologyindex
10574 (name "r-ontologyindex")
10579 (uri (cran-uri "ontologyIndex" version))
10582 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
10583 (properties `((upstream-name . "ontologyIndex")))
10584 (build-system r-build-system)
10585 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
10586 (synopsis "Functions for processing ontologies in R")
10588 "This package provides functions for reading ontologies into R as lists
10589 and manipulating sets of ontological terms.")
10590 (license license:gpl2+)))
10592 (define-public r-gargle
10599 (uri (cran-uri "gargle" version))
10602 "08zhfk2sl342w35i5n2c93ayypg3z0kbl0020l3y9adqka1vazgx"))))
10603 (build-system r-build-system)
10608 ("r-jsonlite" ,r-jsonlite)
10609 ("r-rlang" ,r-rlang)
10610 ("r-withr" ,r-withr)))
10611 (home-page "https://gargle.r-lib.org")
10612 (synopsis "Utilities for working with Google APIs")
10614 "This package provides utilities for working with Google APIs. This
10615 includes functions and classes for handling common credential types and for
10616 preparing, executing, and processing HTTP requests.")
10617 (license license:expat)))
10619 (define-public r-bigrquery
10621 (name "r-bigrquery")
10626 (uri (cran-uri "bigrquery" version))
10629 "1ggh2gngr5x0g6y7d55y6kvn94anf7qi1bkc28cjmw61hxjq38fb"))))
10630 (build-system r-build-system)
10632 `(("r-assertthat" ,r-assertthat)
10633 ("r-bit64" ,r-bit64)
10636 ("r-gargle" ,r-gargle)
10639 ("r-jsonlite" ,r-jsonlite)
10640 ("r-prettyunits" ,r-prettyunits)
10641 ("r-progress" ,r-progress)
10642 ("r-rapidjsonr" ,r-rapidjsonr)
10644 ("r-rlang" ,r-rlang)
10645 ("r-tibble" ,r-tibble)))
10646 (home-page "https://github.com/rstats-db/bigrquery")
10647 (synopsis "R interface to Google's BigQuery API")
10649 "This package provides an R interface to Google's BigQuery database.")
10650 (license license:gpl3)))
10652 (define-public r-gmp
10655 (version "0.5-13.6")
10659 (uri (cran-uri "gmp" version))
10662 "0j2sz2nw41y9306rl1b8hbn0spz7453z5iawcq0bvslyrhc1d9ir"))))
10663 (build-system r-build-system)
10666 (modify-phases %standard-phases
10667 (add-after 'unpack 'set-CC
10668 (lambda _ (setenv "CC" "gcc") #t)))))
10669 (inputs `(("gmp" ,gmp)))
10670 (home-page "https://cran.r-project.org/web/packages/gmp")
10671 (synopsis "Multiple precision arithmetic")
10673 "This package supports multiple precision arithmetic (big integers and
10674 rationals, prime number tests, matrix computation), \"arithmetic without
10675 limitations\" using the GNU Multiple Precision library.")
10676 ;; Any version of the GPL.
10677 (license license:gpl3+)))
10679 (define-public r-rmpfr
10686 (uri (cran-uri "Rmpfr" version))
10689 "09kw7hyca8xc09r2d88qj81cclar8acaq5q9q5rw9f49iffda0rr"))))
10690 (properties `((upstream-name . "Rmpfr")))
10691 (build-system r-build-system)
10696 `(("r-gmp" ,r-gmp)))
10698 `(("pkg-config" ,pkg-config)))
10699 (home-page "http://rmpfr.r-forge.r-project.org/")
10700 (synopsis "R bindings to the MPFR library")
10702 "This package supports arithmetic (via S4 classes and methods) for
10703 arbitrary precision floating point numbers, including transcendental
10704 functions. To this end, the package interfaces with the @dfn{Multiple
10705 Precision Floating-Point Reliable} (MPFR) library.")
10706 (license license:gpl2+)))
10708 (define-public r-assertive-base
10710 (name "r-assertive-base")
10715 (uri (cran-uri "assertive.base" version))
10718 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
10720 `((upstream-name . "assertive.base")))
10721 (build-system r-build-system)
10722 (home-page "https://bitbucket.org/richierocks/assertive.base")
10723 (synopsis "Core of the assertive package")
10725 "This package provides a minimal set of predicates and assertions used by
10726 the assertive package. This is mainly for use by other package developers who
10727 want to include run-time testing features in their own packages.")
10728 (license license:gpl3+)))
10730 (define-public r-assertive-properties
10732 (name "r-assertive-properties")
10737 (uri (cran-uri "assertive.properties" version))
10740 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
10742 `((upstream-name . "assertive.properties")))
10743 (build-system r-build-system)
10745 `(("r-assertive-base" ,r-assertive-base)))
10746 (home-page "https://bitbucket.org/richierocks/assertive.properties")
10747 (synopsis "Assertions to check properties of variables")
10749 "This package provides a set of predicates and assertions for checking
10750 the properties of variables, such as length, names and attributes. This is
10751 mainly for use by other package developers who want to include run-time
10752 testing features in their own packages.")
10753 (license license:gpl3+)))
10755 (define-public r-assertive-numbers
10757 (name "r-assertive-numbers")
10762 (uri (cran-uri "assertive.numbers" version))
10765 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
10767 `((upstream-name . "assertive.numbers")))
10768 (build-system r-build-system)
10770 `(("r-assertive-base" ,r-assertive-base)))
10771 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
10772 (synopsis "Assertions to check properties of numbers")
10774 "This package provides a set of predicates and assertions for checking
10775 the properties of numbers. This is mainly for use by other package developers
10776 who want to include run-time testing features in their own packages.")
10777 (license license:gpl3+)))
10779 (define-public r-assertive-sets
10781 (name "r-assertive-sets")
10786 (uri (cran-uri "assertive.sets" version))
10789 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
10791 `((upstream-name . "assertive.sets")))
10792 (build-system r-build-system)
10794 `(("r-assertive-base" ,r-assertive-base)))
10795 (home-page "https://bitbucket.org/richierocks/assertive.sets")
10796 (synopsis "Assertions to check properties of sets")
10798 "This package provides a set of predicates and assertions for checking
10799 the properties of sets. This is mainly for use by other package developers
10800 who want to include run-time testing features in their own packages.")
10801 (license license:gpl3+)))
10803 (define-public r-assertive-matrices
10805 (name "r-assertive-matrices")
10810 (uri (cran-uri "assertive.matrices" version))
10813 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
10815 `((upstream-name . "assertive.matrices")))
10816 (build-system r-build-system)
10818 `(("r-assertive-base" ,r-assertive-base)))
10819 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
10820 (synopsis "Assertions to check properties of matrices")
10822 "This package provides a set of predicates and assertions for checking
10823 the properties of matrices. This is mainly for use by other package
10824 developers who want to include run-time testing features in their own
10826 (license license:gpl3+)))
10828 (define-public r-assertive-models
10830 (name "r-assertive-models")
10835 (uri (cran-uri "assertive.models" version))
10838 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
10840 `((upstream-name . "assertive.models")))
10841 (build-system r-build-system)
10843 `(("r-assertive-base" ,r-assertive-base)))
10844 (home-page "https://bitbucket.org/richierocks/assertive.models")
10845 (synopsis "Assertions to check properties of models")
10847 "This package provides a set of predicates and assertions for checking
10848 the properties of models. This is mainly for use by other package developers
10849 who want to include run-time testing features in their own packages.")
10850 (license license:gpl3+)))
10852 (define-public r-assertive-reflection
10854 (name "r-assertive-reflection")
10859 (uri (cran-uri "assertive.reflection" version))
10862 "19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj"))))
10864 `((upstream-name . "assertive.reflection")))
10865 (build-system r-build-system)
10867 `(("r-assertive-base" ,r-assertive-base)))
10868 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
10869 (synopsis "Assertions for checking the state of R")
10871 "This package provides a set of predicates and assertions for checking
10872 the state and capabilities of R, the operating system it is running on, and
10873 the IDE being used. This is mainly for use by other package developers who
10874 want to include run-time testing features in their own packages.")
10875 (license license:gpl3+)))
10877 (define-public r-assertive-types
10879 (name "r-assertive-types")
10884 (uri (cran-uri "assertive.types" version))
10887 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
10889 `((upstream-name . "assertive.types")))
10890 (build-system r-build-system)
10892 `(("r-assertive-base" ,r-assertive-base)
10893 ("r-assertive-properties" ,r-assertive-properties)
10894 ("r-codetools" ,r-codetools)))
10895 (home-page "https://bitbucket.org/richierocks/assertive.types")
10896 (synopsis "Assertions to check types of variables")
10898 "This package provides a set of predicates and assertions for checking
10899 the types of variables. This is mainly for use by other package developers
10900 who want to include run-time testing features in their own packages.")
10901 (license license:gpl3+)))
10903 (define-public r-assertive-files
10905 (name "r-assertive-files")
10910 (uri (cran-uri "assertive.files" version))
10913 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
10915 `((upstream-name . "assertive.files")))
10916 (build-system r-build-system)
10918 `(("r-assertive-base" ,r-assertive-base)
10919 ("r-assertive-numbers" ,r-assertive-numbers)))
10920 (home-page "https://bitbucket.org/richierocks/assertive.files")
10921 (synopsis "Assertions to check properties of files")
10923 "This package provides a set of predicates and assertions for checking
10924 the properties of files and connections. This is mainly for use by other
10925 package developers who want to include run-time testing features in their own
10927 (license license:gpl3+)))
10929 (define-public r-assertive-code
10931 (name "r-assertive-code")
10936 (uri (cran-uri "assertive.code" version))
10939 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
10941 `((upstream-name . "assertive.code")))
10942 (build-system r-build-system)
10944 `(("r-assertive-base" ,r-assertive-base)
10945 ("r-assertive-properties" ,r-assertive-properties)
10946 ("r-assertive-types" ,r-assertive-types)))
10947 (home-page "https://bitbucket.org/richierocks/assertive.code")
10948 (synopsis "Assertions to check properties of code")
10950 "This package provides a set of predicates and assertions for checking
10951 the properties of code. This is mainly for use by other package developers
10952 who want to include run-time testing features in their own packages.")
10953 (license license:gpl3+)))
10955 (define-public r-assertive-datetimes
10957 (name "r-assertive-datetimes")
10962 (uri (cran-uri "assertive.datetimes" version))
10965 "00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78"))))
10967 `((upstream-name . "assertive.datetimes")))
10968 (build-system r-build-system)
10970 `(("r-assertive-base" ,r-assertive-base)
10971 ("r-assertive-types" ,r-assertive-types)))
10972 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
10973 (synopsis "Assertions to check properties of dates and times")
10975 "This package provides a set of predicates and assertions for checking
10976 the properties of dates and times. This is mainly for use by other package
10977 developers who want to include run-time testing features in their own
10979 (license license:gpl3+)))
10981 (define-public r-assertive-strings
10983 (name "r-assertive-strings")
10988 (uri (cran-uri "assertive.strings" version))
10991 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
10993 `((upstream-name . "assertive.strings")))
10994 (build-system r-build-system)
10996 `(("r-assertive-base" ,r-assertive-base)
10997 ("r-assertive-types" ,r-assertive-types)
10998 ("r-stringi" ,r-stringi)))
10999 (home-page "https://bitbucket.org/richierocks/assertive.strings")
11000 (synopsis "Assertions to check properties of strings")
11002 "This package provides a set of predicates and assertions for checking
11003 the properties of strings. This is mainly for use by other package developers
11004 who want to include run-time testing features in their own packages.")
11005 (license license:gpl3+)))
11007 (define-public r-assertive-data-us
11009 (name "r-assertive-data-us")
11014 (uri (cran-uri "assertive.data.us" version))
11017 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
11019 `((upstream-name . "assertive.data.us")))
11020 (build-system r-build-system)
11022 `(("r-assertive-base" ,r-assertive-base)
11023 ("r-assertive-strings" ,r-assertive-strings)))
11024 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
11025 (synopsis "Assertions to check properties of strings")
11027 "This package provides a set of predicates and assertions for checking
11028 the properties of US-specific complex data types. This is mainly for use by
11029 other package developers who want to include run-time testing features in
11030 their own packages.")
11031 (license license:gpl3+)))
11033 (define-public r-assertive-data-uk
11035 (name "r-assertive-data-uk")
11040 (uri (cran-uri "assertive.data.uk" version))
11043 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
11045 `((upstream-name . "assertive.data.uk")))
11046 (build-system r-build-system)
11048 `(("r-assertive-base" ,r-assertive-base)
11049 ("r-assertive-strings" ,r-assertive-strings)))
11050 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
11051 (synopsis "Assertions to check properties of strings")
11053 "This package provides a set of predicates and assertions for checking
11054 the properties of UK-specific complex data types. This is mainly for use by
11055 other package developers who want to include run-time testing features in
11056 their own packages.")
11057 (license license:gpl3+)))
11059 (define-public r-assertive-data
11061 (name "r-assertive-data")
11066 (uri (cran-uri "assertive.data" version))
11069 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
11071 `((upstream-name . "assertive.data")))
11072 (build-system r-build-system)
11074 `(("r-assertive-base" ,r-assertive-base)
11075 ("r-assertive-strings" ,r-assertive-strings)))
11076 (home-page "https://bitbucket.org/richierocks/assertive.data")
11077 (synopsis "Assertions to check properties of data")
11079 "This package provides a set of predicates and assertions for checking
11080 the properties of (country independent) complex data types. This is mainly
11081 for use by other package developers who want to include run-time testing
11082 features in their own packages.")
11083 (license license:gpl3+)))
11085 (define-public r-assertive
11087 (name "r-assertive")
11092 (uri (cran-uri "assertive" version))
11095 "0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3"))))
11096 (build-system r-build-system)
11098 `(("r-assertive-base" ,r-assertive-base)
11099 ("r-assertive-code" ,r-assertive-code)
11100 ("r-assertive-data" ,r-assertive-data)
11101 ("r-assertive-data-uk" ,r-assertive-data-uk)
11102 ("r-assertive-data-us" ,r-assertive-data-us)
11103 ("r-assertive-datetimes" ,r-assertive-datetimes)
11104 ("r-assertive-files" ,r-assertive-files)
11105 ("r-assertive-matrices" ,r-assertive-matrices)
11106 ("r-assertive-models" ,r-assertive-models)
11107 ("r-assertive-numbers" ,r-assertive-numbers)
11108 ("r-assertive-properties" ,r-assertive-properties)
11109 ("r-assertive-reflection" ,r-assertive-reflection)
11110 ("r-assertive-sets" ,r-assertive-sets)
11111 ("r-assertive-strings" ,r-assertive-strings)
11112 ("r-assertive-types" ,r-assertive-types)
11113 ("r-knitr" ,r-knitr)))
11114 (home-page "https://bitbucket.org/richierocks/assertive")
11115 (synopsis "Readable check functions to ensure code integrity")
11117 "This package provides lots of predicates (@code{is_*} functions) to
11118 check the state of your variables, and assertions (@code{assert_*} functions)
11119 to throw errors if they aren't in the right form.")
11120 (license license:gpl3+)))
11122 (define-public r-dotcall64
11124 (name "r-dotcall64")
11129 (uri (cran-uri "dotCall64" version))
11132 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
11133 (properties `((upstream-name . "dotCall64")))
11134 (build-system r-build-system)
11135 (native-inputs `(("gfortran" ,gfortran)))
11136 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
11137 (synopsis "Enhanced foreign function interface supporting long vectors")
11139 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
11140 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
11141 supports long vectors, arguments of type 64-bit integer, and provides a
11142 mechanism to avoid unnecessary copies of read-only and write-only arguments.
11143 This makes it a convenient and fast interface to C/C++ and Fortran code.")
11144 (license license:gpl2+)))
11146 (define-public r-spam
11153 (uri (cran-uri "spam" version))
11155 (base32 "0ry0a76cljlmilrzcriiizcidxyhq1i7i9bqhvl1qda81ld8hifi"))))
11156 (build-system r-build-system)
11158 `(("r-dotcall64" ,r-dotcall64)))
11159 (native-inputs `(("gfortran" ,gfortran)))
11160 (home-page "https://www.math.uzh.ch/pages/spam/")
11161 (synopsis "Sparse matrix algebra")
11163 "This package provides a set of functions for sparse matrix algebra.
11164 Differences with other sparse matrix packages are:
11167 @item it only supports (essentially) one sparse matrix format;
11168 @item it is based on transparent and simple structure(s);
11169 @item it is tailored for MCMC calculations within G(M)RF;
11170 @item and it is fast and scalable (with the extension package @code{spam64}).
11172 ;; Either of these licenses
11173 (license (list license:bsd-3 license:lgpl2.0))))
11175 (define-public r-fields
11182 (uri (cran-uri "fields" version))
11184 (base32 "12k97vfjlz5h8vynirnvik1nyj1iw25n8xl7awmx9mpd6wvgy2s9"))))
11185 (build-system r-build-system)
11187 `(("r-maps" ,r-maps)
11188 ("r-spam" ,r-spam)))
11190 `(("gfortran" ,gfortran)))
11191 (home-page "https://www.image.ucar.edu/fields")
11192 (synopsis "Tools for spatial data")
11194 "This is a package for curve, surface and function fitting with an
11195 emphasis on splines, spatial data and spatial statistics. The major methods
11196 include cubic, and thin plate splines, Kriging, and compactly supported
11197 covariance functions for large data sets.")
11198 (license license:gpl2+)))
11200 (define-public r-spatialextremes
11202 (name "r-spatialextremes")
11203 (version "2.0-7.2")
11207 (uri (cran-uri "SpatialExtremes" version))
11210 "0aqq9ryxi4xsdqjhc1lhb7ai8szs7m2vys6nn0ygps1w3pm4xwj8"))))
11212 `((upstream-name . "SpatialExtremes")))
11213 (build-system r-build-system)
11215 `(("r-fields" ,r-fields)
11216 ("r-maps" ,r-maps)))
11217 (home-page "http://spatialextremes.r-forge.r-project.org/")
11218 (synopsis "Modelling spatial extremes")
11220 "This package provides tools for the statistical modelling of spatial
11221 extremes using max-stable processes, copula or Bayesian hierarchical models.
11222 More precisely, this package allows (conditional) simulations from various
11223 parametric max-stable models, analysis of the extremal spatial dependence, the
11224 fitting of such processes using composite likelihoods or least square (simple
11225 max-stable processes only), model checking and selection and prediction.")
11226 (license license:gpl2+)))
11228 (define-public r-drc
11235 (uri (cran-uri "drc" version))
11238 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
11239 (build-system r-build-system)
11242 ("r-gtools" ,r-gtools)
11244 ("r-multcomp" ,r-multcomp)
11245 ("r-plotrix" ,r-plotrix)
11246 ("r-scales" ,r-scales)))
11247 (home-page "https://cran.r-project.org/web/packages/drc")
11248 (synopsis "Analysis of dose-response curves")
11250 "This package provides a suite of flexible and versatile model fitting
11251 and after-fitting functions for the analysis of dose-response data.")
11252 (license license:gpl2+)))
11254 (define-public r-rmeta
11261 (uri (cran-uri "rmeta" version))
11264 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
11265 (build-system r-build-system)
11266 (home-page "https://cran.r-project.org/web/packages/rmeta")
11267 (synopsis "Tools for meta-analysis")
11269 "This package provides functions for simple fixed and random effects
11270 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
11271 draws standard summary plots, funnel plots, and computes summaries and tests
11272 for association and heterogeneity.")
11273 (license license:gpl2)))
11275 (define-public r-bootstrap
11277 (name "r-bootstrap")
11282 (uri (cran-uri "bootstrap" version))
11285 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
11286 (build-system r-build-system)
11287 (native-inputs `(("gfortran" ,gfortran)))
11288 (home-page "https://cran.r-project.org/web/packages/bootstrap")
11289 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
11291 "This package provides software and data for the book \"An Introduction
11292 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
11293 This package is primarily provided for projects already based on it, and for
11294 support of the book. New projects should preferentially use the recommended
11295 package \"boot\".")
11296 (license license:bsd-3)))
11298 (define-public r-survivalroc
11300 (name "r-survivalroc")
11305 (uri (cran-uri "survivalROC" version))
11308 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
11309 (properties `((upstream-name . "survivalROC")))
11310 (build-system r-build-system)
11311 (home-page "https://cran.r-project.org/web/packages/survivalROC")
11312 (synopsis "Time-dependent ROC curve estimation from censored survival data")
11314 "Compute time-dependent ROC curve from censored survival data using
11315 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
11316 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
11317 (license license:gpl2+)))
11319 (define-public r-longitudinal
11321 (name "r-longitudinal")
11326 (uri (cran-uri "longitudinal" version))
11329 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
11330 (build-system r-build-system)
11331 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
11332 (home-page "http://strimmerlab.org/software/longitudinal/")
11333 (synopsis "Analysis of multiple time course data")
11335 "This package contains general data structures and functions for
11336 longitudinal data with multiple variables, repeated measurements, and
11337 irregularly spaced time points. It also implements a shrinkage estimator of
11338 dynamical correlation and dynamical covariance.")
11339 (license license:gpl3+)))
11341 (define-public r-genenet
11348 (uri (cran-uri "GeneNet" version))
11351 "0cdhrj15rz0w0pyw3r8mikrzsdh95y5i1c0pa3cn0c2bjnjx3x3n"))))
11352 (properties `((upstream-name . "GeneNet")))
11353 (build-system r-build-system)
11355 `(("r-corpcor" ,r-corpcor)
11356 ("r-fdrtool" ,r-fdrtool)
11357 ("r-longitudinal" ,r-longitudinal)))
11358 (home-page "http://strimmerlab.org/software/genenet/")
11359 (synopsis "Modeling and inferring gene networks")
11361 "This package analyzes gene expression (time series) data with focus on
11362 the inference of gene networks. In particular, GeneNet implements the methods
11363 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
11364 for learning large-scale gene association networks (including assignment of
11365 putative directions).")
11366 (license license:gpl3+)))
11368 (define-public r-rbamtools
11370 (name "r-rbamtools")
11371 (version "2.16.17")
11375 (uri (cran-uri "rbamtools" version))
11378 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
11379 (build-system r-build-system)
11380 (inputs `(("zlib" ,zlib)))
11382 `(("r-refgenome" ,r-refgenome)))
11383 (home-page "https://cran.r-project.org/web/packages/rbamtools")
11384 (synopsis "Read and write BAM (binary alignment) files")
11386 "This package provides an R interface to functions of the SAMtools
11388 (license license:artistic2.0)))
11390 (define-public r-protviz
11397 (uri (cran-uri "protViz" version))
11400 "1ldciqh3f43xr9663yyhd9r6qwrg4c4vmkprlcancbnd460wakg7"))))
11401 (properties `((upstream-name . "protViz")))
11402 (build-system r-build-system)
11403 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11404 (home-page "https://github.com/protViz/protViz/")
11405 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
11407 "This package helps with quality checks, visualizations and analysis of
11408 mass spectrometry data, coming from proteomics experiments. The package is
11409 developed, tested and used at the Functional Genomics Center Zurich, where it
11410 is used mainly for prototyping, teaching, and having fun with proteomics data.
11411 But it can also be used to do data analysis for small scale data sets.")
11412 (license license:gpl3)))
11414 (define-public r-cmprsk
11421 (uri (cran-uri "cmprsk" version))
11423 (base32 "0xhgfg5b4i9skkaxp7gzkafgg5bqs5q1rp4hpw2jjmykg2nifn99"))))
11424 (build-system r-build-system)
11426 `(("r-survival" ,r-survival)))
11428 `(("gfortran" ,gfortran)))
11429 (home-page "https://cran.r-project.org/web/packages/cmprsk")
11430 (synopsis "Subdistribution analysis of competing risks")
11432 "This package provides tool for estimation, testing and regression
11433 modeling of subdistribution functions in competing risks, as described in
11434 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
11435 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
11436 A proportional hazards model for the subdistribution of a competing risk,
11437 JASA, 94:496-509.")
11438 (license license:gpl2+)))
11440 (define-public r-etm
11443 (version "1.0.5.1")
11447 (uri (cran-uri "etm" version))
11450 "0m41pm277sd50pharigcqzr1a2g92wnmdf6fcab6fx16ia2fzrm7"))))
11451 (build-system r-build-system)
11453 `(("r-data-table" ,r-data-table)
11454 ("r-lattice" ,r-lattice)
11456 ("r-rcpparmadillo" ,r-rcpparmadillo)
11457 ("r-survival" ,r-survival)))
11458 (home-page "https://cran.r-project.org/web/packages/etm")
11459 (synopsis "Empirical transition matrix")
11461 "The @dfn{empirical transition matrix} (etm) package permits to estimate
11462 the matrix of transition probabilities for any time-inhomogeneous multistate
11463 model with finite state space using the Aalen-Johansen estimator.")
11464 (license license:expat)))
11466 (define-public r-epi
11473 (uri (cran-uri "Epi" version))
11476 "046y10vwks5y84pzccmrn6d4pd6qz70imvp1hw5ywp8fnwzfh4g5"))))
11477 (properties `((upstream-name . "Epi")))
11478 (build-system r-build-system)
11480 `(("r-cmprsk" ,r-cmprsk)
11481 ("r-data-table" ,r-data-table)
11484 ("r-matrix" ,r-matrix)
11486 ("r-numderiv" ,r-numderiv)
11488 ("r-survival" ,r-survival)
11490 (home-page "http://BendixCarstensen.com/Epi/")
11491 (synopsis "Statistical analysis in epidemiology")
11493 "This package provides functions for demographic and epidemiological
11494 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
11495 particular representation, manipulation and simulation of multistate data -
11496 the Lexis suite of functions, which includes interfaces to the @code{mstate},
11497 @code{etm} and @code{cmprsk} packages. It also contains functions for
11498 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
11499 data and some useful functions for tabulation and plotting, as well as a
11500 number of epidemiological data sets.")
11501 (license license:gpl2)))
11503 (define-public r-ppls
11506 (version "1.6-1.1")
11510 (uri (cran-uri "ppls" version))
11513 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
11514 (build-system r-build-system)
11515 (propagated-inputs `(("r-mass" ,r-mass)))
11516 (home-page "https://cran.r-project.org/web/packages/ppls")
11517 (synopsis "Penalized partial least squares")
11519 "This package contains linear and nonlinear regression methods based on
11520 partial least squares and penalization techniques. Model parameters are
11521 selected via cross-validation, and confidence intervals ans tests for the
11522 regression coefficients can be conducted via jackknifing.")
11523 (license license:gpl2+)))
11525 (define-public r-huge
11532 (uri (cran-uri "huge" version))
11534 (base32 "07n3j1va2z4v30rj22cww72khgzbz2xsp0yc0qswlrwyxi4my5i3"))))
11535 (build-system r-build-system)
11537 `(("r-igraph" ,r-igraph)
11539 ("r-matrix" ,r-matrix)
11541 ("r-rcppeigen" ,r-rcppeigen)))
11542 (home-page "https://cran.r-project.org/web/packages/huge")
11543 (synopsis "High-dimensional undirected graph estimation")
11545 "This package provides a general framework for high-dimensional
11546 undirected graph estimation. It integrates data preprocessing, neighborhood
11547 screening, graph estimation, and model selection techniques into a pipeline.")
11548 (license license:gpl2)))
11550 (define-public r-parcor
11557 (uri (cran-uri "parcor" version))
11560 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
11561 (build-system r-build-system)
11564 ("r-genenet" ,r-genenet)
11565 ("r-glmnet" ,r-glmnet)
11567 ("r-ppls" ,r-ppls)))
11568 (home-page "https://cran.r-project.org/web/packages/parcor")
11569 (synopsis "Regularized estimation of partial correlation matrices")
11571 "This package estimates the matrix of partial correlations based on
11572 different regularized regression methods: lasso, adaptive lasso, PLS, and
11573 Ridge Regression. In addition, the package provides model selection for
11574 lasso, adaptive lasso and Ridge regression based on cross-validation.")
11575 (license license:gpl2+)))
11577 (define-public r-mcmc
11580 (version "0.9-6.1")
11584 (uri (cran-uri "mcmc" version))
11587 "1i1nhdapyijvm58zx38q28zk01ndmi6smjivxk5xs2cx9b6v2av9"))))
11588 (build-system r-build-system)
11589 (home-page "http://www.stat.umn.edu/geyer/mcmc/")
11590 (synopsis "Markov chain Monte Carlo")
11592 "This package simulates continuous distributions of random vectors using
11593 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
11594 function that evaluates the log unnormalized density. Algorithms are random
11595 walk Metropolis algorithm (function @code{metrop}), simulated
11596 tempering (function @code{temper}), and morphometric random walk
11597 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
11598 by change of variable.")
11599 (license license:expat)))
11601 (define-public r-listenv
11608 (uri (cran-uri "listenv" version))
11611 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
11612 (build-system r-build-system)
11614 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11615 (home-page "https://github.com/HenrikBengtsson/listenv")
11616 (synopsis "Environments behaving (almost) as lists")
11618 "This package implements list environments. List environments are
11619 environments that have list-like properties. For instance, the elements of a
11620 list environment are ordered and can be accessed and iterated over using index
11622 (license license:lgpl2.1+)))
11624 (define-public r-globals
11631 (uri (cran-uri "globals" version))
11634 "1ha8iasgijp4q3v2b0b17y1wh7cd3nvzd9b03w49qm2bidkaf68m"))))
11635 (build-system r-build-system)
11637 `(("r-codetools" ,r-codetools)))
11638 (home-page "https://github.com/HenrikBengtsson/globals")
11639 (synopsis "Identify global objects in R expressions")
11641 "This package provides tools to identify global (\"unknown\" or \"free\")
11642 objects in R expressions by code inspection using various strategies, e.g.
11643 conservative or liberal. The objective of this package is to make it as
11644 simple as possible to identify global objects for the purpose of exporting
11645 them in distributed compute environments.")
11646 (license license:lgpl2.1+)))
11648 (define-public r-future
11655 (uri (cran-uri "future" version))
11658 "1xaqh0b2knf5bp23mc0kriq0iqhqna31q3b7d960piqjhzrb03dm"))))
11659 (build-system r-build-system)
11661 `(("r-digest" ,r-digest)
11662 ("r-globals" ,r-globals)
11663 ("r-listenv" ,r-listenv)))
11665 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11666 (home-page "https://github.com/HenrikBengtsson/future")
11667 (synopsis "Unified parallel and distributed processing in R")
11669 "The purpose of this package is to provide a lightweight and unified
11670 Future API for sequential and parallel processing of R expression via futures.
11671 This package implements sequential, multicore, multisession, and cluster
11672 futures. With these, R expressions can be evaluated on the local machine, in
11673 parallel a set of local machines, or distributed on a mix of local and remote
11674 machines. Extensions to this package implement additional backends for
11675 processing futures via compute cluster schedulers etc. Because of its unified
11676 API, there is no need to modify any code in order to switch from sequential on
11677 the local machine to, say, distributed processing on a remote compute cluster.")
11678 (license license:lgpl2.1+)))
11680 (define-public r-future-apply
11682 (name "r-future-apply")
11687 (uri (cran-uri "future.apply" version))
11690 "1kgq6dv96hdy35kysqkn606nj7s9dp4ibgpm6n46gqhc5n75lzkk"))))
11691 (properties `((upstream-name . "future.apply")))
11692 (build-system r-build-system)
11694 `(("r-future" ,r-future)
11695 ("r-globals" ,r-globals)))
11697 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11698 (home-page "https://github.com/HenrikBengtsson/future.apply")
11699 (synopsis "Apply function to elements in parallel using futures")
11701 "This package provides implementations of @code{apply()},
11702 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
11703 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
11704 can be resolved using any future-supported backend, e.g. parallel on the local
11705 machine or distributed on a compute cluster.")
11706 (license license:gpl2+)))
11708 (define-public r-rsvd
11715 (uri (cran-uri "rsvd" version))
11718 "1fvrw46fl5xb2akaa4mp8nja4h7nn4bdhnjdrk22fsdfqc7hwmhk"))))
11719 (build-system r-build-system)
11721 `(("r-matrix" ,r-matrix)))
11722 (home-page "https://github.com/erichson/rSVD")
11723 (synopsis "Randomized singular value decomposition")
11725 "Low-rank matrix decompositions are fundamental tools and widely used for
11726 data analysis, dimension reduction, and data compression. Classically, highly
11727 accurate deterministic matrix algorithms are used for this task. However, the
11728 emergence of large-scale data has severely challenged our computational
11729 ability to analyze big data. The concept of randomness has been demonstrated
11730 as an effective strategy to quickly produce approximate answers to familiar
11731 problems such as the @dfn{singular value decomposition} (SVD). This package
11732 provides several randomized matrix algorithms such as the randomized singular
11733 value decomposition (@code{rsvd}), randomized principal component
11734 analysis (@code{rpca}), randomized robust principal component
11735 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
11736 and the randomized CUR decomposition (@code{rcur}). In addition several plot
11737 functions are provided.")
11738 (license license:gpl3+)))
11740 (define-public r-sloop
11747 (uri (cran-uri "sloop" version))
11750 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
11751 (build-system r-build-system)
11753 `(("r-codetools" ,r-codetools)
11754 ("r-crayon" ,r-crayon)
11755 ("r-purrr" ,r-purrr)
11756 ("r-rlang" ,r-rlang)
11757 ("r-tibble" ,r-tibble)))
11758 (home-page "https://github.com/r-lib/sloop")
11759 (synopsis "Helpers for object-oriented programming in R")
11761 "This package provides a collection of helper functions designed to
11762 help you to better understand object oriented programming in R, particularly
11764 (license license:gpl3)))
11766 (define-public r-capushe
11773 (uri (cran-uri "capushe" version))
11776 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
11777 (build-system r-build-system)
11778 (propagated-inputs `(("r-mass" ,r-mass)))
11779 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
11780 (synopsis "Calibrating penalties using slope heuristics")
11782 "This package provides tools for the calibration of penalized criteria
11783 for model selection. The calibration methods available are based on the slope
11785 (license license:gpl2+)))
11787 (define-public r-dorng
11794 (uri (cran-uri "doRNG" version))
11797 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
11798 (properties `((upstream-name . "doRNG")))
11799 (build-system r-build-system)
11801 `(("r-foreach" ,r-foreach)
11802 ("r-iterators" ,r-iterators)
11803 ("r-rngtools" ,r-rngtools)))
11804 (home-page "https://renozao.github.io/doRNG/")
11805 (synopsis "Generic reproducible parallel backend for foreach loops")
11807 "This package provides functions to perform reproducible parallel
11808 @code{foreach} loops, using independent random streams as generated by
11809 L'Ecuyer's combined multiple-recursive generator. It enables to easily
11810 convert standard @code{%dopar%} loops into fully reproducible loops,
11811 independently of the number of workers, the task scheduling strategy, or the
11812 chosen parallel environment and associated foreach backend.")
11813 (license license:gpl2+)))
11815 (define-public r-blockmodeling
11817 (name "r-blockmodeling")
11822 (uri (cran-uri "blockmodeling" version))
11825 "12paf76l3wlxad14bkxn37lw9rg6ka473m86wlcf3yhriw8kbaiz"))))
11826 (build-system r-build-system)
11828 `(("r-matrix" ,r-matrix)))
11829 (native-inputs `(("gfortran" ,gfortran)))
11830 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
11831 (synopsis "Generalized and classical blockmodeling of valued networks")
11833 "This package is primarily meant as an implementation of generalized
11834 blockmodeling for valued networks. In addition, measures of similarity or
11835 dissimilarity based on structural equivalence and regular equivalence (REGE
11836 algorithms) can be computed and partitioned matrices can be plotted.")
11837 (license license:gpl2+)))
11839 (define-public r-upsetr
11846 (uri (cran-uri "UpSetR" version))
11849 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
11850 (properties `((upstream-name . "UpSetR")))
11851 (build-system r-build-system)
11853 `(("r-ggplot2" ,r-ggplot2)
11854 ("r-gridextra" ,r-gridextra)
11856 ("r-scales" ,r-scales)))
11857 (home-page "https://github.com/hms-dbmi/UpSetR")
11858 (synopsis "Visualize intersecting sets")
11860 "This package provides a more scalable alternative to Venn and Euler
11861 diagrams for visualizing intersecting sets. Create visualizations of
11862 intersecting sets using a novel matrix design, along with visualizations of
11863 several common set, element and attribute related tasks.")
11864 (license license:expat)))
11866 ;; This package includes a JavaScript file, which is not minified. When
11867 ;; upgrading please check that there are no new minified JavaScript files.
11868 (define-public r-shinybs
11875 (uri (cran-uri "shinyBS" version))
11878 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
11879 (properties `((upstream-name . "shinyBS")))
11880 (build-system r-build-system)
11881 ;; The tests spawn Shiny browser apps. They cannot be run
11882 ;; non-interactively.
11883 (arguments '(#:tests? #f))
11885 `(("r-htmltools" ,r-htmltools)
11886 ("r-shiny" ,r-shiny)))
11887 (home-page "https://ebailey78.github.io/shinyBS/")
11888 (synopsis "Twitter Bootstrap components for Shiny")
11890 "This package adds additional Twitter Bootstrap components to Shiny.")
11891 (license license:gpl3)))
11893 (define-public r-outliers
11895 (name "r-outliers")
11900 (uri (cran-uri "outliers" version))
11903 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
11904 (build-system r-build-system)
11905 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
11906 (synopsis "Tests for outliers")
11908 "This package provides a collection of some tests commonly used for
11909 identifying outliers.")
11910 (license license:gpl2+)))
11912 (define-public r-bayesm
11919 (uri (cran-uri "bayesm" version))
11921 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
11922 (build-system r-build-system)
11924 `(("r-rcpp" ,r-rcpp)
11925 ("r-rcpparmadillo" ,r-rcpparmadillo)))
11926 (home-page "http://www.perossi.org/home/bsm-1")
11927 (synopsis "Bayesian inference for marketing/micro-econometrics")
11929 "This package covers many important models used in marketing and
11930 micro-econometrics applications, including Bayes Regression (univariate or
11931 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
11932 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
11933 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
11934 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
11935 Estimation with normal base, Hierarchical Linear Models with normal prior and
11936 covariates, Hierarchical Linear Models with a mixture of normals prior and
11937 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
11938 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
11939 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
11940 analysis of choice-based conjoint data, Bayesian treatment of linear
11941 instrumental variables models, Analysis of Multivariate Ordinal survey data
11942 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
11943 Coefficient Logit Models.")
11944 (license license:gpl2+)))
11946 (define-public r-tensora
11953 (uri (cran-uri "tensorA" version))
11956 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
11957 (properties `((upstream-name . "tensorA")))
11958 (build-system r-build-system)
11959 (home-page "http://www.stat.boogaart.de/tensorA")
11960 (synopsis "Advanced tensor arithmetic with named indices")
11962 "This package provides convenience functions for advanced linear algebra
11963 with tensors and computation with datasets of tensors on a higher level
11964 abstraction. It includes Einstein and Riemann summing conventions, dragging,
11965 co- and contravariate indices, and parallel computations on sequences of
11967 (license license:gpl2+)))
11969 (define-public r-rarpack
11976 (uri (cran-uri "rARPACK" version))
11979 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
11980 (properties `((upstream-name . "rARPACK")))
11981 (build-system r-build-system)
11982 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
11983 (home-page "https://github.com/yixuan/rARPACK")
11984 (synopsis "Solvers for large scale eigenvalue and SVD problems")
11986 "This package was previously an R wrapper of the ARPACK library, and now
11987 a shell of the R package RSpectra, an R interface to the Spectra library for
11988 solving large scale eigenvalue/vector problems. The current version of
11989 rARPACK simply imports and exports the functions provided by RSpectra. New
11990 users of rARPACK are advised to switch to the RSpectra package.")
11991 (license license:bsd-3)))
11993 (define-public r-compositions
11995 (name "r-compositions")
12000 (uri (cran-uri "compositions" version))
12003 "0z40llyij3cc80ac1vzzrpykk6ysp89bn6dyyh40fbnc4anwx69a"))))
12004 (build-system r-build-system)
12006 `(("r-bayesm" ,r-bayesm)
12007 ("r-robustbase" ,r-robustbase)
12008 ("r-tensora" ,r-tensora)))
12009 (home-page "http://www.stat.boogaart.de/compositions")
12010 (synopsis "Compositional data analysis")
12012 "This package provides functions for the consistent analysis of
12013 compositional data (e.g. portions of substances) and positive
12014 numbers (e.g. concentrations).")
12015 (license license:gpl2+)))
12017 (define-public r-cobs
12024 (uri (cran-uri "cobs" version))
12027 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
12028 (build-system r-build-system)
12030 `(("r-quantreg" ,r-quantreg)
12031 ("r-sparsem" ,r-sparsem)))
12032 (home-page "https://cran.r-project.org/web/packages/cobs")
12033 (synopsis "Constrained B-Splines (sparse matrix based)")
12035 "This package provides qualitatively constrained (regression) smoothing
12036 splines via linear programming and sparse matrices.")
12037 (license license:gpl2+)))
12039 (define-public r-drimpute
12041 (name "r-drimpute")
12046 (uri (cran-uri "DrImpute" version))
12049 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
12050 (properties `((upstream-name . "DrImpute")))
12051 (build-system r-build-system)
12053 `(("r-rcpp" ,r-rcpp)
12054 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12055 (home-page "https://github.com/ikwak2/DrImpute")
12056 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
12058 "This is an R package for imputing dropout events. Many statistical
12059 methods in cell type identification, visualization and lineage reconstruction
12060 do not account for dropout events. DrImpute can improve the performance of
12061 such software by imputing dropout events.")
12062 (license license:gpl3)))
12064 (define-public r-gamlss-dist
12066 (name "r-gamlss-dist")
12071 (uri (cran-uri "gamlss.dist" version))
12073 (base32 "1p904x0b07z4amaqdn2xhs7qzbq8lisr6lqc844s3pkxzmny7w1z"))))
12074 (properties `((upstream-name . "gamlss.dist")))
12075 (build-system r-build-system)
12076 (propagated-inputs `(("r-mass" ,r-mass)))
12077 (home-page "http://www.gamlss.org/")
12078 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
12080 "This package provides a set of distributions which can be used for
12081 modelling the response variables in Generalized Additive Models for Location
12082 Scale and Shape. The distributions can be continuous, discrete or mixed
12083 distributions. Extra distributions can be created, by transforming, any
12084 continuous distribution defined on the real line, to a distribution defined on
12085 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
12086 transformation, respectively.")
12087 ;; Either version of the GPL.
12088 (license (list license:gpl2 license:gpl3))))
12090 ;; This package includes JavaScript files, which are not minified. When
12091 ;; upgrading please check that there are no new minified JavaScript files.
12092 (define-public r-shinyjs
12099 (uri (cran-uri "shinyjs" version))
12102 "14k8y313ppj23m9rhlk8jc94x6sbn3qrsnx6xrijiyv8m8dii1l9"))))
12103 (build-system r-build-system)
12105 `(("r-digest" ,r-digest)
12106 ("r-htmltools" ,r-htmltools)
12107 ("r-jsonlite" ,r-jsonlite)
12108 ("r-shiny" ,r-shiny)))
12109 (home-page "https://deanattali.com/shinyjs")
12110 (synopsis "Improve the user experience of your Shiny apps")
12112 "Perform common useful JavaScript operations in Shiny apps that will
12113 greatly improve your apps without having to know any JavaScript. Examples
12114 include: hiding an element, disabling an input, resetting an input back to its
12115 original value, delaying code execution by a few seconds, and many more useful
12116 functions for both the end user and the developer. Shinyjs can also be used
12117 to easily call your own custom JavaScript functions from R.")
12118 (license license:agpl3+)))
12120 ;; This package includes minified JavaScript files. When upgrading please
12121 ;; check that there are no new minified JavaScript files.
12122 (define-public r-colourpicker
12124 (name "r-colourpicker")
12129 (uri (cran-uri "colourpicker" version))
12132 "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
12133 (build-system r-build-system)
12135 `(#:modules ((guix build utils)
12136 (guix build r-build-system)
12140 (modify-phases %standard-phases
12141 (add-after 'unpack 'process-javascript
12142 (lambda* (#:key inputs #:allow-other-keys)
12143 (with-directory-excursion "inst"
12147 `((,(assoc-ref inputs "js-salvattore")
12148 "examples/colourInput/www/salvattore.min.js")
12149 (,(assoc-ref inputs "js-jquery")
12150 "htmlwidgets/lib/jquery/jquery.min.js")
12151 ("www/shared/colourpicker/js/colourpicker.js"
12152 "www/shared/colourpicker/js/colourpicker.min.js"))))
12153 (lambda (sources targets)
12154 (for-each (lambda (source target)
12155 (format #t "Processing ~a --> ~a~%"
12157 (delete-file target)
12158 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
12159 (call-with-output-file target
12161 (dump-port minified port)))))
12162 sources targets))))
12165 `(("r-ggplot2" ,r-ggplot2)
12166 ("r-htmltools" ,r-htmltools)
12167 ("r-htmlwidgets" ,r-htmlwidgets)
12168 ("r-jsonlite" ,r-jsonlite)
12169 ("r-miniui" ,r-miniui)
12170 ("r-shiny" ,r-shiny)
12171 ("r-shinyjs" ,r-shinyjs)))
12173 `(("uglify-js" ,uglify-js)
12177 (uri "https://code.jquery.com/jquery-3.3.1.js")
12180 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
12184 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
12187 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
12188 (home-page "https://github.com/daattali/colourpicker")
12189 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
12191 "This package provides a color picker that can be used as an input in
12192 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
12193 custom color palettes, and many more options. A plot color helper tool is
12194 available as an RStudio Addin, which helps you pick colors to use in your
12195 plots. A more generic color picker RStudio Addin is also provided to let you
12196 select colors to use in your R code.")
12197 (license license:expat)))
12199 (define-public r-ggextra
12206 (uri (cran-uri "ggExtra" version))
12209 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
12210 (properties `((upstream-name . "ggExtra")))
12211 (build-system r-build-system)
12213 `(("r-colourpicker" ,r-colourpicker)
12214 ("r-ggplot2" ,r-ggplot2)
12215 ("r-gtable" ,r-gtable)
12216 ("r-miniui" ,r-miniui)
12218 ("r-scales" ,r-scales)
12219 ("r-shiny" ,r-shiny)
12220 ("r-shinyjs" ,r-shinyjs)))
12221 (home-page "https://github.com/daattali/ggExtra")
12222 (synopsis "Marginal histograms for ggplot2 and other enhancements")
12224 "This package is a collection of functions and layers to enhance ggplot2.
12225 The flagship function is @code{ggMarginal()}, which can be used to add
12226 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
12227 (license license:expat)))
12229 (define-public r-minpack-lm
12231 (name "r-minpack-lm")
12236 (uri (cran-uri "minpack.lm" version))
12239 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
12240 (properties `((upstream-name . "minpack.lm")))
12241 (build-system r-build-system)
12242 (native-inputs `(("gfortran" ,gfortran)))
12243 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
12244 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
12246 "The @code{nls.lm} function provides an R interface to @code{lmder} and
12247 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
12248 problems by a modification of the Levenberg-Marquardt algorithm, with support
12249 for lower and upper parameter bounds. The implementation can be used via
12250 @code{nls}-like calls using the @code{nlsLM} function.")
12251 (license license:gpl3)))
12253 (define-public r-moments
12260 (uri (cran-uri "moments" version))
12263 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
12264 (build-system r-build-system)
12265 (home-page "https://cran.r-project.org/web/packages/moments")
12266 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
12268 "This package provides functions to calculate: moments, Pearson's
12269 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
12270 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
12271 (license license:gpl2+)))
12273 (define-public r-msir
12280 (uri (cran-uri "msir" version))
12283 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
12284 (build-system r-build-system)
12286 `(("r-mclust" ,r-mclust)))
12287 (home-page "https://cran.r-project.org/web/packages/msir")
12288 (synopsis "Model-based sliced inverse regression")
12290 "This is an R package for dimension reduction based on finite Gaussian
12291 mixture modeling of inverse regression.")
12292 (license license:gpl2+)))
12294 (define-public r-pbivnorm
12296 (name "r-pbivnorm")
12301 (uri (cran-uri "pbivnorm" version))
12304 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
12305 (build-system r-build-system)
12306 (native-inputs `(("gfortran" ,gfortran)))
12307 (home-page "https://github.com/brentonk/pbivnorm")
12308 (synopsis "Vectorized bivariate normal CDF")
12310 "This package provides a vectorized R function for calculating
12311 probabilities from a standard bivariate normal CDF.")
12312 (license license:gpl2+)))
12314 (define-public r-lavaan
12321 (uri (cran-uri "lavaan" version))
12324 "04kvsh2m6mnzlhv83phr3hjzy4sx1ck6f7dgsm7xb8cs84dnxszy"))))
12325 (build-system r-build-system)
12327 `(("r-mass" ,r-mass)
12328 ("r-mnormt" ,r-mnormt)
12329 ("r-numderiv" ,r-numderiv)
12330 ("r-pbivnorm" ,r-pbivnorm)))
12331 (home-page "http://lavaan.ugent.be")
12332 (synopsis "Latent variable analysis")
12334 "This package provides tools to fit a variety of latent variable models,
12335 including confirmatory factor analysis, structural equation modeling and
12336 latent growth curve models.")
12337 (license license:gpl2+)))
12339 (define-public r-nonnest2
12341 (name "r-nonnest2")
12346 (uri (cran-uri "nonnest2" version))
12349 "1bq44qqmm59j91m0sny4xnqmxqlga4cm48qdsw8xfs3x19xwmxk6"))))
12350 (build-system r-build-system)
12352 `(("r-compquadform" ,r-compquadform)
12353 ("r-lavaan" ,r-lavaan)
12354 ("r-mvtnorm" ,r-mvtnorm)
12355 ("r-sandwich" ,r-sandwich)))
12356 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
12357 (synopsis "Tests of non-nested models")
12359 "This package allows for testing of non-nested models. It includes tests
12360 of model distinguishability and of model fit that can be applied to both
12361 nested and non-nested models. The package also includes functionality to
12362 obtain confidence intervals associated with AIC and BIC.")
12363 ;; Either version of the GPL.
12364 (license (list license:gpl2 license:gpl3))))
12366 (define-public r-penalized
12368 (name "r-penalized")
12373 (uri (cran-uri "penalized" version))
12376 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
12377 (build-system r-build-system)
12379 `(("r-rcpp" ,r-rcpp)
12380 ("r-rcpparmadillo" ,r-rcpparmadillo)
12381 ("r-survival" ,r-survival)))
12382 (home-page "https://cran.r-project.org/web/packages/penalized/")
12383 (synopsis "Penalized estimation in GLMs and in the Cox model")
12385 "This package provides tools for fitting possibly high dimensional
12386 penalized regression models. The penalty structure can be any combination of
12387 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
12388 constraint on the regression coefficients. The supported regression models
12389 are linear, logistic and Poisson regression and the Cox Proportional Hazards
12390 model. Cross-validation routines allow optimization of the tuning
12392 (license license:gpl2+)))
12394 (define-public r-zim
12401 (uri (cran-uri "ZIM" version))
12404 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
12405 (properties `((upstream-name . "ZIM")))
12406 (build-system r-build-system)
12407 (propagated-inputs `(("r-mass" ,r-mass)))
12408 (home-page "https://github.com/biostatstudio/ZIM")
12409 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
12411 "Analyze count time series with excess zeros. Two types of statistical
12412 models are supported: Markov regression and state-space models. They are also
12413 known as observation-driven and parameter-driven models respectively in the
12414 time series literature. The functions used for Markov regression or
12415 observation-driven models can also be used to fit ordinary regression models
12416 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
12417 negative binomial (ZINB) assumption. The package also contains miscellaneous
12418 functions to compute density, distribution, quantile, and generate random
12419 numbers from ZIP and ZINB distributions.")
12420 (license license:gpl3)))
12422 (define-public r-nor1mix
12429 (uri (cran-uri "nor1mix" version))
12432 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
12433 (build-system r-build-system)
12434 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
12435 (synopsis "Normal (1-d) mixture models")
12437 "This package provides S3 classes and methods for one-dimensional normal
12438 mixture models, for, e.g., density estimation or clustering algorithms
12439 research and teaching; it provides the widely used Marron-Wand densities. It
12440 also provides tools for efficient random number generation and graphics.")
12441 (license license:gpl2+)))
12443 (define-public r-beanplot
12445 (name "r-beanplot")
12450 (uri (cran-uri "beanplot" version))
12453 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
12454 (build-system r-build-system)
12455 (home-page "https://cran.r-project.org/web/packages/beanplot/")
12456 (synopsis "Visualization via beanplots")
12458 "This package provides beanplots, an alternative to
12459 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
12461 (license license:gpl2)))
12463 (define-public r-pbdzmq
12470 (uri (cran-uri "pbdZMQ" version))
12473 "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
12474 (properties `((upstream-name . "pbdZMQ")))
12475 (build-system r-build-system)
12477 `(("zeromq" ,zeromq)
12480 `(("pkg-config" ,pkg-config)))
12481 (home-page "https://pbdr.org/")
12482 (synopsis "R interface to ZeroMQ")
12484 "ZeroMQ is a well-known library for high-performance asynchronous
12485 messaging in scalable, distributed applications. This package provides high
12486 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
12487 interactive client/server programming frameworks. A few wrapper functions
12488 compatible with @code{rzmq} are also provided.")
12489 (license license:gpl3)))
12491 (define-public r-repr
12498 (uri (cran-uri "repr" version))
12501 "15jz780w4nd9qjd1g3gq8f5lkh60p2v3ig3hm5kl1rg3z4cf0gvl"))))
12502 (build-system r-build-system)
12504 `(("r-base64enc" ,r-base64enc)
12505 ("r-htmltools" ,r-htmltools)
12506 ("r-jsonlite" ,r-jsonlite)
12507 ("r-pillar" ,r-pillar)))
12508 (home-page "https://cran.r-project.org/web/packages/repr/")
12509 (synopsis "Serializable representations")
12511 "This package provides string and binary representations of objects for
12512 several formats and MIME types.")
12513 (license license:gpl3)))
12515 (define-public r-irdisplay
12517 (name "r-irdisplay")
12522 (uri (cran-uri "IRdisplay" version))
12525 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
12526 (properties `((upstream-name . "IRdisplay")))
12527 (build-system r-build-system)
12529 `(("r-repr" ,r-repr)))
12530 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
12531 (synopsis "Jupyter display machinery")
12533 "This package provides an interface to the rich display capabilities of
12534 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
12535 running IRkernel session.")
12536 (license license:expat)))
12538 (define-public r-irkernel
12540 (name "r-irkernel")
12545 (uri (cran-uri "IRkernel" version))
12548 "1viqxs91dys1z4cf7gb59rmqvzb8lc7jdp4azrpmhgwa8qf46s94"))))
12549 (properties `((upstream-name . "IRkernel")))
12550 (build-system r-build-system)
12553 (modify-phases %standard-phases
12554 (add-after 'install 'install-kernelspec
12555 (lambda* (#:key outputs #:allow-other-keys)
12556 (let ((out (assoc-ref outputs "out")))
12557 (setenv "HOME" "/tmp")
12558 (invoke "jupyter" "kernelspec" "install"
12561 (string-append out "/site-library/IRkernel/kernelspec"))
12562 ;; Record the absolute file name of the 'R' executable in
12564 (substitute* (string-append out "/share/jupyter"
12565 "/kernels/ir/kernel.json")
12567 (string-append "[\"" (which "R") "\",")))
12570 `(("jupyter" ,jupyter)))
12572 `(("r-crayon" ,r-crayon)
12573 ("r-digest" ,r-digest)
12574 ("r-evaluate" ,r-evaluate)
12575 ("r-irdisplay" ,r-irdisplay)
12576 ("r-jsonlite" ,r-jsonlite)
12577 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
12578 ("r-minimal" ,r-minimal)
12579 ("r-pbdzmq" ,r-pbdzmq)
12581 ("r-uuid" ,r-uuid)))
12582 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
12583 (synopsis "Native R kernel for Jupyter")
12585 "The R kernel for the Jupyter environment executes R code which the
12586 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
12588 (license license:expat)))
12590 (define-public r-gmodels
12597 (uri (cran-uri "gmodels" version))
12600 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
12601 (build-system r-build-system)
12603 `(("r-gdata" ,r-gdata)
12604 ("r-mass" ,r-mass)))
12605 (home-page "https://cran.r-project.org/web/packages/gmodels/")
12606 (synopsis "Various R programming tools for model fitting")
12608 "This package provides various R programming tools for model fitting.")
12609 (license license:gpl2)))
12611 (define-public r-apcluster
12613 (name "r-apcluster")
12618 (uri (cran-uri "apcluster" version))
12621 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
12622 (build-system r-build-system)
12624 `(("r-matrix" ,r-matrix)
12625 ("r-rcpp" ,r-rcpp)))
12626 (home-page "https://cran.r-project.org/web/packages/apcluster/")
12627 (synopsis "Affinity propagation clustering")
12629 "This package implements affinity propagation clustering introduced by
12630 Frey and Dueck (2007). The package further provides leveraged affinity
12631 propagation and an algorithm for exemplar-based agglomerative clustering that
12632 can also be used to join clusters obtained from affinity propagation. Various
12633 plotting functions are available for analyzing clustering results.")
12634 (license license:gpl2+)))
12636 (define-public r-valr
12643 (uri (cran-uri "valr" version))
12646 "14jhrwkiwmha3vlmm7b50n2xxyizj6ddmy89gb20mpzq7qhz1ika"))))
12647 (build-system r-build-system)
12649 `(("r-broom" ,r-broom)
12650 ("r-dplyr" ,r-dplyr)
12651 ("r-ggplot2" ,r-ggplot2)
12653 ("r-readr" ,r-readr)
12654 ("r-rlang" ,r-rlang)
12655 ("r-stringr" ,r-stringr)
12656 ("r-tibble" ,r-tibble)))
12657 (home-page "http://github.com/rnabioco/valr")
12658 (synopsis "Genome interval arithmetic in R")
12660 "This package enables you to read and manipulate genome intervals and
12661 signals. It provides functionality similar to command-line tool suites within
12662 R, enabling interactive analysis and visualization of genome-scale data.")
12663 (license license:expat)))
12665 (define-public r-rematch2
12667 (name "r-rematch2")
12672 (uri (cran-uri "rematch2" version))
12675 "00cznm6rk33b53w7zybkz7549bnydc66znpi5mb0xd24pmqp0rvq"))))
12676 (build-system r-build-system)
12678 `(("r-tibble" ,r-tibble)))
12679 (home-page "https://github.com/r-lib/rematch2")
12680 (synopsis "Tidy output from regular expression matching")
12682 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
12683 return the match results in tidy data frames.")
12684 (license license:expat)))
12686 (define-public r-picante
12693 (uri (cran-uri "picante" version))
12696 "1b16zm8zjjsl181b8krkdcrbcw347kf772c4w7y5332qmfi7jhz0"))))
12697 (build-system r-build-system)
12701 ("r-vegan" ,r-vegan)))
12702 (home-page "https://cran.r-project.org/web/packages/picante/")
12703 (synopsis "Integrating phylogenies and ecology")
12705 "This package provides functions for phylocom integration, community
12706 analyses, null-models, traits and evolution. It implements numerous
12707 ecophylogenetic approaches including measures of community phylogenetic and
12708 trait diversity, phylogenetic signal, estimation of trait values for
12709 unobserved taxa, null models for community and phylogeny randomizations, and
12710 utility functions for data input/output and phylogeny plotting. A full
12711 description of package functionality and methods are provided by Kembel et
12713 (license license:gpl2)))
12715 (define-public r-reinforcelearn
12717 (name "r-reinforcelearn")
12722 (uri (cran-uri "reinforcelearn" version))
12725 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
12726 (build-system r-build-system)
12728 `(("r-checkmate" ,r-checkmate)
12730 ("r-purrr" ,r-purrr)
12732 (home-page "https://markusdumke.github.io/reinforcelearn")
12733 (synopsis "Reinforcement learning")
12735 "This package implements reinforcement learning environments and
12736 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
12737 can be used with function approximation, eligibility traces (Singh & Sutton,
12738 1996) and experience replay (Mnih et al., 2013).")
12739 (license license:expat)))
12741 (define-public r-lemon
12748 (uri (cran-uri "lemon" version))
12751 "0wsn5bfg10wq4dnrgpyraz2bzx9p19c7hf1pwj3h4zmpqfgsdbpw"))))
12752 (build-system r-build-system)
12754 `(("r-ggplot2" ,r-ggplot2)
12755 ("r-gridextra" ,r-gridextra)
12756 ("r-gtable" ,r-gtable)
12757 ("r-knitr" ,r-knitr)
12758 ("r-lattice" ,r-lattice)
12760 ("r-scales" ,r-scales)))
12761 (home-page "https://github.com/stefanedwards/lemon")
12762 (synopsis "Freshen up your ggplot2 plots")
12764 "This package provides functions for working with legends and axis lines
12765 of ggplot2, facets that repeat axis lines on all panels, and some knitr
12767 (license license:gpl3)))
12769 (define-public r-wgaim
12776 (uri (cran-uri "wgaim" version))
12778 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
12779 (build-system r-build-system)
12781 `(("r-ggplot2" ,r-ggplot2)
12783 (home-page "https://cran.r-project.org/web/packages/wgaim")
12784 (synopsis "Whole genome average interval mapping for QTL detection")
12786 "This package integrates sophisticated mixed modelling methods with a
12787 whole genome approach to detecting significant QTL in linkage maps.")
12788 (license license:gpl2+)))
12790 (define-public r-bedr
12797 (uri (cran-uri "bedr" version))
12800 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
12801 (build-system r-build-system)
12803 `(("r-data-table" ,r-data-table)
12804 ("r-r-utils" ,r-r-utils)
12805 ("r-testthat" ,r-testthat)
12806 ("r-venndiagram" ,r-venndiagram)
12809 ("bedtools" ,bedtools)
12810 ("htslib" ,htslib))) ; for tabix
12812 `(("r-knitr" ,r-knitr))) ; for vignettes
12813 (home-page "https://cran.r-project.org/web/packages/bedr")
12814 (synopsis "Genomic region processing")
12816 "This package is for genomic regions processing using command line tools
12817 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
12818 utilities to perform genome arithmetic e.g indexing, formatting and merging.
12819 The bedr package's API enhances access to these tools as well as offers
12820 additional utilities for genomic regions processing.")
12821 (license license:gpl2)))
12823 (define-public r-sets
12830 (uri (cran-uri "sets" version))
12833 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
12834 (properties `((upstream-name . "sets")))
12835 (build-system r-build-system)
12836 (home-page "https://cran.r-project.org/web/packages/sets")
12837 (synopsis "Sets, generalized sets, customizable sets and intervals")
12839 "This package provides data structures and basic operations for ordinary
12840 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
12841 customizable sets, and intervals.")
12842 (license license:gpl2)))
12844 (define-public r-partitions
12846 (name "r-partitions")
12851 (uri (cran-uri "partitions" version))
12854 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
12855 (build-system r-build-system)
12858 ("r-polynom" ,r-polynom)
12859 ("r-sets" ,r-sets)))
12860 (home-page "https://cran.r-project.org/web/packages/partitions")
12861 (synopsis "Additive partitions of integers")
12863 "This package provides tools to enumerates the partitions, unequal
12864 partitions, and restricted partitions of an integer; the three corresponding
12865 partition functions are also given.")
12866 ;; Any version of the GPL
12867 (license license:gpl2+)))
12869 (define-public r-brobdingnag
12871 (name "r-brobdingnag")
12876 (uri (cran-uri "Brobdingnag" version))
12879 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
12880 (properties `((upstream-name . "Brobdingnag")))
12881 (build-system r-build-system)
12882 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
12883 (synopsis "Very large numbers in R")
12885 "This package handles very large numbers in R. Real numbers are held
12886 using their natural logarithms, plus a logical flag indicating sign. The
12887 package includes a vignette that gives a step-by-step introduction to using S4
12889 ;; Any version of the GPL
12890 (license license:gpl2+)))
12892 (define-public r-untb
12899 (uri (cran-uri "untb" version))
12902 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
12903 (build-system r-build-system)
12905 `(("r-brobdingnag" ,r-brobdingnag)
12906 ("r-partitions" ,r-partitions)
12907 ("r-polynom" ,r-polynom)))
12908 (home-page "https://github.com/RobinHankin/untb.git")
12909 (synopsis "Ecological drift under the UNTB")
12911 "This package provides numerical simulations, and visualizations, of
12912 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
12913 (license license:gpl2+)))
12915 (define-public r-stepwise
12917 (name "r-stepwise")
12922 (uri (cran-uri "stepwise" version))
12925 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
12926 (build-system r-build-system)
12927 (home-page "http://stat.sfu.ca/statgen/research/stepwise.html")
12928 (synopsis "Stepwise detection of recombination breakpoints")
12930 "This package provides a stepwise approach to identifying recombination
12931 breakpoints in a genomic sequence alignment.")
12932 (license license:gpl2+)))
12934 (define-public r-snpmaxsel
12936 (name "r-snpmaxsel")
12941 (uri (cran-uri "SNPmaxsel" version))
12944 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
12945 (properties `((upstream-name . "SNPmaxsel")))
12946 (build-system r-build-system)
12948 `(("r-combinat" ,r-combinat)
12949 ("r-mvtnorm" ,r-mvtnorm)))
12950 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
12951 (synopsis "Maximally selected statistics for SNP data")
12953 "This package implements asymptotic methods related to maximally selected
12954 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
12956 (license license:gpl2+)))
12958 (define-public r-acsnminer
12960 (name "r-acsnminer")
12961 (version "0.16.8.25")
12964 (uri (cran-uri "ACSNMineR" version))
12967 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
12968 (properties `((upstream-name . "ACSNMineR")))
12969 (build-system r-build-system)
12971 `(("r-ggplot2" ,r-ggplot2)
12972 ("r-gridextra" ,r-gridextra)))
12973 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
12974 (synopsis "Gene enrichment analysis")
12976 "This package provides tools to compute and represent gene set enrichment
12977 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
12978 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
12979 enrichment can be run with hypergeometric test or Fisher exact test, and can
12980 use multiple corrections. Visualization of data can be done either by
12981 barplots or heatmaps.")
12982 (license license:gpl2+)))
12984 (define-public r-seqinr
12991 (uri (cran-uri "seqinr" version))
12994 "0j30za6kji6y3v09cvcydiacnp65pv6ig8aw7cydl47l5s9chky4"))))
12995 (build-system r-build-system)
12997 `(("r-ade4" ,r-ade4)
12998 ("r-segmented" ,r-segmented)))
13001 (home-page "http://seqinr.r-forge.r-project.org/")
13002 (synopsis "Biological sequences retrieval and analysis")
13004 "This package provides tools for exploratory data analysis and data
13005 visualization of biological sequence (DNA and protein) data. It also includes
13006 utilities for sequence data management under the ACNUC system.")
13007 (license license:gpl2+)))
13009 (define-public r-units
13016 (uri (cran-uri "units" version))
13019 "02nls8m0r1r7kljs4x35naz3szq62hyqyd5vracf1xwi1kz5kdsh"))))
13020 (build-system r-build-system)
13022 `(("udunits" ,udunits)))
13024 `(("r-rcpp" ,r-rcpp)))
13025 (home-page "https://github.com/r-quantities/units/")
13026 (synopsis "Measurement Units for R Vectors")
13028 "This package provides support for measurement units in R vectors,
13029 matrices and arrays: automatic propagation, conversion, derivation and
13030 simplification of units; raising errors in case of unit incompatibility. It
13031 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
13033 (license license:gpl2)))
13035 (define-public r-classint
13037 (name "r-classint")
13042 (uri (cran-uri "classInt" version))
13045 "0w980hrw8sgfdfyd5dsimalq7gwhvqm7507abk7k363pvgks23dv"))))
13046 (properties `((upstream-name . "classInt")))
13047 (build-system r-build-system)
13049 `(("r-class" ,r-class)
13050 ("r-e1071" ,r-e1071)
13051 ("r-kernsmooth" ,r-kernsmooth)))
13052 (native-inputs `(("gfortran" ,gfortran)))
13053 (home-page "https://github.com/r-spatial/classInt/")
13054 (synopsis "Choose univariate class intervals")
13056 "This package provides selected commonly used methods for choosing
13057 univariate class intervals for mapping or other graphics purposes.")
13058 (license license:gpl2+)))
13060 (define-public r-spdata
13067 (uri (cran-uri "spData" version))
13070 "1v66qkvsx77hvv5c78v760yp0hknf7xzcjir2ri3ha456mz79yl5"))))
13071 (properties `((upstream-name . "spData")))
13072 (build-system r-build-system)
13074 `(("r-raster" ,r-raster)
13076 (home-page "https://github.com/Nowosad/spData")
13077 (synopsis "Datasets for spatial analysis")
13079 "This a package containing diverse spatial datasets for demonstrating,
13080 benchmarking and teaching spatial data analysis. It includes R data of class
13081 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
13082 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
13083 of the datasets are designed to illustrate specific analysis techniques.
13084 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
13085 illustrate point pattern analysis techniques.")
13086 (license license:cc0)))
13088 (define-public r-learnbayes
13090 (name "r-learnbayes")
13095 (uri (cran-uri "LearnBayes" version))
13098 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
13099 (properties `((upstream-name . "LearnBayes")))
13100 (build-system r-build-system)
13101 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
13102 (synopsis "Functions for learning Bayesian inference")
13104 "This package provides a collection of functions helpful in learning the
13105 basic tenets of Bayesian statistical inference. It contains functions for
13106 summarizing basic one and two parameter posterior distributions and predictive
13107 distributions. It contains MCMC algorithms for summarizing posterior
13108 distributions defined by the user. It also contains functions for regression
13109 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
13111 (license license:gpl2+)))
13113 (define-public r-deldir
13120 (uri (cran-uri "deldir" version))
13123 "0kdglv8rc1pb4ilcid4xc9wpv5kkj2y6x6wg7919k3hya7mz58ph"))))
13124 (build-system r-build-system)
13125 (native-inputs `(("gfortran" ,gfortran)))
13126 (home-page "https://cran.r-project.org/web/packages/deldir")
13127 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
13129 "This package provides tools for calculating the Delaunay triangulation
13130 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
13131 of a planar point set. It plots triangulations and tessellations in various
13132 ways, clips tessellations to sub-windows, calculates perimeters of
13133 tessellations, and summarizes information about the tiles of the
13135 (license license:gpl2+)))
13137 (define-public r-sf
13144 (uri (cran-uri "sf" version))
13147 "17wyv74m1ppc3s5jdv60r74jj23nidxpzl46vjhfclfhnpvm7sx9"))))
13148 (build-system r-build-system)
13155 `(("r-classint" ,r-classint)
13157 ("r-magrittr" ,r-magrittr)
13159 ("r-units" ,r-units)))
13160 (native-inputs `(("pkg-config" ,pkg-config)))
13161 (home-page "https://github.com/r-spatial/sf/")
13162 (synopsis "Simple features for R")
13164 "This package provides support for simple features, a standardized way to
13165 encode spatial vector data. It binds to GDAL for reading and writing data, to
13166 GEOS for geometrical operations, and to PROJ for projection conversions and
13167 datum transformations.")
13168 ;; Either of these licenses
13169 (license (list license:gpl2 license:expat))))
13171 (define-public r-spdep
13178 (uri (cran-uri "spdep" version))
13181 "1f8cjffqqc6rnb3n4qym70ca6nz2kvrsd3g587wrqdr79nnbwnrk"))))
13182 (build-system r-build-system)
13184 `(("r-boot" ,r-boot)
13186 ("r-deldir" ,r-deldir)
13188 ("r-gmodels" ,r-gmodels)
13189 ("r-learnbayes" ,r-learnbayes)
13191 ("r-matrix" ,r-matrix)
13195 ("r-spdata" ,r-spdata)))
13196 (home-page "https://github.com/r-spatial/spdep/")
13197 (synopsis "Spatial dependence: weighting schemes, statistics and models")
13199 "This package provides a collection of functions to create spatial
13200 weights matrix objects from polygon contiguities, from point patterns by
13201 distance and tessellations, for summarizing these objects, and for permitting
13202 their use in spatial data analysis, including regional aggregation by minimum
13204 (license license:gpl2+)))
13206 (define-public r-adegenet
13208 (name "r-adegenet")
13213 (uri (cran-uri "adegenet" version))
13216 "01fgrgbiddz2q4l3mx637hhwbs7r0c43yw7vpwl8p8pwbm3nykz0"))))
13217 (build-system r-build-system)
13219 `(("r-ade4" ,r-ade4)
13222 ("r-dplyr" ,r-dplyr)
13223 ("r-ggplot2" ,r-ggplot2)
13224 ("r-igraph" ,r-igraph)
13226 ("r-reshape2" ,r-reshape2)
13227 ("r-seqinr" ,r-seqinr)
13228 ("r-shiny" ,r-shiny)
13229 ("r-spdep" ,r-spdep)
13230 ("r-vegan" ,r-vegan)))
13231 (home-page "https://github.com/thibautjombart/adegenet")
13232 (synopsis "Exploratory analysis of genetic and genomic data")
13234 "This package provides a toolset for the exploration of genetic and
13235 genomic data. Adegenet provides formal (S4) classes for storing and handling
13236 various genetic data, including genetic markers with varying ploidy and
13237 hierarchical population structure (@code{genind} class), alleles counts by
13238 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
13239 also implements original multivariate methods (DAPC, sPCA), graphics,
13240 statistical tests, simulation tools, distance and similarity measures, and
13241 several spatial methods. A range of both empirical and simulated datasets is
13242 also provided to illustrate various methods.")
13243 (license license:gpl2+)))
13245 (define-public r-pegas
13252 (uri (cran-uri "pegas" version))
13254 (base32 "0sb8cmz4d238mcb56hv9fa0cagm00k82r7aj4cj4lxa1flxlpy8p"))))
13255 (build-system r-build-system)
13257 `(("r-adegenet" ,r-adegenet)
13259 (home-page "http://ape-package.ird.fr/pegas.html")
13260 (synopsis "Population and evolutionary genetics analysis system")
13262 "This package provides functions for reading, writing, plotting,
13263 analysing, and manipulating allelic and haplotypic data, including from VCF
13264 files, and for the analysis of population nucleotide sequences and
13265 micro-satellites including coalescent analyses, linkage disequilibrium,
13266 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
13267 minimum spanning tree and network, and median-joining networks.")
13268 (license license:gpl2+)))
13270 (define-public r-rmetasim
13272 (name "r-rmetasim")
13277 (uri (cran-uri "rmetasim" version))
13280 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
13281 (build-system r-build-system)
13283 `(("r-ade4" ,r-ade4)
13284 ("r-adegenet" ,r-adegenet)
13285 ("r-gtools" ,r-gtools)
13286 ("r-pegas" ,r-pegas)))
13287 (home-page "https://cran.r-project.org/web/packages/rmetasim")
13288 (synopsis "Individual-based population genetic simulation environment")
13290 "This package provides an interface between R and the metasim simulation
13291 engine. The simulation environment is documented in: Strand, A.(2002),
13292 Metasim 1.0: an individual-based environment for simulating population
13293 genetics of complex population dynamics.")
13295 (license license:gpl2+)))
13297 (define-public r-genetics
13299 (name "r-genetics")
13300 (version "1.3.8.1.2")
13304 (uri (cran-uri "genetics" version))
13307 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
13308 (build-system r-build-system)
13310 `(("r-combinat" ,r-combinat)
13311 ("r-gdata" ,r-gdata)
13312 ("r-gtools" ,r-gtools)
13314 ("r-mvtnorm" ,r-mvtnorm)))
13315 (home-page "https://cran.r-project.org/web/packages/genetics/")
13316 (synopsis "Population genetics")
13318 "This package provides classes and methods for handling genetic data.
13319 It includes classes to represent genotypes and haplotypes at single markers up
13320 to multiple markers on multiple chromosomes. Function include allele
13321 frequencies, flagging homo/heterozygotes, flagging carriers of certain
13322 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
13323 and testing for linkage disequilibrium, ...")
13324 ;; Any GPL version.
13325 (license license:gpl2+)))
13327 (define-public r-snp-plotter
13329 (name "r-snp-plotter")
13334 (uri (cran-uri "snp.plotter" version))
13337 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
13338 (properties `((upstream-name . "snp.plotter")))
13339 (build-system r-build-system)
13340 (propagated-inputs `(("r-genetics" ,r-genetics)))
13341 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
13342 (synopsis "Plot p-values using single SNP and/or haplotype data")
13344 "This package helps you create plots of p-values using single SNP and/or
13345 haplotype data. Main features of the package include options to display a
13346 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
13347 datasets simultaneously. Plots can be created using global and/or individual
13348 haplotype p-values along with single SNP p-values. Images are created as
13349 either PDF/EPS files.")
13350 (license license:gpl2+)))
13352 (define-public r-polspline
13354 (name "r-polspline")
13359 (uri (cran-uri "polspline" version))
13361 (base32 "0c7fnxpqpy3hibiim4yib6l6bq363s97wwvllxp4lp8h06fjcyyn"))))
13362 (build-system r-build-system)
13363 (native-inputs `(("gfortran" ,gfortran)))
13364 (home-page "https://cran.r-project.org/web/packages/polspline/")
13365 (synopsis "Polynomial spline routines")
13367 "This package provides routines for the polynomial spline fitting
13368 routines hazard regression, hazard estimation with flexible tails, logspline,
13369 lspec, polyclass, and polymars.")
13370 (license license:gpl2+)))
13372 (define-public r-rms
13379 (uri (cran-uri "rms" version))
13381 (base32 "19knh1sw0icw6jh9wfb2hq5jf49i2qfvp9myvqm5paa495689x9q"))))
13382 (build-system r-build-system)
13384 `(("r-ggplot2" ,r-ggplot2)
13385 ("r-hmisc" ,r-hmisc)
13386 ("r-htmltable" ,r-htmltable)
13387 ("r-htmltools" ,r-htmltools)
13388 ("r-lattice" ,r-lattice)
13389 ("r-multcomp" ,r-multcomp)
13391 ("r-polspline" ,r-polspline)
13392 ("r-quantreg" ,r-quantreg)
13393 ("r-rpart" ,r-rpart)
13394 ("r-sparsem" ,r-sparsem)
13395 ("r-survival" ,r-survival)))
13396 (native-inputs `(("gfortran" ,gfortran)))
13397 (home-page "http://biostat.mc.vanderbilt.edu/rms")
13398 (synopsis "Regression modeling strategies")
13400 "This is a package for regression modeling, testing, estimation,
13401 validation, graphics, prediction, and typesetting by storing enhanced model
13402 design attributes in the fit. The rms package is a collection of functions
13403 that assist with and streamline modeling. It also contains functions for
13404 binary and ordinal logistic regression models, ordinal models for continuous Y
13405 with a variety of distribution families, and the Buckley-James multiple
13406 regression model for right-censored responses, and implements penalized
13407 maximum likelihood estimation for logistic and ordinary linear models. The
13408 package works with almost any regression model, but it was especially written
13409 to work with binary or ordinal regression models, Cox regression, accelerated
13410 failure time models, ordinary linear models, the Buckley-James model,
13411 generalized least squares for serially or spatially correlated observations,
13412 generalized linear models, and quantile regression.")
13413 (license license:gpl2+)))
13415 (define-public r-haplo-stats
13417 (name "r-haplo-stats")
13422 (uri (cran-uri "haplo.stats" version))
13425 "19kxascqq5qz0zdxx0w837ji207y1z2ggxkl4vmlbay03k2dw2mx"))))
13426 (properties `((upstream-name . "haplo.stats")))
13427 (build-system r-build-system)
13429 `(("r-rms" ,r-rms)))
13431 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
13432 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
13433 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
13435 "This package provides routines for the analysis of indirectly measured
13436 haplotypes. The statistical methods assume that all subjects are unrelated
13437 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
13438 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
13439 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
13440 examples in the vignette.")
13441 (license license:gpl2+)))
13443 (define-public r-bqtl
13450 (uri (cran-uri "bqtl" version))
13453 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
13454 (build-system r-build-system)
13455 (native-inputs `(("gfortran" ,gfortran)))
13456 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
13457 (synopsis "Bayesian QTL mapping toolkit")
13459 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
13460 lines. It includes maximum likelihood and Bayesian tools.")
13461 (license license:gpl2+)))
13463 (define-public r-ibdreg
13470 (uri (cran-uri "ibdreg" version))
13473 "1kaa5q1byi30wzr0mw4w2cv1ssxprzcwf91wrpqwkgcsdy7dkh2g"))))
13474 (build-system r-build-system)
13475 (home-page "https://www.mayo.edu/research/labs/\
13476 statistical-genetics-genetic-epidemiology/software")
13477 (synopsis "Regression methods for IBD linkage with covariates")
13479 "This package provides a method to test genetic linkage with covariates
13480 by regression methods with response IBD sharing for relative pairs. Account
13481 for correlations of IBD statistics and covariates for relative pairs within
13482 the same pedigree.")
13483 (license license:gpl2+)))
13485 (define-public r-dlmap
13492 (uri (cran-uri "dlmap" version))
13495 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
13496 (build-system r-build-system)
13498 `(("r-ibdreg" ,r-ibdreg)
13502 ("r-wgaim" ,r-wgaim)))
13503 (home-page "https://cran.r-project.org/web/packages/dlmap/")
13504 (synopsis "Detection localization mapping for QTL")
13506 "This is package for QTL mapping in a mixed model framework with separate
13507 detection and localization stages. The first stage detects the number of QTL
13508 on each chromosome based on the genetic variation due to grouped markers on
13509 the chromosome; the second stage uses this information to determine the most
13510 likely QTL positions. The mixed model can accommodate general fixed and
13511 random effects, including spatial effects in field trials and pedigree
13512 effects. It is applicable to backcrosses, doubled haploids, recombinant
13513 inbred lines, F2 intercrosses, and association mapping populations.")
13514 (license license:gpl2)))
13516 (define-public r-ldheatmap
13518 (name "r-ldheatmap")
13523 (uri (cran-uri "LDheatmap" version))
13526 "1r0j8bihi5z1x0sgaf7dwzpsw9i0nc1vylvipvc0cia2ka1lr9dc"))))
13527 (properties `((upstream-name . "LDheatmap")))
13528 (build-system r-build-system)
13530 `(("r-genetics" ,r-genetics)
13532 ("r-snpstats" ,r-snpstats)))
13533 (home-page "http://stat.sfu.ca/statgen/research/ldheatmap.html")
13534 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
13536 "This package provides tools to produce a graphical display, as a heat
13537 map, of measures of pairwise linkage disequilibria between SNPs. Users may
13538 optionally include the physical locations or genetic map distances of each SNP
13540 (license license:gpl3)))
13542 (define-public r-hwde
13549 (uri (cran-uri "hwde" version))
13552 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
13553 (build-system r-build-system)
13554 (home-page "https://cran.r-project.org/web/packages/hwde/")
13555 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
13557 "This package fits models for genotypic disequilibria, as described in
13558 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
13559 terms are available that account for first order interactions between loci.
13560 It also implements, for a single locus in a single population, a conditional
13561 exact test for Hardy-Weinberg equilibrium.")
13562 (license license:gpl2+)))
13564 (define-public r-tdthap
13571 (uri (cran-uri "tdthap" version))
13574 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
13575 (build-system r-build-system)
13576 (home-page "https://cran.r-project.org/web/packages/tdthap/")
13577 (synopsis "TDT tests for extended haplotypes")
13579 "Functions and examples are provided for transmission/disequilibrium
13580 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
13581 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
13582 (license license:artistic2.0)))
13584 (define-public r-sparql
13590 (uri (cran-uri "SPARQL" version))
13593 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
13594 (properties `((upstream-name . "SPARQL")))
13595 (build-system r-build-system)
13597 `(("r-rcurl" ,r-rcurl)
13599 (home-page "https://cran.r-project.org/web/packages/SPARQL")
13600 (synopsis "SPARQL client for R")
13601 (description "This package provides an interface to use SPARQL to pose
13602 SELECT or UPDATE queries to an end-point.")
13603 ;; The only license indication is found in the DESCRIPTION file,
13604 ;; which states GPL-3. So we cannot assume GPLv3+.
13605 (license license:gpl3)))
13607 (define-public r-bookdown
13609 (name "r-bookdown")
13613 (uri (cran-uri "bookdown" version))
13616 "1my6g16phx21v5cvfqcnjibh3zcv02xkix347aafd6a7r3hnxpq5"))))
13617 (build-system r-build-system)
13619 `(("r-htmltools" ,r-htmltools)
13620 ("r-knitr" ,r-knitr)
13621 ("r-rmarkdown" ,r-rmarkdown)
13622 ("r-tinytex" ,r-tinytex)
13624 ("pandoc" ,ghc-pandoc)))
13625 (home-page "https://github.com/rstudio/bookdown")
13626 (synopsis "Authoring books and technical documents with R markdown")
13627 (description "This package provides output formats and utilities for
13628 authoring books and technical documents with R Markdown.")
13629 (license license:gpl3)))
13631 (define-public r-optparse
13633 (name "r-optparse")
13638 (uri (cran-uri "optparse" version))
13641 "0wyrc42ja3ab5szx46zmz8lm7vzfqxkjca0m0sms8g9hqbmmay6d"))))
13642 (build-system r-build-system)
13644 `(("r-getopt" ,r-getopt)))
13645 (home-page "https://github.com/trevorld/optparse")
13646 (synopsis "Command line option parser")
13648 "This package provides a command line parser inspired by Python's
13649 @code{optparse} library to be used with Rscript to write shebang scripts
13650 that accept short and long options.")
13651 (license license:gpl2+)))
13653 (define-public r-wgcna
13660 (uri (cran-uri "WGCNA" version))
13663 "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f"))))
13664 (properties `((upstream-name . "WGCNA")))
13665 (build-system r-build-system)
13667 `(("r-annotationdbi" ,r-annotationdbi)
13668 ("r-doparallel" ,r-doparallel)
13669 ("r-dynamictreecut" ,r-dynamictreecut)
13670 ("r-fastcluster" ,r-fastcluster)
13671 ("r-foreach" ,r-foreach)
13672 ("r-go-db" ,r-go-db)
13673 ("r-hmisc" ,r-hmisc)
13674 ("r-impute" ,r-impute)
13676 ("r-survival" ,r-survival)
13677 ("r-matrixstats" ,r-matrixstats)
13678 ("r-preprocesscore" ,r-preprocesscore)))
13680 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
13681 (synopsis "Weighted correlation network analysis")
13683 "This package provides functions necessary to perform Weighted
13684 Correlation Network Analysis on high-dimensional data. It includes functions
13685 for rudimentary data cleaning, construction and summarization of correlation
13686 networks, module identification and functions for relating both variables and
13687 modules to sample traits. It also includes a number of utility functions for
13688 data manipulation and visualization.")
13689 (license license:gpl2+)))
13691 (define-public r-kernlab
13698 (uri (cran-uri "kernlab" version))
13700 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
13701 (build-system r-build-system)
13702 (home-page "https://cran.r-project.org/web/packages/kernlab")
13703 (synopsis "Kernel-based machine learning tools")
13705 "This package provides kernel-based machine learning methods for
13706 classification, regression, clustering, novelty detection, quantile regression
13707 and dimensionality reduction. Among other methods @code{kernlab} includes
13708 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
13710 (license license:gpl2)))
13712 (define-public r-hierfstat
13714 (name "r-hierfstat")
13715 (version "0.04-22")
13719 (uri (cran-uri "hierfstat" version))
13722 "1fav2v2996v5kb1ffa6v5wxfm921syxg6as034vd3j4jfhdibyfx"))))
13723 (build-system r-build-system)
13725 `(("r-ade4" ,r-ade4)
13726 ("r-adegenet" ,r-adegenet)
13727 ("r-gtools" ,r-gtools)))
13728 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
13729 (synopsis "Estimation and tests of hierarchical F-statistics")
13731 "This package allows the estimation of hierarchical F-statistics from
13732 haploid or diploid genetic data with any numbers of levels in the hierarchy,
13733 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
13734 are also given to test via randomisations the significance of each F and
13735 variance components, using the likelihood-ratio statistics G.")
13736 (license license:gpl2+)))
13738 (define-public r-hapassoc
13740 (name "r-hapassoc")
13745 (uri (cran-uri "hapassoc" version))
13748 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
13749 (build-system r-build-system)
13750 (home-page "http://stat.sfu.ca/statgen/research/hapassoc.html")
13751 (synopsis "Inference of trait associations with SNP haplotypes")
13753 "Hapassoc performs likelihood inference of trait associations with
13754 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
13755 functions are developed primarily for data collected in cohort or
13756 cross-sectional studies. They can accommodate uncertain haplotype phase and
13757 handle missing genotypes at some SNPs.")
13758 (license license:gpl2)))
13760 (define-public r-sampling
13762 (name "r-sampling")
13767 (uri (cran-uri "sampling" version))
13770 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
13771 (build-system r-build-system)
13773 `(("r-lpsolve" ,r-lpsolve)
13774 ("r-mass" ,r-mass)))
13775 (home-page "https://cran.r-project.org/web/packages/sampling/")
13776 (synopsis "Survey sampling")
13778 "This package provides functions for drawing and calibrating samples.")
13779 (license license:gpl2+)))
13781 (define-public r-r2html
13788 (uri (cran-uri "R2HTML" version))
13791 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
13792 (properties `((upstream-name . "R2HTML")))
13793 (build-system r-build-system)
13794 (home-page "https://github.com/nalimilan/R2HTML")
13795 (synopsis "HTML export for R objects")
13797 "This package includes HTML functions and methods to write in an HTML
13798 file. Thus, making HTML reports is easy. It includes a function that allows
13799 redirection on the fly, which appears to be very useful for teaching purposes,
13800 as the student can keep a copy of the produced output to keep all that they
13801 did during the course. The package comes with a vignette describing how to
13802 write HTML reports for statistical analysis. Finally, a driver for Sweave
13803 allows to parse HTML flat files containing R code and to automatically write
13804 the corresponding outputs (tables and graphs).")
13805 (license license:gpl2+)))
13807 (define-public r-rjava
13814 (uri (cran-uri "rJava" version))
13817 "0s9cjy1wh7snmbqwznh8f1r4ipylr7mgda4a979z963a8lqy32n2"))))
13818 (properties `((upstream-name . "rJava")))
13819 (build-system r-build-system)
13821 `(#:modules ((guix build utils)
13822 (guix build r-build-system)
13825 (modify-phases %standard-phases
13826 (add-after 'unpack 'set-JAVA_HOME
13827 (lambda* (#:key inputs #:allow-other-keys)
13828 (let ((jdk (assoc-ref inputs "jdk")))
13829 (setenv "JAVA_HOME" jdk)
13830 (setenv "JAVA" (which "java"))
13831 (setenv "JAR" (which "jar"))
13832 (setenv "JAVAC" (which "javac"))
13833 (setenv "JAVAH" (which "javah"))
13834 (setenv "JAVA_CPPFLAGS"
13835 (string-append "-I" jdk "/include "
13836 "-I" jdk "/include/linux"))
13837 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
13838 ((lib) (setenv "JAVA_LIBS" lib))
13839 (_ (error "Could not find libjvm.so"))))
13843 ("jdk" ,icedtea-8 "jdk")
13846 (home-page "http://www.rforge.net/rJava/")
13847 (synopsis "Low-Level R to Java interface")
13849 "This package provides a low-level interface to the Java VM very much
13850 like .C/.Call and friends. It allows the creation of objects, calling methods
13851 and accessing fields.")
13852 (license license:gpl2)))
13854 (define-public r-svmisc
13861 (uri (cran-uri "svMisc" version))
13864 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
13865 (properties `((upstream-name . "svMisc")))
13866 (build-system r-build-system)
13867 (home-page "https://github.com/SciViews/svMisc")
13868 (synopsis "Miscellaneous functions for SciViews")
13870 "This package provides miscellaneous functions for SciViews or general
13871 use, including tools to manage a temporary environment attached to the search
13872 path for temporary variables you do not want to @code{save()} or
13873 @code{load()}; test the current platform; showing progress bars, etc.")
13874 (license license:gpl2)))
13876 (define-public r-xyz
13883 (uri (cran-uri "xyz" version))
13886 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
13887 (build-system r-build-system)
13889 `(("r-rcpp" ,r-rcpp)))
13890 (home-page "https://cran.r-project.org/web/packages/xyz/")
13891 (synopsis "Algorithm for fast interaction search in high-dimensional data")
13893 "High dimensional interaction search by brute force requires a quadratic
13894 computational cost in the number of variables. The xyz algorithm provably
13895 finds strong interactions in almost linear time. For details of the algorithm
13896 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
13897 interaction search in high-dimensional data.")
13898 ;; Any version of the GPL.
13899 (license license:gpl2+)))
13901 (define-public r-rttf2pt1
13903 (name "r-rttf2pt1")
13908 (uri (cran-uri "Rttf2pt1" version))
13911 "0b3f2zkmbyshn19cnaaf042d0zwf43l9jnkqizfhxxwb93a4c1jn"))))
13912 (properties `((upstream-name . "Rttf2pt1")))
13913 (build-system r-build-system)
13914 (home-page "https://github.com/wch/Rttf2pt1")
13915 (synopsis "Font conversion utility")
13917 "This package contains the program @code{ttf2pt1}, for use with the
13918 @code{extrafont} package.")
13919 ;; Most of the files are covered under the Expat license. Some files are
13920 ;; covered under BSD-3. Deviations for individual files are recorded in
13921 ;; the LICENSE file.
13922 (license (list license:bsd-3 license:expat
13923 (license:non-copyleft "file://LICENSE")))))
13925 (define-public r-extrafontdb
13927 (name "r-extrafontdb")
13932 (uri (cran-uri "extrafontdb" version))
13935 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
13936 (build-system r-build-system)
13937 (home-page "https://github.com/wch/extrafontdb")
13938 (synopsis "Database for the extrafont package")
13940 "This package holds the database for the @code{extrafont} package.")
13941 (license license:gpl2)))
13943 (define-public r-extrafont
13945 (name "r-extrafont")
13950 (uri (cran-uri "extrafont" version))
13953 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
13954 (build-system r-build-system)
13956 `(("r-extrafontdb" ,r-extrafontdb)
13957 ("r-rttf2pt1" ,r-rttf2pt1)))
13958 (home-page "https://github.com/wch/extrafont")
13959 (synopsis "Tools for using fonts in R")
13961 "The extrafont package makes it easier to use fonts other than the basic
13962 PostScript fonts that R uses. Fonts that are imported into extrafont can be
13963 used with PDF or PostScript output files. There are two hurdles for using
13964 fonts in PDF (or Postscript) output files:
13967 @item Making R aware of the font and the dimensions of the characters.
13968 @item Embedding the fonts in the PDF file so that the PDF can be displayed
13969 properly on a device that doesn't have the font. This is usually needed if
13970 you want to print the PDF file or share it with others.
13973 The extrafont package makes both of these things easier.")
13974 (license license:gpl2)))
13976 (define-public r-xkcd
13983 (uri (cran-uri "xkcd" version))
13986 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
13987 (build-system r-build-system)
13989 `(("r-extrafont" ,r-extrafont)
13990 ("r-ggplot2" ,r-ggplot2)
13991 ("r-hmisc" ,r-hmisc)))
13992 (home-page "https://cran.r-project.org/web/packages/xkcd/")
13993 (synopsis "Plot ggplot2 graphics in the XKCD style")
13995 "This package provides the means to plot ggplot2 graphs in the style of
13996 the XKCD web comic.")
13997 (license license:gpl3)))
13999 (define-public r-msigdbr
14006 (uri (cran-uri "msigdbr" version))
14009 "19p8z617m3my8la7n1qgb1s2msf940r372im3q30qkbcx3qxg3sd"))))
14010 (build-system r-build-system)
14012 `(("r-dplyr" ,r-dplyr)
14013 ("r-magrittr" ,r-magrittr)
14014 ("r-rlang" ,r-rlang)
14015 ("r-tibble" ,r-tibble)))
14016 (home-page "https://github.com/igordot/msigdbr")
14017 (synopsis "MSigDB gene sets for multiple organisms")
14019 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
14020 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
14021 software in a standard R data frame with key-value pairs. Included are the
14022 original human gene symbols and Entrez IDs as well as the equivalents for
14023 various frequently studied model organisms such as mouse, rat, pig, fly, and
14025 ;; The package is covered under the Expat license, but the upstream MSigDB
14026 ;; files are made available under the Creative Commons Attribution 4.0
14027 ;; International license.
14028 (license (list license:expat license:cc-by4.0))))
14030 (define-public r-gridgraphics
14032 (name "r-gridgraphics")
14037 (uri (cran-uri "gridGraphics" version))
14040 "0rlyc3xk8kfrfzbfd8n4javq3yxqd7lsfmi4q5n6s61srnrl6c1r"))))
14041 (properties `((upstream-name . "gridGraphics")))
14042 (build-system r-build-system)
14043 (home-page "https://github.com/pmur002/gridgraphics")
14044 (synopsis "Redraw base graphics using @code{grid} graphics")
14046 "This package provides functions to convert a page of plots drawn with
14047 the @code{graphics} package into identical output drawn with the @code{grid}
14048 package. The result looks like the original @code{graphics}-based plot, but
14049 consists of @code{grid} grobs and viewports that can then be manipulated with
14050 @code{grid} functions (e.g., edit grobs and revisit viewports).")
14051 (license license:gpl2+)))
14053 (define-public r-farver
14060 (uri (cran-uri "farver" version))
14063 "1k75v07dsfkjra2gsgxg9s55cw3b46b1nh960kqphq7cg7gr058f"))))
14064 (build-system r-build-system)
14065 (home-page "https://github.com/thomasp85/farver")
14066 (synopsis "Vectorized color conversion and comparison")
14068 "The encoding of color can be handled in many different ways, using
14069 different color spaces. As different color spaces have different uses,
14070 efficient conversion between these representations are important. This
14071 package provides a set of functions that gives access to very fast color space
14072 conversion and comparisons implemented in C++, and offers 100-fold speed
14073 improvements over the @code{convertColor} function in the @code{grDevices}
14075 (license license:expat)))
14077 (define-public r-ggplotify
14079 (name "r-ggplotify")
14084 (uri (cran-uri "ggplotify" version))
14087 "0nv3wdmxnc5ww9m3xlgnb0jp30j45dg33nqc6gg3y36svg8anjcg"))))
14088 (build-system r-build-system)
14090 `(("r-ggplot2" ,r-ggplot2)
14091 ("r-gridgraphics" ,r-gridgraphics)
14092 ("r-rvcheck" ,r-rvcheck)))
14093 (home-page "https://github.com/GuangchuangYu/ggplotify")
14094 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
14096 "This package provides tools to convert plot function calls (using
14097 expression or formula) to @code{grob} or @code{ggplot} objects that are
14098 compatible with the @code{grid} and @code{ggplot2} environment. With this
14099 package, we are able to e.g. use @code{cowplot} to align plots produced by
14100 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
14101 converting them to @code{ggplot} objects.")
14102 (license license:artistic2.0)))
14104 (define-public r-triebeard
14106 (name "r-triebeard")
14111 (uri (cran-uri "triebeard" version))
14114 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
14115 (build-system r-build-system)
14116 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
14117 (home-page "https://github.com/Ironholds/triebeard/")
14118 (synopsis "Radix trees in Rcpp")
14120 "Radix trees, or tries, are key-value data structures optimized for
14121 efficient lookups, similar in purpose to hash tables. This package provides
14122 an implementation of radix trees for use in R programming and in developing
14123 packages with Rcpp.")
14124 (license license:expat)))
14126 (define-public r-tweenr
14133 (uri (cran-uri "tweenr" version))
14136 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
14137 (build-system r-build-system)
14139 `(("r-farver" ,r-farver)
14140 ("r-magrittr" ,r-magrittr)
14142 ("r-rlang" ,r-rlang)))
14143 (home-page "https://github.com/thomasp85/tweenr")
14144 (synopsis "Interpolate data for smooth animations")
14146 "In order to create smooth animation between states of data, tweening is
14147 necessary. This package provides a range of functions for creating tweened
14148 data that can be used as basis for animation. Furthermore it adds a number of
14149 vectorized interpolaters for common R data types such as numeric, date and
14151 (license license:expat)))
14153 (define-public r-polyclip
14155 (name "r-polyclip")
14160 (uri (cran-uri "polyclip" version))
14163 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
14164 (build-system r-build-system)
14165 (native-inputs `(("pkg-config" ,pkg-config)))
14166 (home-page "http://www.angusj.com/delphi/clipper.php")
14167 (synopsis "Polygon clipping")
14169 "This package provides an R port of the library Clipper. It performs
14170 polygon clipping operations (intersection, union, set minus, set difference)
14171 for polygonal regions of arbitrary complexity, including holes. It computes
14172 offset polygons (spatial buffer zones, morphological dilations, Minkowski
14173 dilations) for polygonal regions and polygonal lines. It computes the
14174 Minkowski Sum of general polygons. There is a function for removing
14175 self-intersections from polygon data.")
14176 (license license:boost1.0)))
14178 (define-public r-urltools
14180 (name "r-urltools")
14185 (uri (cran-uri "urltools" version))
14188 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
14189 (build-system r-build-system)
14191 `(("r-rcpp" ,r-rcpp)
14192 ("r-triebeard" ,r-triebeard)))
14193 (home-page "https://github.com/Ironholds/urltools/")
14194 (synopsis "Vectorized tools for URL handling and parsing")
14196 "This package provides a toolkit for all URL-handling needs, including
14197 encoding and decoding, parsing, parameter extraction and modification. All
14198 functions are designed to be both fast and entirely vectorized. It is
14199 intended to be useful for people dealing with web-related datasets, such as
14200 server-side logs, although may be useful for other situations involving large
14202 (license license:expat)))
14204 (define-public r-ggforce
14211 (uri (cran-uri "ggforce" version))
14214 "04926cqrda6psvy2nzkkw4czwyxdp7fnxg76byp14v12kgd72lm0"))))
14215 (build-system r-build-system)
14217 `(("r-ggplot2" ,r-ggplot2)
14218 ("r-gtable" ,r-gtable)
14220 ("r-polyclip" ,r-polyclip)
14222 ("r-rcppeigen" ,r-rcppeigen)
14223 ("r-rlang" ,r-rlang)
14224 ("r-scales" ,r-scales)
14225 ("r-tidyselect" ,r-tidyselect)
14226 ("r-tweenr" ,r-tweenr)
14227 ("r-withr" ,r-withr)))
14228 (home-page "https://ggforce.data-imaginist.com")
14229 (synopsis "Accelerating ggplot2")
14231 "The aim of the ggplot2 package is to aid in visual data investigations.
14232 This focus has led to a lack of facilities for composing specialized plots.
14233 Thi package aims to be a collection of mainly new statistics and geometries
14234 that fills this gap.")
14235 (license license:expat)))
14237 (define-public r-europepmc
14239 (name "r-europepmc")
14244 (uri (cran-uri "europepmc" version))
14247 "1ngqs1sqzkbwv98dd5z4cxj8bnz41wyd0g060a2vpqi3s99s4i2h"))))
14248 (build-system r-build-system)
14250 `(("r-dplyr" ,r-dplyr)
14252 ("r-jsonlite" ,r-jsonlite)
14254 ("r-progress" ,r-progress)
14255 ("r-purrr" ,r-purrr)
14256 ("r-urltools" ,r-urltools)
14257 ("r-xml2" ,r-xml2)))
14258 (home-page "https://github.com/ropensci/europepmc/")
14259 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
14261 "This package provides an R Client for the
14262 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
14263 Service}. It gives access to both metadata on life science literature and
14264 open access full texts. Europe PMC indexes all PubMed content and other
14265 literature sources including Agricola, a bibliographic database of citations
14266 to the agricultural literature, or Biological Patents. In addition to
14267 bibliographic metadata, the client allows users to fetch citations and
14268 reference lists. Links between life-science literature and other EBI
14269 databases, including ENA, PDB or ChEMBL are also accessible.")
14270 (license license:gpl3)))
14272 (define-public r-ggraph
14279 (uri (cran-uri "ggraph" version))
14282 "0q2yqsb981a2arf9j530kqs61vw38ixyxbhb6yvv7skgbck02r6y"))))
14283 (build-system r-build-system)
14285 `(("r-digest" ,r-digest)
14286 ("r-dplyr" ,r-dplyr)
14287 ("r-ggforce" ,r-ggforce)
14288 ("r-ggplot2" ,r-ggplot2)
14289 ("r-ggrepel" ,r-ggrepel)
14290 ("r-graphlayouts" ,r-graphlayouts)
14291 ("r-gtable" ,r-gtable)
14292 ("r-igraph" ,r-igraph)
14295 ("r-rlang" ,r-rlang)
14296 ("r-scales" ,r-scales)
14297 ("r-tidygraph" ,r-tidygraph)
14298 ("r-viridis" ,r-viridis)))
14299 (home-page "https://cran.r-project.org/web/packages/ggraph/")
14300 (synopsis "Implementation of grammar of graphics for graphs and networks")
14302 "The grammar of graphics as implemented in ggplot2 is a poor fit for
14303 graph and network visualizations due to its reliance on tabular data input.
14304 The ggraph package is an extension of the ggplot2 API tailored to graph
14305 visualizations and provides the same flexible approach to building up plots
14307 (license license:gpl3)))
14309 (define-public r-varselrf
14311 (name "r-varselrf")
14316 (uri (cran-uri "varSelRF" version))
14319 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
14320 (properties `((upstream-name . "varSelRF")))
14321 (build-system r-build-system)
14323 `(("r-randomforest" ,r-randomforest)))
14324 (home-page "http://ligarto.org/rdiaz/Software/Software.html")
14325 (synopsis "Variable selection using random forests")
14327 "This package provides tools for the variable selection from random
14328 forests using both backwards variable elimination (for the selection of small
14329 sets of non-redundant variables) and selection based on the importance
14330 spectrum (somewhat similar to scree plots; for the selection of large,
14331 potentially highly-correlated variables). The main applications are in
14332 high-dimensional data (e.g., microarray data, and other genomics and
14333 proteomics applications).")
14334 (license license:gpl2+)))
14336 (define-public r-pamr
14343 (uri (cran-uri "pamr" version))
14346 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
14347 (build-system r-build-system)
14349 `(("r-cluster" ,r-cluster)
14350 ("r-survival" ,r-survival)))
14351 (native-inputs `(("gfortran" ,gfortran)))
14352 (home-page "https://cran.r-project.org/web/packages/pamr/")
14353 (synopsis "Prediction Analysis for Microarrays")
14355 "This package provides some functions for sample classification in
14357 (license license:gpl2)))
14359 (define-public r-rda
14362 (version "1.0.2-2.1")
14366 (uri (cran-uri "rda" version))
14369 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
14370 (build-system r-build-system)
14371 (home-page "https://cran.r-project.org/web/packages/rda/")
14372 (synopsis "Shrunken centroids regularized discriminant analysis")
14374 "This package provides tools for shrunken centroids regularized
14375 discriminant analysis for the purpose of classifying high dimensional data.")
14376 (license license:gpl2+)))
14378 (define-public r-ggvis
14385 (uri (cran-uri "ggvis" version))
14388 "091i9f17912j8qcyxppjgwzjnyqj7769ixs9d2gjg6f2clskqdw2"))))
14389 (build-system r-build-system)
14391 `(("r-assertthat" ,r-assertthat)
14392 ("r-dplyr" ,r-dplyr)
14393 ("r-htmltools" ,r-htmltools)
14394 ("r-jsonlite" ,r-jsonlite)
14395 ("r-lazyeval" ,r-lazyeval)
14396 ("r-magrittr" ,r-magrittr)
14397 ("r-shiny" ,r-shiny)))
14398 (home-page "https://ggvis.rstudio.com/")
14399 (synopsis "Interactive grammar of graphics")
14401 "This package is a data visualization package for R providing an
14402 implementation of an interactive grammar of graphics, taking the best parts of
14403 ggplot2, combining them with the reactive framework of Shiny and drawing web
14404 graphics using Vega.")
14405 (license license:gpl2)))
14407 (define-public r-gbm
14414 (uri (cran-uri "gbm" version))
14417 "0vs6ljaqhwwpgr8wlbhmm4v147rd82kl16rpaijqiylxcc8dxyq6"))))
14418 (build-system r-build-system)
14420 `(("r-gridextra" ,r-gridextra)
14421 ("r-lattice" ,r-lattice)
14422 ("r-survival" ,r-survival)))
14423 (home-page "https://github.com/gbm-developers/gbm")
14424 (synopsis "Generalized boosted regression models")
14426 "This package is an implementation of extensions to Freund and Schapire's
14427 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
14428 regression methods for least squares, absolute loss, t-distribution loss,
14429 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
14430 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
14431 and Learning to Rank measures (LambdaMart).")
14432 (license license:gpl2+)))
14434 (define-public r-threejs
14441 (uri (cran-uri "threejs" version))
14444 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
14445 (build-system r-build-system)
14447 `(#:modules ((guix build utils)
14448 (guix build r-build-system)
14452 (modify-phases %standard-phases
14453 (add-after 'unpack 'process-javascript
14454 (lambda* (#:key inputs #:allow-other-keys)
14455 (with-directory-excursion "inst"
14459 `((,(assoc-ref inputs "js-jquery")
14460 "htmlwidgets/lib/jquery/jquery.min.js")
14461 (,(assoc-ref inputs "js-threejs-111")
14462 "htmlwidgets/lib/threejs-111/three.min.js"))))
14463 (lambda (sources targets)
14464 (for-each (lambda (source target)
14465 (format #t "Processing ~a --> ~a~%"
14467 (delete-file target)
14468 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14469 (call-with-output-file target
14471 (dump-port minified port)))))
14472 sources targets))))
14475 `(("r-base64enc" ,r-base64enc)
14476 ("r-crosstalk" ,r-crosstalk)
14477 ("r-htmlwidgets" ,r-htmlwidgets)
14478 ("r-igraph" ,r-igraph)))
14480 `(("uglify-js" ,uglify-js)
14484 (uri "https://code.jquery.com/jquery-1.12.4.js")
14487 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
14491 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
14494 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
14495 (home-page "https://bwlewis.github.io/rthreejs")
14496 (synopsis "Interactive 3D scatter plots, networks and globes")
14498 "Create interactive 3D scatter plots, network plots, and globes in R
14499 using the three.js visualization library.")
14500 (license license:expat)))
14502 (define-public r-mlbench
14509 (uri (cran-uri "mlbench" version))
14512 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
14513 (build-system r-build-system)
14514 (home-page "https://cran.r-project.org/web/packages/mlbench/")
14515 (synopsis "Machine learning benchmark problems")
14517 "This package provides a collection of artificial and real-world machine
14518 learning benchmark problems, including, e.g., several data sets from the UCI
14520 (license license:gpl2)))
14522 (define-public r-mpm
14529 (uri (cran-uri "mpm" version))
14532 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
14533 (build-system r-build-system)
14535 `(("r-kernsmooth" ,r-kernsmooth)
14536 ("r-mass" ,r-mass)))
14537 (home-page "http://mpm.r-forge.r-project.org")
14538 (synopsis "Multivariate projection methods")
14540 "This is a package for exploratory graphical analysis of multivariate
14541 data, specifically gene expression data with different projection methods:
14542 principal component analysis, correspondence analysis, spectral map
14544 (license license:gpl2+)))
14546 (define-public r-png
14552 (uri (cran-uri "png" version))
14555 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
14556 (build-system r-build-system)
14558 `(("libpng" ,libpng)
14560 (home-page "https://www.rforge.net/png/")
14561 (synopsis "Read and write PNG images")
14563 "This package provides an easy and simple way to read, write and display
14564 bitmap images stored in the PNG format. It can read and write both files and
14565 in-memory raw vectors.")
14566 ;; Any of these GPL versions.
14567 (license (list license:gpl2 license:gpl3))))
14569 (define-public r-ggcorrplot
14571 (name "r-ggcorrplot")
14576 (uri (cran-uri "ggcorrplot" version))
14579 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
14580 (build-system r-build-system)
14582 `(("r-ggplot2" ,r-ggplot2)
14583 ("r-reshape2" ,r-reshape2)))
14584 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
14585 (synopsis "Visualization of a correlation matrix using ggplot2")
14587 "The ggcorrplot package can be used to visualize easily a correlation
14588 matrix using ggplot2. It provides a solution for reordering the correlation
14589 matrix and displays the significance level on the plot. It also includes a
14590 function for computing a matrix of correlation p-values.")
14591 (license license:gpl2)))
14593 (define-public r-flexdashboard
14595 (name "r-flexdashboard")
14596 (version "0.5.1.1")
14600 (uri (cran-uri "flexdashboard" version))
14603 "0fy3nbrr67zqgd44r2mc850s5sp0hzfcw3zqs15m8kxzj1aw067x"))))
14604 (build-system r-build-system)
14606 `(#:modules ((guix build utils)
14607 (guix build r-build-system)
14611 (ice-9 textual-ports))
14613 (modify-phases %standard-phases
14614 (add-after 'unpack 'process-javascript
14615 (lambda* (#:key inputs #:allow-other-keys)
14616 (with-directory-excursion "inst"
14617 ;; Concatenate all components of prism.js
14618 (let ((contents (string-join
14619 (map (lambda (name)
14620 (call-with-input-file
14621 (assoc-ref inputs name)
14625 "js-prism-line-numbers"))
14627 (call-with-output-file "prism-src.js"
14628 (cut display contents <>)))
14632 `(("www/stickytableheaders/jquery.stickytableheaders.js"
14633 "www/stickytableheaders/jquery.stickytableheaders.min.js")
14635 "www/sly/sly.min.js")
14637 "www/prism/prism.js")
14638 (,(assoc-ref inputs "js-raphael")
14639 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
14640 (,(assoc-ref inputs "js-featherlight")
14641 "www/featherlight/featherlight.min.js"))))
14642 (lambda (sources targets)
14643 (for-each (lambda (source target)
14644 (format #t "Processing ~a --> ~a~%"
14646 (delete-file target)
14647 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14648 (call-with-output-file target
14650 (dump-port minified port)))))
14651 sources targets))))
14654 `(("r-htmltools" ,r-htmltools)
14655 ("r-htmlwidgets" ,r-htmlwidgets)
14656 ("r-jsonlite" ,r-jsonlite)
14657 ("r-knitr" ,r-knitr)
14658 ("r-rmarkdown" ,r-rmarkdown)
14659 ("r-shiny" ,r-shiny)))
14661 `(("uglify-js" ,uglify-js)
14665 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
14668 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
14672 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
14675 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
14679 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
14682 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
14683 ("js-prism-line-numbers"
14686 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
14689 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
14693 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
14696 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
14697 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
14698 (synopsis "R Markdown format for flexible dashboards")
14700 "This package provides an R Markdown format for converting an R Markdown
14701 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
14702 of its components to the containing web page.")
14703 (license license:expat)))
14705 (define-public r-preseqr
14712 (uri (cran-uri "preseqR" version))
14715 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
14716 (properties `((upstream-name . "preseqR")))
14717 (build-system r-build-system)
14719 `(("r-polynom" ,r-polynom)))
14720 (home-page "https://cran.r-project.org/web/packages/preseqR/")
14721 (synopsis "Predicting species accumulation curves")
14723 "This package can be used to predict the r-species accumulation
14724 curve (r-SAC), which is the number of species represented at least r times as
14725 a function of the sampling effort. When r = 1, the curve is known as the
14726 species accumulation curve, or the library complexity curve in high-throughput
14727 genomic sequencing. The package includes both parametric and nonparametric
14728 methods, as described by Deng C, et al. (2018).")
14729 (license license:gpl3)))
14731 (define-public r-mapplots
14733 (name "r-mapplots")
14738 (uri (cran-uri "mapplots" version))
14741 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
14742 (build-system r-build-system)
14743 (home-page "https://cran.r-project.org/web/packages/mapplots/")
14744 (synopsis "Data visualization on maps")
14746 "This package helps you create simple maps; add sub-plots like pie plots
14747 to a map or any other plot; format, plot and export gridded data. The package
14748 was developed for displaying fisheries data but most functions can be used for
14749 more generic data visualisation.")
14750 (license license:gpl2+)))
14752 (define-public r-pmcmr
14759 (uri (cran-uri "PMCMR" version))
14762 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
14763 (properties `((upstream-name . "PMCMR")))
14764 (build-system r-build-system)
14765 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
14766 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
14768 "This is a deprecated package for calculating pairwise multiple
14769 comparisons of mean rank sums. This package is superseded by the novel
14770 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
14771 compatibility of dependent packages for some time.")
14772 (license license:gpl3+)))
14774 (define-public r-downloader
14776 (name "r-downloader")
14781 (uri (cran-uri "downloader" version))
14784 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
14785 (build-system r-build-system)
14787 `(("r-digest" ,r-digest)))
14788 (home-page "https://github.com/wch/downloader")
14789 (synopsis "Download files over HTTP and HTTPS")
14791 "This package provides a wrapper for the @code{download.file} function,
14792 making it possible to download files over HTTPS across platforms. The
14793 @code{RCurl} package provides this functionality (and much more) but has
14794 external dependencies. This package has is implemented purely in R.")
14795 (license license:gpl2)))
14797 (define-public r-rex
14804 (uri (cran-uri "rex" version))
14807 "0alsadgjgass3wr8y5d247j12qqzg454sc84vpskclrkmz778g5x"))))
14808 (build-system r-build-system)
14810 `(("r-lazyeval" ,r-lazyeval)
14811 ("r-magrittr" ,r-magrittr)))
14812 (home-page "https://github.com/kevinushey/rex")
14813 (synopsis "Friendly regular expressions")
14815 "This package provides a friendly interface for the construction of
14816 regular expressions. Regular expressions are a very powerful feature, however
14817 they are often difficult to interpret. Rex allows you to build complex
14818 regular expressions from human readable expressions")
14819 (license license:expat)))
14821 (define-public r-xmlparsedata
14823 (name "r-xmlparsedata")
14828 (uri (cran-uri "xmlparsedata" version))
14831 "0gjr3l5z5dp276lchr2649as1rkj56d2mlvbr66yg393zzw50lsh"))))
14832 (properties `((upstream-name . "xmlparsedata")))
14833 (build-system r-build-system)
14834 (home-page "https://github.com/r-lib/xmlparsedata#readme")
14835 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
14837 "This package provides tools to convert the output of
14838 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
14839 @code{XPath}, and is easier to manipulate in general.")
14840 (license license:expat)))
14842 (define-public r-cyclocomp
14844 (name "r-cyclocomp")
14849 (uri (cran-uri "cyclocomp" version))
14852 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
14853 (properties `((upstream-name . "cyclocomp")))
14854 (build-system r-build-system)
14856 `(("r-callr" ,r-callr)
14857 ("r-crayon" ,r-crayon)
14859 ("r-remotes" ,r-remotes)
14860 ("r-withr" ,r-withr)))
14861 (home-page "https://github.com/MangoTheCat/cyclocomp")
14862 (synopsis "Cyclomatic complexity of R code")
14864 "Cyclomatic complexity is a software metric, used to indicate the
14865 complexity of a program. It is a quantitative measure of the number of
14866 linearly independent paths through a program's source code. This package
14867 provides tools to compute this metric.")
14868 (license license:expat)))
14870 (define-public r-lintr
14877 (uri (cran-uri "lintr" version))
14880 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
14881 (properties `((upstream-name . "lintr")))
14882 (build-system r-build-system)
14884 `(("r-codetools" ,r-codetools)
14885 ("r-crayon" ,r-crayon)
14886 ("r-cyclocomp" ,r-cyclocomp)
14887 ("r-digest" ,r-digest)
14889 ("r-jsonlite" ,r-jsonlite)
14890 ("r-knitr" ,r-knitr)
14892 ("r-rstudioapi" ,r-rstudioapi)
14893 ("r-testthat" ,r-testthat)
14895 ("r-xmlparsedata" ,r-xmlparsedata)))
14896 (home-page "https://github.com/jimhester/lintr")
14897 (synopsis "Linter for R code")
14898 (description "This package checks adherence to a given style, syntax
14899 errors and possible semantic issues. It supports on the fly checking of R
14900 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
14901 (license license:expat)))
14903 (define-public r-sctransform
14905 (name "r-sctransform")
14910 (uri (cran-uri "sctransform" version))
14913 "07v3lzccsrkh1glfxd1q20r8f8gl9ls5az0s1dvxm4vcls0hlhyn"))))
14914 (build-system r-build-system)
14916 `(("r-future-apply" ,r-future-apply)
14917 ("r-ggplot2" ,r-ggplot2)
14918 ("r-gridextra" ,r-gridextra)
14920 ("r-matrix" ,r-matrix)
14922 ("r-rcppeigen" ,r-rcppeigen)
14923 ("r-reshape2" ,r-reshape2)))
14924 (home-page "https://github.com/ChristophH/sctransform")
14925 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
14927 "This package provides a normalization method for single-cell UMI count
14928 data using a variance stabilizing transformation. The transformation is based
14929 on a negative binomial regression model with regularized parameters. As part
14930 of the same regression framework, this package also provides functions for
14931 batch correction, and data correction.")
14932 (license license:gpl3)))
14934 (define-public r-styler
14941 (uri (cran-uri "styler" version))
14944 "1waglhsy2c53qjgd2qhlzda3z0lbzbwx9fkrfhac41y6h91mgkrz"))))
14945 (build-system r-build-system)
14947 `(("r-backports" ,r-backports)
14949 ("r-magrittr" ,r-magrittr)
14950 ("r-purrr" ,r-purrr)
14951 ("r-r-cache" ,r-r-cache)
14952 ("r-rematch2" ,r-rematch2)
14953 ("r-rlang" ,r-rlang)
14954 ("r-rprojroot" ,r-rprojroot)
14955 ("r-tibble" ,r-tibble)
14956 ("r-withr" ,r-withr)
14957 ("r-xfun" ,r-xfun)))
14958 (home-page "https://github.com/r-lib/styler")
14959 (synopsis "Non-invasive pretty printing of R code")
14961 "This is a package for pretty-printing R code without changing the user's
14962 formatting intent.")
14963 (license license:gpl3)))
14965 (define-public r-scrime
14972 (uri (cran-uri "scrime" version))
14975 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
14976 (build-system r-build-system)
14977 (home-page "https://cran.r-project.org/web/packages/scrime/")
14978 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
14980 "This package provides tools for the analysis of high-dimensional data
14981 developed/implemented at the group \"Statistical Complexity Reduction In
14982 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
14983 the functions can also be applied to other types of categorical data.")
14984 (license license:gpl2)))
14986 (define-public r-pbmcapply
14988 (name "r-pbmcapply")
14993 (uri (cran-uri "pbmcapply" version))
14996 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
14997 (build-system r-build-system)
14998 (home-page "https://github.com/kvnkuang/pbmcapply")
14999 (synopsis "Track the progress of apply procedures with a progress bar")
15001 "This light-weight package helps you track and visualize the progress of
15002 parallel versions of vectorized R functions of the @code{mc*apply} family.")
15003 (license license:expat)))
15005 (define-public r-blme
15012 (uri (cran-uri "blme" version))
15015 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
15016 (build-system r-build-system)
15017 (propagated-inputs `(("r-lme4" ,r-lme4)))
15018 (home-page "https://github.com/vdorie/blme")
15019 (synopsis "Bayesian linear mixed-effects models")
15021 "This package provides tools for maximum a posteriori estimation for
15022 linear and generalized linear mixed-effects models in a Bayesian setting. It
15023 extends the lme4 package.")
15024 (license license:gpl2+)))
15026 (define-public r-batchtools
15028 (name "r-batchtools")
15033 (uri (cran-uri "batchtools" version))
15036 "16x524hvy9d8p7r4fi1c8mixcvzgsjbf3y0vxaa56ssbbab4p7f9"))))
15037 (build-system r-build-system)
15039 `(("r-backports" ,r-backports)
15040 ("r-base64url" ,r-base64url)
15042 ("r-checkmate" ,r-checkmate)
15043 ("r-data-table" ,r-data-table)
15044 ("r-digest" ,r-digest)
15046 ("r-progress" ,r-progress)
15048 ("r-rappdirs" ,r-rappdirs)
15049 ("r-stringi" ,r-stringi)
15050 ("r-withr" ,r-withr)))
15051 (home-page "https://github.com/mllg/batchtools")
15052 (synopsis "Tools for computation on batch systems")
15054 "As a successor of the packages BatchJobs and BatchExperiments, this
15055 package provides a parallel implementation of the Map function for high
15056 performance computing systems managed by various schedulers. A multicore and
15057 socket mode allow the parallelization on a local machines, and multiple
15058 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
15059 the package provides an abstraction mechanism to define large-scale computer
15060 experiments in a well-organized and reproducible way.")
15061 (license license:lgpl3)))
15063 (define-public r-clue
15070 (uri (cran-uri "clue" version))
15073 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
15074 (build-system r-build-system)
15075 (propagated-inputs `(("r-cluster" ,r-cluster)))
15076 (home-page "https://cran.r-project.org/web/packages/clue/")
15077 (synopsis "Tools for analyzing cluster ensembles")
15078 (description "Cluster ensembles are collections of individual solutions to
15079 a given clustering problem which are useful or necessary to consider in a wide
15080 range of applications. This R package provides an extensible computational
15081 environment for creating and analyzing cluster ensembles, with basic data
15082 structures for representing partitions and hierarchies, and facilities for
15083 computing on them, including methods for measuring proximity and obtaining
15084 consensus and secondary clusterings.")
15085 (license license:gpl2)))
15087 (define-public r-sitmo
15094 (uri (cran-uri "sitmo" version))
15097 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
15098 (build-system r-build-system)
15099 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
15100 (home-page "https://github.com/coatless/sitmo/")
15101 (synopsis "Parallel pseudo random number generator header files")
15103 "This package provides two high quality and fast PPRNGs that may be used
15104 in an OpenMP parallel environment. In addition, there is a generator for one
15105 dimensional low-discrepancy sequence.")
15106 (license license:expat)))
15108 (define-public r-dqrng
15115 (uri (cran-uri "dqrng" version))
15118 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
15119 (build-system r-build-system)
15123 ("r-sitmo" ,r-sitmo)))
15124 (home-page "https://www.daqana.org/dqrng")
15125 (synopsis "Fast pseudo random number generators")
15127 "Several fast random number generators are provided as C++ header-only
15128 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
15129 Additionally, fast functions for generating random numbers according to a
15130 uniform, normal and exponential distribution are included. The latter two use
15131 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
15132 functions are exported to R and as a C++ interface and are enabled for use
15133 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
15134 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
15135 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
15136 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
15137 ;; whole is distributed under the terms of the AGPL 3.
15138 (license license:agpl3)))
15140 (define-public r-dalex
15147 (uri (cran-uri "DALEX" version))
15150 "1jbyn57vn6d281a5y15h5d8ljin8cdb9lr7lbgggc950blyfv4g0"))))
15151 (properties `((upstream-name . "DALEX")))
15152 (build-system r-build-system)
15153 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
15154 (home-page "https://pbiecek.github.io/DALEX/")
15155 (synopsis "Descriptive machine learning explanations")
15157 "Machine Learning models are widely used and have various applications in
15158 classification or regression. Models created with boosting, bagging, stacking
15159 or similar techniques are often used due to their high performance, but such
15160 black-box models usually lack interpretability. The DALEX package contains
15161 various explainers that help to understand the link between input variables
15162 and model output.")
15163 ;; Any version of the GPL
15164 (license license:gpl3+)))
15166 (define-public r-enrichr
15173 (uri (cran-uri "enrichR" version))
15176 "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
15177 (properties `((upstream-name . "enrichR")))
15178 (build-system r-build-system)
15180 `(("r-httr" ,r-httr)
15181 ("r-rjson" ,r-rjson)))
15182 (home-page "https://cran.r-project.org/web/packages/enrichR/")
15183 (synopsis "R Interface to Enrichr database for analyzing gene sets")
15185 "This package provides an R interface to all Enrichr databases, a
15186 web-based tool for analyzing gene sets and returns any enrichment of common
15187 annotated biological functions.")
15188 (license license:gpl2+)))
15190 (define-public r-plot3d
15197 (uri (cran-uri "plot3D" version))
15200 "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
15201 (properties `((upstream-name . "plot3D")))
15202 (build-system r-build-system)
15203 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
15204 (home-page "https://cran.r-project.org/web/packages/plot3D")
15205 (synopsis "Plot multi-dimensional data")
15207 "This package provides functions for viewing 2D and 3D data, including
15208 perspective plots, slice plots, surface plots, scatter plots, etc. It
15209 includes data sets from oceanography.")
15210 (license license:gpl3+)))
15212 (define-public r-ggfortify
15214 (name "r-ggfortify")
15219 (uri (cran-uri "ggfortify" version))
15222 "191q2z7w0l4v7swjlxs2hjgbjngw2838688s7ygnj0kigsm310f3"))))
15223 (build-system r-build-system)
15225 `(("r-dplyr" ,r-dplyr)
15226 ("r-ggplot2" ,r-ggplot2)
15227 ("r-gridextra" ,r-gridextra)
15228 ("r-scales" ,r-scales)
15229 ("r-stringr" ,r-stringr)
15230 ("r-tibble" ,r-tibble)
15231 ("r-tidyr" ,r-tidyr)))
15232 (home-page "https://github.com/sinhrks/ggfortify")
15233 (synopsis "Data visualization tools for statistical analysis results")
15235 "This package provides unified plotting tools for statistics commonly
15236 used, such as GLM, time series, PCA families, clustering and survival
15237 analysis. The package offers a single plotting interface for these analysis
15238 results and plots in a unified style using the @code{ggplot2} package.")
15239 (license license:gpl2)))
15241 (define-public r-refmanager
15243 (name "r-refmanager")
15248 (uri (cran-uri "RefManageR" version))
15251 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
15252 (properties `((upstream-name . "RefManageR")))
15253 (build-system r-build-system)
15255 `(("r-bibtex" ,r-bibtex)
15257 ("r-jsonlite" ,r-jsonlite)
15258 ("r-lubridate" ,r-lubridate)
15260 ("r-stringr" ,r-stringr)
15261 ("r-xml2" ,r-xml2)))
15262 (home-page "https://github.com/ropensci/RefManageR/")
15263 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
15265 "This package provides tools for importing and working with bibliographic
15266 references. It greatly enhances the @code{bibentry} class by providing a
15267 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
15268 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
15269 by various formats for name lists (author by last names, translator by full
15270 names, etc.). Entries can be updated, combined, sorted, printed in a number
15271 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
15272 into R and converted to @code{BibEntry} objects.")
15273 ;; Any of these licenses may be picked.
15274 (license (list license:gpl2 license:gpl3 license:bsd-3))))
15276 (define-public r-citr
15283 (uri (cran-uri "citr" version))
15286 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
15287 (build-system r-build-system)
15289 `(("r-assertthat" ,r-assertthat)
15292 ("r-miniui" ,r-miniui)
15293 ("r-refmanager" ,r-refmanager)
15294 ("r-rstudioapi" ,r-rstudioapi)
15295 ("r-shiny" ,r-shiny)
15296 ("r-shinyjs" ,r-shinyjs)
15297 ("r-yaml" ,r-yaml)))
15298 (home-page "https://github.com/crsh/citr")
15299 (synopsis "RStudio add-in to insert Markdown citations")
15301 "This package provides functions and an RStudio add-in that search a
15302 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
15303 the current document.")
15304 (license license:expat)))
15306 (define-public r-xgboost
15309 (version "0.90.0.2")
15313 (uri (cran-uri "xgboost" version))
15316 "1gy9rzg43mjpfis893vf15drmbigfn0481zrzss9ajnmnk0q8194"))))
15317 (build-system r-build-system)
15319 `(("r-data-table" ,r-data-table)
15320 ("r-magrittr" ,r-magrittr)
15321 ("r-matrix" ,r-matrix)
15322 ("r-stringi" ,r-stringi)))
15323 (home-page "https://github.com/dmlc/xgboost")
15324 (synopsis "Extreme gradient boosting")
15326 "This package provides an R interface to Extreme Gradient Boosting, which
15327 is an efficient implementation of the gradient boosting framework from Chen
15328 and Guestrin (2016). The package includes efficient linear model solver and
15329 tree learning algorithms. The package can automatically do parallel
15330 computation on a single machine. It supports various objective functions,
15331 including regression, classification and ranking. The package is made to be
15332 extensible, so that users are also allowed to define their own objectives
15334 (license license:asl2.0)))
15336 (define-public r-umap
15339 (version "0.2.4.1")
15343 (uri (cran-uri "umap" version))
15346 "1pnh3hv8ihiz2nszqp797lkrdhhna2a6mzpizbsk0s9m8cj4wxva"))))
15347 (build-system r-build-system)
15349 `(("r-openssl" ,r-openssl)
15351 ("r-reticulate" ,r-reticulate)
15352 ("r-rspectra" ,r-rspectra)))
15353 (home-page "https://github.com/tkonopka/umap")
15354 (synopsis "Uniform manifold approximation and projection")
15356 "Uniform manifold approximation and projection is a technique for
15357 dimension reduction. This package provides an interface to the UMAP algorithm
15358 in R, including a translation of the original algorithm into R.")
15359 (license license:expat)))
15361 (define-public r-uwot
15368 (uri (cran-uri "uwot" version))
15371 "0pz9wa89xq4d119q86lskrznf979m0r1db8iaprcz7kxbi6b8lrj"))))
15372 (build-system r-build-system)
15374 `(("r-dqrng" ,r-dqrng)
15376 ("r-irlba" ,r-irlba)
15377 ("r-matrix" ,r-matrix)
15379 ("r-rcppannoy" ,r-rcppannoy)
15380 ("r-rcppparallel" ,r-rcppparallel)
15381 ("r-rcppprogress" ,r-rcppprogress)
15382 ("r-rspectra" ,r-rspectra)))
15383 (home-page "https://github.com/jlmelville/uwot")
15384 (synopsis "Uniform manifold approximation and projection")
15386 "This package provides an implementation of the Uniform Manifold
15387 Approximation and Projection dimensionality reduction by McInnes et
15388 al. (2018). It also provides means to transform new data and to carry out
15389 supervised dimensionality reduction. An implementation of the related
15390 LargeVis method of Tang et al. (2016) is also provided.")
15391 (license license:gpl3)))
15393 (define-public r-kableextra
15395 (name "r-kableextra")
15400 (uri (cran-uri "kableExtra" version))
15403 "1nicvw06xsf3a1f5c10mih07b76m2v5s5h165vmz0qx6n1a3492i"))))
15404 (properties `((upstream-name . "kableExtra")))
15405 (build-system r-build-system)
15407 `(("r-digest" ,r-digest)
15409 ("r-htmltools" ,r-htmltools)
15410 ("r-knitr" ,r-knitr)
15411 ("r-magrittr" ,r-magrittr)
15412 ("r-readr" ,r-readr)
15413 ("r-rmarkdown" ,r-rmarkdown)
15414 ("r-rstudioapi" ,r-rstudioapi)
15415 ("r-rvest" ,r-rvest)
15416 ("r-scales" ,r-scales)
15417 ("r-stringr" ,r-stringr)
15418 ("r-viridislite" ,r-viridislite)
15419 ("r-webshot" ,r-webshot)
15420 ("r-xml2" ,r-xml2)))
15421 (home-page "https://haozhu233.github.io/kableExtra/")
15422 (synopsis "Construct complex tables with pipe syntax")
15424 "Build complex HTML or LaTeX tables using @code{kable()} from
15425 @code{knitr} and the piping syntax from @code{magrittr}. The function
15426 @code{kable()} is a light weight table generator coming from @code{knitr}.
15427 This package simplifies the way to manipulate the HTML or LaTeX codes
15428 generated by @code{kable()} and allows users to construct complex tables and
15429 customize styles using a readable syntax.")
15430 (license license:expat)))
15432 (define-public r-glasso
15439 (uri (cran-uri "glasso" version))
15441 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
15442 (build-system r-build-system)
15443 (native-inputs `(("gfortran" ,gfortran)))
15444 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
15445 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
15447 "This is a package for estimation of a sparse inverse covariance matrix
15448 using a lasso (L1) penalty. Facilities are provided for estimates along a
15449 path of values for the regularization parameter.")
15450 (license license:gpl2)))
15452 (define-public r-rhpcblasctl
15454 (name "r-rhpcblasctl")
15455 (version "0.20-17")
15459 (uri (cran-uri "RhpcBLASctl" version))
15462 "0iwc06blr5sx7rylwczi2jrha8sk8qs0jklflwpidl0zj1jxdggp"))))
15463 (properties `((upstream-name . "RhpcBLASctl")))
15464 (build-system r-build-system)
15465 (home-page "http://prs.ism.ac.jp/~nakama/Rhpc/")
15466 (synopsis "Control the number of threads on BLAS")
15468 "This package allows you to control the number of threads the BLAS
15469 library uses. It is also possible to control the number of threads in
15471 (license license:agpl3+)))
15473 (define-public r-lda
15480 (uri (cran-uri "lda" version))
15483 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
15484 (build-system r-build-system)
15485 (home-page "https://cran.r-project.org/web/packages/lda/")
15486 (synopsis "Collapsed Gibbs sampling methods for topic models")
15488 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
15489 related models. This includes (but is not limited to) sLDA, corrLDA, and the
15490 mixed-membership stochastic blockmodel. Inference for all of these models is
15491 implemented via a fast collapsed Gibbs sampler written in C. Utility
15492 functions for reading/writing data typically used in topic models, as well as
15493 tools for examining posterior distributions are also included.")
15494 ;; Any version of the LGPL
15495 (license license:lgpl3+)))
15497 (define-public r-rann-l1
15504 (uri (cran-uri "RANN.L1" version))
15507 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
15508 (properties `((upstream-name . "RANN.L1")))
15509 (build-system r-build-system)
15510 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
15511 (synopsis "Fast nearest neighbour search using L1 metric")
15513 "This package provides tools to find the k nearest neighbours for every
15514 point in a given dataset in O(N log N) time using Arya and Mount's ANN
15515 library. There is support for approximate as well as exact searches, fixed
15516 radius searches and @code{bd} as well as @code{kd} trees. The distance is
15517 computed using the L1 (Manhattan, taxicab) metric.")
15518 (license license:gpl3+)))
15520 (define-public r-leiden
15527 (uri (cran-uri "leiden" version))
15530 "1hh6bmbz6cpqwl4i94gxylgv9x92zbqdg81r8r4ymfy8c70f3df2"))))
15531 (properties `((upstream-name . "leiden")))
15532 (build-system r-build-system)
15534 `(("r-igraph" ,r-igraph)
15535 ("r-matrix" ,r-matrix)
15536 ("r-reticulate" ,r-reticulate)))
15537 (home-page "https://github.com/TomKellyGenetics/leiden")
15538 (synopsis "R implementation of Leiden clustering algorithm")
15540 "This package implements the Python @code{leidenalg} module to be called
15541 in R. It enables clustering using the Leiden algorithm for partitioning a
15542 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
15543 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
15544 (license license:gpl3)))
15546 (define-public r-patchwork
15547 ;; There has been no public release yet.
15548 (let ((commit "fd7958bae3e7a1e30237c751952e412a0a1d1242")
15551 (name "r-patchwork")
15552 (version (git-version "0.0.1" revision commit))
15556 (uri (git-reference
15557 (url "https://github.com/thomasp85/patchwork.git")
15559 (file-name (git-file-name name version))
15562 "00fq520xwy1ysg4k8x48x9b0yy9wyi8y8zj6dvxjg4bwx0yyp6s4"))))
15563 (build-system r-build-system)
15565 `(("r-ggplot2" ,r-ggplot2)
15566 ("r-gtable" ,r-gtable)))
15567 (home-page "https://github.com/thomasp85/patchwork")
15568 (synopsis "Compose ggplot2 plots")
15570 "The @code{ggplot2} package provides a strong API for sequentially
15571 building up a plot, but does not concern itself with composition of multiple
15572 plots. Patchwork is a package that expands the API to allow for arbitrarily
15573 complex composition of plots by providing mathmatical operators for combining
15575 (license license:expat))))
15577 (define-public r-liger
15584 (uri (git-reference
15585 (url "https://github.com/MacoskoLab/liger.git")
15586 (commit (string-append "v" version))))
15587 (file-name (git-file-name name version))
15590 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
15591 (modules '((guix build utils)))
15594 (delete-file "inst/java/ModularityOptimizer.jar")
15596 (build-system r-build-system)
15599 (modify-phases %standard-phases
15600 (add-after 'unpack 'build-java-part
15601 (lambda* (#:key inputs #:allow-other-keys)
15602 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
15603 (for-each (lambda (file) (invoke "javac" file))
15604 (find-files "." "\\.java$"))
15605 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
15606 (find-files "." "\\.class$"))
15609 `(("r-cowplot" ,r-cowplot)
15610 ("r-dosnow" ,r-dosnow)
15611 ("r-dplyr" ,r-dplyr)
15613 ("r-foreach" ,r-foreach)
15614 ("r-ggplot2" ,r-ggplot2)
15615 ("r-ggrepel" ,r-ggrepel)
15616 ("r-hmisc" ,r-hmisc)
15618 ("r-irlba" ,r-irlba)
15619 ("r-matrix" ,r-matrix)
15620 ("r-mclust" ,r-mclust)
15621 ("r-patchwork" ,r-patchwork)
15623 ("r-rann-l1" ,r-rann-l1)
15625 ("r-rcpparmadillo" ,r-rcpparmadillo)
15626 ("r-riverplot" ,r-riverplot)
15627 ("r-rtsne" ,r-rtsne)
15628 ("r-snow" ,r-snow)))
15630 `(("jdk" ,icedtea "jdk")
15631 ;; See https://github.com/MacoskoLab/liger/issues/96
15632 ;; The optimizer is released under the Expat license.
15636 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
15639 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
15641 ("r-knitr" ,r-knitr))) ; for vignettes
15642 (home-page "https://github.com/MacoskoLab/liger")
15643 (synopsis "Integrate and analyze multiple single-cell datasets")
15645 "LIGER is a package for integrating and analyzing multiple single-cell
15646 datasets, developed and maintained by the Macosko lab. It relies on
15647 integrative non-negative matrix factorization to identify shared and
15648 dataset-specific factors.")
15649 (license license:gpl3)))
15651 (define-public r-harmony
15652 ;; There are no tagged commits
15653 (let ((commit "4d1653870d4dd70fff1807c182882db1fbf9af5a")
15657 (version (git-version "1.0" revision commit))
15661 (uri (git-reference
15662 (url "https://github.com/immunogenomics/harmony")
15664 (file-name (git-file-name name version))
15667 "1gasdldr4aalr9h2q9kmm3y4i7azkgnhdn4bmvsszs7lg9xacw85"))))
15668 (build-system r-build-system)
15670 `(("r-cowplot" ,r-cowplot)
15671 ("r-dplyr" ,r-dplyr)
15672 ("r-ggplot2" ,r-ggplot2)
15673 ("r-irlba" ,r-irlba)
15674 ("r-matrix" ,r-matrix)
15676 ("r-rcpparmadillo" ,r-rcpparmadillo)
15677 ("r-rcppprogress" ,r-rcppprogress)
15678 ("r-rlang" ,r-rlang)
15679 ("r-tibble" ,r-tibble)
15680 ("r-tidyr" ,r-tidyr)))
15681 (home-page "https://github.com/immunogenomics/harmony")
15682 (synopsis "Integration of single cell sequencing data")
15684 "This package provides an implementation of the Harmony algorithm for
15685 single cell integration, described in Korsunsky et al
15686 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
15687 function and interfaces to external frameworks.")
15688 (license license:gpl3))))
15690 (define-public r-covr
15697 (uri (cran-uri "covr" version))
15699 (base32 "1pvr95h7jg9hqq1qq1cccy323pkxldrwafl08151cc410499k4fb"))))
15700 (properties `((upstream-name . "covr")))
15701 (build-system r-build-system)
15703 `(("r-crayon" ,r-crayon)
15704 ("r-digest" ,r-digest)
15706 ("r-jsonlite" ,r-jsonlite)
15708 ("r-withr" ,r-withr)
15709 ("r-yaml" ,r-yaml)))
15711 `(("r-knitr" ,r-knitr))) ; for vignettes
15712 (home-page "https://github.com/r-lib/covr")
15713 (synopsis "Test coverage for R packages")
15715 "Thisp package enables you to track and report code coverage for your
15716 package and (optionally) upload the results to a coverage service. Code
15717 coverage is a measure of the amount of code being exercised by a set of tests.
15718 It is an indirect measure of test quality and completeness. This package is
15719 compatible with any testing methodology or framework and tracks coverage of
15720 both R code and compiled C/C++/FORTRAN code.")
15721 (license license:gpl3)))
15723 (define-public r-systemfonts
15725 (name "r-systemfonts")
15730 (uri (cran-uri "systemfonts" version))
15733 "0m0ljid683xcam2f14x7k2zv1yx4npac38a3gfv11vhxfbnpgp0z"))))
15734 (properties `((upstream-name . "systemfonts")))
15735 (build-system r-build-system)
15737 `(("fontconfig" ,fontconfig)
15738 ("freetype" ,freetype)
15741 `(("pkg-config" ,pkg-config)))
15742 (home-page "https://github.com/r-lib/systemfonts")
15743 (synopsis "System native font finding")
15745 "This package provides system native access to the font catalogue. As
15746 font handling varies between systems it is difficult to correctly locate
15747 installed fonts across different operating systems. The 'systemfonts' package
15748 provides bindings to the native libraries for finding font files that can then
15749 be used further by e.g. graphic devices.")
15750 (license license:expat)))
15752 (define-public r-graphlayouts
15754 (name "r-graphlayouts")
15759 (uri (cran-uri "graphlayouts" version))
15762 "03dizbhhdhnzbj2i5zvqgs617kwcv4h2pha4f16adic0fph1rxl3"))))
15763 (properties `((upstream-name . "graphlayouts")))
15764 (build-system r-build-system)
15766 `(("r-igraph" ,r-igraph)
15768 ("r-rcpparmadillo" ,r-rcpparmadillo)))
15769 (home-page "https://github.com/schochastics/graphlayouts")
15770 (synopsis "Additional layout algorithms for network visualizations")
15772 "This package provides several layout algorithms to visualize networks
15773 which are not part of the igraph library. Most are based on the concept of
15774 stress majorization by Gansner et al. (2004)
15775 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms allow to
15776 emphasize hidden group structures in networks or focus on specific nodes.")
15777 (license license:expat)))
15779 (define-public r-tidygraph
15781 (name "r-tidygraph")
15786 (uri (cran-uri "tidygraph" version))
15789 "1zpsarm74afbc7p5dlyb0whc09670qdcddw1ckb25cfc9hfh0hjn"))))
15790 (properties `((upstream-name . "tidygraph")))
15791 (build-system r-build-system)
15793 `(("r-dplyr" ,r-dplyr)
15794 ("r-igraph" ,r-igraph)
15795 ("r-magrittr" ,r-magrittr)
15796 ("r-pillar" ,r-pillar)
15799 ("r-rlang" ,r-rlang)
15800 ("r-tibble" ,r-tibble)
15801 ("r-tidyr" ,r-tidyr)))
15802 (home-page "https://github.com/thomasp85/tidygraph")
15803 (synopsis "Tidy API for graph manipulation")
15805 "This package provides a graph implementation that can be thought of as
15806 two tidy data frames describing node and edge data respectively. It provides
15807 an approach to manipulate these two virtual data frames using the API defined
15808 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
15809 common graph algorithms.")
15810 (license license:expat)))
15812 (define-public r-soupx
15813 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
15817 (version (git-version "0.3.1" revision commit))
15821 (uri (git-reference
15822 (url "https://github.com/constantAmateur/SoupX")
15824 (file-name (git-file-name name version))
15827 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
15828 (properties `((upstream-name . "SoupX")))
15829 (build-system r-build-system)
15831 `(("r-ggplot2" ,r-ggplot2)
15832 ("r-matrix" ,r-matrix)
15833 ("r-seurat" ,r-seurat)))
15834 (home-page "https://github.com/constantAmateur/SoupX")
15835 (synopsis "Single cell mRNA Soup eXterminator")
15837 "This package provides a package for quantifying, profiling and
15838 removing cell free mRNA contamination (the \"soup\") from droplet based single
15839 cell RNA-seq experiments.")
15840 (license license:gpl2))))
15842 (define-public r-assertr
15849 (uri (cran-uri "assertr" version))
15852 "1x868pd4dac1c7b1q5390wqh2f6s50km8nqcpim3nxcj2l4qkqdb"))))
15853 (build-system r-build-system)
15855 `(("r-dplyr" ,r-dplyr)
15857 ("r-rlang" ,r-rlang)))
15859 `(("r-knitr" ,r-knitr))) ; needed for vignette
15860 (home-page "https://github.com/ropensci/assertr")
15861 (synopsis "Assertive programming for R analysis pipelines")
15863 "This package provides functionality to assert conditions that have to be
15864 met so that errors in data used in analysis pipelines can fail quickly. It is
15865 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
15867 (license license:expat)))
15869 (define-public r-parameters
15871 (name "r-parameters")
15876 (uri (cran-uri "parameters" version))
15879 "19cblrq079svp5j3wgikw5fsdbsp1w0f2llm7kcf1rg5w1aagjr7"))))
15880 (properties `((upstream-name . "parameters")))
15881 (build-system r-build-system)
15883 `(("r-bayestestr" ,r-bayestestr)
15884 ("r-insight" ,r-insight)))
15885 (home-page "https://cran.r-project.org/web/packages/parameters")
15886 (synopsis "Processing of model parameters")
15888 "This package provides utilities for processing the parameters of various
15889 statistical models. Beyond computing p values, CIs, and other indices for a
15890 wide variety of models, this package implements features like standardization
15891 or bootstrapping of parameters and models, feature reduction (feature
15892 extraction and variable selection) as well as conversion between indices of
15894 (license license:gpl3)))
15896 (define-public r-rgdal
15903 (uri (cran-uri "rgdal" version))
15905 (base32 "1jd691amf3ghznq5im15gvhl6v6k25klpl75m4ngrqf9xlxaa3as"))))
15906 (properties `((upstream-name . "rgdal")))
15907 (build-system r-build-system)
15915 `(("pkg-config" ,pkg-config)))
15916 (home-page "http://rgdal.r-forge.r-project.org")
15917 (synopsis "Bindings for the Geospatial Data Abstraction Library")
15919 "This package provides bindings to the Geospatial Data Abstraction
15920 Library (GDAL) and access to projection/transformation operations from the
15922 (license license:gpl2+)))
15924 (define-public r-insol
15931 (uri (cran-uri "insol" version))
15934 "1d2vqmbp94ff80mfkmq4a8y12r6ryym8hh1568ip9qbn7snc64v1"))))
15935 (properties `((upstream-name . "insol")))
15936 (build-system r-build-system)
15938 `(("r-raster" ,r-raster)))
15940 `(("gfortran" ,gfortran)))
15941 (home-page "https://meteoexploration.com/R/insol/index.html")
15942 (synopsis "Tools for calculating solar radiation")
15944 "This package provides functions to compute insolation on tilted
15945 surfaces, computes atmospheric transmittance and related parameters such as:
15946 Earth radius vector, declination, sunset and sunrise, daylength, equation of
15947 time, vector in the direction of the sun, vector normal to surface, and some
15948 atmospheric physics.")
15949 (license license:gpl2+)))
15951 (define-public r-lifecycle
15953 (name "r-lifecycle")
15958 (uri (cran-uri "lifecycle" version))
15961 "0912865c6675fsblrfdk6s568krsj1x8qbk1kipy7m05xs6nwx19"))))
15962 (properties `((upstream-name . "lifecycle")))
15963 (build-system r-build-system)
15965 `(("r-glue" ,r-glue)
15966 ("r-rlang" ,r-rlang)))
15968 `(("r-knitr" ,r-knitr))) ; for vignettes
15969 (home-page "https://github.com/r-lib/lifecycle")
15970 (synopsis "Manage the life cycle of your package functions")
15972 "Manage the life cycle of your exported functions with shared
15973 conventions, documentation badges, and non-invasive deprecation warnings. The
15974 lifecycle package defines four development stages (experimental, maturing,
15975 stable, and questioning) and three deprecation stages (soft-deprecated,
15976 deprecated, and defunct). It makes it easy to insert badges corresponding to
15977 these stages in your documentation. Usage of deprecated functions are
15978 signalled with increasing levels of non-invasive verbosity.")
15979 (license license:gpl3)))
15981 (define-public r-assertable
15983 (name "r-assertable")
15988 (uri (cran-uri "assertable" version))
15991 "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
15992 (build-system r-build-system)
15994 `(("r-data-table" ,r-data-table)))
15995 (home-page "https://cran.r-project.org/web/packages/assertable/")
15996 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
15997 (description "This package provides simple, flexible assertions on
15998 data.frame or data.table objects with verbose output for vetting. While other
15999 assertion packages apply towards more general use-cases, @code{assertable} is
16000 tailored towards tabular data. It includes functions to check variable names
16001 and values, whether the dataset contains all combinations of a given set of
16002 unique identifiers, and whether it is a certain length. In addition,
16003 @code{assertable} includes utility functions to check the existence of target
16004 files and to efficiently import multiple tabular data files into one
16006 (license license:gpl3)))
16008 (define-public r-quadprog
16010 (name "r-quadprog")
16015 (uri (cran-uri "quadprog" version))
16017 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
16018 (build-system r-build-system)
16020 `(("gfortran" ,gfortran)))
16021 (home-page "https://cran.r-project.org/web/packages/quadprog")
16022 (synopsis "Functions to solve quadratic programming problems")
16024 "This package contains routines and documentation for solving quadratic
16025 programming problems.")
16026 (license license:gpl3+)))
16028 (define-public r-desolve
16035 (uri (cran-uri "deSolve" version))
16037 (base32 "05sax045qrk550gsn2i7krb9rbg51rx88x4v190acsigqknxffrv"))))
16038 (properties `((upstream-name . "deSolve")))
16039 (build-system r-build-system)
16041 `(("gfortran" ,gfortran)))
16042 (home-page "https://desolve.r-forge.r-project.org/")
16043 (synopsis "Solvers for initial value problems of differential equations")
16044 (description "This package provides functions that solve initial value
16045 problems of a system of first-order @dfn{ordinary differential
16046 equations} (ODE), of @dfn{partial differential equations} (PDE), of
16047 @dfn{differential algebraic equations} (DAE), and of delay differential
16048 equations. The functions provide an interface to the FORTRAN functions
16049 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
16050 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
16051 C-implementation of solvers of the Runge-Kutta family with fixed or variable
16052 time steps. The package contains routines designed for solving ODEs resulting
16053 from 1-D, 2-D and 3-D partial differential equations that have been converted
16054 to ODEs by numerical differencing.")
16055 (license license:gpl2+)))
16057 (define-public r-pracma
16063 (uri (cran-uri "pracma" version))
16065 (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc"))))
16066 (build-system r-build-system)
16067 (home-page "https://cran.r-project.org/web/packages/pracma/")
16068 (synopsis "Practical numerical math functions")
16069 (description "This package provides functions for numerical analysis and
16070 linear algebra, numerical optimization, differential equations, plus some
16071 special functions. It uses Matlab function names where appropriate to simplify
16073 (license license:gpl3+)))
16075 (define-public r-subplex
16082 (uri (cran-uri "subplex" version))
16085 "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d"))))
16086 (build-system r-build-system)
16088 `(("gfortran" ,gfortran)))
16089 (home-page "https://cran.r-project.org/web/packages/subplex")
16090 (synopsis "Unconstrained optimization using the subplex algorithm")
16092 "This package implements the Subplex optimization algorithm.
16093 It solves unconstrained optimization problems using a simplex method on
16094 subspaces. The method is well suited for optimizing objective functions that
16095 are noisy or are discontinuous at the solution.")
16096 (license license:gpl3+)))
16098 (define-public r-txtplot
16105 (uri (cran-uri "txtplot" version))
16108 "1949ab1bzvysdb79g8x1gaknj0ih3d6g63pv9512h5m5l3a6c31h"))))
16109 (build-system r-build-system)
16110 (home-page "https://cran.r-project.org/web/packages/txtplot/")
16111 (synopsis "Text-based plotting")
16112 (description "This package provides functions to produce rudimentary ASCII
16113 graphics directly in the terminal window. This package provides a basic
16114 plotting function (and equivalents of curve, density, acf and barplot) as well
16115 as a boxplot function.")
16116 (license license:lgpl3+)))
16118 (define-public r-bio3d
16125 (uri (cran-uri "bio3d" version))
16128 "07rw6c2d95gb5myxh31727j0jrchd0xisa3x89jjmf4zzs3vv7v7"))))
16129 (properties `((upstream-name . "bio3d")))
16130 (build-system r-build-system)
16131 (inputs `(("zlib" ,zlib)))
16132 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
16133 (home-page "http://thegrantlab.org/bio3d/")
16134 (synopsis "Biological structure analysis")
16136 "This package provides utilities to process, organize and explore protein
16137 structure, sequence and dynamics data. Features include the ability to read
16138 and write structure, sequence and dynamic trajectory data, perform sequence
16139 and structure database searches, data summaries, atom selection, alignment,
16140 superposition, rigid core identification, clustering, torsion analysis,
16141 distance matrix analysis, structure and sequence conservation analysis, normal
16142 mode analysis, principal component analysis of heterogeneous structure data,
16143 and correlation network analysis from normal mode and molecular dynamics data.
16144 In addition, various utility functions are provided to enable the statistical
16145 and graphical power of the R environment to work with biological sequence and
16147 (license license:gpl2+)))
16149 (define-public r-bios2cor
16151 (name "r-bios2cor")
16156 (uri (cran-uri "Bios2cor" version))
16159 "04wk1cjrrxhpv1kdhd67r1qvjv268xxi0z0r105wy912110z9m6x"))))
16160 (properties `((upstream-name . "Bios2cor")))
16161 (build-system r-build-system)
16163 `(("r-bigmemory" ,r-bigmemory)
16164 ("r-bio3d" ,r-bio3d)
16165 ("r-circular" ,r-circular)
16166 ("r-igraph" ,r-igraph)))
16167 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
16168 (synopsis "From biological sequences and simulations to correlation analysis")
16170 "This package provides utilities for computation and analysis of
16171 correlation/covariation in multiple sequence alignments and in side chain
16172 motions during molecular dynamics simulations. Features include the
16173 computation of correlation/covariation scores using a variety of scoring
16174 functions between either sequence positions in alignments or side chain
16175 dihedral angles in molecular dynamics simulations and utilities to analyze the
16176 correlation/covariation matrix through a variety of tools including network
16177 representation and principal components analysis. In addition, several
16178 utility functions are based on the R graphical environment to provide friendly
16179 tools for help in data interpretation.")
16180 (license license:gpl2+)))
16182 ;; This package includes minified JavaScript files. When upgrading please
16183 ;; check that there are no new minified JavaScript files.
16184 (define-public r-networkd3
16186 (name "r-networkd3")
16191 (uri (cran-uri "networkD3" version))
16194 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
16197 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
16199 (properties `((upstream-name . "networkD3")))
16200 (build-system r-build-system)
16202 `(#:modules ((guix build utils)
16203 (guix build r-build-system)
16207 (modify-phases %standard-phases
16208 (add-after 'unpack 'process-javascript
16209 (lambda* (#:key inputs #:allow-other-keys)
16210 (with-directory-excursion "inst/htmlwidgets/lib/"
16214 `((,(assoc-ref inputs "d3.v4.js")
16215 "d3-4.5.0/d3.min.js"))))
16216 (lambda (sources targets)
16217 (for-each (lambda (source target)
16218 (format #t "Processing ~a --> ~a~%"
16220 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16221 (call-with-output-file target
16223 (dump-port minified port)))))
16224 sources targets))))
16227 `(("uglify-js" ,uglify-js)
16228 ;; NOTE: Make sure that this version of d3 is still valid when
16229 ;; upgrading the package.
16233 (uri "https://d3js.org/d3.v4.js")
16236 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
16238 `(("r-htmlwidgets" ,r-htmlwidgets)
16239 ("r-igraph" ,r-igraph)
16240 ("r-magrittr" ,r-magrittr)))
16241 (home-page "https://cran.r-project.org/package=networkD3")
16242 (synopsis "D3 JavaScript network graphs from R")
16244 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
16246 (license license:gpl3+)))
16248 (define-public r-aasea
16255 (uri (cran-uri "aaSEA" version))
16258 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
16259 (properties `((upstream-name . "aaSEA")))
16260 (build-system r-build-system)
16262 `(("r-bios2cor" ,r-bios2cor)
16264 ("r-hmisc" ,r-hmisc)
16265 ("r-magrittr" ,r-magrittr)
16266 ("r-networkd3" ,r-networkd3)
16267 ("r-plotly" ,r-plotly)
16268 ("r-seqinr" ,r-seqinr)
16269 ("r-shiny" ,r-shiny)
16270 ("r-shinydashboard" ,r-shinydashboard)))
16271 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
16272 (synopsis "Amino acid substitution effect analyzer")
16274 "Given a protein multiple sequence alignment, it is a daunting task to
16275 assess the effects of substitutions along sequence length. The aaSEA package
16276 is intended to help researchers to rapidly analyze property changes caused by
16277 single, multiple and correlated amino acid substitutions in proteins.")
16278 (license license:gpl3)))
16280 (define-public r-abacus
16287 (uri (cran-uri "ABACUS" version))
16290 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
16291 (properties `((upstream-name . "ABACUS")))
16292 (build-system r-build-system)
16294 `(("r-ggplot2" ,r-ggplot2)
16295 ("r-shiny" ,r-shiny)))
16296 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
16297 (synopsis "Apps-based activities for communicating and understanding statistics")
16299 "This package provides a set of Shiny apps for effective communication
16300 and understanding in statistics. The current version includes properties of
16301 normal distribution, properties of sampling distribution, one-sample z and t
16302 tests, two samples independent (unpaired) t test and analysis of variance.")
16303 (license license:gpl3)))
16305 (define-public r-abc-rap
16312 (uri (cran-uri "ABC.RAP" version))
16315 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
16316 (properties `((upstream-name . "ABC.RAP")))
16317 (build-system r-build-system)
16318 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
16319 (synopsis "Array-based CpG region analysis pipeline")
16321 "This package aims to identify candidate genes that are differentially
16322 methylated between cases and controls. It applies Student's t-test and delta
16323 beta analysis to identify candidate genes containing multiple CpG sites.")
16324 (license license:gpl3)))
16326 (define-public r-abcadm
16333 (uri (cran-uri "abcADM" version))
16336 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
16337 (properties `((upstream-name . "abcADM")))
16338 (build-system r-build-system)
16341 ("r-rcpp" ,r-rcpp)))
16342 (home-page "https://cran.r-project.org/web/packages/abcADM/")
16343 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
16345 "This package provides tools to estimate parameters of accumulated
16346 damage (load duration) models based on failure time data under a Bayesian
16347 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
16348 long-term reliability under stochastic load profiles.")
16349 (license license:gpl3)))
16351 (define-public r-rglpk
16358 (uri (cran-uri "Rglpk" version))
16361 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
16362 (properties `((upstream-name . "Rglpk")))
16363 (build-system r-build-system)
16365 `(("r-slam" ,r-slam)))
16368 (home-page "https://r-forge.r-project.org/projects/rglp/")
16369 (synopsis "R interface to the GNU Linear Programming Kit")
16371 "This package provides an R interface to the GNU Linear Programming Kit,
16372 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
16373 integer linear programming} (MILP) and other related problems.")
16375 (license (list license:gpl2 license:gpl3))))
16377 (define-public r-abcdefba
16379 (name "r-abcdefba")
16384 (uri (cran-uri "abcdeFBA" version))
16387 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
16388 (properties `((upstream-name . "abcdeFBA")))
16389 (build-system r-build-system)
16391 `(("r-corrplot" ,r-corrplot)
16392 ("r-lattice" ,r-lattice)
16394 ("r-rglpk" ,r-rglpk)))
16395 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
16396 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
16398 "This package provides functions for Constraint Based Simulation using
16399 Flux Balance Analysis and informative analysis of the data generated during
16401 (license license:gpl2)))
16403 (define-public r-abcrlda
16410 (uri (cran-uri "abcrlda" version))
16413 "0zjdrbg3zx0znqnh0dvmifs9c12b8vjhbaf3nbwab9xh25nsmg75"))))
16414 (properties `((upstream-name . "abcrlda")))
16415 (build-system r-build-system)
16416 (home-page "https://ieeexplore.ieee.org/document/8720003/")
16417 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
16419 "This package offers methods to perform @dfn{asymptotically
16420 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
16421 cost-sensitive binary classification. The bias-correction is an estimate of
16422 the bias term added to regularized discriminant analysis that minimizes the
16424 (license license:gpl3)))
16426 (define-public r-abemus
16433 (uri (cran-uri "abemus" version))
16436 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
16437 (properties `((upstream-name . "abemus")))
16438 (build-system r-build-system)
16440 `(("r-data-table" ,r-data-table)))
16441 (home-page "https://cran.r-project.org/web/packages/abemus/")
16442 (synopsis "Adaptive base error model in ultra-deep sequencing data")
16444 "This package provides an implementation of @dfn{Adaptive Base Error
16445 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
16446 platform-specific genetic knowledge and empirical signal to readily detect and
16447 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
16448 cell free DNA} (cfDNA).")
16449 (license license:gpl3)))
16451 ;; This package includes minified JavaScript files. When upgrading please
16452 ;; check that there are no new minified JavaScript files.
16453 (define-public r-rintrojs
16455 (name "r-rintrojs")
16460 (uri (cran-uri "rintrojs" version))
16463 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
16464 (properties `((upstream-name . "rintrojs")))
16465 (build-system r-build-system)
16467 `(#:modules ((guix build utils)
16468 (guix build r-build-system)
16472 (modify-phases %standard-phases
16473 (add-after 'unpack 'process-javascript
16474 (lambda* (#:key inputs #:allow-other-keys)
16475 (with-directory-excursion "inst/javascript/introjs/"
16479 `((,(assoc-ref inputs "intro.js")
16481 (lambda (sources targets)
16482 (for-each (lambda (source target)
16483 (format #t "Processing ~a --> ~a~%"
16485 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16486 (call-with-output-file target
16488 (dump-port minified port)))))
16489 sources targets))))
16492 `(("uglify-js" ,uglify-js)
16496 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
16499 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
16501 `(("r-jsonlite" ,r-jsonlite)
16502 ("r-shiny" ,r-shiny)))
16503 (home-page "https://github.com/carlganz/rintrojs")
16504 (synopsis "Wrapper for the Intro.js library")
16506 "This package provides a wrapper for the @url{http://www.introjs.com,
16507 Intro.js} library. This package makes it easy to include step-by-step
16508 introductions, and clickable hints in a Shiny application. It supports both
16509 static introductions in the UI, and programmatic introductions from the
16511 (license license:agpl3+)))
16513 (define-public r-sysfonts
16515 (name "r-sysfonts")
16520 (uri (cran-uri "sysfonts" version))
16523 "0wng902plryf2d8fc7k7m3jx11acz51kb2d91cqbyhq7xpk06z43"))))
16524 (properties `((upstream-name . "sysfonts")))
16525 (build-system r-build-system)
16527 `(("freetype" ,freetype)
16531 `(("pkg-config" ,pkg-config)))
16532 (home-page "https://github.com/yixuan/sysfonts")
16533 (synopsis "Loading fonts into R")
16535 "This is a package to simplify loading of system fonts and Google Fonts
16536 into R, in order to support other packages.")
16537 (license license:gpl2)))
16539 (define-public r-showtextdb
16541 (name "r-showtextdb")
16546 (uri (cran-uri "showtextdb" version))
16549 "1qwwj9x2jvadvwn60h75k99c9xi7yhqjsgaakahz5paxgj583bsh"))))
16550 (properties `((upstream-name . "showtextdb")))
16551 (build-system r-build-system)
16553 `(("r-sysfonts" ,r-sysfonts)))
16554 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
16555 (synopsis "Font files for the 'showtext' package")
16557 "This package provides font files that can be used by the @code{showtext}
16559 (license license:asl2.0)))
16561 (define-public r-showtext
16563 (name "r-showtext")
16568 (uri (cran-uri "showtext" version))
16571 "0a5gg72bfrc7wm0phj1aflj1wc08kfi81ac32na6ya9s2ivyimw5"))))
16572 (properties `((upstream-name . "showtext")))
16573 (build-system r-build-system)
16575 `(("freetype" ,freetype)
16579 `(("r-showtextdb" ,r-showtextdb)
16580 ("r-sysfonts" ,r-sysfonts)))
16581 (native-inputs `(("pkg-config" ,pkg-config)))
16582 (home-page "https://github.com/yixuan/showtext")
16583 (synopsis "Using fonts more easily in R graphs")
16585 "This package aims to make it easy to use various types of
16586 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
16587 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
16588 will be converted into polygons or raster images, hence after the plot has
16589 been created, it no longer relies on the font files. No external software
16590 such as Ghostscript is needed to use this package.")
16591 (license license:asl2.0)))
16593 (define-public r-emojifont
16595 (name "r-emojifont")
16600 (uri (cran-uri "emojifont" version))
16603 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
16604 (properties `((upstream-name . "emojifont")))
16605 (build-system r-build-system)
16607 `(("r-ggplot2" ,r-ggplot2)
16608 ("r-proto" ,r-proto)
16609 ("r-showtext" ,r-showtext)
16610 ("r-sysfonts" ,r-sysfonts)))
16611 (home-page "https://guangchuangyu.github.io/emojifont")
16612 (synopsis "Emoji and Font Awesome in R graphics")
16614 "This package enables the use of emoji and the Font Awesome glyphs in
16615 both base and ggplot2 graphics.")
16616 (license license:artistic2.0)))
16618 (define-public r-abstractr
16620 (name "r-abstractr")
16625 (uri (cran-uri "abstractr" version))
16628 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
16629 (properties `((upstream-name . "abstractr")))
16630 (build-system r-build-system)
16632 `(("r-colourpicker" ,r-colourpicker)
16633 ("r-emojifont" ,r-emojifont)
16634 ("r-ggplot2" ,r-ggplot2)
16635 ("r-gridextra" ,r-gridextra)
16636 ("r-rintrojs" ,r-rintrojs)
16637 ("r-shiny" ,r-shiny)
16638 ("r-shinythemes" ,r-shinythemes)))
16639 (home-page "https://matt-kumar.shinyapps.io/portfolio")
16640 (synopsis "R-Shiny application for creating visual abstracts")
16642 "This package provides an R Shiny application to create visual abstracts
16643 for original research. A variety of user defined options and formatting are
16645 (license license:gpl3)))
16647 (define-public r-abtest
16654 (uri (cran-uri "abtest" version))
16657 "1ky3cf827kj24bhcpk00v5zl5jdkii1gca0x81ay1cjkzfispgws"))))
16658 (properties `((upstream-name . "abtest")))
16659 (build-system r-build-system)
16661 `(("r-matrix" ,r-matrix)
16662 ("r-mvtnorm" ,r-mvtnorm)
16663 ("r-plotrix" ,r-plotrix)
16664 ("r-rcolorbrewer" ,r-rcolorbrewer)
16667 ("r-truncnorm" ,r-truncnorm)
16668 ("r-vgam" ,r-vgam)))
16669 (home-page "https://cran.r-project.org/web/packages/abtest/")
16670 (synopsis "Bayesian A/B testing")
16672 "This package provides functions for Bayesian A/B testing including prior
16673 elicitation options based on Kass and Vaidyanathan (1992)
16674 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
16675 (license license:gpl2+)))
16677 (define-public r-accept
16684 (uri (cran-uri "accept" version))
16687 "1r4mhy9g4wjcjgdd0gwdarmr09292il3vdkmx0hz7vh9mffyr9kx"))))
16688 (properties `((upstream-name . "accept")))
16689 (build-system r-build-system)
16691 `(("r-dplyr" ,r-dplyr)
16692 ("r-extrafont" ,r-extrafont)
16694 ("r-plotly" ,r-plotly)
16695 ("r-stringr" ,r-stringr)
16696 ("r-viridis" ,r-viridis)))
16697 (home-page "https://cran.r-project.org/web/packages/accept/")
16698 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
16700 "This package allows clinicians to predict the rate and severity of
16701 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
16702 Disease} (COPD) patients, based on the clinical prediction model published in
16703 Adibi et al. (2019) @url{doi:10.1101/651901}.")
16704 (license license:gpl3)))
16706 (define-public r-smpracticals
16708 (name "r-smpracticals")
16713 (uri (cran-uri "SMPracticals" version))
16716 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
16717 (properties `((upstream-name . "SMPracticals")))
16718 (build-system r-build-system)
16720 `(("r-ellipse" ,r-ellipse)
16723 ("r-survival" ,r-survival)))
16724 (home-page "http://statwww.epfl.ch/davison/SM/")
16725 (synopsis "Practicals for use with Davison (2003) Statistical Models")
16727 "This package contains the datasets and a few functions for use with the
16728 practicals outlined in Appendix A of the book Statistical Models (Davison,
16729 2003, Cambridge University Press). The practicals themselves can be found at
16730 @url{http://statwww.epfl.ch/davison/SM/}.")
16731 (license license:gpl2+)))
16733 (define-public r-fgui
16740 (uri (cran-uri "fgui" version))
16743 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
16744 (properties `((upstream-name . "fgui")))
16745 (build-system r-build-system)
16747 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
16748 (synopsis "Create GUI for R functions")
16750 "Rapidly create a GUI for a function you created by automatically
16751 creating widgets for arguments of the function. This package automatically
16752 parses help routines for context-sensitive help to these arguments. The
16753 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
16754 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
16755 incorporated into the interface for greater customization for the more
16757 ;; Any version of the GPL.
16758 (license (list license:gpl2+ license:gpl3+))))
16760 (define-public r-tcltk2
16767 (uri (cran-uri "tcltk2" version))
16770 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
16771 (properties `((upstream-name . "tcltk2")))
16772 (build-system r-build-system)
16776 (home-page "https://www.sciviews.org/SciViews-R")
16777 (synopsis "Tcl/Tk additions")
16779 "This package provides a series of additional Tcl commands and Tk widgets
16780 with style and various functions to supplement the tcltk package")
16781 (license license:lgpl3)))
16783 (define-public r-accrual
16790 (uri (cran-uri "accrual" version))
16793 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
16794 (properties `((upstream-name . "accrual")))
16795 (build-system r-build-system)
16797 `(("r-fgui" ,r-fgui)
16798 ("r-smpracticals" ,r-smpracticals)
16799 ("r-tcltk2" ,r-tcltk2)))
16800 (home-page "https://cran.r-project.org/web/packages/accrual/")
16801 (synopsis "Bayesian accrual prediction")
16803 "Subject recruitment for medical research is challenging. Slow patient
16804 accrual leads to delay in research. Accrual monitoring during the process of
16805 recruitment is critical. Researchers need reliable tools to manage the
16806 accrual rate. This package provides an implementation of a Bayesian method
16807 that integrates researcher's experience on previous trials and data from the
16808 current study, providing reliable prediction on accrual rate for clinical
16809 studies. It provides functions for Bayesian accrual prediction which can be
16810 easily used by statisticians and clinical researchers.")
16811 (license license:gpl2)))
16813 (define-public r-accrued
16820 (uri (cran-uri "accrued" version))
16823 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
16824 (properties `((upstream-name . "accrued")))
16825 (build-system r-build-system)
16826 (home-page "https://cran.r-project.org/web/packages/accrued/")
16827 (synopsis "Data quality visualization tools for partially accruing data")
16829 "This is a package for visualizing data quality of partially accruing
16831 (license license:gpl3)))
16833 (define-public r-mda
16840 (uri (cran-uri "mda" version))
16843 "19g6kn6g0shidrjfffklbmzc5w7mcimrxhagx4nmpslg59ibqdkh"))))
16844 (properties `((upstream-name . "mda")))
16845 (build-system r-build-system)
16846 (propagated-inputs `(("r-class" ,r-class)))
16847 (native-inputs `(("gfortran" ,gfortran)))
16848 (home-page "https://cran.r-project.org/web/packages/mda/")
16849 (synopsis "Mixture and flexible discriminant analysis")
16851 "This is a package for mixture and flexible discriminant analysis,
16852 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
16853 (license license:gpl2)))
16855 (define-public r-elasticnet
16857 (name "r-elasticnet")
16862 (uri (cran-uri "elasticnet" version))
16865 "0p9dplnsp28z4s2fl6afbwrgd0aj339fak8mmndicmrh7bb7rpmb"))))
16866 (properties `((upstream-name . "elasticnet")))
16867 (build-system r-build-system)
16869 `(("r-lars" ,r-lars)))
16870 (home-page "http://www.stat.umn.edu/~hzou")
16871 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
16873 "This package provides functions for fitting the entire solution path of
16874 the Elastic-Net and also provides functions for estimating sparse Principal
16875 Components. The Lasso solution paths can be computed by the same function.")
16876 (license license:gpl2+)))
16878 (define-public r-sparselda
16880 (name "r-sparselda")
16885 (uri (cran-uri "sparseLDA" version))
16888 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
16889 (properties `((upstream-name . "sparseLDA")))
16890 (build-system r-build-system)
16892 `(("r-elasticnet" ,r-elasticnet)
16895 (home-page "http://www.imm.dtu.dk/~lhc")
16896 (synopsis "Sparse discriminant analysis")
16898 "This package performs sparse linear discriminant analysis for Gaussians
16899 and mixture of Gaussian models.")
16900 (license license:gpl2+)))
16902 (define-public r-accsda
16909 (uri (cran-uri "accSDA" version))
16912 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
16913 (properties `((upstream-name . "accSDA")))
16914 (build-system r-build-system)
16916 `(("r-ggplot2" ,r-ggplot2)
16917 ("r-ggthemes" ,r-ggthemes)
16918 ("r-gridextra" ,r-gridextra)
16920 ("r-rarpack" ,r-rarpack)
16921 ("r-sparselda" ,r-sparselda)))
16922 (home-page "https://github.com/gumeo/accSDA/wiki")
16923 (synopsis "Accelerated sparse discriminant analysis")
16925 "This package provides an implementation of sparse linear discriminant
16926 analysis, which is a supervised classification method for multiple classes.
16927 Various novel optimization approaches to this problem are implemented
16928 including @dfn{alternating direction method of multipliers} (ADMM),
16929 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
16930 Functions for performing cross validation are also supplied along with basic
16931 prediction and plotting functions. @dfn{Sparse zero variance
16932 discriminant} (SZVD) analysis is also included in the package.")
16933 (license license:gpl2+)))
16935 (define-public r-ace2fastq
16937 (name "r-ace2fastq")
16942 (uri (cran-uri "ace2fastq" version))
16945 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
16946 (properties `((upstream-name . "ace2fastq")))
16947 (build-system r-build-system)
16949 `(("r-stringr" ,r-stringr)))
16950 (home-page "https://github.com/c5sire/ace2fastq")
16951 (synopsis "ACE file to FASTQ converter")
16953 "The ACE file format is used in genomics to store contigs from sequencing
16954 machines. This tools converts it into FASTQ format. Both formats contain the
16955 sequence characters and their corresponding quality information. Unlike the
16956 FASTQ file, the ACE file stores the quality values numerically. The
16957 conversion algorithm uses the standard Sanger formula. The package
16958 facilitates insertion into pipelines, and content inspection.")
16959 (license license:gpl3)))
16961 (define-public r-rngwell
16968 (uri (cran-uri "rngWELL" version))
16971 "0pjjcs9pqj7mf0mhb2cwd0aanqpwnm65bm86hk6mi2vw8rgnj2vv"))))
16972 (properties `((upstream-name . "rngWELL")))
16973 (build-system r-build-system)
16974 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
16975 (synopsis "Toolbox for WELL random number generators")
16977 "This is a dedicated package to WELL pseudo random generators, which were
16978 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
16979 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
16980 (license license:bsd-3)))
16982 (define-public r-randtoolbox
16984 (name "r-randtoolbox")
16989 (uri (cran-uri "randtoolbox" version))
16992 "0qg20ar6qns858jdzqhmfq7yji81czhr6cim257958gqpj66sn95"))))
16993 (properties `((upstream-name . "randtoolbox")))
16994 (build-system r-build-system)
16996 `(("r-rngwell" ,r-rngwell)))
16998 `(("gfortran" ,gfortran)))
16999 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
17000 (synopsis "Toolbox for pseudo and quasi random number generation")
17002 "This package provides
17005 @item pseudo random generators, such as general linear
17006 congruential generators, multiple recursive generators and generalized
17007 feedback shift register (SF-Mersenne Twister algorithm and WELL
17010 @item quasi random generators, such as the Torus algorithm, the Sobol
17011 sequence, the Halton sequence (including the Van der Corput sequence), and
17013 @item some generator tests: the gap test, the serial test, the poker test.
17016 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
17017 (license license:bsd-3)))
17019 (define-public r-lhs
17026 (uri (cran-uri "lhs" version))
17029 "0lzaqr7xi3ckln5nglv5xf5njm359slpz1jc6s02hpsqdw6armd4"))))
17030 (properties `((upstream-name . "lhs")))
17031 (build-system r-build-system)
17032 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
17033 (home-page "https://github.com/bertcarnell/lhs")
17034 (synopsis "Latin Hypercube Samples")
17036 "This package provides a number of methods for creating and augmenting
17037 Latin Hypercube Samples.")
17038 (license license:gpl3)))
17040 (define-public r-acebayes
17042 (name "r-acebayes")
17047 (uri (cran-uri "acebayes" version))
17050 "1imfwm1vpbb24vfmfn1nljhmaz8429mwjihw34892p387s8h7xz2"))))
17051 (properties `((upstream-name . "acebayes")))
17052 (build-system r-build-system)
17054 `(("r-compare" ,r-compare)
17056 ("r-randtoolbox" ,r-randtoolbox)
17058 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17059 (home-page "https://cran.r-project.org/web/packages/acebayes/")
17060 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
17062 "Finding an optimal Bayesian experimental design involves maximizing an
17063 objective function given by the expectation of some appropriately chosen
17064 utility function with respect to the joint distribution of unknown
17065 quantities (including responses). This objective function is usually not
17066 available in closed form and the design space can be continuous and of high
17067 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
17068 to maximise an approximation to the expectation of the utility function.")
17069 (license license:gpl2)))
17071 (define-public r-acet
17078 (uri (cran-uri "ACEt" version))
17081 "0626d6kg485xjya164wagrr5z223jvi93ywbwpdns7fkm03c0dlq"))))
17082 (properties `((upstream-name . "ACEt")))
17083 (build-system r-build-system)
17088 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17089 (home-page "https://cran.r-project.org/web/packages/ACEt/")
17090 (synopsis "Estimating dynamic heritability and twin model comparison")
17092 "This package supports twin models that are able to estimate the dynamic
17093 behaviour of the variance components in the classical twin models with respect
17094 to age using B-splines and P-splines.")
17095 (license license:gpl2+)))
17097 (define-public r-acfmperiod
17099 (name "r-acfmperiod")
17104 (uri (cran-uri "acfMPeriod" version))
17107 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
17108 (properties `((upstream-name . "acfMPeriod")))
17109 (build-system r-build-system)
17111 `(("r-mass" ,r-mass)))
17112 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
17113 (synopsis "Estimation of the ACF from the M-periodogram")
17115 "This package support non-robust and robust computations of the sample
17116 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
17117 univariate and multivariate processes. The methodology consists in reversing
17118 the diagonalization procedure involving the periodogram or the
17119 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
17120 ACOVF or the ACF as discussed in Fuller (1995)
17121 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
17122 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
17123 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
17124 (license license:gpl2+)))
17126 (define-public r-gamlss-data
17128 (name "r-gamlss-data")
17133 (uri (cran-uri "gamlss.data" version))
17136 "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
17137 (properties `((upstream-name . "gamlss.data")))
17138 (build-system r-build-system)
17139 (home-page "http://www.gamlss.org/")
17140 (synopsis "GAMLSS data")
17142 "This package provides data used as examples to demonstrate GAMLSS
17144 ;; Either version of the license
17145 (license (list license:gpl2 license:gpl3))))
17147 (define-public r-gamlss
17154 (uri (cran-uri "gamlss" version))
17157 "16b7ick1khvldbvfmmpw9cjs1vznnrisvifq7717fxzd8c9s5jdr"))))
17158 (properties `((upstream-name . "gamlss")))
17159 (build-system r-build-system)
17161 `(("r-gamlss-data" ,r-gamlss-data)
17162 ("r-gamlss-dist" ,r-gamlss-dist)
17165 ("r-survival" ,r-survival)))
17166 (home-page "http://www.gamlss.org/")
17167 (synopsis "Generalized additive models for location scale and shape")
17169 "This package provides functions for fitting the generalized additive
17170 models for location scale and shape introduced by Rigby and
17171 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
17172 use a distributional regression approach where all the parameters of the
17173 conditional distribution of the response variable are modelled using
17174 explanatory variables.")
17175 ;; Either version of the license
17176 (license (list license:gpl2 license:gpl3))))
17178 (define-public r-acid
17185 (uri (cran-uri "acid" version))
17188 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
17189 (properties `((upstream-name . "acid")))
17190 (build-system r-build-system)
17192 `(("r-gamlss" ,r-gamlss)
17193 ("r-gamlss-dist" ,r-gamlss-dist)
17194 ("r-hmisc" ,r-hmisc)))
17195 (home-page "https://cran.r-project.org/web/packages/acid/")
17196 (synopsis "Analysing conditional income distributions")
17198 "This package provides functions for the analysis of income distributions
17199 for subgroups of the population as defined by a set of variables like age,
17200 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
17201 distribution as well as functions for moments, inequality measures, entropy
17202 measures and polarisation measures of income distributions. This package thus
17203 aides the analysis of income inequality by offering tools for the exploratory
17204 analysis of income distributions at the disaggregated level.")
17205 (license license:gpl3)))
17207 (define-public r-acm4r
17214 (uri (cran-uri "acm4r" version))
17217 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
17218 (properties `((upstream-name . "acm4r")))
17219 (build-system r-build-system)
17220 (propagated-inputs `(("r-mass" ,r-mass)))
17221 (home-page "https://cran.r-project.org/web/packages/acm4r/")
17222 (synopsis "Align-and-count method comparisons of RFLP data")
17224 "This is a package to compare sequence fragment lengths or molecular
17225 weights from pairs of lanes. The number of matching bands in the
17226 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
17227 the align-and-count method.")
17228 ;; Any version of the GPL
17229 (license (list license:gpl2+ license:gpl3+))))
17231 (define-public r-filematrix
17233 (name "r-filematrix")
17238 (uri (cran-uri "filematrix" version))
17241 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
17242 (properties `((upstream-name . "filematrix")))
17243 (build-system r-build-system)
17244 ;; These inputs are needed for vignettes
17246 `(("r-knitr" ,r-knitr)
17247 ("r-rmarkdown" ,r-rmarkdown)
17248 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
17249 (home-page "https://github.com/andreyshabalin/filematrix")
17250 (synopsis "File-backed matrix class with convenient read and write access")
17252 "This package provides an interface for working with large matrices
17253 stored in files, not in computer memory. It supports multiple non-character
17254 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
17255 byte real values). Access to parts of the matrix is done by indexing, exactly
17256 as with usual R matrices. It supports very large matrices; the package has
17257 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
17258 columns, ad allows for quick addition of extra columns to a filematrix.")
17259 (license license:lgpl3)))
17261 (define-public r-acmeeqtl
17263 (name "r-acmeeqtl")
17268 (uri (cran-uri "ACMEeqtl" version))
17271 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
17272 (properties `((upstream-name . "ACMEeqtl")))
17273 (build-system r-build-system)
17275 `(("r-filematrix" ,r-filematrix)))
17276 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
17277 (synopsis "Estimation of interpretable eQTL effect sizes")
17279 "This package provides a non-linear model, termed ACME, that reflects a
17280 parsimonious biological model for allelic contributions of cis-acting eQTLs.
17281 With non-linear least-squares algorithm the maximum likelihood parameters can
17282 be estimated. The ACME model provides interpretable effect size estimates and
17283 p-values with well controlled Type-I error.")
17284 (license license:lgpl3)))
17286 (define-public r-acmer
17293 (uri (cran-uri "acmeR" version))
17296 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
17297 (properties `((upstream-name . "acmeR")))
17298 (build-system r-build-system)
17299 (propagated-inputs `(("r-foreign" ,r-foreign)))
17300 (home-page "https://cran.r-project.org/web/packages/acmeR/")
17301 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
17303 "This package provides an implementation of the ACME estimator, described
17304 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
17305 Mortality at Wind Turbines. Unlike most other models, this estimator supports
17306 decreasing-hazard Weibull model for persistence; decreasing search proficiency
17307 as carcasses age; variable bleed-through at successive searches; and interval
17308 mortality estimates. The package provides, based on search data, functions
17309 for estimating the mortality inflation factor in Frequentist and Bayesian
17311 (license license:expat)))
17313 (define-public r-r-huge
17320 (uri (cran-uri "R.huge" version))
17323 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
17324 (properties `((upstream-name . "R.huge")))
17325 (build-system r-build-system)
17327 `(("r-r-methodss3" ,r-r-methodss3)
17329 ("r-r-utils" ,r-r-utils)))
17330 (home-page "https://github.com/HenrikBengtsson/R.huge")
17331 (synopsis "Methods for accessing huge amounts of data")
17333 "This is a deprecated package for accessing huge amounts of data.
17334 Cross-platform alternatives are the following packages: bigmemory (CRAN),
17335 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
17336 the @code{aroma.affymetrix} package.")
17337 (license license:lgpl2.1+)))
17339 (define-public r-r-filesets
17341 (name "r-r-filesets")
17346 (uri (cran-uri "R.filesets" version))
17349 "124rygq0bl9n4akxcm868nl30cyk3rz0iprb98zlpk62gci9f5fg"))))
17350 (properties `((upstream-name . "R.filesets")))
17351 (build-system r-build-system)
17353 `(("r-digest" ,r-digest)
17354 ("r-r-cache" ,r-r-cache)
17355 ("r-r-methodss3" ,r-r-methodss3)
17357 ("r-r-utils" ,r-r-utils)))
17358 (home-page "https://github.com/HenrikBengtsson/R.filesets")
17359 (synopsis "Easy handling of and access to files")
17361 "This package provides classes and methods to locate, setup, subset,
17362 navigate and iterate file sets, i.e. sets of files located in one or more
17363 directories on the file system. The API is designed such that these classes
17364 can be extended via inheritance to provide a richer API for special file
17365 formats. Moreover, a specific name format is defined such that filenames and
17366 directories can be considered to have full names which consists of a name
17367 followed by comma-separated tags. This adds additional flexibility to
17368 identify file sets and individual files.")
17369 (license license:lgpl2.1+)))
17371 (define-public r-r-devices
17373 (name "r-r-devices")
17378 (uri (cran-uri "R.devices" version))
17381 "15zlnq3g27whq26fbcy5zfl5hiddm256h4rga4frblg6wqlbkvdd"))))
17382 (properties `((upstream-name . "R.devices")))
17383 (build-system r-build-system)
17385 `(("r-base64enc" ,r-base64enc)
17386 ("r-r-methodss3" ,r-r-methodss3)
17388 ("r-r-utils" ,r-r-utils)))
17389 (home-page "https://github.com/HenrikBengtsson/R.devices")
17390 (synopsis "Unified handling of graphics devices")
17392 "This package provides functions for creating plots and image files in a
17393 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
17394 Default device options as well as scales and aspect ratios are controlled in a
17395 uniform way across all device types. Switching output format requires minimal
17396 changes in code. This package is ideal for large-scale batch processing,
17397 because it will never leave open graphics devices or incomplete image files
17398 behind, even on errors or user interrupts.")
17399 (license license:lgpl2.1+)))
17401 (define-public r-acnr
17408 (uri (cran-uri "acnr" version))
17411 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
17412 (properties `((upstream-name . "acnr")))
17413 (build-system r-build-system)
17414 (home-page "https://github.com/mpierrejean/acnr")
17415 (synopsis "Annotated copy-number regions")
17417 "This package provides SNP array data from different types of copy-number
17418 regions. These regions were identified manually by the authors of the package
17419 and may be used to generate realistic data sets with known truth.")
17420 (license license:lgpl2.1+)))
17422 (define-public r-acopula
17429 (uri (cran-uri "acopula" version))
17432 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
17433 (properties `((upstream-name . "acopula")))
17434 (build-system r-build-system)
17435 (home-page "https://cran.r-project.org/web/packages/acopula/")
17436 (synopsis "Modelling dependence with multivariate Archimax copulas")
17438 "Archimax copulas are a mixture of Archimedean and EV copulas. This
17439 package provides definitions of several parametric families of generator and
17440 dependence function, computes CDF and PDF, estimates parameters, tests for
17441 goodness of fit, generates random sample and checks copula properties for
17442 custom constructs. In the 2-dimensional case explicit formulas for density
17443 are used, contrary to higher dimensions when all derivatives are linearly
17444 approximated. Several non-archimax families (normal, FGM, Plackett) are
17445 provided as well.")
17446 (license license:gpl2)))
17448 (define-public r-tuner
17455 (uri (cran-uri "tuneR" version))
17458 "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
17459 (properties `((upstream-name . "tuneR")))
17460 (build-system r-build-system)
17461 (propagated-inputs `(("r-signal" ,r-signal)))
17462 (home-page "https://cran.r-project.org/web/packages/tuneR/")
17463 (synopsis "Analysis of music and speech")
17465 "This is a package for the analysis of music and speech. Analyze music
17466 and speech, extract features like MFCCs, handle wave files and their
17467 representation in various ways, read MP3, read MIDI, perform steps of a
17468 transcription, ...")
17469 ;; Either of these versions.
17470 (license (list license:gpl2 license:gpl3))))
17472 (define-public r-seewave
17479 (uri (cran-uri "seewave" version))
17482 "1qg8f5gik9pw6f9mcxqmrc9x3003s8vdm6g01pjjpyc9qaqiz2vi"))))
17483 (properties `((upstream-name . "seewave")))
17484 (build-system r-build-system)
17486 `(("r-tuner" ,r-tuner)))
17487 (home-page "http://rug.mnhn.fr/seewave")
17488 (synopsis "Sound analysis and synthesis")
17490 "This package provides functions for analysing, manipulating, displaying,
17491 editing and synthesizing time waves (particularly sound). This package
17492 processes time analysis (oscillograms and envelopes), spectral content,
17493 resonance quality factor, entropy, cross correlation and autocorrelation,
17494 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
17495 and 3D spectrograms and many other analyses.")
17496 (license license:gpl2+)))
17498 (define-public r-acousticndlcoder
17500 (name "r-acousticndlcoder")
17505 (uri (cran-uri "AcousticNDLCodeR" version))
17508 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
17510 `((upstream-name . "AcousticNDLCodeR")))
17511 (build-system r-build-system)
17513 `(("r-seewave" ,r-seewave)
17514 ("r-tuner" ,r-tuner)
17516 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
17517 (synopsis "Coding sound files for use with NDL")
17519 "Make acoustic cues to use with the R package @code{ndl}.
17520 The package implements functions used in the PLoS ONE paper \"Words from
17521 spontaneous conversational speech can be recognized with human-like accuracy
17522 by an error-driven learning algorithm that discriminates between meanings
17523 straight from smart acoustic features, bypassing the phoneme as recognition
17524 unit.\" @url{doi:10.1371/journal.pone.0174623}")
17525 (license license:gpl2+)))
17527 (define-public r-acp
17534 (uri (cran-uri "acp" version))
17537 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
17538 (properties `((upstream-name . "acp")))
17539 (build-system r-build-system)
17541 `(("r-quantmod" ,r-quantmod)
17542 ("r-tseries" ,r-tseries)))
17543 (home-page "https://cran.r-project.org/web/packages/acp/")
17544 (synopsis "Autoregressive conditional Poisson")
17546 "This package supports the analysis of count data exhibiting
17547 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
17548 model (ACP(p,q)) proposed by Heinen (2003).")
17549 (license license:gpl2)))
17551 (define-public r-ada
17558 (uri (cran-uri "ada" version))
17561 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
17562 (properties `((upstream-name . "ada")))
17563 (build-system r-build-system)
17564 (propagated-inputs `(("r-rpart" ,r-rpart)))
17565 (home-page "https://cran.r-project.org/web/packages/ada/")
17566 (synopsis "Stochastic boosting")
17568 "This package provides a straightforward, well-documented, and broad
17569 boosting routine for classification, ideally suited for small to
17570 moderate-sized data sets. It performs discrete, real, and gentle boost under
17571 both exponential and logistic loss on a given data set.")
17572 ;; Any version of the GPL.
17573 (license (list license:gpl2+ license:gpl3+))))
17575 (define-public r-genalg
17582 (uri (cran-uri "genalg" version))
17585 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
17586 (properties `((upstream-name . "genalg")))
17587 (build-system r-build-system)
17588 (home-page "https://github.com/egonw/genalg")
17589 (synopsis "R based genetic algorithm")
17591 "This package provides an R based genetic algorithm for binary and
17592 floating point chromosomes.")
17593 (license license:gpl2)))
17595 (define-public r-kernelfactory
17597 (name "r-kernelfactory")
17602 (uri (cran-uri "kernelFactory" version))
17605 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
17606 (properties `((upstream-name . "kernelFactory")))
17607 (build-system r-build-system)
17610 ("r-genalg" ,r-genalg)
17611 ("r-kernlab" ,r-kernlab)
17612 ("r-randomforest" ,r-randomforest)))
17613 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
17614 (synopsis "Ensemble of kernel machines")
17616 "Kernel factory is an ensemble method where each base classifier (random
17617 forest) is fit on the kernel matrix of a subset of the training data.")
17618 (license license:gpl2+)))
17620 (define-public r-dummies
17627 (uri (cran-uri "dummies" version))
17630 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
17631 (properties `((upstream-name . "dummies")))
17632 (build-system r-build-system)
17633 (home-page "https://decisionpatterns.com")
17634 (synopsis "Create dummy/indicator variables flexibly and efficiently")
17636 "This package lets you expand factors, characters and other eligible
17637 classes into dummy/indicator variables.")
17638 (license license:gpl2+)))
17640 (define-public r-acrm
17647 (uri (cran-uri "aCRM" version))
17650 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
17651 (properties `((upstream-name . "aCRM")))
17652 (build-system r-build-system)
17655 ("r-dummies" ,r-dummies)
17656 ("r-kernelfactory" ,r-kernelfactory)
17657 ("r-randomforest" ,r-randomforest)))
17658 (home-page "https://cran.r-project.org/web/packages/aCRM/")
17659 (synopsis "Convenience functions for analytical customer relationship management")
17661 "This package provides convenience functions for data preparation and
17662 modeling often used in @dfn{analytical customer relationship
17663 management} (aCRM).")
17664 (license license:gpl2+)))
17666 (define-public r-treeclust
17668 (name "r-treeclust")
17673 (uri (cran-uri "treeClust" version))
17676 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
17677 (properties `((upstream-name . "treeClust")))
17678 (build-system r-build-system)
17680 `(("r-cluster" ,r-cluster)
17681 ("r-rpart" ,r-rpart)))
17682 (home-page "https://cran.r-project.org/web/packages/treeClust/")
17683 (synopsis "Cluster distances through trees")
17685 "This package provides tools to create a measure of inter-point
17686 dissimilarity useful for clustering mixed data, and, optionally, perform the
17688 (license license:gpl2+)))
17690 (define-public r-acrosstic
17692 (name "r-acrosstic")
17697 (uri (cran-uri "AcrossTic" version))
17700 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
17701 (properties `((upstream-name . "AcrossTic")))
17702 (build-system r-build-system)
17704 `(("r-lpsolve" ,r-lpsolve)
17705 ("r-treeclust" ,r-treeclust)))
17706 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
17707 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
17709 "This is a package for constructing minimum-cost regular spanning
17710 subgraph as part of a non-parametric two-sample test for equality of
17712 (license license:gpl2+)))
17714 (define-public r-acrt
17721 (uri (cran-uri "acrt" version))
17724 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
17725 (properties `((upstream-name . "acrt")))
17726 (build-system r-build-system)
17728 `(("r-rcpp" ,r-rcpp)
17729 ("r-rcppeigen" ,r-rcppeigen)
17730 ("r-sandwich" ,r-sandwich)))
17731 (home-page "https://cran.r-project.org/web/packages/acrt/")
17732 (synopsis "Autocorrelation robust testing")
17734 "This package provides functions for testing affine hypotheses on the
17735 regression coefficient vector in regression models with autocorrelated
17737 (license license:gpl2)))
17739 (define-public r-acs
17746 (uri (cran-uri "acs" version))
17749 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
17750 (properties `((upstream-name . "acs")))
17751 (build-system r-build-system)
17753 `(("r-httr" ,r-httr)
17756 ("r-stringr" ,r-stringr)
17758 (home-page "http://dusp.mit.edu/faculty/ezra-glenn")
17759 (synopsis "Work with data from the US Census")
17761 "This package provides a general toolkit for downloading, managing,
17762 analyzing, and presenting data from the
17763 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
17764 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
17765 American Community Survey (ACS). Confidence intervals provided with ACS data
17766 are converted to standard errors to be bundled with estimates in complex
17767 @code{acs} objects. The package provides new methods to conduct standard
17768 operations on @code{acs} objects and present/plot data in statistically
17769 appropriate ways.")
17770 (license license:gpl3)))
17772 (define-public r-acss-data
17774 (name "r-acss-data")
17779 (uri (cran-uri "acss.data" version))
17782 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
17783 (properties `((upstream-name . "acss.data")))
17784 (build-system r-build-system)
17785 (home-page "http://complexitycalculator.com/methodology.html")
17786 (synopsis "Data for algorithmic complexity of short strings")
17788 "This is a data only package providing the algorithmic complexity of
17789 short strings, computed using the coding theorem method. For a given set of
17790 symbols in a string, all possible or a large number of random samples of
17791 Turing machines with a given number of states (e.g., 5) and number of symbols
17792 corresponding to the number of symbols in the strings were simulated until
17793 they reached a halting state or failed to end. This package contains data on
17794 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
17795 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
17796 distribution of the halting states.")
17797 (license license:gpl2+)))
17799 (define-public r-acss
17806 (uri (cran-uri "acss" version))
17809 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
17810 (properties `((upstream-name . "acss")))
17811 (build-system r-build-system)
17813 `(("r-acss-data" ,r-acss-data)
17815 (home-page "http://complexitycalculator.com/methodology.html")
17816 (synopsis "Algorithmic complexity for short strings")
17818 "The main purpose of this package is to provide the algorithmic
17819 complexity for short strings, an approximation of the Kolmogorov Complexity of
17820 a short string using the coding theorem method. While the database containing
17821 the complexity is provided in the data only package @code{acss.data}, this
17822 package provides functions accessing the data such as @code{prob_random}
17823 returning the posterior probability that a given string was produced by a
17824 random process. In addition, two traditional (but problematic) measures of
17825 complexity are also provided: entropy and change complexity.")
17826 (license license:gpl2+)))
17828 (define-public r-acswr
17835 (uri (cran-uri "ACSWR" version))
17838 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
17839 (properties `((upstream-name . "ACSWR")))
17840 (build-system r-build-system)
17842 `(("r-mass" ,r-mass)))
17843 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
17844 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
17846 "This is a companion package for the book \"A Course in Statistics with
17847 R\" (ISBN 978-1-119-15272-9.)")
17848 (license license:gpl2)))
17850 (define-public r-alabama
17853 (version "2015.3-1")
17857 (uri (cran-uri "alabama" version))
17860 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
17861 (properties `((upstream-name . "alabama")))
17862 (build-system r-build-system)
17863 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
17864 (home-page "https://cran.r-project.org/web/packages/alabama/")
17865 (synopsis "Constrained nonlinear optimization")
17867 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
17868 Algorithm; it is used for optimizing smooth nonlinear objective functions with
17869 constraints. Linear or nonlinear equality and inequality constraints are
17871 (license license:gpl2+)))
17873 (define-public r-gdina
17880 (uri (cran-uri "GDINA" version))
17883 "13pmj069r04h38hg61ibyn1ab15zdy9m0qv60vi25ahgsmg6ccvx"))))
17884 (properties `((upstream-name . "GDINA")))
17885 (build-system r-build-system)
17887 `(("r-alabama" ,r-alabama)
17888 ("r-ggplot2" ,r-ggplot2)
17890 ("r-nloptr" ,r-nloptr)
17891 ("r-numderiv" ,r-numderiv)
17893 ("r-rcpparmadillo" ,r-rcpparmadillo)
17894 ("r-rsolnp" ,r-rsolnp)
17895 ("r-shiny" ,r-shiny)
17896 ("r-shinydashboard" ,r-shinydashboard)))
17897 (home-page "https://github.com/Wenchao-Ma/GDINA")
17898 (synopsis "Generalized DINA model framework")
17900 "This package provides a set of psychometric tools for cognitive
17901 diagnosis modeling based on the generalized deterministic inputs, noisy and
17902 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
17903 and its extensions, including the sequential G-DINA model by Ma and de la
17904 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
17905 polytomous G-DINA model by Chen and de la Torre
17906 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
17907 distribution can be independent, saturated, higher-order, loglinear smoothed
17908 or structured. Q-matrix validation, item and model fit statistics, model
17909 comparison at test and item level and differential item functioning can also
17910 be conducted. A graphical user interface is also provided.")
17911 (license license:gpl3)))
17913 (define-public r-actcd
17920 (uri (cran-uri "ACTCD" version))
17923 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
17924 (properties `((upstream-name . "ACTCD")))
17925 (build-system r-build-system)
17927 `(("r-gdina" ,r-gdina)
17928 ("r-r-methodss3" ,r-r-methodss3)))
17930 `(("gfortran" ,gfortran)))
17931 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
17932 (synopsis "Asymptotic classification theory for cognitive diagnosis")
17934 "This is a package supporting cluster analysis for cognitive diagnosis
17935 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
17936 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
17937 sum-scores, cluster analysis techniques can be used to classify examinees into
17938 latent classes based on their attribute patterns. In addition to the
17939 algorithms used to classify data, three labeling approaches are proposed to
17940 label clusters so that examinees' attribute profiles can be obtained.")
17941 (license license:gpl2+)))
17943 (define-public r-ineq
17950 (uri (cran-uri "ineq" version))
17953 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
17954 (properties `((upstream-name . "ineq")))
17955 (build-system r-build-system)
17956 (home-page "https://cran.r-project.org/web/packages/ineq/")
17957 (synopsis "Measuring inequality, concentration, and poverty")
17959 "This package provides tools for measuring inequality, concentration, and
17960 poverty measures. It provides both empirical and theoretical Lorenz curves.")
17961 ;; Either of these two versions.
17962 (license (list license:gpl2 license:gpl3))))
17964 (define-public r-actfrag
17971 (uri (cran-uri "ActFrag" version))
17974 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
17975 (properties `((upstream-name . "ActFrag")))
17976 (build-system r-build-system)
17978 `(("r-accelerometry" ,r-accelerometry)
17979 ("r-dplyr" ,r-dplyr)
17981 ("r-survival" ,r-survival)
17982 ("r-tidyr" ,r-tidyr)))
17983 (home-page "https://github.com/junruidi/ActFrag")
17984 (synopsis "Activity fragmentation metrics extraction")
17986 "This package provides functions to extract commonly used fragmentation
17987 metrics to quantify time accumulation strategies based on minute level
17988 actigraphy-measured activity counts data.")
17989 (license license:gpl3)))
17991 (define-public r-fda
17994 (version "2.4.8.1")
17998 (uri (cran-uri "fda" version))
18001 "0g50kj1dx7zarjv0lgwyzd2c7bv6di7nkndmywday5vjywgl8m7a"))))
18002 (properties `((upstream-name . "fda")))
18003 (build-system r-build-system)
18005 `(("r-matrix" ,r-matrix)))
18006 (home-page "http://www.functionaldata.org")
18007 (synopsis "Functional data analysis")
18009 "These functions were developed to support functional data analysis as
18010 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
18011 Analysis. The package includes data sets and script files working many
18013 (license license:gpl2+)))
18015 (define-public r-actigraphy
18017 (name "r-actigraphy")
18022 (uri (cran-uri "Actigraphy" version))
18025 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
18026 (properties `((upstream-name . "Actigraphy")))
18027 (build-system r-build-system)
18029 `(("r-fda" ,r-fda)))
18030 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
18031 (synopsis "Actigraphy data analysis")
18033 "This package provides tools for functional linear modeling and analysis
18034 of actigraphy data.")
18035 (license license:asl2.0)))
18037 (define-public r-activedriver
18039 (name "r-activedriver")
18044 (uri (cran-uri "ActiveDriver" version))
18047 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
18048 (properties `((upstream-name . "ActiveDriver")))
18049 (build-system r-build-system)
18051 `(("r-mass" ,r-mass)))
18052 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
18053 (synopsis "Tools for finding cancer driver proteins")
18055 "This package provides a mutation analysis tool that discovers cancer
18056 driver genes with frequent mutations in protein signalling sites such as
18057 post-translational modifications (phosphorylation, ubiquitination, etc). The
18058 Poisson generalized linear regression model identifies genes where cancer
18059 mutations in signalling sites are more frequent than expected from the
18060 sequence of the entire gene. Integration of mutations with signalling
18061 information helps find new driver genes and propose candidate mechanisms to
18063 (license license:gpl2+)))
18065 (define-public r-activitycounts
18067 (name "r-activitycounts")
18072 (uri (cran-uri "activityCounts" version))
18075 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
18077 `((upstream-name . "activityCounts")))
18078 (build-system r-build-system)
18080 `(("r-lubridate" ,r-lubridate)
18081 ("r-magrittr" ,r-magrittr)
18082 ("r-seewave" ,r-seewave)
18083 ("r-signal" ,r-signal)
18084 ("r-tibble" ,r-tibble)))
18085 (home-page "https://github.com/walkabillylab/activityCounts")
18086 (synopsis "Generate ActiLife counts")
18088 "ActiLife generates activity counts from data collected by Actigraph
18089 accelerometers. Actigraph is one of the most common research-grade
18090 accelerometers. There is considerable research validating and developing
18091 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
18092 counts are proprietary and difficult to implement if researchers use different
18093 accelerometer brands. The code creates ActiLife counts from raw acceleration
18094 data for different accelerometer brands.")
18095 (license license:gpl3)))
18097 (define-public r-activityindex
18099 (name "r-activityindex")
18104 (uri (cran-uri "ActivityIndex" version))
18107 "14k6d78s15j7kb7jhixf4msrdjdl28d0r264cbvy41p8dkq7ysvk"))))
18108 (properties `((upstream-name . "ActivityIndex")))
18109 (build-system r-build-system)
18111 `(("r-data-table" ,r-data-table)
18112 ("r-matrixstats" ,r-matrixstats)
18113 ("r-r-utils" ,r-r-utils)))
18114 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
18115 (synopsis "Activity Index calculation using raw accelerometry data")
18117 "This is a package to read raw accelerometry from GT3X+ accelerometry
18118 data and plain table data to calculate the Activity Index from Bai et
18119 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
18120 (license license:gpl3)))
18122 (define-public r-activpal
18124 (name "r-activpal")
18129 (uri (cran-uri "activPAL" version))
18132 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
18133 (properties `((upstream-name . "activPAL")))
18134 (build-system r-build-system)
18136 `(("r-devtools" ,r-devtools)
18137 ("r-dplyr" ,r-dplyr)
18138 ("r-ggplot2" ,r-ggplot2)
18139 ("r-lubridate" ,r-lubridate)
18140 ("r-magrittr" ,r-magrittr)
18141 ("r-tidyr" ,r-tidyr)))
18142 (home-page "https://cran.r-project.org/web/packages/activPAL")
18143 (synopsis "Processing and chart generation from activPAL events files")
18145 "This package contains functions to generate pre-defined summary
18146 statistics from activPAL events files. The package also contains functions to
18147 produce informative graphics that visualize physical activity behaviour and
18148 trends. This includes generating graphs that align physical activity
18149 behaviour with additional time based observations described by other data
18150 sets, such as sleep diaries and continuous glucose monitoring data.")
18151 (license license:gpl3)))
18153 (define-public r-activpalprocessing
18155 (name "r-activpalprocessing")
18160 (uri (cran-uri "activpalProcessing" version))
18163 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
18165 `((upstream-name . "activpalProcessing")))
18166 (build-system r-build-system)
18168 `(("r-chron" ,r-chron)))
18169 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
18170 (synopsis "Process activPAL events files")
18172 "This package performs estimation of physical activity and sedentary
18173 behavior variables from activPAL events files.")
18174 ;; Either version of the GPL.
18175 (license (list license:gpl2 license:gpl3))))
18177 (define-public r-actogrammr
18179 (name "r-actogrammr")
18184 (uri (cran-uri "actogrammr" version))
18187 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
18188 (properties `((upstream-name . "actogrammr")))
18189 (build-system r-build-system)
18191 `(("r-dplyr" ,r-dplyr)
18192 ("r-ggplot2" ,r-ggplot2)
18193 ("r-lubridate" ,r-lubridate)
18194 ("r-readr" ,r-readr)
18195 ("r-tidyr" ,r-tidyr)))
18196 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
18197 (synopsis "Read in activity data and plot actograms")
18199 "Read in activity measurements from standard file formats used by
18200 circadian rhythm researchers, currently only ClockLab format, and process and
18201 plot the data. The central type of plot is the actogram, as first described
18202 in \"Activity and distribution of certain wild mice in relation to biotic
18203 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
18204 (license license:gpl3)))
18206 (define-public r-expint
18213 (uri (cran-uri "expint" version))
18216 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
18217 (properties `((upstream-name . "expint")))
18218 (build-system r-build-system)
18219 (home-page "https://gitlab.com/vigou3/expint")
18220 (synopsis "Exponential integral and incomplete Gamma function")
18222 "This package provides the exponential integrals @code{E_1(x)},
18223 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
18224 function @code{G(a, x)} defined for negative values of its first argument.
18225 The package also gives easy access to the underlying C routines through an
18226 API; see the package vignette for details.")
18227 (license license:gpl2+)))
18229 (define-public r-actuar
18236 (uri (cran-uri "actuar" version))
18239 "0aw3hlan5y22mdqk1wvnw9ksqhwp4yy5hi0dpv21p7s0hyxhphih"))))
18240 (properties `((upstream-name . "actuar")))
18241 (build-system r-build-system)
18242 (propagated-inputs `(("r-expint" ,r-expint)))
18243 (home-page "https://gitlab.com/vigou3/actuar")
18244 (synopsis "Actuarial functions and heavy tailed distributions")
18246 "This package provides functions and data sets for actuarial science:
18247 modeling of loss distributions; risk theory and ruin theory; simulation of
18248 compound models, discrete mixtures and compound hierarchical models;
18249 credibility theory. It boasts support for many additional probability
18250 distributions to model insurance loss amounts and loss frequency: 19
18251 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
18252 distribution; zero-truncated and zero-modified extensions of the standard
18253 discrete distributions. It also supports phase-type distributions commonly
18254 used to compute ruin probabilities.")
18255 (license license:gpl2+)))
18257 (define-public r-bmp
18264 (uri (cran-uri "bmp" version))
18267 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
18268 (properties `((upstream-name . "bmp")))
18269 (build-system r-build-system)
18270 (home-page "https://cran.r-project.org/web/packages/bmp/")
18271 (synopsis "Read Bitmap (BMP) images")
18273 "This package provides pure R tools to read BMP format images. It is
18274 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
18275 (license license:gpl2+)))
18277 (define-public r-readbitmap
18279 (name "r-readbitmap")
18284 (uri (cran-uri "readbitmap" version))
18287 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
18288 (properties `((upstream-name . "readbitmap")))
18289 (build-system r-build-system)
18291 `(("libjpeg" ,libjpeg)
18292 ("libpng" ,libpng)))
18297 ("r-tiff" ,r-tiff)))
18298 (home-page "https://github.com/jefferis/readbitmap")
18299 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
18301 "This package provides tools to identify and read BMP, JPEG, PNG, and
18302 TIFF format bitmap images. Identification defaults to the use of the magic
18303 number embedded in the file rather than the file extension.")
18304 (license license:gpl2+)))
18306 (define-public r-imager
18313 (uri (cran-uri "imager" version))
18316 "1d7a49lcna77wyfjf5q1b89jck3p3vnysnkgz4drb0qkpy6hz76b"))))
18317 (properties `((upstream-name . "imager")))
18318 (build-system r-build-system)
18321 ("libtiff" ,libtiff)
18325 `(("r-downloader" ,r-downloader)
18326 ("r-igraph" ,r-igraph)
18328 ("r-magrittr" ,r-magrittr)
18330 ("r-purrr" ,r-purrr)
18332 ("r-readbitmap" ,r-readbitmap)
18333 ("r-stringr" ,r-stringr)))
18334 (native-inputs `(("pkg-config" ,pkg-config)))
18335 (home-page "http://dahtah.github.io/imager")
18336 (synopsis "Image processing library")
18338 "This is a package for fast image processing for images in up to 4
18339 dimensions (two spatial dimensions, one time/depth dimension, one color
18340 dimension). It provides most traditional image processing tools (filtering,
18341 morphology, transformations, etc.) as well as various functions for easily
18342 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
18343 simple, modern C++ library for image processing.")
18344 (license license:lgpl3)))
18346 (define-public r-acuityview
18348 (name "r-acuityview")
18353 (uri (cran-uri "AcuityView" version))
18356 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
18357 (properties `((upstream-name . "AcuityView")))
18358 (build-system r-build-system)
18360 `(("r-fftwtools" ,r-fftwtools)
18361 ("r-imager" ,r-imager)
18362 ("r-plotrix" ,r-plotrix)))
18363 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
18364 (synopsis "Display scenes as seen by an animal with less acute vision")
18366 "This package provides a simple method for representing a visual scene as
18367 it may be seen by an animal with less acute vision.")
18368 (license license:gpl2+)))
18370 (define-public r-caret
18377 (uri (cran-uri "caret" version))
18380 "0jxbf2zcvbb5s2pnjzg182awjvylc57q7z5plx6gs6gm62zxjafs"))))
18381 (build-system r-build-system)
18383 `(("r-foreach" ,r-foreach)
18384 ("r-ggplot2" ,r-ggplot2)
18385 ("r-lattice" ,r-lattice)
18386 ("r-modelmetrics" ,r-modelmetrics)
18390 ("r-recipes" ,r-recipes)
18391 ("r-reshape2" ,r-reshape2)
18392 ("r-withr" ,r-withr)))
18393 (home-page "https://github.com/topepo/caret")
18394 (synopsis "Classification and regression training")
18396 "This package provides miscellaneous functions for training and plotting
18397 classification and regression models.")
18398 (license license:gpl2+)))
18400 (define-public r-adabag
18407 (uri (cran-uri "adabag" version))
18410 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
18411 (properties `((upstream-name . "adabag")))
18412 (build-system r-build-system)
18414 `(("r-caret" ,r-caret)
18415 ("r-doparallel" ,r-doparallel)
18416 ("r-foreach" ,r-foreach)
18417 ("r-rpart" ,r-rpart)))
18418 (home-page "https://cran.r-project.org/web/packages/adabag/")
18419 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
18421 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
18422 Breiman's Bagging algorithm using classification trees as individual
18423 classifiers. Once these classifiers have been trained, they can be used to
18424 predict on new data. Also, cross validation estimation of the error can be
18426 (license license:gpl2+)))
18428 (define-public r-adagio
18435 (uri (cran-uri "adagio" version))
18438 "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
18439 (properties `((upstream-name . "adagio")))
18440 (build-system r-build-system)
18441 (native-inputs `(("gfortran" ,gfortran)))
18442 (home-page "https://cran.r-project.org/web/packages/adagio/")
18443 (synopsis "Discrete and global optimization routines")
18445 "This package provides methods and algorithms for discrete optimization,
18446 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
18447 Hooke-Jeeves minimization, and some (evolutionary) global optimization
18449 (license license:gpl3+)))
18451 (define-public r-univoutl
18453 (name "r-univoutl")
18458 (uri (cran-uri "univOutl" version))
18461 "193wrpkvgmlrx43nag8w3ivrlqm37nm6g86wcvd3bgw3hchs70gi"))))
18462 (properties `((upstream-name . "univOutl")))
18463 (build-system r-build-system)
18465 `(("r-hmisc" ,r-hmisc)
18466 ("r-robustbase" ,r-robustbase)))
18467 (home-page "https://github.com/marcellodo/univOutl")
18468 (synopsis "Detection of univariate outliers")
18470 "This package provides well-known outlier detection techniques in the
18471 univariate case. Methods to deal with skewed distribution are included too.
18472 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
18473 historical data is implemented as well. When available, survey weights can be
18474 used in outliers detection.")
18475 (license license:gpl2+)))
18477 (define-public r-tolerance
18479 (name "r-tolerance")
18484 (uri (cran-uri "tolerance" version))
18487 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
18488 (properties `((upstream-name . "tolerance")))
18489 (build-system r-build-system)
18491 `(("r-mass" ,r-mass)
18493 (home-page "https://cran.r-project.org/web/packages/tolerance/")
18494 (synopsis "Statistical tolerance intervals and regions")
18496 "This package provides functions for estimating tolerance
18497 limits (intervals) for various univariate distributions (binomial, Cauchy,
18498 discrete Pareto, exponential, two-parameter exponential, extreme value,
18499 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
18500 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
18501 Bayesian normal tolerance limits, multivariate normal tolerance regions,
18502 nonparametric tolerance intervals, tolerance bands for regression
18503 settings (linear regression, nonlinear regression, nonparametric regression,
18504 and multivariate regression), and analysis of variance tolerance intervals.
18505 Visualizations are also available for most of these settings.")
18506 (license license:gpl2+)))
18508 (define-public r-additivitytests
18510 (name "r-additivitytests")
18515 (uri (cran-uri "additivityTests" version))
18518 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
18520 `((upstream-name . "additivityTests")))
18521 (build-system r-build-system)
18522 (home-page "https://github.com/simecek/additivityTests")
18523 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
18525 "This package provides an implementation of the Tukey, Mandel,
18526 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
18527 (license license:gpl3)))
18529 (define-public r-flexclust
18531 (name "r-flexclust")
18536 (uri (cran-uri "flexclust" version))
18539 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
18540 (properties `((upstream-name . "flexclust")))
18541 (build-system r-build-system)
18543 `(("r-class" ,r-class)
18544 ("r-lattice" ,r-lattice)
18545 ("r-modeltools" ,r-modeltools)))
18546 (home-page "https://cran.r-project.org/web/packages/flexclust/")
18547 (synopsis "Flexible cluster algorithms")
18549 "The main function @code{kcca} implements a general framework for
18550 k-centroids cluster analysis supporting arbitrary distance measures and
18551 centroid computation. Further cluster methods include hard competitive
18552 learning, neural gas, and QT clustering. There are numerous visualization
18553 methods for cluster results (neighborhood graphs, convex cluster hulls,
18554 barcharts of centroids, ...), and bootstrap methods for the analysis of
18555 cluster stability.")
18556 (license license:gpl2)))
18558 (define-public r-biclust
18565 (uri (cran-uri "biclust" version))
18568 "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b"))))
18569 (properties `((upstream-name . "biclust")))
18570 (build-system r-build-system)
18572 `(("r-additivitytests" ,r-additivitytests)
18573 ("r-colorspace" ,r-colorspace)
18574 ("r-flexclust" ,r-flexclust)
18575 ("r-ggplot2" ,r-ggplot2)
18576 ("r-lattice" ,r-lattice)
18578 ("r-tidyr" ,r-tidyr)))
18579 (home-page "https://cran.r-project.org/web/packages/biclust/")
18580 (synopsis "BiCluster algorithms")
18582 "The main function @code{biclust()} provides several algorithms to find
18583 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
18584 In addition, the package provides methods for data
18585 preprocessing (normalization and discretization), visualization, and
18586 validation of bicluster solutions.")
18587 (license license:gpl3)))
18589 (define-public r-icge
18596 (uri (cran-uri "ICGE" version))
18599 "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
18600 (properties `((upstream-name . "ICGE")))
18601 (build-system r-build-system)
18603 `(("r-cluster" ,r-cluster)
18604 ("r-mass" ,r-mass)))
18605 (home-page "https://cran.r-project.org/web/packages/ICGE/")
18606 (synopsis "Cluster estimation and identification of atypical units")
18608 "ICGE is a package that helps to estimate the number of real clusters in
18609 data as well as to identify atypical units. The underlying methods are based
18610 on distances rather than on unit x variables.")
18611 (license license:gpl2+)))
18613 (define-public r-depth
18616 (version "2.1-1.1")
18620 (uri (cran-uri "depth" version))
18623 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
18624 (properties `((upstream-name . "depth")))
18625 (build-system r-build-system)
18627 `(("r-abind" ,r-abind)
18628 ("r-circular" ,r-circular)
18631 `(("gfortran" ,gfortran)))
18632 (home-page "https://cran.r-project.org/web/packages/depth/")
18633 (synopsis "Nonparametric depth functions for multivariate analysis")
18635 "This package provides tools for depth functions methodology applied to
18636 multivariate analysis. Besides allowing calculation of depth values and
18637 depth-based location estimators, the package includes functions or drawing
18638 contour plots and perspective plots of depth functions. Euclidian and
18639 spherical depths are supported.")
18640 (license license:gpl2)))
18642 (define-public r-archetypes
18644 (name "r-archetypes")
18645 (version "2.2-0.1")
18649 (uri (cran-uri "archetypes" version))
18652 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
18653 (properties `((upstream-name . "archetypes")))
18654 (build-system r-build-system)
18656 `(("r-modeltools" ,r-modeltools)
18657 ("r-nnls" ,r-nnls)))
18658 (home-page "https://cran.r-project.org/web/packages/archetypes")
18659 (synopsis "Archetypal analysis")
18661 "The main function @code{archetypes} implements a framework for
18662 archetypal analysis supporting arbitrary problem solving mechanisms for the
18663 different conceptual parts of the algorithm.")
18664 (license license:gpl2+)))
18666 (define-public r-shapes
18673 (uri (cran-uri "shapes" version))
18676 "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s"))))
18677 (properties `((upstream-name . "shapes")))
18678 (build-system r-build-system)
18680 `(("r-mass" ,r-mass)
18681 ("r-minpack-lm" ,r-minpack-lm)
18683 ("r-scatterplot3d" ,r-scatterplot3d)))
18684 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
18685 (synopsis "Statistical shape analysis")
18687 "This package provides routines for the statistical analysis of landmark
18688 shapes, including Procrustes analysis, graphical displays, principal
18689 components analysis, permutation and bootstrap tests, thin-plate spline
18690 transformation grids and comparing covariance matrices. See Dryden, I.L. and
18691 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
18692 Edition), John Wiley and Sons.")
18693 (license license:gpl2)))
18695 (define-public r-anthropometry
18697 (name "r-anthropometry")
18702 (uri (cran-uri "Anthropometry" version))
18705 "1f568ri1s6psaby8y737vrkarbjg64v89d4jyw23hy17apdmszr8"))))
18706 (properties `((upstream-name . "Anthropometry")))
18707 (build-system r-build-system)
18709 `(("r-archetypes" ,r-archetypes)
18710 ("r-biclust" ,r-biclust)
18711 ("r-cluster" ,r-cluster)
18712 ("r-depth" ,r-depth)
18717 ("r-shapes" ,r-shapes)))
18718 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
18719 (synopsis "Statistical methods for anthropometric data")
18721 "This package provides statistical methods especially developed to
18722 analyze anthropometric data. These methods are aimed at providing effective
18723 solutions to some commons problems related to Ergonomics and Anthropometry.
18724 They are based on clustering, the statistical concept of data depth,
18725 statistical shape analysis and archetypal analysis.")
18726 (license license:gpl2+)))
18728 (define-public r-adamethods
18730 (name "r-adamethods")
18735 (uri (cran-uri "adamethods" version))
18738 "0mp73zh5x6h18gv29v981kb9n632kb58lvlcxwr6vcvrx393nrxh"))))
18739 (properties `((upstream-name . "adamethods")))
18740 (build-system r-build-system)
18742 `(("r-anthropometry" ,r-anthropometry)
18743 ("r-archetypes" ,r-archetypes)
18745 ("r-foreach" ,r-foreach)
18747 ("r-tolerance" ,r-tolerance)
18748 ("r-univoutl" ,r-univoutl)))
18749 (home-page "https://cran.r-project.org/web/packages/adamethods/")
18750 (synopsis "Archetypoid algorithms and anomaly detection")
18752 "This package is a collection of several algorithms to obtain
18753 archetypoids with small and large databases and with both classical
18754 multivariate data and functional data (univariate and multivariate). Some of
18755 these algorithms also allow to detect anomalies (outliers).")
18756 (license license:gpl2+)))
18758 (define-public r-idpmisc
18765 (uri (cran-uri "IDPmisc" version))
18768 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
18769 (properties `((upstream-name . "IDPmisc")))
18770 (build-system r-build-system)
18772 `(("r-lattice" ,r-lattice)))
18773 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
18774 (synopsis "Functions for data analyses and visualization")
18776 "This package provides different high-level graphics functions for
18777 displaying large datasets, displaying circular data in a very flexible way,
18778 finding local maxima, brewing color ramps, drawing nice arrows, zooming
18779 2D-plots, creating figures with differently colored margin and plot region.
18780 In addition, the package contains auxiliary functions for data manipulation
18781 like omitting observations with irregular values or selecting data by logical
18782 vectors, which include NAs. Other functions are especially useful in
18783 spectroscopy and analyses of environmental data: robust baseline fitting,
18784 finding peaks in spectra, converting humidity measures.")
18785 (license license:gpl3+)))
18787 (define-public r-qqman
18794 (uri (cran-uri "qqman" version))
18797 "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
18798 (properties `((upstream-name . "qqman")))
18799 (build-system r-build-system)
18801 `(("r-calibrate" ,r-calibrate)))
18802 (home-page "https://cran.r-project.org/web/packages/qqman/")
18803 (synopsis "Q-Q and Manhattan plots for GWAS data")
18805 "This package allows you to create Q-Q and Manhattan plots for GWAS data
18806 from PLINK results.")
18807 (license license:gpl3)))
18809 (define-public r-ggplot-multistats
18811 (name "r-ggplot-multistats")
18816 (uri (cran-uri "ggplot.multistats" version))
18819 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
18821 `((upstream-name . "ggplot.multistats")))
18822 (build-system r-build-system)
18824 `(("r-ggplot2" ,r-ggplot2)
18825 ("r-hexbin" ,r-hexbin)
18826 ("r-rlang" ,r-rlang)
18827 ("r-scales" ,r-scales)))
18828 (home-page "https://github.com/flying-sheep/ggplot.multistats")
18829 (synopsis "Multiple summary statistics for binned stats/geometries")
18831 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
18832 which functions similar to its singular form, but allows the use of multiple
18833 statistics per bin. Those statistics can be mapped to multiple bin
18835 (license license:gpl3)))
18837 (define-public r-knn-covertree
18839 (name "r-knn-covertree")
18844 (uri (cran-uri "knn.covertree" version))
18847 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
18848 (properties `((upstream-name . "knn.covertree")))
18849 (build-system r-build-system)
18851 `(("r-matrix" ,r-matrix)
18853 ("r-rcppeigen" ,r-rcppeigen)))
18854 (home-page "https://github.com/flying-sheep/knn.covertree")
18855 (synopsis "Accurate kNN Implementation with multiple distance measures")
18857 "Similarly to the FNN package, this package allows calculation of the k
18858 nearest neighbors (kNN) of a data matrix. The implementation is based on
18859 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
18860 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
18861 (license license:agpl3+)))
18863 (define-public r-poibin
18870 (uri (cran-uri "poibin" version))
18873 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
18874 (properties `((upstream-name . "poibin")))
18875 (build-system r-build-system)
18876 (home-page "https://cran.r-project.org/web/packages/poibin/")
18877 (synopsis "Poisson binomial distribution")
18879 "This package provides an implementation of both the exact and
18880 approximation methods for computing the @dfn{cumulative distribution
18881 function} (CDF) of the Poisson binomial distribution. It also provides the
18882 @dfn{probability mass function} (PMF), quantile function, and random number
18883 generation for the Poisson binomial distribution.")
18884 (license license:gpl2)))
18886 (define-public r-diagram
18893 (uri (cran-uri "diagram" version))
18896 "0f6ffprn5k0ir1s7m9s7izc64aa17r3gnygagz5bihrlsvawaavw"))))
18897 (properties `((upstream-name . "diagram")))
18898 (build-system r-build-system)
18900 `(("r-shape" ,r-shape)))
18901 (home-page "https://cran.r-project.org/web/packages/diagram/")
18902 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
18904 "This package provides tools to visualize simple graphs (networks) based
18905 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
18906 electrical networks, etc. It also includes supporting material for the book
18907 \"A practical guide to ecological modelling - using R as a simulation
18908 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
18909 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
18910 Francesca Mazzia (2012).")
18911 (license license:gpl2+)))
18913 (define-public r-lim
18920 (uri (cran-uri "LIM" version))
18923 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
18924 (properties `((upstream-name . "LIM")))
18925 (build-system r-build-system)
18927 `(("r-diagram" ,r-diagram)
18928 ("r-limsolve" ,r-limsolve)))
18929 (home-page "https://cran.r-project.org/web/packages/LIM/")
18930 (synopsis "Linear inverse model examples and solution methods")
18932 "This package provides functions that read and solve linear inverse
18933 problems (food web problems, linear programming problems).")
18934 (license license:gpl2+)))
18936 (define-public r-shinycssloaders
18938 (name "r-shinycssloaders")
18943 (uri (cran-uri "shinycssloaders" version))
18946 "1gzq1lhcnhqd145ys3ixf0l13l560fiqr2sc3m2nrijwxlgcw54d"))))
18948 `((upstream-name . "shinycssloaders")))
18949 (build-system r-build-system)
18951 `(("r-digest" ,r-digest)
18953 ("r-shiny" ,r-shiny)))
18954 (home-page "https://github.com/andrewsali/shinycssloaders")
18955 (synopsis "Add CSS loading animations to Shiny outputs")
18957 "This package provides tools to create a lightweight Shiny wrapper for
18958 the css-loaders created by Luke Hass
18959 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
18960 automatically show a loader when the output is (re)calculating.")
18961 (license license:gpl3)))
18963 (define-public r-rsvg
18970 (uri (cran-uri "rsvg" version))
18973 "11mccgf6hfskg45wqc114sx3qy2r494y6axdf73z6xwhs1wpm97g"))))
18974 (properties `((upstream-name . "rsvg")))
18975 (build-system r-build-system)
18977 `(("librsvg" ,librsvg)
18980 `(("pkg-config" ,pkg-config)))
18981 (home-page "https://github.com/jeroen/rsvg#readme")
18982 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
18984 "This package allows you to render vector-based SVG images into
18985 high-quality custom-size bitmap arrays using the librsvg2 library. The
18986 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
18987 addition, the package can convert images directly to various formats such as
18988 PDF or PostScript.")
18989 (license license:expat)))
18991 (define-public r-influencer
18993 (name "r-influencer")
18998 (uri (cran-uri "influenceR" version))
19001 "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
19002 (properties `((upstream-name . "influenceR")))
19003 (build-system r-build-system)
19005 `(("r-igraph" ,r-igraph)
19006 ("r-matrix" ,r-matrix)))
19007 (home-page "https://github.com/rcc-uchicago/influenceR")
19008 (synopsis "Tools to quantify structural importance of nodes in a network")
19010 "This package provides functionality to compute various node centrality
19011 measures on networks. Included are functions to compute betweenness
19012 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
19013 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
19014 algorithm to identify key players, and Valente's bridging metric. The
19015 betweenness, Key Players, and bridging implementations are parallelized with
19017 (license license:gpl2)))
19019 (define-public r-emplik
19022 (version "1.0-4.3")
19026 (uri (cran-uri "emplik" version))
19029 "1g4hz85bvw29c77zs0ig487z92jjl682vv457x81l077h0psvk7c"))))
19030 (properties `((upstream-name . "emplik")))
19031 (build-system r-build-system)
19033 `(("r-quantreg" ,r-quantreg)))
19034 (home-page "http://www.ms.uky.edu/~mai/EmpLik.html")
19035 (synopsis "Empirical likelihood ratio for censored/truncated data")
19037 "This package provides empirical likelihood ratio tests for
19038 means/quantiles/hazards from possibly censored and/or truncated data. It also
19040 (license license:gpl2+)))
19042 (define-public r-imputeyn
19044 (name "r-imputeyn")
19049 (uri (cran-uri "imputeYn" version))
19052 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
19053 (properties `((upstream-name . "imputeYn")))
19054 (build-system r-build-system)
19056 `(("r-boot" ,r-boot)
19057 ("r-emplik" ,r-emplik)
19058 ("r-mvtnorm" ,r-mvtnorm)
19059 ("r-quadprog" ,r-quadprog)
19060 ("r-survival" ,r-survival)))
19061 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
19062 (synopsis "Impute last largest censored observation under weighted least squares")
19064 "This package allows for the imputation of the last largest censored
19065 observantions. This method brings less bias and more efficient estimates for
19067 (license license:gpl2)))
19069 (define-public r-adapenetclass
19071 (name "r-adapenetclass")
19076 (uri (cran-uri "AdapEnetClass" version))
19079 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
19080 (properties `((upstream-name . "AdapEnetClass")))
19081 (build-system r-build-system)
19083 `(("r-glmnet" ,r-glmnet)
19084 ("r-imputeyn" ,r-imputeyn)
19086 ("r-quadprog" ,r-quadprog)))
19087 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
19088 (synopsis "Class of adaptive elastic net methods for censored data")
19090 "This package provides methods for variable selection for AFT models.")
19091 (license license:gpl2)))
19093 (define-public r-flock
19100 (uri (cran-uri "flock" version))
19103 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
19104 (properties `((upstream-name . "flock")))
19105 (build-system r-build-system)
19106 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
19107 (home-page "https://cran.r-project.org/web/packages/flock/")
19108 (synopsis "Process synchronization using file locks")
19110 "This package implements synchronization between R processes (spawned by
19111 using the @code{parallel} package for instance) using file locks. It supports
19112 both exclusive and shared locking.")
19113 (license license:asl2.0)))
19115 (define-public r-archivist
19117 (name "r-archivist")
19122 (uri (cran-uri "archivist" version))
19125 "1i11hrcq1910jgd6diw6h3sxx624v57zjianm49pqvb2dvd0b8y7"))))
19126 (properties `((upstream-name . "archivist")))
19127 (build-system r-build-system)
19130 ("r-digest" ,r-digest)
19131 ("r-flock" ,r-flock)
19133 ("r-lubridate" ,r-lubridate)
19134 ("r-magrittr" ,r-magrittr)
19135 ("r-rcurl" ,r-rcurl)
19136 ("r-rsqlite" ,r-rsqlite)))
19137 (home-page "https://pbiecek.github.io/archivist/")
19138 (synopsis "Tools for storing, restoring and searching for R objects")
19140 "Data exploration and modelling is a process in which a lot of data
19141 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
19142 statistical models, different versions of data sets and different versions of
19143 results. Archivist helps to store and manage artifacts created in R. It
19144 allows you to store selected artifacts as binary files together with their
19145 metadata and relations. Archivist allows sharing artifacts with others. It
19146 can look for already created artifacts by using its class, name, date of the
19147 creation or other properties. It also makes it easy to restore such
19149 (license license:gpl2)))
19151 (define-public r-versions
19153 (name "r-versions")
19158 (uri (cran-uri "versions" version))
19161 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
19162 (properties `((upstream-name . "versions")))
19163 (build-system r-build-system)
19164 (home-page "https://cran.r-project.org/web/packages/versions/")
19165 (synopsis "Query and install specific versions of CRAN packages")
19167 "This package allows you to install specified versions of R packages
19168 hosted on CRAN and provides functions to list available versions and the
19169 versions of currently installed packages.")
19170 (license license:bsd-3)))
19172 (define-public r-adapr
19179 (uri (cran-uri "adapr" version))
19182 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
19183 (properties `((upstream-name . "adapr")))
19184 (build-system r-build-system)
19186 `(("r-archivist" ,r-archivist)
19187 ("r-devtools" ,r-devtools)
19188 ("r-digest" ,r-digest)
19189 ("r-doparallel" ,r-doparallel)
19190 ("r-gdata" ,r-gdata)
19191 ("r-ggplot2" ,r-ggplot2)
19192 ("r-git2r" ,r-git2r)
19193 ("r-igraph" ,r-igraph)
19194 ("r-knitr" ,r-knitr)
19195 ("r-plotly" ,r-plotly)
19197 ("r-rmarkdown" ,r-rmarkdown)
19198 ("r-shiny" ,r-shiny)
19199 ("r-shinydashboard" ,r-shinydashboard)
19200 ("r-versions" ,r-versions)))
19201 (home-page "https://cran.r-project.org/web/packages/adapr/")
19202 (synopsis "Implementation of an accountable data analysis process")
19204 "This package tracks reading and writing within R scripts that are
19205 organized into a directed acyclic graph. It contains an interactive Shiny
19206 application @code{adaprApp()}. It uses Git and file hashes to track version
19207 histories of inputs and outputs.")
19208 (license license:lgpl2.0)))
19210 (define-public r-adapsamp
19212 (name "r-adapsamp")
19217 (uri (cran-uri "AdapSamp" version))
19220 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
19221 (properties `((upstream-name . "AdapSamp")))
19222 (build-system r-build-system)
19223 (propagated-inputs `(("r-pracma" ,r-pracma)))
19224 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
19225 (synopsis "Adaptive sampling algorithms")
19227 "For distributions whose probability density functions are log-concave,
19228 the adaptive rejection sampling algorithm can be used to build envelope
19229 functions for sampling. For others, the modified adaptive rejection sampling
19230 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
19231 adaptive slice sampling algorithm can be used. This R package mainly includes
19232 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
19233 @code{rASS()}. These functions can realize sampling based on the algorithms
19235 (license license:gpl2)))
19237 (define-public r-adaptalint
19239 (name "r-adaptalint")
19244 (uri (cran-uri "adaptalint" version))
19247 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
19248 (properties `((upstream-name . "adaptalint")))
19249 (build-system r-build-system)
19251 `(("r-dplyr" ,r-dplyr)
19252 ("r-lintr" ,r-lintr)
19253 ("r-purrr" ,r-purrr)))
19254 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
19255 (synopsis "Check R code style")
19257 "This package provides tools to infer the code style (which style rules
19258 are followed and which ones are not) from one package and use it to check
19259 another. This makes it easier to find and correct the most important problems
19261 (license license:gpl3)))
19263 (define-public r-fracdiff
19265 (name "r-fracdiff")
19270 (uri (cran-uri "fracdiff" version))
19273 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
19274 (properties `((upstream-name . "fracdiff")))
19275 (build-system r-build-system)
19276 (home-page "https://github.com/mmaechler/fracdiff")
19278 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
19280 "This package provides tools for the maximum likelihood estimation of the
19281 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
19282 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
19283 (license license:gpl2+)))
19285 (define-public r-forecast
19287 (name "r-forecast")
19292 (uri (cran-uri "forecast" version))
19295 "0ayidhnk9cxav2qi83jrvqlg2jh4zlf4lki4xw48gdqsmjvih9x1"))))
19296 (properties `((upstream-name . "forecast")))
19297 (build-system r-build-system)
19299 `(("r-colorspace" ,r-colorspace)
19300 ("r-fracdiff" ,r-fracdiff)
19301 ("r-ggplot2" ,r-ggplot2)
19302 ("r-lmtest" ,r-lmtest)
19303 ("r-magrittr" ,r-magrittr)
19306 ("r-rcpparmadillo" ,r-rcpparmadillo)
19307 ("r-timedate" ,r-timedate)
19308 ("r-tseries" ,r-tseries)
19312 `(("r-knitr" ,r-knitr))) ; needed for vignettes
19313 (home-page "https://pkg.robjhyndman.com/forecast/")
19314 (synopsis "Forecasting functions for time series and linear models")
19316 "This package provides methods and tools for displaying and analysing
19317 univariate time series forecasts including exponential smoothing via state
19318 space models and automatic ARIMA modelling.")
19319 (license license:gpl3)))
19321 (define-public r-xmisc
19328 (uri (cran-uri "Xmisc" version))
19331 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
19332 (properties `((upstream-name . "Xmisc")))
19333 (build-system r-build-system)
19334 (home-page "https://cran.r-project.org/package=Xmisc")
19336 "Xiaobei's miscellaneous classes and functions")
19338 "This package provides Xiaobei's miscellaneous classes and functions,
19339 which are useful when developing R packages for @dfn{object oriented
19340 programming} (OOP) using R Reference Class.")
19341 (license license:gpl2+)))
19343 (define-public r-proxyc
19350 (uri (cran-uri "proxyC" version))
19353 "159bc42x4shm6n3rh9fc8ziv3ivq0ipmpbasrh279hhn1prc8gg6"))))
19354 (properties `((upstream-name . "proxyC")))
19355 (build-system r-build-system)
19357 `(("r-matrix" ,r-matrix)
19359 ("r-rcpparmadillo" ,r-rcpparmadillo)
19360 ("r-rcppparallel" ,r-rcppparallel)))
19361 (home-page "https://cran.r-project.org/package=proxyC")
19362 (synopsis "Compute proximity in large sparse matrices")
19364 "This package provides efficient tools to compute the proximity between
19365 rows or columns of large matrices. Functions are optimised for large sparse
19366 matrices using the Armadillo and Intel TBB libraries. Among several built-in
19367 similarity/distance measures, computation of correlation, cosine similarity
19368 and Euclidean distance is particularly fast.")
19369 (license license:gpl3)))
19371 (define-public r-isocodes
19373 (name "r-isocodes")
19374 (version "2019.12.22")
19378 (uri (cran-uri "ISOcodes" version))
19381 "1k2f2258bwzs0b3nxma9kcw395qkljvk514a7047rx4dn0iwd874"))))
19382 (properties `((upstream-name . "ISOcodes")))
19383 (build-system r-build-system)
19384 (home-page "https://cran.r-project.org/package=ISOcodes")
19385 (synopsis "Selected ISO codes")
19387 "This package provides ISO language, territory, currency, script and
19388 character codes. It provides ISO 639 language codes, ISO 3166 territory
19389 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
19390 character codes as well as the UN M.49 area codes.")
19391 (license license:gpl2)))
19393 (define-public r-stopwords
19395 (name "r-stopwords")
19400 (uri (cran-uri "stopwords" version))
19403 "1nmi0bpd0c238g5b8ch1v034m5ng9llhs519cgxdrj3sh9fplwlv"))))
19404 (properties `((upstream-name . "stopwords")))
19405 (build-system r-build-system)
19406 (propagated-inputs `(("r-isocodes" ,r-isocodes)))
19407 (home-page "https://github.com/quanteda/stopwords")
19408 (synopsis "Multilingual stopword lists")
19410 "This package provides multiple sources of stopwords, for use in text
19411 analysis and natural language processing.")
19412 (license license:expat)))
19414 (define-public r-spacyr
19421 (uri (cran-uri "spacyr" version))
19424 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
19425 (properties `((upstream-name . "spacyr")))
19426 (build-system r-build-system)
19428 `(("r-data-table" ,r-data-table)
19429 ("r-reticulate" ,r-reticulate)))
19430 (home-page "https://spacyr.quanteda.io")
19431 (synopsis "R wrapper for the spaCy NLP library")
19433 "This package provides an R wrapper to the Python @dfn{natural language
19434 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
19435 (license license:gpl3)))
19437 (define-public r-snowballc
19439 (name "r-snowballc")
19444 (uri (cran-uri "SnowballC" version))
19447 "0b7pqdavf5jbf8si4ybnii5fff39p3b1rb5rym05j8s48hs7sqb1"))))
19448 (properties `((upstream-name . "SnowballC")))
19449 (build-system r-build-system)
19450 (home-page "https://r-forge.r-project.org/projects/r-temis/")
19451 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
19453 "This package provides an R interface to the C @code{libstemmer} library
19454 that implements Porter's word stemming algorithm for collapsing words to a
19455 common root to aid comparison of vocabulary. Currently supported languages
19456 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
19457 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
19458 (license license:bsd-3)))
19460 (define-public r-quanteda
19462 (name "r-quanteda")
19467 (uri (cran-uri "quanteda" version))
19470 "0snr610vahbdqkmma0zy5mg5qbb6n1b8sgsclqb2sccn1gg38vyy"))))
19471 (properties `((upstream-name . "quanteda")))
19472 (build-system r-build-system)
19474 `(("r-data-table" ,r-data-table)
19475 ("r-extrafont" ,r-extrafont)
19476 ("r-fastmatch" ,r-fastmatch)
19477 ("r-ggplot2" ,r-ggplot2)
19478 ("r-ggrepel" ,r-ggrepel)
19479 ("r-jsonlite" ,r-jsonlite)
19480 ("r-magrittr" ,r-magrittr)
19481 ("r-matrix" ,r-matrix)
19482 ("r-network" ,r-network)
19483 ("r-proxyc" ,r-proxyc)
19485 ("r-rcpparmadillo" ,r-rcpparmadillo)
19486 ("r-rcppparallel" ,r-rcppparallel)
19488 ("r-snowballc" ,r-snowballc)
19489 ("r-stopwords" ,r-stopwords)
19490 ("r-stringi" ,r-stringi)
19492 ("r-yaml" ,r-yaml)))
19493 (home-page "https://quanteda.io")
19494 (synopsis "Quantitative analysis of textual data")
19496 "This package provides a fast, flexible, and comprehensive framework for
19497 quantitative text analysis in R. It provides functionality for corpus
19498 management, creating and manipulating tokens and ngrams, exploring keywords in
19499 context, forming and manipulating sparse matrices of documents by features and
19500 feature co-occurrences, analyzing keywords, computing feature similarities and
19501 distances, applying content dictionaries, applying supervised and unsupervised
19502 machine learning, visually representing text and text analyses, and more.")
19503 (license license:gpl3)))
19505 (define-public r-topicmodels
19507 (name "r-topicmodels")
19512 (uri (cran-uri "topicmodels" version))
19515 "1757r5x8bsl4dk106xg6481mvdkdz9vwg87n7rpbvdkavsvhyxs0"))))
19516 (properties `((upstream-name . "topicmodels")))
19517 (build-system r-build-system)
19521 `(("r-modeltools" ,r-modeltools)
19524 (home-page "https://cran.r-project.org/package=topicmodels")
19525 (synopsis "Topic models")
19527 "This package provides an interface to the C code for @dfn{Latent
19528 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
19529 David M. Blei and co-authors and the C++ code for fitting LDA models using
19530 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
19531 (license license:gpl2)))
19533 (define-public r-stm
19540 (uri (cran-uri "stm" version))
19543 "1yyfxaxqc6yq0yq68zhdnhpwpvsyp71dlmivn7zxixfmp932s6cn"))))
19544 (properties `((upstream-name . "stm")))
19545 (build-system r-build-system)
19547 `(("r-data-table" ,r-data-table)
19548 ("r-glmnet" ,r-glmnet)
19550 ("r-matrix" ,r-matrix)
19551 ("r-matrixstats" ,r-matrixstats)
19552 ("r-quadprog" ,r-quadprog)
19553 ("r-quanteda" ,r-quanteda)
19555 ("r-rcpparmadillo" ,r-rcpparmadillo)
19557 ("r-stringr" ,r-stringr)))
19558 (home-page "http://www.structuraltopicmodel.com/")
19559 (synopsis "Estimation of the Structural Topic Model")
19561 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
19562 topic models with document-level covariates. The package also includes tools
19563 for model selection, visualization, and estimation of topic-covariate
19565 (license license:expat)))
19567 (define-public r-polycor
19574 (uri (cran-uri "polycor" version))
19577 "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna"))))
19578 (properties `((upstream-name . "polycor")))
19579 (build-system r-build-system)
19581 `(("r-matrix" ,r-matrix)
19582 ("r-mvtnorm" ,r-mvtnorm)))
19583 (home-page "https://r-forge.r-project.org/projects/polycor/")
19584 (synopsis "Polychoric and polyserial correlations")
19586 "This package provides tools to compute polychoric and polyserial
19587 correlations by quick \"two-step\" methods or ML, optionally with standard
19588 errors; tetrachoric and biserial correlations are special cases.")
19589 (license license:gpl2+)))
19591 (define-public r-msm
19598 (uri (cran-uri "msm" version))
19601 "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk"))))
19602 (properties `((upstream-name . "msm")))
19603 (build-system r-build-system)
19605 `(("r-expm" ,r-expm)
19606 ("r-mvtnorm" ,r-mvtnorm)
19607 ("r-survival" ,r-survival)))
19608 (home-page "https://github.com/chjackson/msm")
19609 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
19611 "This package provides functions for fitting continuous-time Markov and
19612 hidden Markov multi-state models to longitudinal data. It was designed for
19613 processes observed at arbitrary times in continuous time (panel data) but some
19614 other observation schemes are supported. Both Markov transition rates and the
19615 hidden Markov output process can be modelled in terms of covariates, which may
19616 be constant or piecewise-constant in time.")
19617 (license license:gpl2+)))
19619 (define-public r-ltm
19626 (uri (cran-uri "ltm" version))
19629 "1qrgzwx5l58qf5rfp1knxc84r0g943q5sdr3ky74zzwpnmrf2vf7"))))
19630 (properties `((upstream-name . "ltm")))
19631 (build-system r-build-system)
19633 `(("r-mass" ,r-mass)
19635 ("r-polycor" ,r-polycor)))
19636 (home-page "https://github.com/drizopoulos/ltm")
19637 (synopsis "Latent trait models under IRT")
19639 "This is a package supporting the analysis of multivariate dichotomous
19640 and polytomous data using latent trait models under the Item Response Theory
19641 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
19642 Three-Parameter, the Graded Response, and the Generalized Partial Credit
19644 (license license:gpl2+)))
19646 (define-public r-mi
19653 (uri (cran-uri "mi" version))
19656 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
19657 (properties `((upstream-name . "mi")))
19658 (build-system r-build-system)
19661 ("r-matrix" ,r-matrix)))
19662 (home-page "http://www.stat.columbia.edu/~gelman/")
19663 (synopsis "Missing data imputation and model checking")
19665 "This package provides functions for data manipulation, imputing missing
19666 values in an approximate Bayesian framework, diagnostics of the models used to
19667 generate the imputations, confidence-building mechanisms to validate some of
19668 the assumptions of the imputation algorithm, and functions to analyze multiply
19669 imputed data sets with the appropriate degree of sampling uncertainty.")
19670 (license license:gpl2+)))
19672 (define-public r-matrixcalc
19674 (name "r-matrixcalc")
19679 (uri (cran-uri "matrixcalc" version))
19682 "1c4w9dhi5w98qj1wwh9bbpnfk39rhiwjbanalr8bi5nmxkpcmrhp"))))
19683 (properties `((upstream-name . "matrixcalc")))
19684 (build-system r-build-system)
19685 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
19686 (synopsis "Collection of functions for matrix calculations")
19688 "This package provides a collection of functions to support matrix
19689 calculations for probability, econometric and numerical analysis. There are
19690 additional functions that are comparable to APL functions which are useful for
19691 actuarial models such as pension mathematics.")
19692 (license license:gpl2+)))
19694 (define-public r-sem
19701 (uri (cran-uri "sem" version))
19704 "1f9c6g6pfx66gd2pappcsqh484ah6a0x4z47hpd46rah0817hcsa"))))
19705 (properties `((upstream-name . "sem")))
19706 (build-system r-build-system)
19708 `(("r-boot" ,r-boot)
19710 ("r-matrixcalc" ,r-matrixcalc)
19712 (home-page "https://cran.r-project.org/package=sem")
19713 (synopsis "Structural equation models")
19715 "This package provides functions for fitting general linear structural
19716 equation models (with observed and latent variables) using the RAM approach,
19717 and for fitting structural equations in observed-variable models by two-stage
19719 (license license:gpl2+)))
19721 (define-public r-semtools
19723 (name "r-semtools")
19728 (uri (cran-uri "semTools" version))
19731 "1zj841pszfsikzp82cmh463qyc4xhdrqjqcnhc2r8mcflv12irv6"))))
19732 (properties `((upstream-name . "semTools")))
19733 (build-system r-build-system)
19735 `(("r-lavaan" ,r-lavaan)))
19736 (home-page "https://github.com/simsem/semTools/wiki")
19737 (synopsis "Useful tools for structural equation modeling")
19739 "This package provides useful tools for structural equation modeling.")
19740 (license license:gpl2+)))
19742 (define-public r-regsem
19749 (uri (cran-uri "regsem" version))
19752 "0ch057010xfsw0nqcsarzakdbiplvxaldyqlbbacspqs65ax1yk7"))))
19753 (properties `((upstream-name . "regsem")))
19754 (build-system r-build-system)
19756 `(("r-lavaan" ,r-lavaan)
19758 ("r-rcpparmadillo" ,r-rcpparmadillo)
19759 ("r-rsolnp" ,r-rsolnp)))
19760 (home-page "https://cran.r-project.org/package=regsem")
19761 (synopsis "Regularized structural equation modeling")
19763 "This package uses both ridge and lasso penalties (and extensions) to
19764 penalize specific parameters in structural equation models. The package
19765 offers additional cost functions, cross validation, and other extensions
19766 beyond traditional structural equation models. It also contains a function to
19767 perform @dfn{exploratory mediation} (XMed).")
19768 (license license:gpl2+)))
19770 (define-public r-stanheaders
19772 (name "r-stanheaders")
19777 (uri (cran-uri "StanHeaders" version))
19780 "0cmk0fzczx7dcywcw1dhm6gfq84qlsx77qrsk4z3bf3dhr4bznam"))))
19781 (properties `((upstream-name . "StanHeaders")))
19782 (build-system r-build-system)
19783 (inputs `(("pandoc" ,ghc-pandoc)))
19785 `(("gfortran" ,gfortran)
19786 ("r-knitr" ,r-knitr))) ; for vignettes
19787 (home-page "https://mc-stan.org/")
19788 (synopsis "C++ header files for Stan")
19790 "The C++ header files of the Stan project are provided by this package.
19791 There is a shared object containing part of the @code{CVODES} library, but it
19792 is not accessible from R. @code{r-stanheaders} is only useful for developers
19793 who want to utilize the @code{LinkingTo} directive of their package's
19794 DESCRIPTION file to build on the Stan library without incurring unnecessary
19797 The Stan project develops a probabilistic programming language that implements
19798 full or approximate Bayesian statistical inference via Markov Chain Monte
19799 Carlo or variational methods and implements (optionally penalized) maximum
19800 likelihood estimation via optimization. The Stan library includes an advanced
19801 automatic differentiation scheme, templated statistical and linear algebra
19802 functions that can handle the automatically differentiable scalar types (and
19803 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
19804 package provides user-facing R functions to parse, compile, test, estimate,
19805 and analyze Stan models.")
19806 (license license:bsd-3)))
19808 (define-public r-rpf
19815 (uri (cran-uri "rpf" version))
19818 "1i2kqd7nx55nn35qnw89xmnqk23x9c8xhkh736c2xg7k2ai84ybl"))))
19819 (properties `((upstream-name . "rpf")))
19820 (build-system r-build-system)
19822 `(("r-lifecycle" ,r-lifecycle)
19823 ("r-mvtnorm" ,r-mvtnorm)
19825 ("r-rcppeigen" ,r-rcppeigen)))
19826 (home-page "https://github.com/jpritikin/rpf")
19827 (synopsis "Response probability functions")
19829 "The purpose of this package is to factor out logic and math common to
19830 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
19831 core support code suitable for more specialized IRT packages to build upon.
19832 Complete access to optimized C functions is made available with
19833 @code{R_RegisterCCallable()}.")
19834 (license license:gpl3+)))
19836 (define-public r-openmx
19843 (uri (cran-uri "OpenMx" version))
19846 "1s2pcg281ag3qz2wz8yi826f2d3kj3qg916js7zz0nsrljcyv5bc"))))
19847 (properties `((upstream-name . "OpenMx")))
19848 (build-system r-build-system)
19851 ("r-digest" ,r-digest)
19853 ("r-matrix" ,r-matrix)
19855 ("r-rcppeigen" ,r-rcppeigen)
19857 ("r-stanheaders" ,r-stanheaders)))
19858 (native-inputs `(("gfortran" ,gfortran)))
19859 (home-page "http://openmx.ssri.psu.edu")
19860 (synopsis "Extended structural equation modelling")
19862 "This package allows for the estimation of a wide variety of advanced
19863 multivariate statistical models. It consists of a library of functions and
19864 optimizers that allow you to quickly and flexibly define an SEM model and
19865 estimate parameters given observed data.")
19866 (license license:asl2.0)))
19868 (define-public r-kutils
19875 (uri (cran-uri "kutils" version))
19878 "12pg26a85h0jxlfcyai68dbh4bq1gnq8v1ngi8k9qvafbrpc6gx8"))))
19879 (properties `((upstream-name . "kutils")))
19880 (build-system r-build-system)
19882 `(("r-foreign" ,r-foreign)
19883 ("r-lavaan" ,r-lavaan)
19884 ("r-openxlsx" ,r-openxlsx)
19886 ("r-runit" ,r-runit)
19887 ("r-xtable" ,r-xtable)))
19888 (home-page "https://cran.r-project.org/package=kutils")
19889 (synopsis "Project management tools")
19891 "This package provides tools for data importation, recoding, and
19892 inspection. There are functions to create new project folders, R code
19893 templates, create uniquely named output directories, and to quickly obtain a
19894 visual summary for each variable in a data frame. The main feature here is
19895 the systematic implementation of the \"variable key\" framework for data
19896 importation and recoding.")
19897 (license license:gpl2)))
19899 (define-public r-rockchalk
19901 (name "r-rockchalk")
19902 (version "1.8.144")
19906 (uri (cran-uri "rockchalk" version))
19909 "07dp1n155b9gfvk8l30h6bhjbhbylsjxfzns08mryn4mxj3nqpnb"))))
19910 (properties `((upstream-name . "rockchalk")))
19911 (build-system r-build-system)
19913 `(("r-cardata" ,r-cardata)
19914 ("r-kutils" ,r-kutils)
19916 ("r-mass" ,r-mass)))
19917 (home-page "https://cran.r-project.org/package=rockchalk")
19918 (synopsis "Regression estimation and presentation")
19920 "This package provides a collection of functions for interpretation and
19921 presentation of regression analysis. These functions are used to produce the
19922 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
19923 includes regression diagnostics, regression tables, and plots of interactions
19924 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
19925 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
19926 fairly comprehensive overview.")
19927 (license license:gpl3+)))
19929 (define-public r-lisreltor
19931 (name "r-lisreltor")
19936 (uri (cran-uri "lisrelToR" version))
19939 "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
19940 (properties `((upstream-name . "lisrelToR")))
19941 (build-system r-build-system)
19942 (home-page "https://cran.r-project.org/package=lisrelToR")
19943 (synopsis "Import output from LISREL into R")
19945 "This is an unofficial package aimed at automating the import of LISREL
19947 (license license:gpl2)))
19949 (define-public r-bdgraph
19956 (uri (cran-uri "BDgraph" version))
19959 "1b1vfar940swvn3pcil848qsp8ji50fjjll8jjzp6y2adx0f8pby"))))
19960 (properties `((upstream-name . "BDgraph")))
19961 (build-system r-build-system)
19963 `(("r-igraph" ,r-igraph)))
19964 (home-page "https://www.uva.nl/profile/a.mohammadi")
19965 (synopsis "Bayesian structure learning in graphical models")
19967 "This package provides statistical tools for Bayesian structure learning
19968 in undirected graphical models for continuous, discrete, and mixed data. It
19969 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
19970 on a continuous-time birth-death process.")
19971 (license license:gpl2+)))
19973 (define-public r-d3network
19975 (name "r-d3network")
19976 (version "0.5.2.1")
19980 (uri (cran-uri "d3Network" version))
19983 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
19984 (properties `((upstream-name . "d3Network")))
19985 (build-system r-build-system)
19987 `(("r-plyr" ,r-plyr)
19988 ("r-rjson" ,r-rjson)
19989 ("r-whisker" ,r-whisker)))
19990 (home-page "http://christophergandrud.github.io/d3Network/")
19991 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
19993 "This package is intended to make it easy to create D3 JavaScript
19994 network, tree, dendrogram, and Sankey graphs from R using data frames.")
19995 (license license:gpl3+)))
19997 (define-public r-qgraph
20004 (uri (cran-uri "qgraph" version))
20007 "0pwys9irxvp0ap158drplyypkplbmwqinv0fmlsblk7q875cr592"))))
20008 (properties `((upstream-name . "qgraph")))
20009 (build-system r-build-system)
20011 `(("r-abind" ,r-abind)
20012 ("r-bdgraph" ,r-bdgraph)
20013 ("r-colorspace" ,r-colorspace)
20014 ("r-corpcor" ,r-corpcor)
20015 ("r-d3network" ,r-d3network)
20016 ("r-dplyr" ,r-dplyr)
20017 ("r-fdrtool" ,r-fdrtool)
20018 ("r-ggplot2" ,r-ggplot2)
20019 ("r-ggraph" ,r-ggraph)
20020 ("r-glasso" ,r-glasso)
20021 ("r-gtools" ,r-gtools)
20022 ("r-hmisc" ,r-hmisc)
20024 ("r-igraph" ,r-igraph)
20026 ("r-lavaan" ,r-lavaan)
20027 ("r-matrix" ,r-matrix)
20028 ("r-pbapply" ,r-pbapply)
20031 ("r-psych" ,r-psych)
20033 ("r-reshape2" ,r-reshape2)
20034 ("r-tidygraph" ,r-tidygraph)))
20035 (home-page "http://sachaepskamp.com/qgraph/")
20036 (synopsis "Weighted network visualization and analysis")
20038 "This package implements tools for weighted network visualization and
20039 analysis, as well as Gaussian graphical model computation. It contains graph
20040 plotting methods, and tools for psychometric data visualization and graphical
20041 model estimation. See Epskamp et al. (2012)
20042 @url{doi:10.18637/jss.v048.i04}.")
20043 (license license:gpl2)))
20045 (define-public r-semplot
20052 (uri (cran-uri "semPlot" version))
20055 "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr"))))
20056 (properties `((upstream-name . "semPlot")))
20057 (build-system r-build-system)
20059 `(("r-colorspace" ,r-colorspace)
20060 ("r-corpcor" ,r-corpcor)
20061 ("r-igraph" ,r-igraph)
20062 ("r-lavaan" ,r-lavaan)
20063 ("r-lisreltor" ,r-lisreltor)
20064 ("r-openmx" ,r-openmx)
20066 ("r-qgraph" ,r-qgraph)
20067 ("r-regsem" ,r-regsem)
20068 ("r-rockchalk" ,r-rockchalk)
20071 (home-page "https://github.com/SachaEpskamp/semPlot")
20072 (synopsis "Unified visualizations of structural equation models")
20074 "Structural equation modeling (SEM) has a long history of representing
20075 models graphically as path diagrams. The semPlot package for R fills the gap
20076 between advanced, but time-consuming, graphical software and the limited
20077 graphics produced automatically by SEM software. In addition, semPlot offers
20078 more functionality than drawing path diagrams: it can act as a common ground
20079 for importing SEM results into R. Any result usable as input to semPlot can
20080 also be represented in any of the three popular SEM frame-works, as well as
20081 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
20082 (license license:gpl2)))
20084 (define-public r-cdm
20091 (uri (cran-uri "CDM" version))
20094 "1ln1r3rk004fmk55iy08bjh3vv4wnkb8zg2wj3r9rq7pi8jn8fv4"))))
20095 (properties `((upstream-name . "CDM")))
20096 (build-system r-build-system)
20098 `(("r-mvtnorm" ,r-mvtnorm)
20099 ("r-polycor" ,r-polycor)
20101 ("r-rcpparmadillo" ,r-rcpparmadillo)))
20103 "https://github.com/alexanderrobitzsch/CDM")
20104 (synopsis "Cognitive diagnosis modeling")
20106 "This package provides functions for cognitive diagnosis modeling and
20107 multidimensional item response modeling for dichotomous and polytomous item
20108 responses. It enables the estimation of the DINA and DINO model, the multiple
20109 group (polytomous) GDINA model, the multiple choice DINA model, the general
20110 diagnostic model (GDM), the structured latent class model (SLCA), and
20111 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
20112 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
20113 estimation and the package structure. For tutorials on how to use the CDM
20114 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
20115 well as Ravand and Robitzsch (2015).")
20116 (license license:gpl2+)))
20118 (define-public r-tam
20125 (uri (cran-uri "TAM" version))
20128 "1rkjp5x6wrk1dfspp1imvfals0wvy4w1wb8a5mhfbnilc7vgnlbq"))))
20129 (properties `((upstream-name . "TAM")))
20130 (build-system r-build-system)
20134 ("r-rcpparmadillo" ,r-rcpparmadillo)))
20135 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
20136 (synopsis "Test analysis modules")
20138 "This package includes tools for marginal maximum likelihood estimation
20139 and joint maximum likelihood estimation for unidimensional and
20140 multidimensional item response models. The package functionality covers the
20141 Rasch model, 2PL model, 3PL model, generalized partial credit model,
20142 multi-faceted Rasch model, nominal item response model, structured latent
20143 class model, mixture distribution IRT models, and located latent class models.
20144 Latent regression models and plausible value imputation are also supported.")
20145 (license license:gpl2+)))
20147 (define-public r-erm
20154 (uri (cran-uri "eRm" version))
20157 "0njqzznnhnkvalmhiq5yq1w7gwp2myki5cv61w42ydvd27hdyyg9"))))
20158 (properties `((upstream-name . "eRm")))
20159 (build-system r-build-system)
20161 `(("r-colorspace" ,r-colorspace)
20162 ("r-lattice" ,r-lattice)
20164 ("r-matrix" ,r-matrix)
20165 ("r-psych" ,r-psych)))
20166 (native-inputs `(("gfortran" ,gfortran)))
20167 (home-page "https://cran.r-project.org/package=eRm")
20168 (synopsis "Extended Rasch modeling")
20170 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
20171 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
20172 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
20173 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
20174 data matrix. Additional features are the ML estimation of the person
20175 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
20176 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
20177 infit and outfit measures, ICC and other plots, automated stepwise item
20178 elimination, and a simulation module for various binary data matrices.")
20179 (license license:gpl3)))
20181 (define-public r-irtoys
20188 (uri (cran-uri "irtoys" version))
20191 "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
20192 (properties `((upstream-name . "irtoys")))
20193 (build-system r-build-system)
20197 (home-page "https://cran.r-project.org/package=irtoys")
20198 (synopsis "Collection of functions related to Item Response Theory (IRT)")
20200 "This package provides a collection of functions useful in learning and
20201 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
20202 programs. It provides basic CTT analysis, a simple common interface to the
20203 estimation of item parameters in IRT models for binary responses with three
20204 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
20205 EAP, WLE, plausible values), item and person fit statistics, scaling
20206 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
20207 array of parametric and non-parametric (kernel) plots. It estimates and plots
20208 Haberman's interaction model when all items are dichotomously scored.")
20209 (license license:gpl2+)))
20211 (define-public r-iheatmapr
20213 (name "r-iheatmapr")
20218 (uri (cran-uri "iheatmapr" version))
20221 "0s479j9l35xiss599vablxgvg6i2j9zq9sxphsq4vdk3bafg84bw"))))
20222 (properties `((upstream-name . "iheatmapr")))
20223 (build-system r-build-system)
20225 `(("r-fastcluster" ,r-fastcluster)
20226 ("r-ggdendro" ,r-ggdendro)
20227 ("r-htmlwidgets" ,r-htmlwidgets)
20228 ("r-jsonlite" ,r-jsonlite)
20229 ("r-knitr" ,r-knitr)
20230 ("r-magrittr" ,r-magrittr)
20232 ("r-rcolorbrewer" ,r-rcolorbrewer)
20233 ("r-s4vectors" ,r-s4vectors)
20234 ("r-scales" ,r-scales)))
20235 (home-page "https://docs.ropensci.org/iheatmapr")
20236 (synopsis "Interactive, Complex Heatmaps")
20238 "iheatmapr is an R package for building complex, interactive heatmaps
20239 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
20240 subplots along the rows or columns of the main heatmap add more information
20241 about each row or column. For example, a one column additional heatmap may
20242 indicate what group a particular row or column belongs to. Complex heatmaps
20243 may also include multiple side by side heatmaps which show different types of
20244 data for the same conditions. Interactivity can improve complex heatmaps by
20245 providing tooltips with information about each cell and enabling zooming into
20246 interesting features. iheatmapr uses the plotly library for interactivity.")
20247 (license license:expat)))
20249 (define-public r-packrat
20256 (uri (cran-uri "packrat" version))
20259 "1xy5dd2hrpqa07jfl4s7dsrya05mf36ms74j833scdz0zf89586n"))))
20260 (properties `((upstream-name . "packrat")))
20261 (build-system r-build-system)
20262 (home-page "https://github.com/rstudio/packrat/")
20263 (synopsis "Dependency management R projects")
20265 "This package provides a dependency manager for R projects that allows
20266 you to manage the R packages your project depends on in an isolated, portable,
20267 and reproducible way.")
20268 (license license:gpl2)))
20270 (define-public r-rsconnect
20272 (name "r-rsconnect")
20277 (uri (cran-uri "rsconnect" version))
20280 "05ii0p0p7xpf8z0c1594s5q7wpwcs7lmlddrd67s5p2ka5m8qwiz"))))
20281 (properties `((upstream-name . "rsconnect")))
20282 (build-system r-build-system)
20284 `(("r-curl" ,r-curl)
20285 ("r-digest" ,r-digest)
20286 ("r-jsonlite" ,r-jsonlite)
20287 ("r-openssl" ,r-openssl)
20288 ("r-packrat" ,r-packrat)
20289 ("r-rstudioapi" ,r-rstudioapi)
20290 ("r-yaml" ,r-yaml)))
20291 (home-page "https://github.com/rstudio/rsconnect")
20292 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
20294 "This package provides a programmatic deployment interface for RPubs,
20295 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
20296 documents, Shiny applications, Plumber APIs, plots, and static web content.")
20297 (license license:gpl2)))
20299 ;; This package includes minified JavaScript files. When upgrading please
20300 ;; check that there are no new minified JavaScript files.
20301 (define-public r-dygraphs
20303 (name "r-dygraphs")
20304 (version "1.1.1.6")
20308 (uri (cran-uri "dygraphs" version))
20311 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
20312 (properties `((upstream-name . "dygraphs")))
20313 (build-system r-build-system)
20315 `(#:modules ((guix build utils)
20316 (guix build r-build-system)
20320 (modify-phases %standard-phases
20321 (add-after 'unpack 'process-javascript
20322 (lambda* (#:key inputs #:allow-other-keys)
20323 (with-directory-excursion "inst/htmlwidgets/lib/"
20327 `(("dygraphs/dygraph-combined-dev.js"
20328 "dygraph-combined.js")
20329 (,(assoc-ref inputs "js-jquery")
20330 "jquery/jquery.min.js")
20331 (,(assoc-ref inputs "js-fquarter")
20332 "fquarter/moment-fquarter.min.js"))))
20333 (lambda (sources targets)
20334 (for-each (lambda (source target)
20335 (format #t "Processing ~a --> ~a~%"
20337 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
20338 (call-with-output-file target
20340 (dump-port minified port)))))
20341 sources targets))))
20344 `(("uglify-js" ,uglify-js)
20345 ;; They actually use version 1.11.1, but this more recent version
20346 ;; should be just fine.
20350 (uri "https://code.jquery.com/jquery-1.12.4.js")
20353 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
20357 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
20358 "moment-fquarter/1.0.1/moment-fquarter.js"))
20361 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
20363 `(("r-htmltools" ,r-htmltools)
20364 ("r-htmlwidgets" ,r-htmlwidgets)
20365 ("r-magrittr" ,r-magrittr)
20368 (home-page "https://github.com/rstudio/dygraphs")
20369 (synopsis "Interface to Dygraphs interactive time series charting library")
20371 "This package provides an R interface to the dygraphs JavaScript charting
20372 library (a copy of which is included in the package). It provides rich
20373 facilities for charting time-series data in R, including highly configurable
20374 series- and axis-display and interactive features like zoom/pan and
20375 series/point highlighting.")
20376 (license license:expat)))
20378 (define-public r-shinystan
20380 (name "r-shinystan")
20385 (uri (cran-uri "shinystan" version))
20388 "18alf5kiqw7y2l6m5nxxizwc2znsf9frxfsqhvgcad8hld9cbya5"))))
20389 (properties `((upstream-name . "shinystan")))
20390 (build-system r-build-system)
20392 `(("r-bayesplot" ,r-bayesplot)
20393 ("r-colourpicker" ,r-colourpicker)
20395 ("r-dygraphs" ,r-dygraphs)
20396 ("r-ggplot2" ,r-ggplot2)
20397 ("r-gridextra" ,r-gridextra)
20398 ("r-gtools" ,r-gtools)
20399 ("r-markdown" ,r-markdown)
20400 ("r-reshape2" ,r-reshape2)
20401 ("r-rsconnect" ,r-rsconnect)
20402 ("r-rstan" ,r-rstan)
20403 ("r-shiny" ,r-shiny)
20404 ("r-shinyjs" ,r-shinyjs)
20405 ("r-shinythemes" ,r-shinythemes)
20406 ("r-threejs" ,r-threejs)
20407 ("r-xtable" ,r-xtable)
20409 (home-page "https://mc-stan.org/")
20410 (synopsis "Interactive visual and numerical analysis for Bayesian models")
20412 "This package provides a graphical user interface for interactive
20413 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
20414 for analyzing a posterior sample. The interface is powered by the Shiny web
20415 application framework and works with the output of MCMC programs written in
20416 any programming language (and has extended functionality for Stan models fit
20417 using the @code{rstan} and @code{rstanarm} packages).")
20418 (license license:gpl3+)))
20420 (define-public r-rstantools
20422 (name "r-rstantools")
20427 (uri (cran-uri "rstantools" version))
20430 "1il0pn4ksbdkska5fmhvgaicvwnnc6cs08g6ags9fj1xkjiqmrsa"))))
20431 (properties `((upstream-name . "rstantools")))
20432 (build-system r-build-system)
20433 (inputs `(("pandoc" ,ghc-pandoc)))
20435 `(("r-desc" ,r-desc)
20436 ("r-rcpp" ,r-rcpp)))
20437 (home-page "https://mc-stan.org/rstantools/")
20438 (synopsis "Tools for developing R packages interfacing with Stan")
20440 "This package provides various tools for developers of R packages
20441 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
20442 up the required package structure, S3 generics and default methods to unify
20443 function naming across Stan-based R packages, and vignettes with
20444 recommendations for developers.")
20445 (license license:gpl3+)))
20447 (define-public r-loo
20454 (uri (cran-uri "loo" version))
20457 "1hq1zcj76x55z9kic6cwf7mfq9pzqfbr341jbc9wp7x8ac4zcva6"))))
20458 (properties `((upstream-name . "loo")))
20459 (build-system r-build-system)
20461 `(("pandoc" ,ghc-pandoc)
20462 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
20464 `(("r-checkmate" ,r-checkmate)
20465 ("r-matrixstats" ,r-matrixstats)))
20466 (home-page "https://mc-stan.org/loo/")
20467 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
20469 "This package provides an implementation of efficient approximate
20470 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
20471 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
20472 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
20473 procedure for regularizing importance weights. As a byproduct of the
20474 calculations, we also obtain approximate standard errors for estimated
20475 predictive errors and for the comparison of predictive errors between models.
20476 The package also provides methods for using stacking and other model weighting
20477 techniques to average Bayesian predictive distributions.")
20478 (license license:gpl3+)))
20480 (define-public r-rstan
20487 (uri (cran-uri "rstan" version))
20490 "128ndwjrhf8b1qvvqz4bl13qlm8718z9qs5ryc6gsdr3vk65s0np"))))
20491 (properties `((upstream-name . "rstan")))
20492 (build-system r-build-system)
20495 (modify-phases %standard-phases
20496 (add-before 'install 'set-timezone
20497 ;; This package is picky about timezones.
20498 (lambda* (#:key inputs #:allow-other-keys)
20499 (setenv "TZ" "UTC+1")
20501 (string-append (assoc-ref inputs "tzdata")
20502 "/share/zoneinfo"))
20505 `(("tzdata" ,tzdata)
20506 ("pandoc" ,ghc-pandoc)))
20509 ("r-ggplot2" ,r-ggplot2)
20510 ("r-gridextra" ,r-gridextra)
20511 ("r-inline" ,r-inline)
20513 ("r-pkgbuild" ,r-pkgbuild)
20515 ("r-rcppeigen" ,r-rcppeigen)
20516 ("r-stanheaders" ,r-stanheaders)))
20517 (home-page "https://discourse.mc-stan.org/")
20518 (synopsis "R interface to Stan")
20520 "User-facing R functions are provided to parse, compile, test, estimate,
20521 and analyze Stan models by accessing the header-only Stan library provided by
20522 the StanHeaders package. The Stan project develops a probabilistic
20523 programming language that implements full Bayesian statistical inference via
20524 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
20525 approximation, and (optionally penalized) maximum likelihood estimation via
20526 optimization. In all three cases, automatic differentiation is used to
20527 quickly and accurately evaluate gradients without burdening the user with the
20528 need to derive the partial derivatives.")
20529 (license license:gpl3+)))
20531 (define-public r-rstanarm
20533 (name "r-rstanarm")
20538 (uri (cran-uri "rstanarm" version))
20541 "0gxjq8bdlvdd8kn3dhp12xlymdab036r7n12lzmd3xlkl4cnxq3s"))))
20542 (properties `((upstream-name . "rstanarm")))
20543 (build-system r-build-system)
20545 `(("pandoc" ,ghc-pandoc)
20546 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
20548 `(("r-bayesplot" ,r-bayesplot)
20550 ("r-ggplot2" ,r-ggplot2)
20553 ("r-matrix" ,r-matrix)
20556 ("r-rcppeigen" ,r-rcppeigen)
20557 ("r-rcppparallel" ,r-rcppparallel)
20558 ("r-rstan" ,r-rstan)
20559 ("r-rstantools" ,r-rstantools)
20560 ("r-shinystan" ,r-shinystan)
20561 ("r-stanheaders" ,r-stanheaders)
20562 ("r-survival" ,r-survival)))
20563 (home-page "https://mc-stan.org/rstanarm/")
20564 (synopsis "Bayesian applied regression modeling via Stan")
20566 "This package estimates previously compiled regression models using the
20567 @code{rstan} package, which provides the R interface to the Stan C++ library
20568 for Bayesian estimation. Users specify models via the customary R syntax with
20569 a formula and @code{data.frame} plus some additional arguments for priors.")
20570 (license license:gpl3+)))
20572 (define-public r-kendall
20579 (uri (cran-uri "Kendall" version))
20582 "0z2yr3x2nvdm81w2imb61hxwcbmg14kfb2bxgh3wmkmv3wfjwkwn"))))
20583 (properties `((upstream-name . "Kendall")))
20584 (build-system r-build-system)
20586 `(("r-boot" ,r-boot)))
20588 `(("gfortran" ,gfortran)))
20589 (home-page "https://cran.r-project.org/web/packages/Kendall/")
20590 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
20592 "This package computes the Kendall rank correlation and Mann-Kendall
20594 (license license:gpl2+)))
20596 (define-public r-zyp
20599 (version "0.10-1.1")
20603 (uri (cran-uri "zyp" version))
20606 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
20607 (properties `((upstream-name . "zyp")))
20608 (build-system r-build-system)
20610 `(("r-kendall" ,r-kendall)))
20611 (home-page "https://cran.r-project.org/web/packages/zyp/")
20612 (synopsis "Zhang + Yue-Pilon Trends Package")
20614 "This package contains an efficient implementation of Sen's slope
20615 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
20616 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
20618 (license license:lgpl2.1)))
20620 (define-public r-zvcv
20627 (uri (cran-uri "ZVCV" version))
20630 "1npw836q2skx54843lgxvb0rfwafckjc8k8dljykm60ad3z7zak8"))))
20631 (properties `((upstream-name . "ZVCV")))
20632 (build-system r-build-system)
20634 `(("r-abind" ,r-abind)
20635 ("r-glmnet" ,r-glmnet)
20636 ("r-mvtnorm" ,r-mvtnorm)
20637 ("r-partitions" ,r-partitions)
20639 ("r-rcpparmadillo" ,r-rcpparmadillo)))
20640 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
20641 (synopsis "Zero-Variance Control Variates")
20643 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
20644 to reduce the variance of Monte Carlo estimators of expectations using the
20645 derivatives of the log target. Once the derivatives are available, the only
20646 additional computational effort is in solving a linear regression problem.
20647 This method has been extended to higher dimensions using regularisation. This
20648 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
20649 samples, derivatives and function evaluations are available. Additional
20650 functions for applying ZV-CV to two estimators for the normalising constant of
20651 the posterior distribution in Bayesian statistics are also supplied.")
20652 (license license:gpl2+)))
20654 (define-public r-ztype
20661 (uri (cran-uri "ztype" version))
20664 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
20665 (properties `((upstream-name . "ztype")))
20666 (build-system r-build-system)
20668 `(("r-assertthat" ,r-assertthat)
20669 ("r-dplyr" ,r-dplyr)
20670 ("r-ggplot2" ,r-ggplot2)
20671 ("r-lubridate" ,r-lubridate)
20672 ("r-magrittr" ,r-magrittr)
20673 ("r-rvest" ,r-rvest)
20674 ("r-stringr" ,r-stringr)))
20675 (home-page "https://cran.r-project.org/web/packages/ztype/")
20676 (synopsis "Run a Ztype game loaded with R functions")
20678 "How fast can you type R functions on your keyboard? Find out by running
20679 a @code{zty.pe} game: export R functions as instructions to type to destroy
20680 opponents' vessels.")
20681 (license license:gpl3)))
20683 (define-public r-zseq
20690 (uri (cran-uri "Zseq" version))
20693 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
20694 (properties `((upstream-name . "Zseq")))
20695 (build-system r-build-system)
20697 `(("r-gmp" ,r-gmp)))
20698 (home-page "https://cran.r-project.org/web/packages/Zseq/")
20699 (synopsis "Integer sequence generator")
20701 "This package generates well-known integer sequences. The @code{gmp}
20702 package is adopted for computing with arbitrarily large numbers. Every
20703 function has a hyperlink to its corresponding item in the @dfn{On-Line
20704 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
20705 (license license:gpl3+)))
20707 (define-public r-isoband
20714 (uri (cran-uri "isoband" version))
20717 "1r023s73qypnvpx18znr9ymylr022m90v65mz2jasn0a1kjrfcbq"))))
20718 (properties `((upstream-name . "isoband")))
20719 (build-system r-build-system)
20721 `(("r-rcpp" ,r-rcpp)
20722 ("r-testthat" ,r-testthat)))
20723 (home-page "https://github.com/wilkelab/isoband")
20724 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
20726 "This package provides a fast C++ implementation to generate contour
20727 lines (isolines) and contour polygons (isobands) from regularly spaced grids
20728 containing elevation data.")
20729 (license license:expat)))