1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
4 ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
5 ;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
6 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
7 ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
8 ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
9 ;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net>
10 ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
11 ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
12 ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
13 ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
14 ;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com>
15 ;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
16 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
17 ;;; Copyright © 2018 Eric Brown <brown@fastmail.com>
18 ;;; Copyright © 2018, 2019 Brett Gilio <brettg@posteo.net>
19 ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
20 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
22 ;;; This file is part of GNU Guix.
24 ;;; GNU Guix is free software; you can redistribute it and/or modify it
25 ;;; under the terms of the GNU General Public License as published by
26 ;;; the Free Software Foundation; either version 3 of the License, or (at
27 ;;; your option) any later version.
29 ;;; GNU Guix is distributed in the hope that it will be useful, but
30 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
31 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
32 ;;; GNU General Public License for more details.
34 ;;; You should have received a copy of the GNU General Public License
35 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
37 (define-module (gnu packages cran)
38 #:use-module ((guix licenses) #:prefix license:)
39 #:use-module (guix packages)
40 #:use-module (guix download)
41 #:use-module (guix git-download)
42 #:use-module (guix utils)
43 #:use-module (guix build-system r)
44 #:use-module (gnu packages algebra)
45 #:use-module (gnu packages base)
46 #:use-module (gnu packages bioinformatics)
47 #:use-module (gnu packages c)
48 #:use-module (gnu packages compression)
49 #:use-module (gnu packages curl)
50 #:use-module (gnu packages databases)
51 #:use-module (gnu packages fontutils)
52 #:use-module (gnu packages gcc)
53 #:use-module (gnu packages geo)
54 #:use-module (gnu packages ghostscript)
55 #:use-module (gnu packages gl)
56 #:use-module (gnu packages gnome)
57 #:use-module (gnu packages graph)
58 #:use-module (gnu packages gtk)
59 #:use-module (gnu packages haskell-xyz)
60 #:use-module (gnu packages icu4c)
61 #:use-module (gnu packages image)
62 #:use-module (gnu packages imagemagick)
63 #:use-module (gnu packages java)
64 #:use-module (gnu packages javascript)
65 #:use-module (gnu packages machine-learning)
66 #:use-module (gnu packages maths)
67 #:use-module (gnu packages mpi)
68 #:use-module (gnu packages multiprecision)
69 #:use-module (gnu packages networking)
70 #:use-module (gnu packages pcre)
71 #:use-module (gnu packages perl)
72 #:use-module (gnu packages pkg-config)
73 #:use-module (gnu packages python)
74 #:use-module (gnu packages python-xyz)
75 #:use-module (gnu packages statistics)
76 #:use-module (gnu packages tls)
77 #:use-module (gnu packages web)
78 #:use-module (gnu packages xorg))
80 (define-public r-clipr
87 (uri (cran-uri "clipr" version))
90 "1qn2p13d0c1bpqss6mv9hk60980rzhznfqpyaf5x0fy65svy9903"))))
91 (build-system r-build-system)
92 (home-page "https://github.com/mdlincoln/clipr")
93 (synopsis "Read and write from the system clipboard")
95 "This package provides simple utility functions to read from and write to
96 the system clipboards.")
97 (license license:gpl3)))
99 (define-public r-scales
106 (uri (cran-uri "scales" version))
108 (base32 "00rdbfj5mwc3kr8pskidn3n2zkp4ms6cx36xazz54pxw3pysdr0y"))))
109 (build-system r-build-system)
111 `(("r-farver" ,r-farver)
112 ("r-labeling" ,r-labeling)
113 ("r-lifecycle" ,r-lifecycle)
114 ("r-munsell" ,r-munsell)
115 ("r-rcolorbrewer" ,r-rcolorbrewer)
117 ("r-viridislite" ,r-viridislite)))
118 (home-page "https://github.com/hadley/scales")
119 (synopsis "Scale functions for visualization")
121 "This package provides graphical scales that map data to aesthetics, and
122 provides methods for automatically determining breaks and labels for axes and
124 (license license:expat)))
126 (define-public r-pheatmap
133 (uri (cran-uri "pheatmap" version))
136 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
137 (build-system r-build-system)
139 `(("r-gtable" ,r-gtable)
140 ("r-rcolorbrewer" ,r-rcolorbrewer)
141 ("r-scales" ,r-scales)))
142 (home-page "https://cran.r-project.org/web/packages/pheatmap")
143 (synopsis "Pretty heatmaps")
145 "This package provides an implementation of heatmaps that offers more
146 control over dimensions and appearance.")
147 (license license:gpl2+)))
149 (define-public r-ellipsis
156 (uri (cran-uri "ellipsis" version))
159 "01z9gq311nzwv3a0sa49jhm5ylqd59srip4vjkrf23hzgb5i9y0b"))))
160 (build-system r-build-system)
162 `(("r-rlang" ,r-rlang)))
163 (home-page "https://github.com/hadley/ellipsis")
164 (synopsis "Tools for working with additional arguments")
166 "In S3 generics, it's useful to take @code{...} so that methods can have
167 additional arguments. But this flexibility comes at a cost: misspelled
168 arguments will be silently ignored. The @code{ellipsis} package is an
169 experiment that allows a generic to warn if any arguments passed in @code{...}
171 (license license:gpl3)))
180 (uri (cran-uri "grr" version))
183 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
184 (build-system r-build-system)
185 (home-page "https://cran.r-project.org/web/packages/grr")
186 (synopsis "Alternative implementations of base R functions")
188 "This package provides alternative implementations of some base R
189 functions, including @code{sort}, @code{order}, and @code{match}. The
190 functions are simplified but can be faster or have other advantages.")
191 (license license:gpl3)))
193 (define-public r-matrix-utils
195 (name "r-matrix-utils")
200 (uri (cran-uri "Matrix.utils" version))
203 "1x64r4aj3gy1dzjjysyrk1j9jq3qsnyrqws8i6bs7q8pf6gvr7va"))))
204 (properties `((upstream-name . "Matrix.utils")))
205 (build-system r-build-system)
208 ("r-matrix" ,r-matrix)))
209 (home-page "https://github.com/cvarrichio/Matrix.utils")
211 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
213 "This package implements data manipulation methods such as @code{cast},
214 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
216 (license license:gpl3)))
225 (uri (cran-uri "sys" version))
228 "14wvy46i2iz9jn7lj3cvifmps932s3395wq681hniva0f8m7q8d6"))))
229 (build-system r-build-system)
230 (home-page "https://github.com/jeroen/sys")
231 (synopsis "Powerful and reliable tools for running system commands in R")
233 "This package provides drop-in replacements for the base @code{system2()}
234 function with fine control and consistent behavior across platforms. It
235 supports clean interruption, timeout, background tasks, and streaming STDIN /
236 STDOUT / STDERR over binary or text connections. The package also provides
237 functions for evaluating expressions inside a temporary fork. Such
238 evaluations have no side effects on the main R process, and support reliable
239 interrupts and timeouts. This provides the basis for a sandboxing
241 (license license:expat)))
243 (define-public r-askpass
250 (uri (cran-uri "askpass" version))
253 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
254 (build-system r-build-system)
255 (propagated-inputs `(("r-sys" ,r-sys)))
256 (home-page "https://github.com/jeroen/askpass")
257 (synopsis "Safe password entry for R")
259 "This package provides cross-platform utilities for prompting the user
260 for credentials or a passphrase, for example to authenticate with a server or
261 read a protected key.")
262 (license license:expat)))
264 (define-public r-vegan
271 (uri (cran-uri "vegan" version))
274 "0g60rgn1i7wqf9pf5m1yki1m45gcp7i5hmjic0ci0f6vng70mh5k"))))
275 (build-system r-build-system)
277 `(("gfortran" ,gfortran)))
279 `(("r-cluster" ,r-cluster)
280 ("r-knitr" ,r-knitr) ; needed for vignettes
281 ("r-lattice" ,r-lattice)
284 ("r-permute" ,r-permute)))
285 (home-page "https://cran.r-project.org/web/packages/vegan")
286 (synopsis "Functions for community ecology")
288 "The vegan package provides tools for descriptive community ecology. It
289 has most basic functions of diversity analysis, community ordination and
290 dissimilarity analysis. Most of its multivariate tools can be used for other
291 data types as well.")
292 (license license:gpl2+)))
294 (define-public r-tidyverse
301 (uri (cran-uri "tidyverse" version))
304 "02gyys08qv2v4cl2d66gml4d31ipxay0iyfwwksvxyclx60wp2kd"))))
305 (build-system r-build-system)
307 `(("r-broom" ,r-broom)
309 ("r-crayon" ,r-crayon)
310 ("r-dbplyr" ,r-dbplyr)
312 ("r-forcats" ,r-forcats)
313 ("r-ggplot2" ,r-ggplot2)
317 ("r-jsonlite" ,r-jsonlite)
318 ("r-lubridate" ,r-lubridate)
319 ("r-magrittr" ,r-magrittr)
320 ("r-modelr" ,r-modelr)
321 ("r-pillar" ,r-pillar)
324 ("r-readxl" ,r-readxl)
325 ("r-reprex" ,r-reprex)
327 ("r-rstudioapi" ,r-rstudioapi)
329 ("r-stringr" ,r-stringr)
330 ("r-tibble" ,r-tibble)
333 (home-page "https://tidyverse.tidyverse.org")
334 (synopsis "Install and load packages from the \"Tidyverse\"")
336 "The @code{tidyverse} is a set of packages that work in harmony because
337 they share common data representations and API design. This package is
338 designed to make it easy to install and load multiple tidyverse packages in a
340 (license license:gpl3)))
342 (define-public r-rvest
349 (uri (cran-uri "rvest" version))
351 (base32 "0r0a5jic09xw5pk0x42pr99r3zab5m9s4x85ymx1sl769jz42zqf"))))
352 (build-system r-build-system)
355 ("r-magrittr" ,r-magrittr)
356 ("r-selectr" ,r-selectr)
358 (home-page "https://github.com/hadley/rvest")
359 (synopsis "Simple web scraping for R")
361 "@code{r-rvest} helps you scrape information from web pages. It is
362 designed to work with @code{magrittr} to make it easy to express common web
363 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
364 (license license:gpl3)))
366 (define-public r-selectr
373 (uri (cran-uri "selectr" version))
375 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
376 (build-system r-build-system)
378 `(("r-stringr" ,r-stringr)
380 (home-page "https://sjp.co.nz/projects/selectr/")
381 (synopsis "Translate CSS selectors to XPath expressions")
383 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
384 expression. This allows you to use CSS selectors when working with the XML
385 package as it can only evaluate XPath expressions. Also provided are
386 convenience functions useful for using CSS selectors on XML nodes. This
387 package is a port of the Python package @code{cssselect}.")
388 (license license:bsd-3)))
390 (define-public r-reprex
397 (uri (cran-uri "reprex" version))
400 "0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10"))))
401 (build-system r-build-system)
403 `(("r-callr" ,r-callr)
407 ("r-rmarkdown" ,r-rmarkdown)
408 ("r-whisker" ,r-whisker)
409 ("r-withr" ,r-withr)))
410 (home-page "https://github.com/tidyverse/reprex")
411 (synopsis "Prepare reproducible R code examples for sharing")
413 "This package provides a convenience wrapper that uses the
414 @code{rmarkdown} package to render small snippets of code to target formats
415 that include both code and output. The goal is to encourage the sharing of
416 small, reproducible, and runnable examples on code-oriented websites or email.
417 @code{reprex} also extracts clean, runnable R code from various common formats,
418 such as copy/paste from an R session.")
419 (license license:expat)))
421 (define-public r-callr
428 (uri (cran-uri "callr" version))
431 "1hvxw2glizq8g0qnxakcxh8jc5scn0hp1x8i70fdpqwwbgx49slr"))))
432 (build-system r-build-system)
435 ("r-processx" ,r-processx)))
436 (home-page "https://github.com/r-lib/callr#readme")
437 (synopsis "Call R from R")
439 "It is sometimes useful to perform a computation in a separate R process,
440 without affecting the current R process at all. This package does exactly
442 (license license:expat)))
444 (define-public r-readxl
451 (uri (cran-uri "readxl" version))
454 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
455 (build-system r-build-system)
457 `(("r-cellranger" ,r-cellranger)
458 ("r-progress" ,r-progress)
460 ("r-tibble" ,r-tibble)))
461 (home-page "https://readxl.tidyverse.org")
462 (synopsis "Read Excel files")
464 "This package lets you import Excel files into R. It supports
465 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
466 the embedded @code{RapidXML} C++ library.")
467 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
468 ;; 'rapidxml' which is Boost.
469 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
471 (define-public r-modelr
478 (uri (cran-uri "modelr" version))
481 "0nnfhlzz75ihs8azy963cc4cwg1kx81rybk4z3wm98bbghwfxfs5"))))
482 (build-system r-build-system)
484 `(("r-broom" ,r-broom)
486 ("r-magrittr" ,r-magrittr)
489 ("r-tibble" ,r-tibble)
490 ("r-tidyr" ,r-tidyr)))
491 (home-page "https://github.com/tidyverse/modelr")
492 (synopsis "Helper functions for modelling in pipelines")
494 "Functions for modelling that help you seamlessly integrate modelling
495 into a pipeline of data manipulation and visualisation.")
496 (license license:gpl3)))
498 (define-public r-httpuv
504 (uri (cran-uri "httpuv" version))
507 "13ax0hs2lc39ilznh1zarwqdzahcbhb8adilrfik3xg0fkljpcwk"))))
508 (build-system r-build-system)
512 ("r-promises" ,r-promises)
515 (home-page "https://github.com/rstudio/httpuv")
516 (synopsis "HTTP and WebSocket server library for R")
518 "The httpuv package provides low-level socket and protocol support for
519 handling HTTP and WebSocket requests directly from within R. It is primarily
520 intended as a building block for other packages, rather than making it
521 particularly easy to create complete web applications using httpuv alone.")
522 ;; This package includes third-party code that was originally released
523 ;; under various non-copyleft licenses. Full licensing information can be
524 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
525 (license license:gpl3+)))
527 (define-public r-jsonlite
533 (uri (cran-uri "jsonlite" version))
536 "0lyvhnr6n57h3a89bvipii7x17nvfaycm9j5j50bfrlr48jv9ic8"))))
537 (build-system r-build-system)
538 (home-page "http://arxiv.org/abs/1403.2805")
539 (synopsis "Robust, high performance JSON parser and generator for R")
541 "The jsonlite package provides a fast JSON parser and generator optimized
542 for statistical data and the web. It offers flexible, robust, high
543 performance tools for working with JSON in R and is particularly powerful for
544 building pipelines and interacting with a web API. In addition to converting
545 JSON data from/to R objects, jsonlite contains functions to stream, validate,
546 and prettify JSON data. The unit tests included with the package verify that
547 all edge cases are encoded and decoded consistently for use with dynamic data
548 in systems and applications.")
549 (license license:expat)))
551 (define-public r-servr
557 (uri (cran-uri "servr" version))
560 "199k9aghwk9rf1rm8pjg60xacqww25cza259h5dfj1ixil0m6dxi"))))
561 (build-system r-build-system)
563 `(("r-httpuv" ,r-httpuv)
564 ("r-jsonlite" ,r-jsonlite)
567 (home-page "https://github.com/yihui/servr")
568 (synopsis "Simple HTTP server to serve static files or dynamic documents")
570 "Servr provides an HTTP server in R to serve static files, or dynamic
571 documents that can be converted to HTML files (e.g., R Markdown) under a given
573 (license license:expat)))
575 (define-public r-htmltools
581 (uri (cran-uri "htmltools" version))
584 "06l17d8jkf438yk2mchpsp4j90bynnapz3nabh5vkcc324p5a62v"))))
585 (build-system r-build-system)
587 `(("r-digest" ,r-digest)
589 ("r-rlang" ,r-rlang)))
590 (home-page "https://cran.r-project.org/web/packages/htmltools")
591 (synopsis "R tools for HTML")
593 "This package provides tools for HTML generation and output in R.")
594 (license license:expat)))
596 (define-public r-htmlwidgets
598 (name "r-htmlwidgets")
602 (uri (cran-uri "htmlwidgets" version))
605 "10fp306l1nybkah6jrlrqwwdb6zvklbddp8i3w9v9naj8la5jbnl"))))
606 (build-system r-build-system)
608 `(("r-htmltools" ,r-htmltools)
609 ("r-jsonlite" ,r-jsonlite)
611 (home-page "https://github.com/ramnathv/htmlwidgets")
612 (synopsis "HTML Widgets for R")
614 "HTML widgets is a framework for creating HTML widgets that render in
615 various contexts including the R console, R Markdown documents, and Shiny web
617 (license license:expat)))
619 (define-public r-htmltable
626 (uri (cran-uri "htmlTable" version))
629 "0g9r156k9yl1f092hfw3b9wjx11akf0shbi3x0d0mvpnflvc8nfl"))))
630 (properties `((upstream-name . "htmlTable")))
631 (build-system r-build-system)
633 `(("r-checkmate" ,r-checkmate)
634 ("r-htmltools" ,r-htmltools)
635 ("r-htmlwidgets" ,r-htmlwidgets)
637 ("r-magrittr" ,r-magrittr)
638 ("r-rstudioapi" ,r-rstudioapi)
639 ("r-stringr" ,r-stringr)))
640 (home-page "http://gforge.se/packages/")
641 (synopsis "Advanced tables for Markdown/HTML")
643 "This package provides functions to build tables with advanced layout
644 elements such as row spanners, column spanners, table spanners, zebra
645 striping, and more. While allowing advanced layout, the underlying
646 CSS-structure is simple in order to maximize compatibility with word
647 processors such as LibreOffice. The package also contains a few text
648 formatting functions that help outputting text compatible with HTML or
650 (license license:gpl3+)))
652 (define-public r-curl
658 (uri (cran-uri "curl" version))
661 "1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl"))))
662 (build-system r-build-system)
665 (modify-phases %standard-phases
666 ;; The environment variable CURL_CA_BUNDLE is only respected when
667 ;; running Windows, so we disable the platform checks.
668 ;; This can be removed once the libcurl has been patched.
669 (add-after 'unpack 'allow-CURL_CA_BUNDLE
671 (substitute* "R/onload.R"
672 (("if \\(!grepl\\(\"mingw\".*")
674 (substitute* "src/handle.c"
675 (("#ifdef _WIN32") "#if 1"))
681 `(("pkg-config" ,pkg-config)))
682 (home-page "https://github.com/jeroenooms/curl")
683 (synopsis "HTTP client for R")
685 "The @code{curl()} and @code{curl_download()} functions provide highly
686 configurable drop-in replacements for base @code{url()} and
687 @code{download.file()} with better performance, support for encryption, gzip
688 compression, authentication, and other @code{libcurl} goodies. The core of
689 the package implements a framework for performing fully customized requests
690 where data can be processed either in memory, on disk, or streaming via the
691 callback or connection interfaces.")
692 (license license:expat)))
694 (define-public r-hwriter
701 (uri (cran-uri "hwriter" version))
704 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
705 (build-system r-build-system)
706 (home-page "https://cran.r-project.org/web/packages/hwriter")
707 (synopsis "Output R objects in HTML format")
709 "This package provides easy-to-use and versatile functions to output R
710 objects in HTML format.")
711 (license license:lgpl2.1+)))
713 (define-public r-rjson
720 (uri (cran-uri "rjson" version))
723 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
724 (build-system r-build-system)
725 (home-page "https://cran.r-project.org/web/packages/rjson")
726 (synopsis "JSON library for R")
728 "This package provides functions to convert R objects into JSON objects
730 (license license:gpl2+)))
732 (define-public r-shiny
740 (url "https://github.com/rstudio/shiny.git")
741 (commit (string-append "v" version))))
742 (file-name (git-file-name name version))
745 "1kl3dh68h4cnrm3rqn9pddk5n6bsmr5x0626bkfv0qqi0q92zin4"))))
746 (build-system r-build-system)
748 `(#:modules ((guix build r-build-system)
749 (guix build minify-build-system)
752 #:imported-modules (,@%r-build-system-modules
753 (guix build minify-build-system))
755 (modify-phases (@ (guix build r-build-system) %standard-phases)
756 (add-after 'unpack 'replace-bundled-minified-JavaScript
757 (lambda* (#:key inputs #:allow-other-keys)
758 (let ((replace-file (lambda (old new)
759 (format #t "replacing ~a with ~a\n" old new)
762 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
763 ;; contain just data. They are not minified code, so we don't
765 (with-directory-excursion "inst/www/shared"
766 (replace-file "bootstrap/shim/respond.min.js"
767 (string-append (assoc-ref inputs "js-respond")
768 "/share/javascript/respond.min.js"))
769 (replace-file "bootstrap/shim/html5shiv.min.js"
770 (string-append (assoc-ref inputs "js-html5shiv")
771 "/share/javascript/html5shiv.min.js"))
772 (replace-file "json2-min.js"
773 (string-append (assoc-ref inputs "js-json2")
774 "/share/javascript/json2.min.js"))
775 (replace-file "strftime/strftime-min.js"
776 (string-append (assoc-ref inputs "js-strftime")
777 "/share/javascript/strftime.min.js"))
778 (replace-file "highlight/highlight.pack.js"
779 (string-append (assoc-ref inputs "js-highlight")
780 "/share/javascript/highlight.min.js"))
781 (replace-file "datatables/js/jquery.dataTables.min.js"
782 (string-append (assoc-ref inputs "js-datatables")
783 "/share/javascript/jquery.dataTables.min.js"))
784 (replace-file "selectize/js/selectize.min.js"
785 (string-append (assoc-ref inputs "js-selectize")
786 "/share/javascript/selectize.min.js"))
787 (replace-file "selectize/js/es5-shim.min.js"
788 (string-append (assoc-ref inputs "js-es5-shim")
789 "/share/javascript/es5-shim.min.js"))
790 (for-each (match-lambda
793 (minify source #:target target)))
794 '(("jqueryui/jquery-ui.js" .
795 "jqueryui/jquery-ui.min.js")
796 ("datepicker/js/bootstrap-datepicker.js" .
797 "datepicker/js/bootstrap-datepicker.min.js")
798 ("ionrangeslider/js/ion.rangeSlider.js" .
799 "ionrangeslider/js/ion.rangeSlider.min.js")
800 ("bootstrap/js/bootstrap.js" .
801 "bootstrap/js/bootstrap.min.js")
808 `(("r-crayon" ,r-crayon)
809 ("r-httpuv" ,r-httpuv)
811 ("r-jsonlite" ,r-jsonlite)
812 ("r-xtable" ,r-xtable)
813 ("r-digest" ,r-digest)
814 ("r-htmltools" ,r-htmltools)
816 ("r-sourcetools" ,r-sourcetools)))
818 `(("js-datatables" ,js-datatables)
819 ("js-html5shiv" ,js-html5shiv)
820 ("js-json2" ,js-json2)
821 ("js-respond" ,js-respond)
822 ("js-selectize" ,js-selectize)
823 ("js-strftime" ,js-strftime)
824 ("js-highlight" ,js-highlight)
825 ("js-es5-shim" ,js-es5-shim)))
827 `(("uglify-js" ,uglify-js)))
828 (home-page "http://shiny.rstudio.com")
829 (synopsis "Easy interactive web applications with R")
831 "Makes it incredibly easy to build interactive web applications
832 with R. Automatic \"reactive\" binding between inputs and outputs and
833 extensive prebuilt widgets make it possible to build beautiful,
834 responsive, and powerful applications with minimal effort.")
835 (license license:artistic2.0)))
837 ;; This package includes minified JavaScript files. When upgrading please
838 ;; check that there are no new minified JavaScript files.
839 (define-public r-shinytree
846 (uri (cran-uri "shinyTree" version))
849 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
850 (modules '((guix build utils)))
853 ;; Delete minified JavaScript
854 (for-each delete-file
855 '("inst/www/jsTree-3.3.7/libs/require.js"
856 "inst/www/jsTree-3.3.7/libs/jquery.js"
857 "inst/www/jsTree-3.3.7/jstree.min.js"))
859 (properties `((upstream-name . "shinyTree")))
860 (build-system r-build-system)
862 `(#:modules ((guix build utils)
863 (guix build r-build-system)
867 (modify-phases %standard-phases
868 (add-after 'unpack 'replace-minified-javascript
869 (lambda* (#:key inputs #:allow-other-keys)
870 (with-directory-excursion "inst/www/jsTree-3.3.7/"
871 (symlink (string-append (assoc-ref inputs "js-requirejs")
872 "/share/javascript/require.min.js")
877 `((,(assoc-ref inputs "js-jquery")
881 (lambda (sources targets)
882 (for-each (lambda (source target)
883 (format #t "Processing ~a --> ~a~%"
885 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
886 (call-with-output-file target
888 (dump-port minified port)))))
892 `(("r-htmlwidgets" ,r-htmlwidgets)
893 ("r-jsonlite" ,r-jsonlite)
894 ("r-promises" ,r-promises)
896 ("r-stringr" ,r-stringr)))
898 `(("js-requirejs" ,js-requirejs)))
900 `(("uglify-js" ,uglify-js)
904 (uri "https://code.jquery.com/jquery-3.3.1.js")
907 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
908 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
909 (synopsis "jsTree bindings for Shiny")
911 "This package exposes R bindings to jsTree, a JavaScript library that
912 supports interactive trees, to enable rich, editable trees in Shiny.")
913 (license license:expat)))
915 (define-public r-shinydashboard
917 (name "r-shinydashboard")
921 (uri (cran-uri "shinydashboard" version))
924 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
925 (build-system r-build-system)
926 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
927 ;; Regenerate it from the included sources.
929 `(#:modules ((guix build utils)
930 (guix build r-build-system)
933 (modify-phases %standard-phases
934 (add-after 'unpack 'generate-minified-javascript
936 (with-directory-excursion "inst/AdminLTE"
937 (delete-file "app.min.js")
938 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
939 (call-with-output-file "app.min.js"
941 (dump-port minified port))))))))))
943 `(("r-htmltools" ,r-htmltools)
944 ("r-promises" ,r-promises)
945 ("r-shiny" ,r-shiny)))
947 `(("uglify-js" ,uglify-js)))
948 (home-page "http://rstudio.github.io/shinydashboard/")
949 (synopsis "Create dashboards with shiny")
950 (description "This package provides an extension to the Shiny web
951 application framework for R, making it easy to create attractive dashboards.")
952 ;; This package includes software that was released under the Expat
953 ;; license, but the whole package is released under GPL version 2 or
955 (license license:gpl2+)))
957 (define-public r-shinyfiles
959 (name "r-shinyfiles")
964 (uri (cran-uri "shinyFiles" version))
966 (base32 "1143m941hma9hc77c3xcw26c0ygfhn9ii2sbp9wrydxv4gc7mr8a"))))
967 (properties `((upstream-name . "shinyFiles")))
968 (build-system r-build-system)
971 ("r-htmltools" ,r-htmltools)
972 ("r-jsonlite" ,r-jsonlite)
974 ("r-tibble" ,r-tibble)))
975 (home-page "https://github.com/thomasp85/shinyFiles")
976 (synopsis "Server-side file system viewer for Shiny")
978 "This package provides functionality for client-side navigation of the
979 server side file system in shiny apps. In case the app is running locally
980 this gives the user direct access to the file system without the need to
981 \"download\" files to a temporary location. Both file and folder selection as
982 well as file saving is available.")
983 (license license:gpl2+)))
985 (define-public r-shinythemes
987 (name "r-shinythemes")
992 (uri (cran-uri "shinythemes" version))
995 "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf"))))
996 (properties `((upstream-name . "shinythemes")))
997 (build-system r-build-system)
998 (propagated-inputs `(("r-shiny" ,r-shiny)))
999 (home-page "http://rstudio.github.io/shinythemes/")
1000 (synopsis "Themes for Shiny")
1002 "This package provides themes for use with Shiny. It includes several
1003 Bootstrap themes, which are packaged for use with Shiny applications.")
1004 ;; The package is released under version 3 of the GPL, but it includes
1005 ;; source files that are covered by the Expat license. It also includes
1006 ;; fonts under SIL or the ASL.
1007 (license (list license:gpl3 license:expat
1008 license:silofl1.1 license:asl2.0))))
1010 ;; The package sources include minified variants of d3.js and non-minified
1011 ;; source code of d3-jetpack.
1012 (define-public r-d3r
1019 (uri (cran-uri "d3r" version))
1022 "0xl3im76lp7pd5lhp8jfyqdm4j4zvjrx5a5fl81xv2cf7x3n4f2a"))))
1023 (build-system r-build-system)
1025 `(#:modules ((guix build utils)
1026 (guix build r-build-system)
1030 (modify-phases %standard-phases
1031 (add-after 'unpack 'process-javascript
1032 (lambda* (#:key inputs #:allow-other-keys)
1033 (with-directory-excursion "inst/www/d3/"
1037 `((,(assoc-ref inputs "d3.v3.js")
1038 "v3/dist/d3.min.js")
1039 (,(assoc-ref inputs "d3.v4.js")
1040 "v4/dist/d3.min.js")
1041 (,(assoc-ref inputs "d3.v5.js")
1042 "v5/dist/d3.min.js"))))
1043 (lambda (sources targets)
1044 (for-each (lambda (source target)
1045 (format #t "Processing ~a --> ~a~%"
1047 (delete-file target)
1048 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1049 (call-with-output-file target
1051 (dump-port minified port)))))
1055 `(("r-dplyr" ,r-dplyr)
1056 ("r-htmltools" ,r-htmltools)
1057 ("r-tidyr" ,r-tidyr)))
1059 `(("uglify-js" ,uglify-js)
1063 (uri "https://d3js.org/d3.v3.js")
1066 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
1070 (uri "https://d3js.org/d3.v4.js")
1073 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
1077 (uri "https://d3js.org/d3.v5.js")
1080 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))))
1081 (home-page "https://github.com/timelyportfolio/d3r")
1082 (synopsis "d3.js utilities for R")
1084 "This package provides a suite of functions to help ease the use of the
1085 d3.js visualization library in R. These helpers include
1086 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
1087 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
1088 R objects into the JSON format that the d3.js library expects.")
1089 (license license:bsd-3)))
1091 ;; We use the latest commit here because the last release was in 2016 while
1092 ;; the latest commit was in 2018.
1093 (define-public r-sankeyd3
1094 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
1098 (version (git-version "0.3.2" revision commit))
1103 (url "https://github.com/fbreitwieser/sankeyD3.git")
1105 (file-name (git-file-name name version))
1108 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
1109 (build-system r-build-system)
1112 ("r-htmlwidgets" ,r-htmlwidgets)
1113 ("r-shiny" ,r-shiny)
1114 ("r-magrittr" ,r-magrittr)))
1115 (home-page "https://github.com/fbreitwieser/sankeyD3")
1116 (synopsis "Sankey network graphs from R")
1118 "This package provides an R library to generate Sankey network graphs
1119 in R and Shiny via the D3 visualization library.")
1120 ;; The R code is licensed under GPLv3+. It includes the non-minified
1121 ;; JavaScript source code of d3-sankey, which is released under the
1122 ;; 3-clause BSD license.
1123 (license (list license:gpl3+ license:bsd-3)))))
1125 (define-public r-crosstalk
1127 (name "r-crosstalk")
1132 (uri (cran-uri "crosstalk" version))
1135 "0lfa89vhrzi7a1rghmygcjr8gzddw35sinb3jx6g49mc9jias7mk"))))
1136 (build-system r-build-system)
1138 `(("r-ggplot2" ,r-ggplot2)
1139 ("r-htmltools" ,r-htmltools)
1140 ("r-jsonlite" ,r-jsonlite)
1141 ("r-lazyeval" ,r-lazyeval)
1143 ("r-shiny" ,r-shiny)))
1144 (home-page "https://rstudio.github.io/crosstalk/")
1145 (synopsis "Inter-widget interactivity for HTML widgets")
1147 "This package provides building blocks for allowing HTML widgets to
1148 communicate with each other, with Shiny or without (i.e. static @code{.html}
1149 files). It currently supports linked brushing and filtering.")
1150 (license license:expat)))
1152 (define-public r-rook
1159 (uri (cran-uri "Rook" version))
1162 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
1163 (properties `((upstream-name . "Rook")))
1164 (build-system r-build-system)
1165 (propagated-inputs `(("r-brew" ,r-brew)))
1166 (home-page "https://cran.r-project.org/web/packages/Rook")
1167 (synopsis "Web server interface for R")
1169 "This package contains the Rook specification and convenience software
1170 for building and running Rook applications. A Rook application is an R
1171 reference class object that implements a @code{call} method or an R closure
1172 that takes exactly one argument, an environment, and returns a list with three
1173 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
1174 (license license:gpl2)))
1176 (define-public r-miniui
1183 (uri (cran-uri "miniUI" version))
1186 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
1187 (properties `((upstream-name . "miniUI")))
1188 (build-system r-build-system)
1190 `(("r-htmltools" ,r-htmltools)
1191 ("r-shiny" ,r-shiny)))
1192 (home-page "https://cran.r-project.org/web/packages/miniUI/")
1193 (synopsis "Shiny UI widgets for small screens")
1195 "This package provides UI widget and layout functions for writing Shiny apps that
1196 work well on small screens.")
1197 (license license:gpl3)))
1199 (define-public r-feather
1206 (uri (cran-uri "feather" version))
1209 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
1210 (build-system r-build-system)
1214 ("r-tibble" ,r-tibble)))
1215 (home-page "https://github.com/wesm/feather")
1216 (synopsis "R Bindings to the Feather API")
1217 (description "Read and write feather files, a lightweight binary columnar
1218 data store designed for maximum speed.")
1219 (license license:asl2.0)))
1221 (define-public r-maps
1228 (uri (cran-uri "maps" version))
1231 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
1232 (build-system r-build-system)
1233 (home-page "https://cran.r-project.org/web/packages/maps")
1234 (synopsis "Draw geographical maps")
1235 (description "This package provides an R module for display of maps.
1236 Projection code and larger maps are in separate packages (@code{mapproj} and
1238 (license license:gpl2)))
1240 (define-public r-mapproj
1247 (uri (cran-uri "mapproj" version))
1250 "1rggww8cbwv0vzlj5afzhbsbngg4bzj5znbkz7wmxsbshfbsm9b2"))))
1251 (build-system r-build-system)
1252 (propagated-inputs `(("r-maps" ,r-maps)))
1253 (home-page "https://cran.r-project.org/web/packages/mapproj")
1254 (synopsis "Map projection in R")
1255 (description "This package converts latitude/longitude into projected
1257 (license (list license:gpl2 ; The R interface
1258 (license:non-copyleft ; The C code
1259 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
1260 "Lucent Public License Version 1.02")))))
1262 (define-public r-rgooglemaps
1264 (name "r-rgooglemaps")
1269 (uri (cran-uri "RgoogleMaps" version))
1272 "0sbklacc4jl5524ixhc11mh6smrzdz4l9pji6cn402i6zdn9z05x"))))
1273 (properties `((upstream-name . "RgoogleMaps")))
1274 (build-system r-build-system)
1275 (propagated-inputs `(("r-png" ,r-png)))
1276 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
1277 (synopsis "Use Google Maps in R")
1278 (description "This package serves two purposes:
1280 @item Provide a comfortable R interface to query the Google server for static
1282 @item Use the map as a background image to overlay plots within R. This
1283 requires proper coordinate scaling.
1285 (license license:gpl2+)))
1287 (define-public r-geosphere
1289 (name "r-geosphere")
1294 (uri (cran-uri "geosphere" version))
1297 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
1298 (build-system r-build-system)
1299 (propagated-inputs `(("r-sp" ,r-sp)))
1300 (home-page "https://cran.r-project.org/web/packages/geosphere")
1301 (synopsis "Spherical trigonometry")
1302 (description "This package computes spherical trigonometry for geographic
1303 applications. That is, compute distances and related measures for angular
1304 (longitude/latitude) locations.")
1305 (license license:gpl3+)))
1307 (define-public r-jpeg
1314 (uri (cran-uri "jpeg" version))
1317 "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
1318 (build-system r-build-system)
1319 (inputs `(("libjpeg" ,libjpeg)))
1320 (home-page "http://www.rforge.net/jpeg/")
1321 (synopsis "Read and write JPEG images with R")
1322 (description "This package provides a way to read, write and display
1323 bitmap images stored in the JPEG format with R. It can read and write both
1324 files and in-memory raw vectors.")
1325 (license license:gpl2+)))
1327 (define-public r-ggmap
1334 (uri (cran-uri "ggmap" version))
1337 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
1338 (build-system r-build-system)
1340 `(("r-bitops" ,r-bitops)
1341 ("r-digest" ,r-digest)
1342 ("r-dplyr" ,r-dplyr)
1343 ("r-ggplot2" ,r-ggplot2)
1347 ("r-magrittr" ,r-magrittr)
1350 ("r-purrr" ,r-purrr)
1351 ("r-rgooglemaps" ,r-rgooglemaps)
1352 ("r-rjson" ,r-rjson)
1353 ("r-scales" ,r-scales)
1354 ("r-stringr" ,r-stringr)
1355 ("r-tibble" ,r-tibble)
1356 ("r-tidyr" ,r-tidyr)))
1357 (home-page "https://github.com/dkahle/ggmap")
1358 (synopsis "Spatial visualization with ggplot2")
1359 (description "This package provides a collection of functions to visualize
1360 spatial data and models on top of static maps from various online sources (e.g
1361 Google Maps and Stamen Maps). It includes tools common to those tasks,
1362 including functions for geolocation and routing.")
1363 (license license:gpl2)))
1365 (define-public r-haven
1372 (uri (cran-uri "haven" version))
1375 "0g9d6mxqmrw2zdms78jpx2sx73pczlyy771v1h5hmxqz9sqyk7hr"))))
1376 (build-system r-build-system)
1380 `(("r-forcats" ,r-forcats)
1383 ("r-rlang" ,r-rlang)
1384 ("r-readr" ,r-readr)
1385 ("r-tibble" ,r-tibble)
1386 ("r-tidyselect" ,r-tidyselect)))
1387 (home-page "https://haven.tidyverse.org")
1388 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
1390 "This package lets you mport foreign statistical formats into R via the
1391 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
1392 (license license:expat)))
1394 (define-public r-amap
1400 (uri (cran-uri "amap" version))
1403 "1il94bkhl8192vawq4gr2gwyhqhid27jr2312rhvr72ssg8p713b"))))
1404 (build-system r-build-system)
1406 `(("gfortran" ,gfortran)))
1407 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
1408 (synopsis "Another multidimensional analysis package")
1409 (description "This package provides tools for clustering and principal
1410 component analysis (with robust methods, and parallelized functions).")
1411 (license license:gpl2+)))
1413 (define-public r-ape
1420 (uri (cran-uri "ape" version))
1423 "08wbk1kxhs32bmmvqlqanbdg1w235amd35k8m00fngsj9h9xzc08"))))
1424 (build-system r-build-system)
1426 `(("r-lattice" ,r-lattice)
1428 ("r-rcpp" ,r-rcpp)))
1429 (home-page "http://ape-package.ird.fr/")
1430 (synopsis "Analyses of phylogenetics and evolution")
1432 "This package provides functions for reading, writing, plotting, and
1433 manipulating phylogenetic trees, analyses of comparative data in a
1434 phylogenetic framework, ancestral character analyses, analyses of
1435 diversification and macroevolution, computing distances from DNA sequences,
1436 and several other tools.")
1437 (license license:gpl2+)))
1439 (define-public r-abbyyr
1446 (uri (cran-uri "abbyyR" version))
1449 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
1450 (properties `((upstream-name . "abbyyR")))
1451 (build-system r-build-system)
1453 `(("r-curl" ,r-curl)
1456 ("r-progress" ,r-progress)
1457 ("r-readr" ,r-readr)
1459 (home-page "https://github.com/soodoku/abbyyR")
1460 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
1462 "This package provides tools to get text from images of text using Abbyy
1463 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
1464 OCR images, barcodes, forms, documents with machine readable zones, e.g.
1465 passports and get the results in a variety of formats including plain text and
1466 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
1467 (license license:expat)))
1469 (define-public r-colorspace
1471 (name "r-colorspace")
1476 (uri (cran-uri "colorspace" version))
1478 (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9"))))
1479 (build-system r-build-system)
1480 (home-page "https://cran.r-project.org/web/packages/colorspace")
1481 (synopsis "Color space manipulation")
1483 "This package carries out a mapping between assorted color spaces
1484 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
1485 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
1486 colors are provided.")
1487 (license license:bsd-3)))
1489 (define-public r-glue
1496 (uri (cran-uri "glue" version))
1499 "1a1ycg9r3gd91visp49q49rsrdgyf8kr9dxdy3hk99kikn4z5hag"))))
1500 (build-system r-build-system)
1501 (home-page "https://github.com/tidyverse/glue")
1502 (synopsis "Interpreted string literals")
1504 "This package provides an implementation of interpreted string literals,
1505 inspired by Python's Literal String Interpolation (PEP-0498) and
1506 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
1507 (license license:expat)))
1509 (define-public r-pastecs
1515 (uri (cran-uri "pastecs" version))
1518 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
1519 (build-system r-build-system)
1521 `(("r-boot" ,r-boot)))
1522 (home-page "http://www.sciviews.org/pastecs")
1523 (synopsis "Analysis of space-time ecological series")
1525 "This package provides functions for regulation, decomposition and analysis
1526 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
1527 initiative to bring PASSTEC 2000 functionalities to R.")
1528 (license license:gpl2+)))
1530 (define-public r-plogr
1537 (uri (cran-uri "plogr" version))
1540 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
1541 (build-system r-build-system)
1542 (home-page "https://github.com/krlmlr/plogr")
1543 (synopsis "R bindings for the plog C++ logging library")
1545 "This package provides the header files for a stripped-down version of
1546 the plog header-only C++ logging library, and a method to log to R's standard
1548 (license license:expat)))
1550 (define-public r-pls
1557 (uri (cran-uri "pls" version))
1559 (base32 "121byimd6bg7jbrq5wz5fpi0vxq0vh8g724vkhnjzszbvcv1xsb7"))))
1560 (build-system r-build-system)
1561 (home-page "http://mevik.net/work/software/pls.html")
1562 (synopsis "Partial Least Squares and Principal Component Regression")
1564 "The pls package implements multivariate regression methods: Partial Least
1565 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
1566 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
1569 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
1570 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
1571 @item multi-response models (or @dfn{PLS2})
1572 @item flexible cross-validation
1573 @item Jackknife variance estimates of regression coefficients
1574 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
1575 (R)MSEP, R², and correlation loadings
1576 @item formula interface, modelled after @code{lm()}, with methods for predict,
1577 print, summary, plot, update, etc.
1578 @item extraction functions for coefficients, scores, and loadings
1579 @item MSEP, RMSEP, and R² estimates
1580 @item multiplicative scatter correction (@dfn{MSC})
1582 (license license:gpl2)))
1591 (uri (cran-uri "ps" version))
1593 (base32 "1lcq7r0q4jb8x6k023zr2ydj2dg925bqqbkhx1phpnyjrk897498"))))
1594 (build-system r-build-system)
1595 (home-page "http://ps.r-lib.org")
1596 (synopsis "List, query, and manipulate system processes")
1598 "The ps package implements an API to list, query, and manipulate system
1599 processes. Most of its code is based on the @code{psutil} Python package.")
1600 (license license:bsd-3)))
1602 (define-public r-pkgbuild
1609 (uri (cran-uri "pkgbuild" version))
1611 (base32 "0xnlz6ivhkbmncg9hfw5p69lm4rjy3wn5lyxmygxyf4rrfnnqwxx"))))
1612 (build-system r-build-system)
1614 `(("r-callr" ,r-callr)
1616 ("r-crayon" ,r-crayon)
1618 ("r-prettyunits" ,r-prettyunits)
1620 ("r-rprojroot" ,r-rprojroot)
1621 ("r-withr" ,r-withr)))
1622 (home-page "https://github.com/r-pkgs/pkgbuild")
1623 (synopsis "Find tools needed to build R packages")
1625 "This package provides functions used to build R packages. It locates
1626 compilers needed to build R packages on various platforms and ensures the PATH
1627 is configured appropriately so R can use them.")
1628 (license license:gpl3)))
1630 (define-public r-pkgload
1637 (uri (cran-uri "pkgload" version))
1640 "0z7jvharafahi2gv5547mk1n499isjzw06kfwymmxc0gd575d1ii"))))
1641 (build-system r-build-system)
1643 `(("r-desc" ,r-desc)
1644 ("r-pkgbuild" ,r-pkgbuild)
1645 ("r-rlang" ,r-rlang)
1646 ("r-rprojroot" ,r-rprojroot)
1647 ("r-rstudioapi" ,r-rstudioapi)
1648 ("r-withr" ,r-withr)))
1649 (home-page "https://github.com/r-lib/pkgload")
1650 (synopsis "Simulate package installation and attach")
1652 "This package simulates the process of installing a package and then
1653 attaching it. This is a key part of the @code{devtools} package as it allows
1654 you to rapidly iterate while developing a package.")
1655 (license license:gpl3)))
1657 (define-public r-rcpp
1664 (uri (cran-uri "Rcpp" version))
1666 (base32 "03h3zyjq948y0hrrs95lfk4zgx6wfrg64hjlrfrzf5na7bfh0d9b"))))
1667 (build-system r-build-system)
1669 `(("r-knitr" ,r-knitr))) ; for vignettes
1670 (home-page "http://www.rcpp.org")
1671 (synopsis "Seamless R and C++ integration")
1673 "The Rcpp package provides R functions as well as C++ classes which offer
1674 a seamless integration of R and C++. Many R data types and objects can be
1675 mapped back and forth to C++ equivalents which facilitates both writing of new
1676 code as well as easier integration of third-party libraries. Documentation
1677 about Rcpp is provided by several vignettes included in this package, via the
1678 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
1679 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
1680 @code{citation(\"Rcpp\")} for details on these last two.")
1681 (license license:gpl2+)))
1683 (define-public r-bindr
1690 (uri (cran-uri "bindr" version))
1693 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
1694 (build-system r-build-system)
1695 (home-page "https://github.com/krlmlr/bindr")
1696 (synopsis "Parametrized active bindings")
1698 "This package provides a simple interface for creating active bindings
1699 where the bound function accepts additional arguments.")
1700 (license license:expat)))
1702 (define-public r-bindrcpp
1709 (uri (cran-uri "bindrcpp" version))
1712 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
1713 (build-system r-build-system)
1715 `(("r-bindr" ,r-bindr)
1716 ("r-plogr" ,r-plogr)
1717 ("r-rcpp" ,r-rcpp)))
1718 (home-page "https://github.com/krlmlr/bindrcpp")
1719 (synopsis "Rcpp interface to active bindings")
1721 "This package provides an easy way to fill an environment with active
1722 bindings that call a C++ function.")
1723 (license license:expat)))
1725 (define-public r-auc
1732 (uri (cran-uri "AUC" version))
1735 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
1736 (properties `((upstream-name . "AUC")))
1737 (build-system r-build-system)
1738 (home-page "https://cran.r-project.org/web/packages/AUC")
1739 (synopsis "Compute the area under the curve of selected measures")
1741 "This package includes functions to compute the area under the curve of
1742 selected measures: the area under the sensitivity curve (AUSEC), the area
1743 under the specificity curve (AUSPC), the area under the accuracy
1744 curve (AUACC), and the area under the receiver operating characteristic
1745 curve (AUROC). The curves can also be visualized. Support for partial areas
1747 (license license:gpl2+)))
1749 (define-public r-calibrate
1751 (name "r-calibrate")
1756 (uri (cran-uri "calibrate" version))
1758 (base32 "1s423nr176l2sc66wp7hzgqkv7c2bq8d2bjrrvrrm5qa9y3zdx1k"))))
1759 (build-system r-build-system)
1761 `(("r-mass" ,r-mass)))
1762 (home-page "https://cran.r-project.org/web/packages/calibrate")
1763 (synopsis "Calibration of scatterplot and biplot axes")
1765 "This is a package for drawing calibrated scales with tick marks
1766 on (non-orthogonal) variable vectors in scatterplots and biplots.")
1767 (license license:gpl2)))
1769 (define-public r-shape
1776 (uri (cran-uri "shape" version))
1779 "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
1780 (build-system r-build-system)
1781 (home-page "https://cran.r-project.org/web/packages/shape")
1782 (synopsis "Functions for plotting graphical shapes")
1784 "This package provides functions for plotting graphical shapes such as
1785 ellipses, circles, cylinders, arrows, ...")
1786 (license license:gpl3+)))
1788 (define-public r-globaloptions
1790 (name "r-globaloptions")
1795 (uri (cran-uri "GlobalOptions" version))
1797 (base32 "0x89hfz80avq4zcskxl71i4zi0mgniqqxfrvz050aa2189wfyja2"))))
1798 (properties `((upstream-name . "GlobalOptions")))
1799 (build-system r-build-system)
1800 (home-page "https://github.com/jokergoo/GlobalOptions")
1801 (synopsis "Generate functions to get or set global options")
1803 "This package provides more controls on the option values such as
1804 validation and filtering on the values, making options invisible or private.")
1805 (license license:gpl2+)))
1807 (define-public r-circlize
1814 (uri (cran-uri "circlize" version))
1817 "0jvr9hmxyhg0zx101iiqkrg8wfaj86kp62xpv42n2j9fkn5r1mi2"))))
1818 (build-system r-build-system)
1820 `(("r-colorspace" ,r-colorspace)
1821 ("r-globaloptions" ,r-globaloptions)
1822 ("r-shape" ,r-shape)))
1823 (home-page "https://github.com/jokergoo/circlize")
1824 (synopsis "Circular visualization")
1826 "Circular layout is an efficient way to visualise huge amounts of
1827 information. This package provides an implementation of circular layout
1828 generation in R as well as an enhancement of available software. Its
1829 flexibility is based on the usage of low-level graphics functions such that
1830 self-defined high-level graphics can be easily implemented by users for
1831 specific purposes. Together with the seamless connection between the powerful
1832 computational and visual environment in R, it gives users more convenience and
1833 freedom to design figures for better understanding complex patterns behind
1834 multi-dimensional data.")
1835 (license license:gpl2+)))
1837 (define-public r-powerlaw
1844 (uri (cran-uri "poweRlaw" version))
1847 "1asr6ikr7hmj78jyg8r1gwvcjg14addkxdiz92nh06lv71a183r4"))))
1848 (properties `((upstream-name . "poweRlaw")))
1849 (build-system r-build-system)
1851 `(("r-vgam" ,r-vgam)))
1852 (home-page "https://github.com/csgillespie/poweRlaw")
1853 (synopsis "Tools for the analysis of heavy tailed distributions")
1855 "This package provides an implementation of maximum likelihood estimators
1856 for a variety of heavy tailed distributions, including both the discrete and
1857 continuous power law distributions. Additionally, a goodness-of-fit based
1858 approach is used to estimate the lower cut-off for the scaling region.")
1859 ;; Any of these GPL versions.
1860 (license (list license:gpl2 license:gpl3))))
1862 (define-public r-compare
1869 (uri (cran-uri "compare" version))
1872 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
1873 (build-system r-build-system)
1874 (home-page "https://cran.r-project.org/web/packages/compare")
1875 (synopsis "Comparing objects for differences")
1877 "This package provides functions to compare a model object to a
1878 comparison object. If the objects are not identical, the functions can be
1879 instructed to explore various modifications of the objects (e.g., sorting
1880 rows, dropping names) to see if the modified versions are identical.")
1881 (license license:gpl2+)))
1883 (define-public r-dendextend
1885 (name "r-dendextend")
1890 (uri (cran-uri "dendextend" version))
1893 "1iclvd9cyckd4djpa87ynm05fk6zl4b4m735za1w4irimc130m3r"))))
1894 (build-system r-build-system)
1896 `(("r-ggplot2" ,r-ggplot2)
1897 ("r-magrittr" ,r-magrittr)
1898 ("r-viridis" ,r-viridis)))
1899 (home-page "https://cran.r-project.org/web/packages/dendextend")
1900 (synopsis "Extending 'dendrogram' functionality in R")
1902 "This package offers a set of functions for extending @code{dendrogram}
1903 objects in R, letting you visualize and compare trees of hierarchical
1904 clusterings. You can adjust a tree's graphical parameters (the color, size,
1905 type, etc of its branches, nodes and labels) and visually and statistically
1906 compare different dendrograms to one another.")
1907 ;; Any of these versions
1908 (license (list license:gpl2 license:gpl3))))
1910 (define-public r-getoptlong
1912 (name "r-getoptlong")
1917 (uri (cran-uri "GetoptLong" version))
1920 "1fl3w2n602ldybc5qj7qw4xmzzb804bsjkqwf6dswzj0vf0qiadr"))))
1921 (properties `((upstream-name . "GetoptLong")))
1922 (build-system r-build-system)
1926 `(("r-globaloptions" ,r-globaloptions)
1927 ("r-rjson" ,r-rjson)))
1928 (home-page "https://github.com/jokergoo/GetoptLong")
1929 (synopsis "Parsing command-line arguments and variable interpolation")
1931 "This is yet another command-line argument parser which wraps the
1932 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
1933 use in R. It also provides a simple way for variable interpolation in R.")
1934 (license license:gpl2+)))
1936 (define-public r-fastmatch
1938 (name "r-fastmatch")
1943 (uri (cran-uri "fastmatch" version))
1946 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
1947 (build-system r-build-system)
1948 (home-page "http://www.rforge.net/fastmatch")
1949 (synopsis "Fast match function")
1951 "This package provides a fast @code{match} replacement for cases that
1952 require repeated look-ups. It is slightly faster that R's built-in
1953 @code{match} function on first match against a table, but extremely fast on
1954 any subsequent lookup as it keeps the hash table in memory.")
1955 (license license:gpl2)))
1964 (uri (cran-uri "ff" version))
1967 "1w724q4jpzbvzpilb2ifviaxkjgk9lzwxz9gksnvicbmfa20fqqw"))))
1968 (build-system r-build-system)
1969 (propagated-inputs `(("r-bit" ,r-bit)))
1970 (home-page "http://ff.r-forge.r-project.org/")
1971 (synopsis "Memory-efficient storage of large data on disk and access functions")
1973 "This package provides data structures that are stored on disk but
1974 behave (almost) as if they were in RAM by transparently mapping only a section
1976 ;; error Architecture not supported.
1977 (supported-systems (delete "aarch64-linux" %supported-systems))
1978 (license license:gpl2)))
1980 (define-public r-ffbase
1987 (uri (cran-uri "ffbase" version))
1990 "04kxx2f3f0743c5nvpb7x1x0pcd220dazpd5ag1pidxbz3xa85nw"))))
1991 (build-system r-build-system)
1994 ("r-fastmatch" ,r-fastmatch)
1996 (home-page "http://github.com/edwindj/ffbase")
1997 (synopsis "Basic statistical functions for package 'ff'")
1999 "This package extends the out of memory vectors of @code{ff} with
2000 statistical functions and other utilities to ease their usage.")
2001 (license license:gpl3)))
2003 (define-public r-prettyunits
2005 (name "r-prettyunits")
2010 (uri (cran-uri "prettyunits" version))
2013 "0p3z42hnk53x7ky4d1dr2brf7p8gv3agxr71i99m01n2hq2ri91m"))))
2014 (build-system r-build-system)
2016 `(("r-assertthat" ,r-assertthat)
2017 ("r-magrittr" ,r-magrittr)))
2018 (home-page "https://github.com/gaborcsardi/prettyunits")
2019 (synopsis "Pretty, human readable formatting of quantities")
2021 "This package provides tools for pretty, human readable formatting of
2023 (license license:expat)))
2025 (define-public r-reshape
2032 (uri (cran-uri "reshape" version))
2035 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
2036 (build-system r-build-system)
2038 `(("r-plyr" ,r-plyr)
2039 ("r-rcpp" ,r-rcpp)))
2040 (home-page "http://had.co.nz/reshape")
2041 (synopsis "Flexibly reshape data")
2043 "Flexibly restructure and aggregate data using just two functions:
2044 @code{melt} and @code{cast}. This package provides them.")
2045 (license license:expat)))
2047 (define-public r-progress
2054 (uri (cran-uri "progress" version))
2057 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
2058 (build-system r-build-system)
2060 `(("r-crayon" ,r-crayon)
2062 ("r-prettyunits" ,r-prettyunits)
2064 (home-page "https://github.com/gaborcsardi/progress")
2065 (synopsis "Terminal progress bars")
2067 "This package provides configurable progress bars. They may include
2068 percentage, elapsed time, and/or the estimated completion time. They work in
2069 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
2070 package also provides a C++ API, that works with or without Rcpp.")
2071 (license license:expat)))
2073 (define-public r-ggally
2080 (uri (cran-uri "GGally" version))
2083 "1zjmcc5bzagvy7c5cmdcl39xmx07fwi98yrj4i05w7y40kqcsiws"))))
2084 (properties `((upstream-name . "GGally")))
2085 (build-system r-build-system)
2087 `(("libressl" ,libressl)))
2089 `(("r-ggplot2" ,r-ggplot2)
2090 ("r-gtable" ,r-gtable)
2092 ("r-progress" ,r-progress)
2093 ("r-rcolorbrewer" ,r-rcolorbrewer)
2094 ("r-reshape" ,r-reshape)
2095 ("r-rlang" ,r-rlang)))
2096 (home-page "https://ggobi.github.io/ggally")
2097 (synopsis "Extension to ggplot2")
2099 "The R package ggplot2 is a plotting system based on the grammar of
2100 graphics. GGally extends ggplot2 by adding several functions to reduce the
2101 complexity of combining geometric objects with transformed data. Some of
2102 these functions include a pairwise plot matrix, a two group pairwise plot
2103 matrix, a parallel coordinates plot, a survival plot, and several functions to
2105 (license license:gpl2+)))
2107 (define-public r-proxy
2114 (uri (cran-uri "proxy" version))
2117 "17b6qfllqrhzrxqgx7dccffgybnkcria5a68ap5ly3plg04ypm4x"))))
2118 (build-system r-build-system)
2119 (home-page "https://cran.r-project.org/web/packages/proxy")
2120 (synopsis "Distance and similarity measures")
2122 "This package provides an extensible framework for the efficient
2123 calculation of auto- and cross-proximities, along with implementations of the
2124 most popular ones.")
2125 (license license:gpl2)))
2134 (uri (cran-uri "sp" version))
2136 (base32 "0kpjsqh3lzqp1m0avsvm54lazlgwfx3hyf0av3mvbyslsanj42ll"))))
2137 (build-system r-build-system)
2139 `(("r-lattice" ,r-lattice)))
2140 (home-page "https://cran.r-project.org/web/packages/sp")
2141 (synopsis "Classes and methods for spatial data")
2143 "This package provides classes and methods for spatial data; the classes
2144 document where the spatial location information resides, for 2D or 3D data.
2145 Utility functions are provided, e.g. for plotting data as maps, spatial
2146 selection, as well as methods for retrieving coordinates, for subsetting,
2147 print, summary, etc.")
2148 (license license:gpl2+)))
2150 (define-public r-rmtstat
2157 (uri (cran-uri "RMTstat" version))
2160 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
2161 (properties `((upstream-name . "RMTstat")))
2162 (build-system r-build-system)
2163 (home-page "https://cran.r-project.org/web/packages/RMTstat")
2164 (synopsis "Distributions, statistics and tests derived from random matrix theory")
2166 "This package provides functions for working with the Tracy-Widom laws
2167 and other distributions related to the eigenvalues of large Wishart
2169 (license license:bsd-3)))
2171 (define-public r-rmpi
2177 (uri (cran-uri "Rmpi" version))
2180 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
2181 (properties `((upstream-name . "Rmpi")))
2182 (build-system r-build-system)
2184 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
2185 #:phases (modify-phases %standard-phases
2186 (add-before 'install 'mpi-setup
2189 `(("openmpi" ,openmpi)))
2191 `(("pkg-config" ,pkg-config)))
2192 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
2193 (synopsis "R interface to message-passing interface (MPI)")
2195 "This package provides an interface (wrapper) to MPI APIs. It also
2196 provides an interactive R manager and worker environment.")
2197 (license license:gpl2+)))
2199 (define-public r-lmoments
2206 (uri (cran-uri "Lmoments" version))
2209 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
2210 (properties `((upstream-name . "Lmoments")))
2211 (build-system r-build-system)
2213 `(("r-rcpp" ,r-rcpp)
2214 ("r-rcpparmadillo" ,r-rcpparmadillo)))
2215 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
2216 (synopsis "L-moments and quantile mixtures")
2218 "This package contains functions to estimate L-moments and trimmed
2219 L-moments from the data. It also contains functions to estimate the
2220 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
2221 quantile mixture from L-moments and trimmed L-moments.")
2222 (license license:gpl2)))
2224 (define-public r-distillery
2226 (name "r-distillery")
2231 (uri (cran-uri "distillery" version))
2234 "1mi3ig9jq0kd7yrwc5m37lmrw04p1b4lirnbsxi10z3n5yay4429"))))
2235 (build-system r-build-system)
2236 (home-page "http://www.ral.ucar.edu/staff/ericg")
2237 (synopsis "Functions for confidence intervals and object information")
2239 "This package provides some very simple method functions for confidence
2240 interval calculation and to distill pertinent information from a potentially
2241 complex object; primarily used in common with the packages extRemes and
2243 (license license:gpl2+)))
2245 (define-public r-extremes
2252 (uri (cran-uri "extRemes" version))
2255 "0hmgynxhzswqnhwb2sxrkczgam8c17s3vpxqc5bcz0bwczpxxyvm"))))
2256 (properties `((upstream-name . "extRemes")))
2257 (build-system r-build-system)
2259 `(("r-distillery" ,r-distillery)
2260 ("r-lmoments" ,r-lmoments)))
2261 (home-page "http://www.assessment.ucar.edu/toolkit/")
2262 (synopsis "Extreme value analysis")
2264 "ExtRemes is a suite of functions for carrying out analyses on the
2265 extreme values of a process of interest; be they block maxima over long blocks
2266 or excesses over a high threshold.")
2267 (license license:gpl2+)))
2269 (define-public r-lmtest
2276 (uri (cran-uri "lmtest" version))
2279 "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx"))))
2280 (build-system r-build-system)
2282 `(("r-zoo" ,r-zoo)))
2284 `(("gfortran" ,gfortran)))
2285 (home-page "https://cran.r-project.org/web/packages/lmtest")
2286 (synopsis "Testing linear regression models")
2288 "This package provides a collection of tests, data sets, and examples for
2289 diagnostic checking in linear regression models. Furthermore, some generic
2290 tools for inference in parametric models are provided.")
2291 ;; Either version is okay
2292 (license (list license:gpl2 license:gpl3))))
2294 (define-public r-idr
2300 (uri (cran-uri "idr" version))
2303 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
2304 (build-system r-build-system)
2305 (home-page "https://cran.r-project.org/web/packages/idr/")
2306 (synopsis "Irreproducible discovery rate")
2308 "This is a package for estimating the copula mixture model and plotting
2309 correspondence curves in \"Measuring reproducibility of high-throughput
2310 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
2311 by Li, Brown, Huang, and Bickel")
2312 (license license:gpl2+)))
2314 (define-public r-inline
2320 (uri (cran-uri "inline" version))
2323 "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
2324 (build-system r-build-system)
2325 (home-page "https://cran.r-project.org/web/packages/inline")
2326 (synopsis "Functions to inline C, C++, Fortran function calls from R")
2328 "This package provides functionality to dynamically define R functions
2329 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
2330 @code{.Call} calling conventions.")
2331 ;; Any version of the LGPL.
2332 (license license:lgpl3+)))
2334 (define-public r-bbmle
2341 (uri (cran-uri "bbmle" version))
2344 "1xzij7swrrzl5ly8l3lw6awh486zcm00251dwqws1y23fbgyh3vc"))))
2345 (build-system r-build-system)
2347 `(("r-lattice" ,r-lattice)
2349 ("r-numderiv" ,r-numderiv)))
2350 (home-page "https://cran.r-project.org/web/packages/bbmle")
2351 (synopsis "Tools for General Maximum Likelihood Estimation")
2353 "This package provides methods and functions for fitting maximum
2354 likelihood models in R. This package modifies and extends the @code{mle}
2355 classes in the @code{stats4} package.")
2356 ;; Any version of the GPL
2357 (license license:gpl2+)))
2359 (define-public r-emdbook
2366 (uri (cran-uri "emdbook" version))
2369 "0a515jdzvg87npvrh7md7zp0v5nlz7c2jr7pba5dql6slb0d8j7q"))))
2370 (build-system r-build-system)
2372 `(("r-bbmle" ,r-bbmle)
2374 ("r-lattice" ,r-lattice)
2377 ("r-rcpp" ,r-rcpp)))
2378 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
2379 (synopsis "Support functions and data for \"Ecological Models and Data\"")
2381 "This package provides auxiliary functions and data sets for \"Ecological
2382 Models and Data\", a book presenting maximum likelihood estimation and related
2383 topics for ecologists (ISBN 978-0-691-12522-0).")
2385 (license (list license:gpl2 license:gpl3))))
2387 (define-public r-lpsolve
2390 (version "5.6.13.3")
2394 (uri (cran-uri "lpSolve" version))
2397 "1xazby8amb47vw5n12k13awv7x3bjci3q8vdd3vk1ms0ii16ahg6"))))
2398 (properties `((upstream-name . "lpSolve")))
2399 (build-system r-build-system)
2400 (home-page "https://cran.r-project.org/web/packages/lpSolve")
2401 (synopsis "R interface to Lp_solve to solve linear/integer programs")
2403 "Lp_solve is software for solving linear, integer and mixed integer
2404 programs. This implementation supplies a \"wrapper\" function in C and some R
2405 functions that solve general linear/integer problems, assignment problems, and
2406 transportation problems.")
2407 (license license:lgpl2.0)))
2409 (define-public r-limsolve
2416 (uri (cran-uri "limSolve" version))
2419 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
2420 (properties `((upstream-name . "limSolve")))
2421 (build-system r-build-system)
2423 `(("r-lpsolve" ,r-lpsolve)
2425 ("r-quadprog" ,r-quadprog)))
2426 (native-inputs `(("gfortran" ,gfortran)))
2427 (home-page "https://cran.r-project.org/web/packages/limSolve")
2428 (synopsis "Solving linear inverse models")
2430 "This package provides functions that:
2433 @item find the minimum/maximum of a linear or quadratic function,
2434 @item sample an underdetermined or overdetermined system,
2435 @item solve a linear system Ax=B for the unknown x.
2438 It includes banded and tridiagonal linear systems. The package calls Fortran
2439 functions from LINPACK.")
2441 (license (list license:gpl2+ license:gpl3+))))
2443 (define-public r-fitdistrplus
2445 (name "r-fitdistrplus")
2450 (uri (cran-uri "fitdistrplus" version))
2453 "10q08wsv8v3w7797jdvvv60bgrf1bi6438wf0jcqv81ays82a245"))))
2454 (build-system r-build-system)
2456 `(("r-mass" ,r-mass)
2457 ("r-npsurv" ,r-npsurv)
2458 ("r-survival" ,r-survival)))
2459 (home-page "http://riskassessment.r-forge.r-project.org")
2460 (synopsis "Fitting a parametric distribution from data")
2462 "This package extends the @code{fitdistr} function of the MASS package
2463 with several functions to help the fit of a parametric distribution to
2464 non-censored or censored data. Censored data may contain left-censored,
2465 right-censored and interval-censored values, with several lower and upper
2466 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
2467 provides moment matching (MME), quantile matching (QME) and maximum
2468 goodness-of-fit estimation (MGE) methods (available only for non-censored
2469 data). Weighted versions of MLE, MME and QME are available.")
2470 (license license:gpl2+)))
2472 (define-public r-energy
2479 (uri (cran-uri "energy" version))
2482 "13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37"))))
2483 (build-system r-build-system)
2485 `(("r-boot" ,r-boot)
2486 ("r-rcpp" ,r-rcpp)))
2487 (home-page "https://cran.r-project.org/web/packages/energy")
2488 (synopsis "Multivariate inference via the energy of data")
2490 "This package provides e-statistics (energy) tests and statistics for
2491 multivariate and univariate inference, including distance correlation,
2492 one-sample, two-sample, and multi-sample tests for comparing multivariate
2493 distributions, are implemented. Measuring and testing multivariate
2494 independence based on distance correlation, partial distance correlation,
2495 multivariate goodness-of-fit tests, clustering based on energy distance,
2496 testing for multivariate normality, distance components (disco) for
2497 non-parametric analysis of structured data, and other energy
2498 statistics/methods are implemented.")
2499 (license license:gpl2+)))
2501 (define-public r-suppdists
2503 (name "r-suppdists")
2508 (uri (cran-uri "SuppDists" version))
2511 "1ffx8wigqqvz2pnh06jjc0fnf4vq9z2rhwk2y3f9aszn18ap3dgw"))))
2512 (properties `((upstream-name . "SuppDists")))
2513 (build-system r-build-system)
2514 (home-page "https://cran.r-project.org/web/packages/SuppDists")
2515 (synopsis "Supplementary distributions")
2517 "This package provides ten distributions supplementing those built into
2518 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
2519 Spearman's rho, maximum F ratio, the Pearson product moment correlation
2520 coefficient, Johnson distributions, normal scores and generalized
2521 hypergeometric distributions. In addition two random number generators of
2522 George Marsaglia are included.")
2523 (license license:gpl2+)))
2525 (define-public r-ksamples
2532 (uri (cran-uri "kSamples" version))
2535 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
2536 (properties `((upstream-name . "kSamples")))
2537 (build-system r-build-system)
2539 `(("r-suppdists" ,r-suppdists)))
2540 (home-page "https://cran.r-project.org/web/packages/kSamples")
2541 (synopsis "K-Sample rank tests and their combinations")
2543 "This package provides tools to compares k samples using the
2544 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
2545 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
2546 test. It computes asymptotic, simulated or (limited) exact P-values, all
2547 valid under randomization, with or without ties, or conditionally under random
2548 sampling from populations, given the observed tie pattern. Except for Steel's
2549 test and the JT test it also combines these tests across several blocks of
2551 (license license:gpl2+)))
2553 (define-public r-cvst
2560 (uri (cran-uri "CVST" version))
2563 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
2564 (properties `((upstream-name . "CVST")))
2565 (build-system r-build-system)
2567 `(("r-kernlab" ,r-kernlab)
2568 ("r-matrix" ,r-matrix)))
2569 (home-page "https://cran.r-project.org/web/packages/CVST")
2570 (synopsis "Fast cross-validation via sequential testing")
2572 "This package implements the fast cross-validation via sequential
2573 testing (CVST) procedure. CVST is an improved cross-validation procedure
2574 which uses non-parametric testing coupled with sequential analysis to
2575 determine the best parameter set on linearly increasing subsets of the data.
2576 Additionally to the CVST the package contains an implementation of the
2577 ordinary k-fold cross-validation with a flexible and powerful set of helper
2578 objects and methods to handle the overall model selection process. The
2579 implementations of the Cochran's Q test with permutations and the sequential
2580 testing framework of Wald are generic and can therefore also be used in other
2582 (license license:gpl2+)))
2584 (define-public r-squarem
2587 (version "2017.10-1")
2591 (uri (cran-uri "SQUAREM" version))
2594 "10xj26x7qjyvzndnbjl5krr9wabnb9cbrnp3m7xg673g8ddr12cv"))))
2595 (properties `((upstream-name . "SQUAREM")))
2596 (build-system r-build-system)
2597 (home-page "http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.html")
2598 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
2600 "This package provides algorithms for accelerating the convergence of
2601 slow, monotone sequences from smooth, contraction mapping such as the EM
2602 algorithm. It can be used to accelerate any smooth, linearly convergent
2603 acceleration scheme. A tutorial style introduction to this package is
2604 available in a vignette.")
2605 (license license:gpl2+)))
2607 (define-public r-lava
2614 (uri (cran-uri "lava" version))
2617 "0nfab5fgnmxh8cplg8rd8cp34fny5j0k5wn4baj51r6ck7fq9g3s"))))
2618 (build-system r-build-system)
2620 `(("r-numderiv" ,r-numderiv)
2621 ("r-squarem" ,r-squarem)
2622 ("r-survival" ,r-survival)))
2623 (home-page "https://github.com/kkholst/lava")
2624 (synopsis "Latent variable models")
2626 "This package provides tools for the estimation and simulation of latent
2628 (license license:gpl3)))
2630 (define-public r-drr
2637 (uri (cran-uri "DRR" version))
2640 "1yd1fvllfkcrwg9v322n4wkk4q4q84nvy58y4vac9pdr3yf3i4vl"))))
2641 (properties `((upstream-name . "DRR")))
2642 (build-system r-build-system)
2644 `(("r-cvst" ,r-cvst)
2645 ("r-kernlab" ,r-kernlab)
2646 ("r-matrix" ,r-matrix)))
2647 (home-page "https://cran.r-project.org/web/packages/DRR")
2648 (synopsis "Dimensionality reduction via regression")
2650 "This package provides an implementation of dimensionality reduction via
2651 regression using Kernel Ridge Regression.")
2652 (license license:gpl3)))
2654 (define-public r-prodlim
2657 (version "2019.11.13")
2661 (uri (cran-uri "prodlim" version))
2664 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
2665 (build-system r-build-system)
2667 `(("r-kernsmooth" ,r-kernsmooth)
2670 ("r-survival" ,r-survival)))
2671 (home-page "https://cran.r-project.org/web/packages/prodlim")
2672 (synopsis "Product-limit estimation for censored event history analysis")
2674 "This package provides a fast and user-friendly implementation of
2675 nonparametric estimators for censored event history (survival) analysis with
2676 the Kaplan-Meier and Aalen-Johansen methods.")
2677 (license license:gpl2+)))
2679 (define-public r-dimred
2686 (uri (cran-uri "dimRed" version))
2689 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
2690 (properties `((upstream-name . "dimRed")))
2691 (build-system r-build-system)
2694 ("r-magrittr" ,r-magrittr)))
2695 (home-page "https://github.com/gdkrmr/dimRed")
2696 (synopsis "Framework for dimensionality reduction")
2698 "This package provides a collection of dimensionality reduction
2699 techniques from R packages and provides a common interface for calling the
2701 (license license:gpl3)))
2703 (define-public r-timedate
2706 (version "3043.102")
2710 (uri (cran-uri "timeDate" version))
2713 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
2714 (properties `((upstream-name . "timeDate")))
2715 (build-system r-build-system)
2716 (home-page "https://www.rmetrics.org")
2717 (synopsis "Chronological and calendar objects")
2719 "This package provides an environment for teaching \"Financial
2720 Engineering and Computational Finance\" and for managing chronological and
2722 (license license:gpl2+)))
2724 (define-public r-magic
2731 (uri (cran-uri "magic" version))
2734 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
2735 (build-system r-build-system)
2737 `(("r-abind" ,r-abind)))
2738 (home-page "https://github.com/RobinHankin/magic.git")
2739 (synopsis "Create and investigate magic squares")
2741 "This package provides a collection of efficient, vectorized algorithms
2742 for the creation and investigation of magic squares and hypercubes, including
2743 a variety of functions for the manipulation and analysis of arbitrarily
2744 dimensioned arrays.")
2745 (license license:gpl2)))
2747 (define-public r-rmysql
2754 (uri (cran-uri "RMySQL" version))
2757 "1xamf99ih44dvaxg5x4ivj0hkqssmabgqd7gh8b8q1srw7yg8kbm"))))
2758 (properties `((upstream-name . "RMySQL")))
2759 (build-system r-build-system)
2761 `(("mariadb" ,mariadb "lib")
2762 ("mariadb-dev" ,mariadb "dev")
2765 `(("r-dbi" ,r-dbi)))
2766 (home-page "https://github.com/r-dbi/RMySQL")
2767 (synopsis "Database interface and MySQL driver for R")
2769 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
2770 package contains an old implementation based on legacy code from S-PLUS which
2771 is being phased out. A modern MySQL client based on Rcpp is available from
2772 the RMariaDB package.")
2773 (license license:gpl2)))
2775 (define-public r-rpostgresql
2777 (name "r-rpostgresql")
2782 (uri (cran-uri "RPostgreSQL" version))
2785 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
2786 (properties `((upstream-name . "RPostgreSQL")))
2787 (build-system r-build-system)
2789 `(("postgresql" ,postgresql)))
2791 `(("r-dbi" ,r-dbi)))
2792 (home-page "https://github.com/tomoakin/RPostgreSQL")
2793 (synopsis "R interface to the PostgreSQL database system")
2795 "This package provides a Database Interface (DBI) compliant driver for R
2796 to access PostgreSQL database systems.")
2797 ;; The whole package is released under GPL version 2. It includes code
2798 ;; under the PostgreSQL license.
2799 (license license:gpl2)))
2801 (define-public r-linprog
2808 (uri (cran-uri "linprog" version))
2811 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
2812 (build-system r-build-system)
2813 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
2814 (home-page "http://linprog.r-forge.r-project.org/")
2815 (synopsis "Linear programming and optimization")
2817 "This package can be used to solve Linear Programming / Linear
2818 Optimization problems by using the simplex algorithm.")
2819 (license license:gpl2+)))
2821 (define-public r-geometry
2828 (uri (cran-uri "geometry" version))
2831 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
2832 (build-system r-build-system)
2834 `(("r-magic" ,r-magic)
2835 ("r-linprog" ,r-linprog)
2836 ("r-lpsolve" ,r-lpsolve)
2838 ("r-rcppprogress" ,r-rcppprogress)))
2839 (home-page "http://geometry.r-forge.r-project.org/")
2840 (synopsis "Mesh generation and surface tesselation")
2842 "This package makes the qhull library available in R, in a similar manner
2843 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
2844 intersections about a point, Voronoi diagrams, furthest-site Delaunay
2845 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
2846 and higher dimensions. It implements the Quickhull algorithm for computing
2847 the convex hull. Qhull does not support constrained Delaunay triangulations,
2848 or mesh generation of non-convex objects, but the package does include some R
2849 functions that allow for this. Currently the package only gives access to
2850 Delaunay triangulation and convex hull computation.")
2851 ;; The Qhull sources are included and are distributed under a custom
2852 ;; non-copyleft license. The R sources are released under GPL version 2.
2853 (license (list license:gpl2
2854 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
2856 (define-public r-ddalpha
2863 (uri (cran-uri "ddalpha" version))
2866 "1064g7y8d7kmvd5kjc2m48yvidmh2ci1y0xgil3pcx4ix6mf0ljz"))))
2867 (build-system r-build-system)
2870 ("r-class" ,r-class)
2871 ("r-geometry" ,r-geometry)
2874 ("r-robustbase" ,r-robustbase)
2875 ("r-sfsmisc" ,r-sfsmisc)))
2877 `(("gfortran" ,gfortran)))
2878 (home-page "https://cran.r-project.org/web/packages/ddalpha")
2879 (synopsis "Depth-Based classification and calculation of data depth")
2881 "This package contains procedures for depth-based supervised learning,
2882 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
2883 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
2884 statistical depth function to a compact low-dimensional space, where the final
2885 classification is done. It also offers an extension to functional data and
2886 routines for calculating certain notions of statistical depth functions. 50
2887 multivariate and 5 functional classification problems are included.")
2888 (license license:gpl2)))
2890 (define-public r-gower
2897 (uri (cran-uri "gower" version))
2900 "007ivwn1nagpi26qq8iih1c2l61c53glvv60n90hi341ry8vwgxg"))))
2901 (build-system r-build-system)
2902 (home-page "https://github.com/markvanderloo/gower")
2903 (synopsis "Gower's distance")
2905 "This package provides tools to compute Gower's distance (or similarity)
2906 coefficient between records, and to compute the top-n matches between records.
2907 Core algorithms are executed in parallel on systems supporting OpenMP.")
2908 (license license:gpl3)))
2910 (define-public r-rcpproll
2917 (uri (cran-uri "RcppRoll" version))
2920 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
2921 (properties `((upstream-name . "RcppRoll")))
2922 (build-system r-build-system)
2924 `(("r-rcpp" ,r-rcpp)))
2925 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
2926 (synopsis "Efficient rolling and windowed operations")
2928 "This package provides fast and efficient routines for common rolling /
2929 windowed operations. Routines for the efficient computation of windowed mean,
2930 median, sum, product, minimum, maximum, standard deviation and variance are
2932 (license license:gpl2+)))
2934 (define-public r-ipred
2941 (uri (cran-uri "ipred" version))
2944 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
2945 (build-system r-build-system)
2947 `(("r-class" ,r-class)
2950 ("r-prodlim" ,r-prodlim)
2951 ("r-rpart" ,r-rpart)
2952 ("r-survival" ,r-survival)))
2953 (home-page "https://cran.r-project.org/web/packages/ipred")
2954 (synopsis "Improved predictors")
2956 "This package provides improved predictive models by indirect
2957 classification and bagging for classification, regression and survival
2958 problems as well as resampling based estimators of prediction error.")
2959 (license license:gpl2+)))
2961 (define-public r-psych
2968 (uri (cran-uri "psych" version))
2971 "0hvp0dkkkn0szaf5rkirr3kb8qmr4bxwl775m5wmpvn1kc25w5vf"))))
2972 (build-system r-build-system)
2974 `(("r-foreign" ,r-foreign)
2975 ("r-lattice" ,r-lattice)
2976 ("r-mnormt" ,r-mnormt)
2977 ("r-nlme" ,r-nlme)))
2978 (home-page "https://cran.r-project.org/web/packages/psych/")
2979 (synopsis "Procedures for psychological, psychometric, and personality research")
2981 "This package provides a general purpose toolbox for personality,
2982 psychometric theory and experimental psychology. Functions are primarily for
2983 multivariate analysis and scale construction using factor analysis, principal
2984 component analysis, cluster analysis and reliability analysis, although others
2985 provide basic descriptive statistics. Item Response Theory is done using
2986 factor analysis of tetrachoric and polychoric correlations. Functions for
2987 analyzing data at multiple levels include within and between group statistics,
2988 including correlations and factor analysis. Functions for simulating and
2989 testing particular item and test structures are included. Several functions
2990 serve as a useful front end for structural equation modeling. Graphical
2991 displays of path diagrams, factor analysis and structural equation models are
2992 created using basic graphics.")
2993 (license license:gpl2+)))
2995 (define-public r-generics
3002 (uri (cran-uri "generics" version))
3005 "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi"))))
3006 (build-system r-build-system)
3007 (home-page "https://github.com/r-lib/generics")
3008 (synopsis "Common S3 generics not provided by base R methods")
3010 "In order to reduce potential package dependencies and conflicts,
3011 generics provides a number of commonly used S3 generics that are not provided
3012 by base R methods related to model fitting.")
3013 (license license:gpl2)))
3015 (define-public r-broom
3022 (uri (cran-uri "broom" version))
3025 "0qmclih5dm5sqzy4hplcfy677kr12pm9pnpv3r319g14dd27pbqn"))))
3026 (build-system r-build-system)
3028 `(("r-backports" ,r-backports)
3029 ("r-dplyr" ,r-dplyr)
3030 ("r-generics" ,r-generics)
3032 ("r-purrr" ,r-purrr)
3033 ("r-reshape2" ,r-reshape2)
3034 ("r-stringr" ,r-stringr)
3035 ("r-tibble" ,r-tibble)
3036 ("r-tidyr" ,r-tidyr)))
3037 (home-page "https://github.com/tidyverse/broom")
3038 (synopsis "Convert statistical analysis objects into tidy data frames")
3040 "This package provides tools to convert statistical analysis objects from
3041 R into tidy data frames, so that they can more easily be combined, reshaped
3042 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
3043 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
3044 summarizes a model's statistical findings such as coefficients of a
3045 regression; @code{augment}, which adds columns to the original data such as
3046 predictions, residuals and cluster assignments; and @code{glance}, which
3047 provides a one-row summary of model-level statistics.")
3048 (license license:expat)))
3050 (define-public r-recipes
3057 (uri (cran-uri "recipes" version))
3060 "1gw8x7vqj7k18mfpiqinyfwzv9i5r0pb51k7xcfxsjap6m9nks98"))))
3061 (build-system r-build-system)
3063 `(("r-dplyr" ,r-dplyr)
3064 ("r-generics" ,r-generics)
3066 ("r-gower" ,r-gower)
3067 ("r-ipred" ,r-ipred)
3068 ("r-lubridate" ,r-lubridate)
3069 ("r-magrittr" ,r-magrittr)
3070 ("r-matrix" ,r-matrix)
3071 ("r-purrr" ,r-purrr)
3072 ("r-rlang" ,r-rlang)
3073 ("r-tibble" ,r-tibble)
3074 ("r-tidyr" ,r-tidyr)
3075 ("r-tidyselect" ,r-tidyselect)
3076 ("r-timedate" ,r-timedate)
3077 ("r-withr" ,r-withr)))
3078 (home-page "https://github.com/topepo/recipes")
3079 (synopsis "Preprocessing tools to create design matrices")
3081 "Recipes is an extensible framework to create and preprocess design
3082 matrices. Recipes consist of one or more data manipulation and analysis
3083 \"steps\". Statistical parameters for the steps can be estimated from an
3084 initial data set and then applied to other data sets. The resulting design
3085 matrices can then be used as inputs into statistical or machine learning
3087 (license license:gpl2)))
3089 (define-public r-pdist
3096 (uri (cran-uri "pdist" version))
3099 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
3100 (build-system r-build-system)
3101 (home-page "https://github.com/jeffwong/pdist")
3102 (synopsis "Partitioned distance function")
3104 "Pdist computes the euclidean distance between rows of a matrix X and
3105 rows of another matrix Y. Previously, this could be done by binding the two
3106 matrices together and calling @code{dist}, but this creates unnecessary
3107 computation by computing the distances between a row of X and another row of
3108 X, and likewise for Y. Pdist strictly computes distances across the two
3109 matrices, not within the same matrix, making computations significantly faster
3110 for certain use cases.")
3111 (license license:gpl3+)))
3113 (define-public r-ggrepel
3120 (uri (cran-uri "ggrepel" version))
3123 "10vjrcmx8yknfbx93d9a4y3z8gafri0fhimw6hcq733dmdvkml6m"))))
3124 (build-system r-build-system)
3126 `(("r-ggplot2" ,r-ggplot2)
3128 ("r-scales" ,r-scales)))
3129 (home-page "http://github.com/slowkow/ggrepel")
3130 (synopsis "Repulsive text and label geometries for ggplot2")
3132 "This package provides text and label geometries for ggplot2 that help to
3133 avoid overlapping text labels. Labels repel away from each other and away
3134 from the data points.")
3135 (license license:gpl3)))
3137 (define-public r-corrplot
3144 (uri (cran-uri "corrplot" version))
3147 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
3148 (build-system r-build-system)
3149 (home-page "https://github.com/taiyun/corrplot")
3150 (synopsis "Visualization of a correlation matrix")
3152 "This package provides a graphical display of a correlation matrix or
3153 general matrix. It also contains some algorithms to do matrix reordering. In
3154 addition, corrplot is good at details, including choosing color, text labels,
3155 color labels, layout, etc.")
3156 ;; Any version of the GPL
3157 (license license:gpl2+)))
3159 (define-public r-stringdist
3161 (name "r-stringdist")
3166 (uri (cran-uri "stringdist" version))
3168 (base32 "1dqfakclzaf878x7mhwmqrcpcql2h9cv19fz5f3ygpajf3si5kqi"))))
3169 (build-system r-build-system)
3170 (home-page "https://github.com/markvanderloo/stringdist")
3171 (synopsis "Approximate string matching and string distance functions")
3173 "This package implements an approximate string matching version of R's
3174 native @code{match} function. It can calculate various string distances based
3175 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
3176 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
3177 Jaro-Winkler). An implementation of soundex is provided as well. Distances
3178 can be computed between character vectors while taking proper care of encoding
3179 or between integer vectors representing generic sequences.")
3180 (license license:gpl3+)))
3182 (define-public r-ucminf
3189 (uri (cran-uri "ucminf" version))
3192 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
3193 (build-system r-build-system)
3194 (native-inputs `(("gfortran" ,gfortran)))
3195 (home-page "https://cran.r-project.org/web/packages/ucminf/")
3196 (synopsis "General-purpose unconstrained non-linear optimization")
3198 "This package provides an implementation of an algorithm for
3199 general-purpose unconstrained non-linear optimization. The algorithm is of
3200 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
3201 search with a trust region type monitoring of the input to the line search
3202 algorithm. The interface of @code{ucminf} is designed for easy interchange
3203 with the package @code{optim}.")
3204 (license license:gpl2+)))
3206 (define-public r-ordinal
3209 (version "2019.4-25")
3213 (uri (cran-uri "ordinal" version))
3216 "1pvrkly4x12w32n7w1qljdwzqnlkv7rfa7rx0nz5vbiw29xas4i8"))))
3217 (build-system r-build-system)
3219 `(("r-mass" ,r-mass)
3220 ("r-matrix" ,r-matrix)
3221 ("r-numderiv" ,r-numderiv)
3222 ("r-ucminf" ,r-ucminf)))
3223 (home-page "https://github.com/runehaubo/ordinal")
3224 (synopsis "Regression models for ordinal data")
3226 "This package provides an implementation of cumulative link (mixed)
3227 models also known as ordered regression models, proportional odds models,
3228 proportional hazards models for grouped survival times and ordered models.
3229 Estimation is via maximum likelihood and mixed models are fitted with the
3230 Laplace approximation and adaptive Gauss-Hermite quadrature.")
3231 (license license:gpl2+)))
3233 (define-public r-jomo
3240 (uri (cran-uri "jomo" version))
3243 "1k9l4290g350zbw1pjs871q9bxj3j2h1dilxpp06v4wy4n7d8qs0"))))
3244 (build-system r-build-system)
3246 `(("r-lme4" ,r-lme4)
3248 ("r-ordinal" ,r-ordinal)
3249 ("r-survival" ,r-survival)))
3250 (home-page "https://cran.r-project.org/web/packages/jomo/")
3251 (synopsis "Multilevel Joint Modelling Multiple Imputation")
3253 "Similarly to Schafer's package pan, jomo is a package for multilevel
3254 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
3255 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
3256 possibility of handling binary and categorical data through latent normal
3257 variables, the option to use cluster-specific covariance matrices and to
3258 impute compatibly with the substantive model.")
3259 (license license:gpl2)))
3261 (define-public r-pan
3268 (uri (cran-uri "pan" version))
3271 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
3272 (build-system r-build-system)
3273 (native-inputs `(("gfortran" ,gfortran)))
3274 (home-page "https://cran.r-project.org/web/packages/pan/")
3275 (synopsis "Multiple imputation for multivariate panel or clustered data")
3277 "This package implements multiple imputation for multivariate panel or
3279 (license license:gpl3)))
3281 (define-public r-mitml
3288 (uri (cran-uri "mitml" version))
3291 "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
3292 (build-system r-build-system)
3294 `(("r-haven" ,r-haven)
3297 (home-page "https://cran.r-project.org/web/packages/mitml/")
3298 (synopsis "Tools for multiple imputation in multilevel modeling")
3300 "This package provides tools for multiple imputation of missing data in
3301 multilevel modeling. It includes a user-friendly interface to the packages
3302 pan and jomo, and several functions for visualization, data management and the
3303 analysis of multiply imputed data sets.")
3304 (license license:gpl2+)))
3306 (define-public r-mice
3313 (uri (cran-uri "mice" version))
3316 "0pgcxdmp77604h6f4x8hhs6j4xdjgf5b9zvnixyzdj8vcgdjpivv"))))
3317 (build-system r-build-system)
3319 `(("r-broom" ,r-broom)
3320 ("r-dplyr" ,r-dplyr)
3321 ("r-lattice" ,r-lattice)
3323 ("r-mitml" ,r-mitml)
3326 ("r-rlang" ,r-rlang)
3327 ("r-rpart" ,r-rpart)
3328 ("r-survival" ,r-survival)))
3329 (home-page "https://cran.r-project.org/web/packages/mice/")
3330 (synopsis "Multivariate imputation by chained equations")
3332 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
3333 implemented by the MICE algorithm as described in @url{Van Buuren and
3334 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
3335 variable has its own imputation model. Built-in imputation models are
3336 provided for continuous data (predictive mean matching, normal), binary
3337 data (logistic regression), unordered categorical data (polytomous logistic
3338 regression) and ordered categorical data (proportional odds). MICE can also
3339 impute continuous two-level data (normal model, pan, second-level variables).
3340 Passive imputation can be used to maintain consistency between variables.
3341 Various diagnostic plots are available to inspect the quality of the
3343 ;; Any of these two versions.
3344 (license (list license:gpl2 license:gpl3))))
3346 (define-public r-truncnorm
3348 (name "r-truncnorm")
3353 (uri (cran-uri "truncnorm" version))
3356 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
3357 (build-system r-build-system)
3358 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
3359 (synopsis "Truncated normal distribution")
3360 (description "This package provides functions for the truncated normal
3361 distribution with mean equal to @code{mean} and standard deviation equal to
3362 @code{sd}. It includes density, distribution, quantile, and expected value
3363 functions, as well as a random generation function.")
3364 (license license:gpl2)))
3366 (define-public r-rsolnp
3373 (uri (cran-uri "Rsolnp" version))
3376 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
3377 (properties `((upstream-name . "Rsolnp")))
3378 (build-system r-build-system)
3380 `(("r-truncnorm" ,r-truncnorm)))
3381 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
3382 (synopsis "General non-linear optimization")
3383 (description "The Rsolnp package implements a general non-linear augmented
3384 Lagrange multiplier method solver, a @dfn{sequential quadratic
3385 programming} (SQP) based solver).")
3386 ;; Any version of the GPL.
3387 (license license:gpl2+)))
3389 (define-public r-hardyweinberg
3391 (name "r-hardyweinberg")
3396 (uri (cran-uri "HardyWeinberg" version))
3399 "1irz44q6nf95h37av868f47aakwv3jgwgw217xfsfw0afkm7s25f"))))
3400 (properties `((upstream-name . "HardyWeinberg")))
3401 (build-system r-build-system)
3403 `(("r-mice" ,r-mice)
3405 ("r-rsolnp" ,r-rsolnp)))
3406 (home-page "https://cran.r-project.org/package=HardyWeinberg")
3407 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
3409 "This package contains tools for exploring Hardy-Weinberg equilibrium for
3410 diallelic genetic marker data. All classical tests (chi-square, exact,
3411 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
3412 included in the package, as well as functions for power computation and for
3413 the simulation of marker data under equilibrium and disequilibrium. Routines
3414 for dealing with markers on the X-chromosome are included. Functions for
3415 testing equilibrium in the presence of missing data by using multiple
3416 imputation are also provided. Implements several graphics for exploring the
3417 equilibrium status of a large set of diallelic markers: ternary plots with
3418 acceptance regions, log-ratio plots and Q-Q plots.")
3419 (license license:gpl2+)))
3428 (uri (cran-uri "sm" version))
3431 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
3432 (build-system r-build-system)
3433 (native-inputs `(("gfortran" ,gfortran)))
3434 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
3435 (synopsis "Smoothing methods for nonparametric regression and density estimation")
3437 "This is software accompanying the book 'Applied Smoothing Techniques for
3438 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
3439 University Press. It provides smoothing methods for nonparametric regression
3440 and density estimation")
3441 (license license:gpl2+)))
3443 (define-public r-venndiagram
3445 (name "r-venndiagram")
3449 (uri (cran-uri "VennDiagram" version))
3452 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
3453 (properties `((upstream-name . "VennDiagram")))
3454 (build-system r-build-system)
3456 `(("r-futile-logger" ,r-futile-logger)))
3457 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
3458 (synopsis "Generate High-Resolution Venn and Euler Plots")
3460 "This package provides a set of functions to generate high-resolution
3461 Venn and Euler plots. It includes handling for several special cases,
3462 including two-case scaling, and extensive customization of plot shape and
3464 (license license:gpl2+)))
3466 (define-public r-vioplot
3473 (uri (cran-uri "vioplot" version))
3476 "1fsklymilspzz5fzlj7666x09aglaw0v4x0yfjjzy4vr5qpjc529"))))
3477 (build-system r-build-system)
3481 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
3482 (synopsis "Violin plot")
3484 "This package provides a violin plot, which is a combination of a box
3485 plot and a kernel density plot.")
3486 (license license:bsd-3)))
3488 (define-public r-rsofia
3494 ;; This package has been removed from CRAN, so we can
3495 ;; only fetch it from the archives.
3496 (uri (string-append "https://cran.r-project.org/src/"
3497 "contrib/Archive/RSofia/RSofia_"
3501 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
3502 (properties `((upstream-name . "RSofia")))
3503 (build-system r-build-system)
3505 `(("r-rcpp" ,r-rcpp)))
3506 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
3507 (synopsis "Port of sofia-ml to R")
3508 (description "This package is a port of sofia-ml to R. Sofia-ml is a
3509 suite of fast incremental algorithms for machine learning that can be used for
3510 training models for classification or ranking.")
3511 (license license:asl2.0)))
3513 (define-public r-xts
3520 (uri (cran-uri "xts" version))
3523 "1f0kxrvn13py3hk2gh2m56cqm39x3bqp1i350r5viddacrm2yxqj"))))
3524 (build-system r-build-system)
3525 (propagated-inputs `(("r-zoo" ,r-zoo)))
3526 (home-page "https://github.com/joshuaulrich/xts")
3527 (synopsis "Extensible time series")
3529 "This package provides for uniform handling of R's different time-based
3530 data classes by extending @code{zoo}, maximizing native format information
3531 preservation and allowing for user-level customization and extension, while
3532 simplifying cross-class interoperability.")
3533 (license license:gpl2+)))
3535 (define-public r-performanceanalytics
3537 (name "r-performanceanalytics")
3542 (uri (cran-uri "PerformanceAnalytics" version))
3545 "0jhjldwyxwq7a47zmk5y1jjck7hvq92p8rlgjvdfy51hx2dmlqqd"))))
3547 `((upstream-name . "PerformanceAnalytics")))
3548 (build-system r-build-system)
3550 `(("r-quadprog" ,r-quadprog)
3553 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
3554 (synopsis "Econometric tools for performance and risk analysis")
3555 (description "This is a collection of econometric functions for
3556 performance and risk analysis. This package aims to aid practitioners and
3557 researchers in utilizing the latest research in analysis of non-normal return
3558 streams. In general, it is most tested on return (rather than price) data on
3559 a regular scale, but most functions will work with irregular return data as
3560 well, and increasing numbers of functions will work with P&L or price data
3562 ;; Either version may be picked.
3563 (license (list license:gpl2 license:gpl3))))
3565 (define-public r-laeken
3572 (uri (cran-uri "laeken" version))
3575 "1g9r3y7b0gl91hijk9awa8rjk97mqpkxinzq2cgmx0m38ng9ylpa"))))
3576 (build-system r-build-system)
3578 `(("r-boot" ,r-boot)
3579 ("r-mass" ,r-mass)))
3580 (home-page "https://cran.r-project.org/web/packages/laeken/")
3581 (synopsis "Estimation of indicators on social exclusion and poverty")
3582 (description "This package provides tools for the estimation of indicators
3583 on social exclusion and poverty, as well as an implementation of Pareto tail
3584 modeling for empirical income distributions.")
3585 (license license:gpl2+)))
3587 (define-public r-vcd
3594 (uri (cran-uri "vcd" version))
3597 "1lp99h0wvsc61l1dgcqjxdrcgpgw88ak430cdsv43kmm43qssqd5"))))
3598 (build-system r-build-system)
3600 `(("r-colorspace" ,r-colorspace)
3601 ("r-lmtest" ,r-lmtest)
3602 ("r-mass" ,r-mass)))
3603 (home-page "https://cran.r-project.org/web/packages/vcd/")
3604 (synopsis "Visualizing categorical data")
3605 (description "This package provides visualization techniques, data sets,
3606 summary and inference procedures aimed particularly at categorical data.
3607 Special emphasis is given to highly extensible grid graphics. The package was
3608 originally inspired by the book \"Visualizing Categorical Data\" by Michael
3609 Friendly and is now the main support package for a new book, \"Discrete Data
3610 Analysis with R\" by Michael Friendly and David Meyer (2015).")
3611 (license license:gpl2)))
3613 (define-public r-ica
3620 (uri (cran-uri "ica" version))
3623 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
3624 (build-system r-build-system)
3625 (home-page "https://cran.r-project.org/web/packages/ica/")
3626 (synopsis "Independent component analysis")
3627 (description "This package provides tools for @dfn{Independent Component
3628 Analysis} (ICA) using various algorithms: FastICA,
3629 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
3630 of Eigenmatrices} (JADE).")
3631 (license license:gpl2+)))
3633 (define-public r-dtw
3640 (uri (cran-uri "dtw" version))
3643 "02hyhx1sy5h3vzh9zixy18a7d47df4k5d0wyflcvlcbsbcl6p90s"))))
3644 (build-system r-build-system)
3645 (propagated-inputs `(("r-proxy" ,r-proxy)))
3646 (home-page "http://dtw.r-forge.r-project.org/")
3647 (synopsis "Dynamic Time Warping Algorithms")
3648 (description "This package provides a comprehensive implementation of
3649 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
3650 optimal (least cumulative distance) alignment between points of two time
3651 series. Common DTW variants covered include local (slope) and global (window)
3652 constraints, subsequence matches, arbitrary distance definitions,
3653 normalizations, minimum variance matching, and so on.")
3654 (license license:gpl2+)))
3656 (define-public r-sdmtools
3659 (version "1.1-221.2")
3663 (uri (cran-uri "SDMTools" version))
3666 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
3667 (properties `((upstream-name . "SDMTools")))
3668 (build-system r-build-system)
3669 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
3670 (home-page "http://www.rforge.net/SDMTools/")
3671 (synopsis "Species distribution modelling tools")
3672 (description "This package provides a set of tools for post processing
3673 the outcomes of species distribution modeling exercises. It includes novel
3674 methods for comparing models and tracking changes in distributions through
3675 time. It further includes methods for visualizing outcomes, selecting
3676 thresholds, calculating measures of accuracy and landscape fragmentation
3678 (license license:gpl3+)))
3680 (define-public r-scatterplot3d
3682 (name "r-scatterplot3d")
3687 (uri (cran-uri "scatterplot3d" version))
3690 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
3691 (build-system r-build-system)
3692 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
3693 (synopsis "3D scatter plot")
3694 (description "This package provides an implementation of scatter plots for
3695 plotting. a three dimensional point cloud.")
3696 (license license:gpl2)))
3698 (define-public r-ggridges
3705 (uri (cran-uri "ggridges" version))
3708 "0dhwcpy785ac2ny5bjp284595nnybi3554wd0yffsli0vzf7ry01"))))
3709 (build-system r-build-system)
3711 `(("r-ggplot2" ,r-ggplot2)
3713 ("r-scales" ,r-scales)
3714 ("r-withr" ,r-withr)))
3715 (home-page "https://github.com/clauswilke/ggridges")
3716 (synopsis "Ridgeline plots in ggplot2")
3718 "Ridgeline plots provide a convenient way of visualizing changes in
3719 distributions over time or space. This package enables the creation of such
3720 plots in @code{ggplot2}.")
3721 (license license:gpl2)))
3723 (define-public r-ggjoy
3730 (uri (cran-uri "ggjoy" version))
3733 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
3734 (build-system r-build-system)
3736 `(("r-ggplot2" ,r-ggplot2)
3737 ("r-ggridges" ,r-ggridges)))
3738 (home-page "https://github.com/clauswilke/ggjoy")
3739 (synopsis "Joyplots in ggplot2")
3740 (description "Joyplots provide a convenient way of visualizing changes in
3741 distributions over time or space. This package enables the creation of such
3742 plots in @code{ggplot2}.")
3743 (license license:gpl2)))
3745 (define-public r-cli
3752 (uri (cran-uri "cli" version))
3755 "1gv3zqdipj29ivkw5dsi1qdlra7q4lcrcqvlg9fns7d670yglfki"))))
3756 (build-system r-build-system)
3758 `(("r-assertthat" ,r-assertthat)
3759 ("r-crayon" ,r-crayon)
3760 ("r-fansi" ,r-fansi)
3761 ("r-glue" ,r-glue)))
3762 (home-page "https://github.com/r-lib/cli#readme")
3763 (synopsis "Helpers for developing command line interfaces")
3764 (description "This package provides a suite of tools designed to build
3765 attractive command line interfaces (CLIs). It includes tools for drawing
3766 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
3767 (license license:expat)))
3769 (define-public r-argparser
3771 (name "r-argparser")
3776 (uri (cran-uri "argparser" version))
3779 "0s1wxshx4jk69wfxhycx973q6y8cmqrfymyjklhq1i8xrj0kmmx9"))))
3780 (build-system r-build-system)
3781 (home-page "https://bitbucket.org/djhshih/argparser")
3782 (synopsis "Command-line argument parser")
3784 "This package provides a cross-platform command-line argument parser
3785 written purely in R with no external dependencies. It is useful with the
3786 Rscript front-end and facilitates turning an R script into an executable
3788 (license license:gpl3+)))
3790 (define-public r-debugme
3797 (uri (cran-uri "debugme" version))
3800 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
3801 (build-system r-build-system)
3802 (propagated-inputs `(("r-crayon" ,r-crayon)))
3803 (home-page "https://github.com/r-lib/debugme#readme")
3804 (synopsis "Debug R packages")
3806 "This package allows the user to specify debug messages as special string
3807 constants, and control debugging of packages via environment variables.")
3808 (license license:expat)))
3810 (define-public r-processx
3817 (uri (cran-uri "processx" version))
3820 "1g6ipcaxg9y94lyrnbp7kkbqfkcdh1fyrqjjclbjp3x7iysdvazi"))))
3821 (build-system r-build-system)
3825 (home-page "https://github.com/r-lib/processx3")
3826 (synopsis "Execute and control system processes")
3828 "This package provides portable tools to run system processes in the
3829 background. It can check if a background process is running; wait on a
3830 background process to finish; get the exit status of finished processes; kill
3831 background processes and their children; restart processes. It can read the
3832 standard output and error of the processes, using non-blocking connections.
3833 @code{processx} can poll a process for standard output or error, with a
3834 timeout. It can also poll several processes at once.")
3835 (license license:expat)))
3837 (define-public r-tsp
3844 (uri (cran-uri "TSP" version))
3847 "0rxxhvqi55869dg2p82hzg5kvgcqf9h60cjcg00k3pv9aw4x07kb"))))
3848 (properties `((upstream-name . "TSP")))
3849 (build-system r-build-system)
3850 (propagated-inputs `(("r-foreach" ,r-foreach)))
3851 (home-page "https://cran.r-project.org/web/packages/TSP/")
3852 (synopsis "Traveling salesperson problem (TSP)")
3853 (description "This package provides basic infrastructure and some
3854 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
3855 traveling salesman problem).")
3856 (license license:gpl3)))
3858 (define-public r-qap
3865 (uri (cran-uri "qap" version))
3868 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
3869 (build-system r-build-system)
3870 (native-inputs `(("gfortran" ,gfortran)))
3871 (home-page "https://cran.r-project.org/web/packages/qap/")
3872 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
3873 (description "This package implements heuristics for the @dfn{quadratic
3874 assignment problem} (QAP). Currently only a simulated annealing heuristic is
3876 (license license:gpl3)))
3878 (define-public r-gclus
3885 (uri (cran-uri "gclus" version))
3888 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
3889 (build-system r-build-system)
3890 (propagated-inputs `(("r-cluster" ,r-cluster)))
3891 (home-page "https://cran.r-project.org/web/packages/gclus/")
3892 (synopsis "Clustering graphics")
3893 (description "This package orders panels in scatterplot matrices and
3894 parallel coordinate displays by some merit index. It contains various indices
3895 of merit, ordering functions, and enhanced versions of @code{pairs} and
3896 @code{parcoord} which color panels according to their merit level.")
3897 (license license:gpl2+)))
3899 (define-public r-webshot
3906 (uri (cran-uri "webshot" version))
3909 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
3910 (build-system r-build-system)
3912 `(("r-callr" ,r-callr)
3913 ("r-jsonlite" ,r-jsonlite)
3914 ("r-magrittr" ,r-magrittr)))
3915 (home-page "https://github.com/wch/webshot/")
3916 (synopsis "Take screenshots of web pages")
3918 "Webshot makes it easy to take screenshots of web pages from within R.
3919 It can also run Shiny applications locally and take screenshots of the
3920 application; and it can render and screenshot static as well as interactive R
3921 Markdown documents.")
3922 (license license:gpl2)))
3924 (define-public r-seriation
3926 (name "r-seriation")
3931 (uri (cran-uri "seriation" version))
3934 "1zbdxq0s5rc5v307b69fw9k52m0654ls7pf22lh35ggirig6lwsk"))))
3935 (build-system r-build-system)
3937 `(("r-cluster" ,r-cluster)
3938 ("r-colorspace" ,r-colorspace)
3939 ("r-dendextend" ,r-dendextend)
3940 ("r-gclus" ,r-gclus)
3941 ("r-gplots" ,r-gplots)
3944 ("r-registry" ,r-registry)
3946 (native-inputs `(("gfortran" ,gfortran)))
3947 (home-page "http://s2.smu.edu/IDA/seriation/")
3948 (synopsis "Infrastructure for ordering objects using seriation")
3950 "This package provides infrastructure for seriation with an
3951 implementation of several seriation/sequencing techniques to reorder matrices,
3952 dissimilarity matrices, and dendrograms. It also provides (optimally)
3953 reordered heatmaps, color images and clustering visualizations like
3954 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
3956 (license license:gpl3)))
3958 (define-public r-xfun
3965 (uri (cran-uri "xfun" version))
3967 (base32 "0dncw6bqkal7nyarrrrj9arxy0y3nkdzmrbibcjh84m1cxd4phiw"))))
3968 (build-system r-build-system)
3969 (home-page "https://github.com/yihui/xfun")
3970 (synopsis "Miscellaneous functions")
3972 "This package provides miscellaneous functions commonly used in other
3973 packages maintained by Yihui Xie.")
3974 (license license:expat)))
3976 (define-public r-utf8
3983 (uri (cran-uri "utf8" version))
3986 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
3987 (build-system r-build-system)
3988 (home-page "https://github.com/patperry/r-utf8")
3989 (synopsis "Unicode text processing")
3991 "This package provides tools to process and print UTF-8 encoded
3992 international text (Unicode). Input, validate, normalize, encode, format, and
3994 (license license:asl2.0)))
3996 (define-public r-zeallot
4003 (uri (cran-uri "zeallot" version))
4006 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
4007 (build-system r-build-system)
4008 (home-page "https://github.com/nteetor/zeallot")
4009 (synopsis "Multiple, unpacking, and destructuring assignment")
4011 "This package provides a @code{%<-%} operator to perform multiple,
4012 unpacking, and destructuring assignment in R. The operator unpacks the
4013 right-hand side of an assignment into multiple values and assigns these values
4014 to variables on the left-hand side of the assignment.")
4015 (license license:expat)))
4017 (define-public r-vctrs
4024 (uri (cran-uri "vctrs" version))
4027 "05h0y8qzwc899qj84gkhg4jwzscd065as00d4d8smv42h4i8zkjv"))))
4028 (build-system r-build-system)
4030 `(("r-backports" ,r-backports)
4031 ("r-digest" ,r-digest)
4032 ("r-ellipsis" ,r-ellipsis)
4034 ("r-rlang" ,r-rlang)
4035 ("r-zeallot" ,r-zeallot)))
4036 (home-page "https://github.com/r-lib/vctrs")
4037 (synopsis "Vector helpers")
4039 "There are three main goals to the @code{vctrs} package:
4042 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
4043 @code{length()} and @code{class()}. These definitions are paired with a
4044 framework for type-coercion and size-recycling.
4045 @item To define type- and size-stability as desirable function properties, use
4046 them to analyse existing base function, and to propose better alternatives.
4047 This work has been particularly motivated by thinking about the ideal
4048 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
4049 @item To provide a new @code{vctr} base class that makes it easy to create new
4050 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
4051 a few new @code{vctrs} generics, making implementation considerably simpler
4054 (license license:gpl3)))
4056 (define-public r-pillar
4063 (uri (cran-uri "pillar" version))
4066 "0988047mf0xdhdkqqmavzx4ifjhndjnxniyrrhrdq1nvnrvbpfms"))))
4067 (build-system r-build-system)
4070 ("r-crayon" ,r-crayon)
4071 ("r-fansi" ,r-fansi)
4072 ("r-rlang" ,r-rlang)
4074 ("r-vctrs" ,r-vctrs)))
4075 (home-page "https://github.com/r-lib/pillar")
4076 (synopsis "Coloured formatting for columns")
4078 "This package provides a @code{pillar} generic designed for formatting
4079 columns of data using the full range of colours provided by modern
4081 (license license:gpl3)))
4083 (define-public r-uuid
4090 (uri (cran-uri "uuid" version))
4093 "1gmisd630fc8ybg845hbg13wmm3pk3npaamrh5wqbc1nqd6p0wfx"))))
4094 (build-system r-build-system)
4095 (home-page "http://www.rforge.net/uuid")
4096 (synopsis "Tools for generating and handling of UUIDs")
4098 "This package provides tools for generating and handling of
4099 @dfn{Universally Unique Identifiers} (UUIDs).")
4100 (license license:expat)))
4102 (define-public r-tinytex
4109 (uri (cran-uri "tinytex" version))
4112 "0mgxrbj4gam2gvxfk26nq820vsfjggj81m2l7j9m8vp361k15r0w"))))
4113 (build-system r-build-system)
4115 `(("r-xfun" ,r-xfun)))
4116 (home-page "https://github.com/yihui/tinytex")
4117 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
4119 "This package provides helper functions to install and maintain the LaTeX
4120 distribution named TinyTeX, a lightweight, cross-platform, portable, and
4121 easy-to-maintain version of TeX Live. This package also contains helper
4122 functions to compile LaTeX documents, and install missing LaTeX packages
4124 (license license:expat)))
4126 (define-public r-network
4133 (uri (cran-uri "network" version))
4136 "0dnf1wl3za2lhx2lwd8smhlijl1cfhckgr8zz9piiirrfi2m2kx2"))))
4137 (build-system r-build-system)
4139 `(("r-magrittr" ,r-magrittr)
4140 ("r-tibble" ,r-tibble)))
4141 (home-page "https://statnet.org/")
4142 (synopsis "Classes for relational data")
4144 "This package provides tools to create and modify network objects. The
4145 @code{network} class can represent a range of relational data types, and
4146 supports arbitrary vertex/edge/graph attributes.")
4147 (license license:gpl2+)))
4149 (define-public r-statnet-common
4151 (name "r-statnet-common")
4156 (uri (cran-uri "statnet.common" version))
4159 "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3"))))
4161 `((upstream-name . "statnet.common")))
4162 (build-system r-build-system)
4164 `(("r-coda" ,r-coda)))
4165 (home-page "https://statnet.org")
4166 (synopsis "R scripts and utilities used by the Statnet software")
4167 (description "This package provides non-statistical utilities used by the
4168 software developed by the Statnet Project.")
4169 (license license:gpl3)))
4171 (define-public r-statcheck
4173 (name "r-statcheck")
4178 (uri (cran-uri "statcheck" version))
4181 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
4182 (build-system r-build-system)
4184 `(("r-ggplot2" ,r-ggplot2)
4186 ("r-rmarkdown" ,r-rmarkdown)))
4187 (home-page "https://cran.r-project.org/web/packages/statcheck/")
4188 (synopsis "Extract statistics from articles and recompute p-values")
4189 (description "This package can automatically extract statistical
4190 null-hypothesis significant testing (NHST) results from articles and recompute
4191 the p-values based on the reported test statistic and degrees of freedom to
4192 detect possible inconsistencies.")
4193 (license license:gpl2)))
4195 (define-public r-sna
4202 (uri (cran-uri "sna" version))
4205 "1ks8819qvpdfansfqj9p32s1rhvl26frvbi78m4rx1wd1qcv74i2"))))
4206 (build-system r-build-system)
4208 `(("r-network" ,r-network)
4209 ("r-statnet-common" ,r-statnet-common)))
4210 (home-page "https://statnet.org")
4211 (synopsis "Tools for social network analysis")
4213 "This package provides a range of tools for social network analysis,
4214 including node and graph-level indices, structural distance and covariance
4215 methods, structural equivalence detection, network regression, random graph
4216 generation, and 2D/3D network visualization.")
4217 (license license:gpl2+)))
4219 (define-public r-tfisher
4226 (uri (cran-uri "TFisher" version))
4229 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
4230 (properties `((upstream-name . "TFisher")))
4231 (build-system r-build-system)
4233 `(("r-matrix" ,r-matrix)
4234 ("r-mvtnorm" ,r-mvtnorm)
4236 (home-page "https://cran.r-project.org/web/packages/TFisher/")
4237 (synopsis "Optimal thresholding Fisher's p-value combination method")
4239 "This package provides the @dfn{cumulative distribution function} (CDF),
4240 quantile, and statistical power calculator for a collection of thresholding
4241 Fisher's p-value combination methods, including Fisher's p-value combination
4242 method, truncated product method and, in particular, soft-thresholding
4243 Fisher's p-value combination method which is proven to be optimal in some
4244 context of signal detection. The p-value calculator for the omnibus version
4245 of these tests are also included.")
4246 (license license:gpl2)))
4248 (define-public r-ttr
4255 (uri (cran-uri "TTR" version))
4258 "0fxipnyxaz55n4camrk9cs71x9w4dsmjrihysv8i1s6khf825rg6"))))
4259 (properties `((upstream-name . "TTR")))
4260 (build-system r-build-system)
4262 `(("r-curl" ,r-curl)
4265 (home-page "https://github.com/joshuaulrich/TTR")
4266 (synopsis "Technical trading rules")
4268 "This package provides functions and data to construct technical trading
4270 (license license:gpl2)))
4272 (define-public r-leaps
4279 (uri (cran-uri "leaps" version))
4282 "11gjmn1azrjw5xlvdb4gknj9985kck9x8zb9np1rnk2smp6pka2m"))))
4283 (build-system r-build-system)
4284 (native-inputs `(("gfortran" ,gfortran)))
4285 (home-page "https://cran.r-project.org/web/packages/leaps/")
4286 (synopsis "Regression subset selection")
4288 "This package provides tools for regression subset selection, including
4289 exhaustive search.")
4290 (license license:gpl2+)))
4292 (define-public r-splus2r
4299 (uri (cran-uri "splus2R" version))
4302 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
4303 (properties `((upstream-name . "splus2R")))
4304 (build-system r-build-system)
4305 (native-inputs `(("gfortran" ,gfortran)))
4306 (home-page "https://cran.r-project.org/web/packages/splus2R/")
4307 (synopsis "Supplemental S-PLUS functionality in R")
4309 "Currently there are many functions in S-PLUS that are missing in R. To
4310 facilitate the conversion of S-PLUS packages to R packages, this package
4311 provides some missing S-PLUS functionality in R.")
4312 (license license:gpl2)))
4314 (define-public r-ifultools
4316 (name "r-ifultools")
4321 (uri (cran-uri "ifultools" version))
4324 "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j"))))
4325 (build-system r-build-system)
4327 `(("r-mass" ,r-mass)
4328 ("r-splus2r" ,r-splus2r)))
4329 (home-page "https://cran.r-project.org/web/packages/ifultools/")
4330 (synopsis "Insightful research tools")
4331 (description "This package provides C code used by the wmtsa, fractal, and
4333 (license license:gpl2)))
4335 (define-public r-sapa
4342 (uri (cran-uri "sapa" version))
4345 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
4346 (build-system r-build-system)
4348 `(("r-ifultools" ,r-ifultools)
4349 ("r-splus2r" ,r-splus2r)))
4350 (home-page "https://cran.r-project.org/web/packages/sapa/")
4351 (synopsis "Spectral analysis for physical applications")
4352 (description "This package provides software for the book Spectral
4353 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
4354 Cambridge University Press, 1993.")
4355 (license license:gpl2)))
4357 (define-public r-aggregation
4359 (name "r-aggregation")
4364 (uri (cran-uri "aggregation" version))
4367 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
4368 (build-system r-build-system)
4369 (home-page "https://cran.r-project.org/web/packages/aggregation/")
4370 (synopsis "Methods for p-value aggregation")
4372 "This package contains functionality for performing the following methods
4373 of p-value aggregation: Fisher's method, the Lancaster method (weighted
4374 Fisher's method), and Sidak correction.")
4375 (license license:gpl3)))
4377 (define-public r-quantmod
4384 (uri (cran-uri "quantmod" version))
4387 "0lyzaf5ypk93v6zj9gdghy05cc7cxgn9yasv1apx5r6qsjcfgwky"))))
4388 (build-system r-build-system)
4390 `(("r-curl" ,r-curl)
4394 (home-page "https://cran.r-project.org/web/packages/quantmod/")
4395 (synopsis "Quantitative financial modelling framework")
4396 (description "This package provides a quantitative financial modelling
4397 framework to allow users to specify, build, trade, and analyse quantitative
4398 financial trading strategies.")
4399 (license license:gpl3)))
4401 (define-public r-tseries
4408 (uri (cran-uri "tseries" version))
4411 "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
4412 (build-system r-build-system)
4414 `(("r-quadprog" ,r-quadprog)
4415 ("r-quantmod" ,r-quantmod)
4418 `(("gfortran" ,gfortran)))
4419 (home-page "https://cran.r-project.org/web/packages/tseries/")
4420 (synopsis "Time series analysis and computational finance")
4422 "This package provides functions relating to time series analysis and
4423 computational finance.")
4424 (license license:gpl2)))
4426 (define-public r-wmtsa
4433 (uri (cran-uri "wmtsa" version))
4436 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
4437 (build-system r-build-system)
4439 `(("r-ifultools" ,r-ifultools)
4441 ("r-splus2r" ,r-splus2r)))
4442 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
4443 (synopsis "Wavelet methods for time series analysis")
4445 "This package provides software to accompany the book \"Wavelet Methods
4446 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
4447 University Press, 2000.")
4448 (license license:gpl2)))
4450 (define-public r-tsa
4457 (uri (cran-uri "TSA" version))
4460 "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q"))))
4461 (properties `((upstream-name . "TSA")))
4462 (build-system r-build-system)
4464 `(("r-leaps" ,r-leaps)
4465 ("r-locfit" ,r-locfit)
4466 ("r-mgcv" ,r-mgcv)))
4467 (home-page "http://www.stat.uiowa.edu/~kchan/TSA.htm")
4468 (synopsis "Time series analysis")
4470 "This package contains R functions and datasets detailed in the book
4471 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
4472 Cryer and Kung-Sik Chan.")
4473 (license license:gpl2+)))
4475 (define-public r-extradistr
4477 (name "r-extradistr")
4482 (uri (cran-uri "extraDistr" version))
4485 "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3"))))
4486 (properties `((upstream-name . "extraDistr")))
4487 (build-system r-build-system)
4489 `(("r-rcpp" ,r-rcpp)))
4490 (home-page "https://github.com/twolodzko/extraDistr")
4491 (synopsis "Additional univariate and multivariate distributions")
4493 "This package implements density, distribution functions, quantile
4494 functions and random generation functions for a large number of univariate and
4495 multivariate distributions.")
4496 (license license:gpl2)))
4498 (define-public r-fractal
4505 (uri (cran-uri "fractal" version))
4508 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
4509 (build-system r-build-system)
4511 `(("r-ifultools" ,r-ifultools)
4514 ("r-scatterplot3d" ,r-scatterplot3d)
4515 ("r-splus2r" ,r-splus2r)
4516 ("r-wmtsa" ,r-wmtsa)))
4517 (home-page "https://cran.r-project.org/web/packages/fractal/")
4518 (synopsis "Fractal time series modeling and analysis")
4520 "This package provides tools for stochastic fractal and deterministic
4521 chaotic time series analysis.")
4522 (license license:gpl2)))
4524 (define-public r-urca
4531 (uri (cran-uri "urca" version))
4534 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
4535 (build-system r-build-system)
4536 (propagated-inputs `(("r-nlme" ,r-nlme)))
4537 (native-inputs `(("gfortran" ,gfortran)))
4538 (home-page "https://cran.r-project.org/web/packages/urca/")
4539 (synopsis "Unit root and cointegration tests for time series data")
4541 "This package provides unit root and cointegration tests encountered in
4542 applied econometric analysis.")
4543 (license license:gpl2+)))
4545 (define-public r-cubature
4552 (uri (cran-uri "cubature" version))
4555 "0jpyq8j7x06dpiz29w48av879ygldzgls9z810192hsymkmfaz6r"))))
4556 (build-system r-build-system)
4558 `(("r-rcpp" ,r-rcpp)))
4559 (home-page "https://github.com/bnaras/cubature")
4560 (synopsis "Adaptive multivariate integration over hypercubes")
4562 "This package is an R wrapper around the cubature C library for adaptive
4563 multivariate integration over hypercubes. This version provides both
4564 @code{hcubature} and @code{pcubature} routines in addition to a vector
4566 ;; The included cubature C library is released under GPLv2+, but the
4567 ;; wrapper declares the license to be GPLv3+.
4568 (license (list license:gpl2+ license:gpl3+))))
4570 (define-public r-trend
4577 (uri (cran-uri "trend" version))
4580 "1bd567n15k2vpmgbx02584k5kglrc58mlb5kgd07wdss3knpa48q"))))
4581 (build-system r-build-system)
4583 `(("r-extradistr" ,r-extradistr)))
4585 `(("gfortran" ,gfortran)))
4586 (home-page "https://cran.r-project.org/web/packages/trend/")
4587 (synopsis "Non-parametric trend tests and change-point detection")
4589 "The analysis of environmental data often requires the detection of
4590 trends and change-points. This package includes tests for trend
4591 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
4592 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
4593 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
4594 correlation trend test), change-point detection (Lanzante's test procedures,
4595 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
4596 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
4597 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
4598 sample Robust Rank-Order Distributional Test.")
4599 (license license:gpl3)))
4601 (define-public r-expm
4608 (uri (cran-uri "expm" version))
4611 "15k0acg2aqb2ajhwal6l7vhhp03m4lg579805d34554cl0kn9l2q"))))
4612 (build-system r-build-system)
4613 (propagated-inputs `(("r-matrix" ,r-matrix)))
4614 (native-inputs `(("gfortran" ,gfortran)))
4615 (home-page "https://r-forge.r-project.org/projects/expm/")
4616 (synopsis "Tools for matrix exponentials and related quantities")
4618 "This package provides tools for the computation of the matrix
4619 exponential, logarithm, square root, and related quantities.")
4620 (license license:gpl2+)))
4622 (define-public r-complexplus
4624 (name "r-complexplus")
4629 (uri (cran-uri "complexplus" version))
4632 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
4633 (build-system r-build-system)
4635 `(("r-expm" ,r-expm)
4636 ("r-matrix" ,r-matrix)))
4637 (home-page "https://cran.r-project.org/web/packages/complexplus/")
4638 (synopsis "Functions of complex or real variables")
4640 "This package extends several functions to the complex domain, including
4641 the matrix exponential and logarithm, and the determinant.")
4642 (license license:gpl2)))
4644 (define-public r-phontools
4646 (name "r-phontools")
4651 (uri (cran-uri "phonTools" version))
4654 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
4655 (properties `((upstream-name . "phonTools")))
4656 (build-system r-build-system)
4657 (home-page "http://www.santiagobarreda.com/rscripts.html")
4658 (synopsis "Tools for phonetic and acoustic analyses")
4660 "This package contains tools for the organization, display, and analysis
4661 of the sorts of data frequently encountered in phonetics research and
4662 experimentation, including the easy creation of IPA vowel plots, and the
4663 creation and manipulation of WAVE audio files.")
4664 (license license:bsd-2)))
4673 (uri (cran-uri "np" version))
4676 "1z4jcpx8bbgwslv42wrphfd1qfq965qjn0kmfxm5f6hbbycahcgy"))))
4677 (build-system r-build-system)
4679 `(("r-boot" ,r-boot)
4680 ("r-cubature" ,r-cubature)
4681 ("r-quadprog" ,r-quadprog)
4682 ("r-quantreg" ,r-quantreg)))
4683 (home-page "https://github.com/JeffreyRacine/R-Package-np")
4684 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
4685 (description "This package provides non-parametric (and semi-parametric)
4686 kernel methods that seamlessly handle a mix of continuous, unordered, and
4687 ordered factor data types.")
4688 ;; Any version of the GPL.
4689 (license license:gpl3+)))
4691 (define-public r-powerplus
4693 (name "r-powerplus")
4698 (uri (cran-uri "powerplus" version))
4701 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
4702 (build-system r-build-system)
4704 `(("r-complexplus" ,r-complexplus)
4707 ("r-matrix" ,r-matrix)
4708 ("r-phontools" ,r-phontools)))
4709 (home-page "https://cran.r-project.org/web/packages/powerplus/")
4710 (synopsis "Exponentiation operations")
4712 "This package provides tools for the computation of matrix and scalar
4714 (license license:gpl2)))
4716 (define-public r-egg
4723 (uri (cran-uri "egg" version))
4726 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
4727 (properties `((upstream-name . "egg")))
4728 (build-system r-build-system)
4730 `(("r-ggplot2" ,r-ggplot2)
4731 ("r-gridextra" ,r-gridextra)
4732 ("r-gtable" ,r-gtable)))
4733 (home-page "https://cran.r-project.org/web/packages/egg")
4734 (synopsis "Extensions for ggplot2")
4736 "This package provides miscellaneous functions to help customize ggplot2
4737 objects. High-level functions are provided to post-process ggplot2 layouts
4738 and allow alignment between plot panels, as well as setting panel sizes to
4739 fixed values. Other functions include a custom @code{geom}, and helper
4740 functions to enforce symmetric scales or add tags to facetted plots.")
4741 (license license:gpl3)))
4743 (define-public r-heatmaply
4745 (name "r-heatmaply")
4750 (uri (cran-uri "heatmaply" version))
4753 "0576gml3bcl7r1biigzj1rag2xzz422knbw7arc8d2gsakjj757g"))))
4754 (build-system r-build-system)
4756 `(("r-assertthat" ,r-assertthat)
4757 ("r-colorspace" ,r-colorspace)
4758 ("r-dendextend" ,r-dendextend)
4760 ("r-ggplot2" ,r-ggplot2)
4761 ("r-htmlwidgets" ,r-htmlwidgets)
4762 ("r-magrittr" ,r-magrittr)
4763 ("r-plotly" ,r-plotly)
4764 ("r-rcolorbrewer" ,r-rcolorbrewer)
4765 ("r-reshape2" ,r-reshape2)
4766 ("r-scales" ,r-scales)
4767 ("r-seriation" ,r-seriation)
4768 ("r-viridis" ,r-viridis)
4769 ("r-webshot" ,r-webshot)))
4770 (home-page "https://cran.r-project.org/package=heatmaply")
4771 (synopsis "Interactive cluster heat maps using plotly")
4773 "This package enables you to create interactive cluster heatmaps that can
4774 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
4775 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
4776 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
4777 a popular graphical method for visualizing high-dimensional data, in which a
4778 table of numbers is encoded as a grid of colored cells. The rows and columns
4779 of the matrix are ordered to highlight patterns and are often accompanied by
4781 ;; Either version of the license.
4782 (license (list license:gpl2 license:gpl3))))
4791 (uri (cran-uri "h5" version))
4794 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
4795 (build-system r-build-system)
4800 `(("which" ,which)))
4802 `(("r-rcpp" ,r-rcpp)))
4803 (home-page "https://github.com/mannau/h5")
4804 (synopsis "Interface to the HDF5 Library")
4806 "This package provides an S4 interface to the HDF5 library supporting
4807 fast storage and retrieval of R-objects like vectors, matrices and arrays to
4808 binary files in a language independent format. The HDF5 format can therefore
4809 be used as an alternative to R's save/load mechanism. Since h5 is able to
4810 access only subsets of stored data it can also handle data sets which do not
4812 (license license:bsd-2)))
4814 (define-public r-cgdsr
4821 (uri (cran-uri "cgdsr" version))
4824 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
4825 (build-system r-build-system)
4827 `(("r-httr" ,r-httr)
4828 ("r-r-methodss3" ,r-r-methodss3)
4829 ("r-r-oo" ,r-r-oo)))
4830 (home-page "https://github.com/cBioPortal/cgdsr")
4831 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
4833 "This package provides a basic set of R functions for querying the Cancer
4834 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
4835 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
4836 (license license:lgpl3)))
4838 (define-public r-import
4845 (uri (cran-uri "import" version))
4848 "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
4849 (build-system r-build-system)
4850 (home-page "https://github.com/smbache/import")
4851 (synopsis "Import mechanism for R")
4853 "This is an alternative mechanism for importing objects from packages.
4854 The syntax allows for importing multiple objects from a package with a single
4855 command in an expressive way. The import package bridges some of the gap
4856 between using @code{library} (or @code{require}) and direct (single-object)
4857 imports. Furthermore the imported objects are not placed in the current
4858 environment. It is also possible to import objects from stand-alone @code{.R}
4860 (license license:expat)))
4862 (define-public r-shinyace
4869 (uri (cran-uri "shinyAce" version))
4872 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
4873 (properties `((upstream-name . "shinyAce")))
4874 (build-system r-build-system)
4876 `(("r-shiny" ,r-shiny)
4877 ("r-jsonlite" ,r-jsonlite)))
4878 (home-page "http://cran.r-project.org/web/packages/shinyAce")
4879 (synopsis "Ace editor bindings for Shiny")
4881 "This package provides Ace editor bindings to enable a rich text editing
4882 environment within Shiny.")
4883 (license license:expat)))
4885 (define-public r-base64url
4887 (name "r-base64url")
4892 (uri (cran-uri "base64url" version))
4895 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
4896 (build-system r-build-system)
4898 `(("r-backports" ,r-backports)))
4899 (home-page "https://github.com/mllg/base64url")
4900 (synopsis "Fast and URL-safe base64 encoder and decoder")
4902 "This package provides a URL-safe base64 encoder and decoder. In
4903 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
4904 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
4905 encoder does not fill the string with trailing @code{=}. The resulting
4906 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
4907 and thus are safe to use in URLs or for file names. The package also comes
4908 with a simple base32 encoder/decoder suited for case insensitive file
4910 (license license:gpl3)))
4912 (define-public r-radiant-data
4914 (name "r-radiant-data")
4919 (uri (cran-uri "radiant.data" version))
4922 "08x7zasxf429m021482p86lx3zc6dqz2mih0id8s34isg4gafapg"))
4923 (modules '((guix build utils)))
4926 ;; Delete files that are under CC-NC-SA.
4927 (delete-file-recursively "inst/app/tools/help")
4929 (properties `((upstream-name . "radiant.data")))
4930 (build-system r-build-system)
4932 `(("r-base64enc" ,r-base64enc)
4933 ("r-broom" ,r-broom)
4936 ("r-dplyr" ,r-dplyr)
4939 ("r-ggplot2" ,r-ggplot2)
4940 ("r-gridextra" ,r-gridextra)
4941 ("r-import" ,r-import)
4942 ("r-jsonlite" ,r-jsonlite)
4943 ("r-knitr" ,r-knitr)
4944 ("r-lubridate" ,r-lubridate)
4945 ("r-magrittr" ,r-magrittr)
4946 ("r-markdown" ,r-markdown)
4947 ("r-plotly" ,r-plotly)
4948 ("r-psych" ,r-psych)
4949 ("r-readr" ,r-readr)
4950 ("r-readxl" ,r-readxl)
4951 ("r-rlang" ,r-rlang)
4952 ("r-rmarkdown" ,r-rmarkdown)
4953 ("r-rstudioapi" ,r-rstudioapi)
4954 ("r-scales" ,r-scales)
4955 ("r-shiny" ,r-shiny)
4956 ("r-shinyfiles" ,r-shinyfiles)
4957 ("r-shinyace" ,r-shinyace)
4958 ("r-stringi" ,r-stringi)
4959 ("r-tibble" ,r-tibble)
4960 ("r-tidyr" ,r-tidyr)
4961 ("r-writexl" ,r-writexl)))
4962 (home-page "https://github.com/radiant-rstats/radiant.data")
4963 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
4965 "The Radiant Data menu includes interfaces for loading, saving, viewing,
4966 visualizing, summarizing, transforming, and combining data. It also contains
4967 functionality to generate reproducible reports of the analyses conducted in
4969 (license license:agpl3)))
4971 (define-public r-algdesign
4973 (name "r-algdesign")
4978 (uri (cran-uri "AlgDesign" version))
4980 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
4981 (properties `((upstream-name . "AlgDesign")))
4982 (build-system r-build-system)
4983 (home-page "https://github.com/jvbraun/AlgDesign")
4984 (synopsis "Algorithmic experimental design")
4986 "This package provides tools to calculate exact and approximate theory
4987 experimental designs for D, A, and I criteria. Very large designs may be
4988 created. Experimental designs may be blocked or blocked designs created from
4989 a candidate list, using several criteria. The blocking can be done when whole
4990 and within plot factors interact.")
4991 (license license:gpl2+)))
4993 (define-public r-signal
5000 (uri (cran-uri "signal" version))
5003 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
5004 (build-system r-build-system)
5005 (propagated-inputs `(("r-mass" ,r-mass)))
5006 (native-inputs `(("gfortran" ,gfortran)))
5007 (home-page "https://cran.r-project.org/web/packages/signal/")
5008 (synopsis "Signal processing")
5010 "This package provides a set of signal processing functions originally
5011 written for Matlab and GNU Octave. It includes filter generation utilities,
5012 filtering functions, resampling routines, and visualization of filter models.
5013 It also includes interpolation functions.")
5014 (license license:gpl2)))
5016 (define-public r-gsubfn
5023 (uri (cran-uri "gsubfn" version))
5026 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
5027 (build-system r-build-system)
5028 (propagated-inputs `(("r-proto" ,r-proto)))
5029 (home-page "http://gsubfn.googlecode.com")
5030 (synopsis "Utilities for strings and function arguments.")
5032 "This package provides @code{gsubfn} which is like @code{gsub} but can
5033 take a replacement function or certain other objects instead of the
5034 replacement string. Matches and back references are input to the replacement
5035 function and replaced by the function output. @code{gsubfn} can be used to
5036 split strings based on content rather than delimiters and for quasi-perl-style
5037 string interpolation. The package also has facilities for translating
5038 formulas to functions and allowing such formulas in function calls instead of
5040 (license license:gpl2+)))
5042 (define-public r-sqldf
5049 (uri (cran-uri "sqldf" version))
5052 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
5053 (build-system r-build-system)
5055 `(("r-chron" ,r-chron)
5057 ("r-gsubfn" ,r-gsubfn)
5058 ("r-proto" ,r-proto)
5059 ("r-rsqlite" ,r-rsqlite)))
5060 (home-page "https://github.com/ggrothendieck/sqldf")
5061 (synopsis "Manipulate R data frames using SQL")
5063 "The @code{sqldf} function is typically passed a single argument which is
5064 an SQL select statement where the table names are ordinary R data frame names.
5065 @code{sqldf} transparently sets up a database, imports the data frames into
5066 that database, performs the SQL statement and returns the result using a
5067 heuristic to determine which class to assign to each column of the returned
5068 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
5069 used to read filtered files into R even if the original files are larger than
5070 R itself can handle.")
5071 (license license:gpl2)))
5073 (define-public r-abind
5080 (uri (cran-uri "abind" version))
5083 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
5084 (build-system r-build-system)
5085 (home-page "https://cran.r-project.org/web/packages/abind/")
5086 (synopsis "Combine multidimensional arrays")
5088 "This package provides tools to combine multidimensional arrays into a
5089 single array. This is a generalization of @code{cbind} and @code{rbind}. It
5090 works with vectors, matrices, and higher-dimensional arrays. It also provides
5091 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
5092 extracting and replacing data in arrays.")
5093 (license license:lgpl2.0+)))
5095 (define-public r-prroc
5102 (uri (cran-uri "PRROC" version))
5105 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
5106 (properties `((upstream-name . "PRROC")))
5107 (build-system r-build-system)
5108 (home-page "https://cran.r-project.org/web/packages/PRROC/")
5109 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
5111 "This package computes the areas under the @dfn{precision-recall} (PR)
5112 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
5113 contrast to other implementations, the interpolation between points of the PR
5114 curve is done by a non-linear piecewise function. In addition to the areas
5115 under the curves, the curves themselves can also be computed and plotted by a
5116 specific S3-method.")
5117 (license license:gpl3)))
5119 (define-public r-vim
5126 (uri (cran-uri "VIM" version))
5129 "08x4a4yzgp8adgrv7a3666yma4b60n64mcsnvhzmwdy023f4ysrw"))))
5130 (properties `((upstream-name . "VIM")))
5131 (build-system r-build-system)
5134 ("r-colorspace" ,r-colorspace)
5135 ("r-data-table" ,r-data-table)
5136 ("r-e1071" ,r-e1071)
5137 ("r-laeken" ,r-laeken)
5140 ("r-ranger" ,r-ranger)
5142 ("r-robustbase" ,r-robustbase)
5145 (home-page "https://github.com/alexkowa/VIM")
5146 (synopsis "Visualization and imputation of missing values")
5148 "This package provides tools for the visualization of missing and/or
5149 imputed values are introduced, which can be used for exploring the data and
5150 the structure of the missing and/or imputed values. Depending on this
5151 structure of the missing values, the corresponding methods may help to
5152 identify the mechanism generating the missing values and allows to explore the
5153 data including missing values. In addition, the quality of imputation can be
5154 visually explored using various univariate, bivariate, multiple and
5155 multivariate plot methods.")
5156 (license license:gpl2+)))
5158 (define-public r-fnn
5165 (uri (cran-uri "FNN" version))
5168 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
5169 (properties `((upstream-name . "FNN")))
5170 (build-system r-build-system)
5171 (home-page "https://cran.r-project.org/web/packages/FNN")
5172 (synopsis "Fast nearest neighbor search algorithms and applications")
5174 "This package provides cover-tree and kd-tree fast k-nearest neighbor
5175 search algorithms. Related applications including KNN classification,
5176 regression and information measures are implemented.")
5177 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
5178 ;; later can be used.
5179 (license license:gpl2+)))
5181 (define-public r-smoother
5188 (uri (cran-uri "smoother" version))
5191 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
5192 (build-system r-build-system)
5194 `(("r-ttr" ,r-ttr)))
5195 (home-page "http://cran.r-project.org/web/packages/smoother")
5196 (synopsis "Functions relating to the smoothing of numerical data")
5198 "This package provides a collection of methods for smoothing numerical
5199 data, commencing with a port of the Matlab gaussian window smoothing function.
5200 In addition, several functions typically used in smoothing of financial data
5202 (license license:gpl2)))
5204 (define-public r-riverplot
5206 (name "r-riverplot")
5211 (uri (cran-uri "riverplot" version))
5214 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
5215 (build-system r-build-system)
5216 (home-page "https://logfc.wordpress.com")
5217 (synopsis "Sankey or ribbon plots")
5219 "Sankey plots are a type of diagram that is convenient to illustrate how
5220 flow of information, resources etc. separates and joins, much like observing
5221 how rivers split and merge. For example, they can be used to compare
5222 different clusterings. This package provides an implementation of Sankey
5224 (license license:gpl2+)))
5226 (define-public r-dyn
5233 (uri (cran-uri "dyn" version))
5236 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
5237 (build-system r-build-system)
5239 `(("r-zoo" ,r-zoo)))
5240 (home-page "https://cran.r-project.org/web/packages/dyn")
5241 (synopsis "Time series regression")
5243 "This package provides the dyn class interfaces @code{ts}, @code{irts},
5244 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
5245 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
5246 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
5247 @code{randomForest::randomForest()} and other regression functions, allowing
5248 those functions to be used with time series including specifications that may
5249 contain lags, diffs and missing values.")
5251 (license license:gpl2+)))
5253 (define-public r-catdap
5260 (uri (cran-uri "catdap" version))
5263 "0i877l61f6c75pczi235rzci67w29zv1d7z5zn5p5ymndclvlpl2"))))
5264 (build-system r-build-system)
5266 `(("gfortran" ,gfortran)))
5267 (home-page "https://cran.r-project.org/web/packages/catdap/")
5268 (synopsis "Tools for categorical data analysis")
5270 "This package provides functions for analyzing multivariate data.
5271 Dependencies of the distribution of the specified variable (response
5272 variable) to other variables (explanatory variables) are derived and
5273 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
5274 (license license:gpl2+)))
5276 (define-public r-arules
5283 (uri (cran-uri "arules" version))
5286 "003c5cd3xzq39h7c19px077ygm0n1v7k83icy5zzrnkagyds2p8n"))))
5287 (build-system r-build-system)
5289 `(("r-matrix" ,r-matrix)))
5290 (home-page "https://github.com/mhahsler/arules")
5291 (synopsis "Mining association rules and frequent itemsets")
5293 "This package provides an infrastructure for representing, manipulating
5294 and analyzing transaction data and patterns (frequent itemsets and association rules).
5295 It also provides C implementations of the association mining algorithms Apriori
5297 (license license:gpl3)))
5299 (define-public r-parsedate
5301 (name "r-parsedate")
5306 (uri (cran-uri "parsedate" version))
5309 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
5310 (build-system r-build-system)
5312 `(("r-rematch2" ,r-rematch2)))
5313 (home-page "https://github.com/gaborcsardi/parsedate")
5315 "Recognize and parse dates in various formats")
5317 "This package provides three functions for dealing with dates:
5318 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
5319 time formats, @code{parse_date} parses dates in unspecified formats,
5320 and @code{format_iso_8601} formats a date in ISO 8601 format.")
5321 (license license:gpl2)))
5323 (define-public r-abc-data
5330 (uri (cran-uri "abc.data" version))
5333 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
5334 (properties `((upstream-name . "abc.data")))
5335 (build-system r-build-system)
5336 (home-page "https://cran.r-project.org/web/packages/abc.data/")
5337 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
5339 "This package contains data which are used by functions of the abc
5340 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
5341 algorithms for performing parameter estimation, model selection, and
5343 (license license:gpl3+)))
5345 (define-public r-abc
5352 (uri (cran-uri "abc" version))
5355 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
5356 (build-system r-build-system)
5358 `(("r-abc-data" ,r-abc-data)
5359 ("r-locfit" ,r-locfit)
5362 ("r-quantreg" ,r-quantreg)))
5363 (home-page "https://cran.r-project.org/web/packages/abc/")
5364 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
5366 "This package implements several @dfn{Approximate Bayesian
5367 Computation} (ABC) algorithms for performing parameter estimation, model
5368 selection, and goodness-of-fit. Cross-validation tools are also available for
5369 measuring the accuracy of ABC estimates, and to calculate the
5370 misclassification probabilities of different models.")
5371 (license license:gpl3+)))
5373 (define-public r-zip
5380 (uri (cran-uri "zip" version))
5383 "1c02amk3pl6xir5jnbfiwiv2wvpkpbkkb1w71y6lf2yk7g3d0pdb"))))
5384 (build-system r-build-system)
5385 (home-page "https://github.com/gaborcsardi/zip")
5386 (synopsis "Cross-platform Zip compression")
5388 "This package provides a cross-platform Zip compression library for R.
5389 It is a replacement for the @code{zip} function, that does not require any
5390 additional external tools on any platform.")
5391 (license license:cc0)))
5393 (define-public r-openxlsx
5400 (uri (cran-uri "openxlsx" version))
5403 "1mwxldw9i9nfksx1i6h1kfs7vmsz9fgyllbsipar4vnfyqhqp8q7"))))
5404 (build-system r-build-system)
5406 `(("r-rcpp" ,r-rcpp)
5407 ("r-stringi" ,r-stringi)
5409 (home-page "https://github.com/awalker89/openxlsx")
5410 (synopsis "Read, write and edit XLSX files")
5412 "This package simplifies the creation of Excel @code{.xlsx} files by
5413 providing a high level interface to writing, styling and editing worksheets.
5414 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
5415 and @code{XLConnect} packages with the added benefit of removing the
5416 dependency on Java.")
5417 (license license:gpl3)))
5419 (define-public r-rio
5426 (uri (cran-uri "rio" version))
5429 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
5430 (build-system r-build-system)
5432 `(("r-curl" ,r-curl)
5433 ("r-data-table" ,r-data-table)
5434 ("r-foreign" ,r-foreign)
5435 ("r-haven" ,r-haven)
5436 ("r-openxlsx" ,r-openxlsx)
5437 ("r-readxl" ,r-readxl)
5438 ("r-tibble" ,r-tibble)))
5439 (home-page "https://github.com/leeper/rio")
5440 (synopsis "Swiss-army knife for data I/O")
5442 "This package provides streamlined data import and export infrastructure
5443 by making assumptions that the user is probably willing to make: @code{import}
5444 and @code{export} determine the data structure from the file extension,
5445 reasonable defaults are used for data import and export (e.g.,
5446 @code{stringsAsFactors=FALSE}), web-based import is natively
5447 supported (including from SSL/HTTPS), compressed files can be read directly
5448 without explicit decompression, and fast import packages are used where
5449 appropriate. An additional convenience function, @code{convert}, provides a
5450 simple method for converting between file types.")
5451 (license license:gpl2)))
5453 (define-public r-maptools
5460 (uri (cran-uri "maptools" version))
5463 "0v4llkxk8qs61vq4ykvaim4k23aagdaz0p62ns7zfq02sln3pfk9"))))
5464 (build-system r-build-system)
5466 `(("r-foreign" ,r-foreign)
5467 ("r-lattice" ,r-lattice)
5469 (home-page "http://r-forge.r-project.org/projects/maptools/")
5470 (synopsis "Tools for reading and handling spatial objects")
5472 "This package provides a set of tools for manipulating and reading
5473 geographic data, in particular ESRI Shapefiles. It includes binary access to
5474 GSHHG shoreline files. The package also provides interface wrappers for
5475 exchanging spatial objects with other R packages.")
5476 ;; The C source files from shapelib are released under the Expat license.
5477 ;; The R code is released under GPL version 2 or later.
5478 (license (list license:gpl2+
5481 (define-public r-later
5488 (uri (cran-uri "later" version))
5491 "11xjavj7siz0xv2ffq1ld4bwl35jyrcfpvvs4p3ilpifxx49hyr7"))))
5492 (build-system r-build-system)
5496 ("r-rlang" ,r-rlang)))
5497 (home-page "https://github.com/r-lib/later")
5498 (synopsis "Utilities for delaying function execution")
5500 "This package provides tools to execute arbitrary R or C functions some
5501 time after the current time, after the R execution stack has emptied.")
5502 (license license:gpl2+)))
5504 (define-public r-promises
5511 (uri (cran-uri "promises" version))
5514 "01l0ydjvvy6afcg5d6pzvk1ikd3djq8n2flv8c831ksn68z0zsn8"))))
5515 (build-system r-build-system)
5517 `(("r-later" ,r-later)
5518 ("r-magrittr" ,r-magrittr)
5521 ("r-rlang" ,r-rlang)))
5522 (home-page "https://rstudio.github.io/promises")
5523 (synopsis "Abstractions for promise-based asynchronous programming")
5525 "This package provides fundamental abstractions for doing asynchronous
5526 programming in R using promises. Asynchronous programming is useful for
5527 allowing a single R process to orchestrate multiple tasks in the background
5528 while also attending to something else. Semantics are similar to JavaScript
5529 promises, but with a syntax that is idiomatic R.")
5530 (license license:expat)))
5532 (define-public r-dosnow
5539 (uri (cran-uri "doSNOW" version))
5542 "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh"))))
5543 (properties `((upstream-name . "doSNOW")))
5544 (build-system r-build-system)
5546 `(("r-foreach" ,r-foreach)
5547 ("r-iterators" ,r-iterators)
5548 ("r-snow" ,r-snow)))
5549 (home-page "https://cran.r-project.org/web/packages/doSNOW")
5550 (synopsis "Foreach parallel adaptor for the snow package")
5552 "This package provides a parallel backend for the @code{%dopar%} function
5553 using the @code{snow} package.")
5554 (license license:gpl2)))
5556 (define-public r-snowfall
5559 (version "1.84-6.1")
5562 (uri (cran-uri "snowfall" version))
5564 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
5565 (build-system r-build-system)
5567 `(("r-snow" ,r-snow)))
5568 (home-page "http://cran.r-project.org/web/packages/snowfall/")
5569 (synopsis "Easier cluster computing")
5570 (description "This package is a usability wrapper around snow for easier
5571 development of parallel R programs. This package offers e.g. extended error
5572 checks, and additional functions. All functions work in sequential mode, too,
5573 if no cluster is present or wished. The package is also designed as connector
5574 to the cluster management tool @code{sfCluster}, but can also used without
5576 (license license:gpl2+)))
5578 (define-public r-rappdirs
5585 (uri (cran-uri "rappdirs" version))
5588 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
5589 (build-system r-build-system)
5590 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
5591 (synopsis "Determine where to save data, caches, and logs")
5593 "This package provides an easy way to determine which directories on the
5594 user's computer should be used to save data, caches and logs. It is a port of
5595 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
5596 (license license:expat)))
5598 (define-public r-renv
5605 (uri (cran-uri "renv" version))
5608 "0mwqpcay6v1hnvhggsrn1chvdlhi9hwvsswas8ysygfy5wxxz1sm"))))
5609 (properties `((upstream-name . "renv")))
5610 (build-system r-build-system)
5611 (home-page "https://rstudio.github.io/renv")
5612 (synopsis "Project environments")
5614 "This package provides a dependency management toolkit for R. Using
5615 renv, you can create and manage project-local R libraries, save the state of
5616 these libraries to a lockfile, and later restore your library as required.
5617 Together, these tools can help make your projects more isolated, portable, and
5619 (license license:expat)))
5621 (define-public r-learnr
5628 (uri (cran-uri "learnr" version))
5631 "0278q9nbkc4nb0rp930kjrwyidf0v7y38d1s187m4f4bs7ha82k6"))))
5632 (build-system r-build-system)
5634 `(("r-checkmate" ,r-checkmate)
5635 ("r-ellipsis" ,r-ellipsis)
5636 ("r-evaluate" ,r-evaluate)
5637 ("r-htmltools" ,r-htmltools)
5638 ("r-htmlwidgets" ,r-htmlwidgets)
5639 ("r-jsonlite" ,r-jsonlite)
5640 ("r-knitr" ,r-knitr)
5641 ("r-markdown" ,r-markdown)
5642 ("r-rappdirs" ,r-rappdirs)
5644 ("r-rmarkdown" ,r-rmarkdown)
5645 ("r-rprojroot" ,r-rprojroot)
5646 ("r-shiny" ,r-shiny)
5647 ("r-withr" ,r-withr)))
5648 (home-page "https://rstudio.github.io/learnr/")
5649 (synopsis "Interactive tutorials for R")
5651 "This package provides tools to create interactive tutorials using R
5652 Markdown. Use a combination of narrative, figures, videos, exercises, and
5653 quizzes to create self-paced tutorials for learning about R and R packages.")
5654 (license license:asl2.0)))
5656 (define-public r-analytics
5658 (name "r-analytics")
5663 (uri (cran-uri "analytics" version))
5666 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
5667 (build-system r-build-system)
5670 ("r-cluster" ,r-cluster)
5671 ("r-fractal" ,r-fractal)
5672 ("r-lmtest" ,r-lmtest)
5675 ("r-powerplus" ,r-powerplus)
5676 ("r-robust" ,r-robust)
5677 ("r-trend" ,r-trend)
5681 (home-page "https://cran.r-project.org/web/packages/analytics/")
5682 (synopsis "Collection of data analysis tools")
5684 "This package is a collection of data analysis tools. It includes tools
5685 for regression outlier detection in a fitted linear model, stationary
5686 bootstrap using a truncated geometric distribution, a comprehensive test for
5687 weak stationarity, column means by group, weighted biplots, and a heuristic to
5688 obtain a better initial configuration in non-metric MDS.")
5689 (license license:gpl2)))
5691 (define-public r-reticulate
5693 (name "r-reticulate")
5698 (uri (cran-uri "reticulate" version))
5701 "1qwxh7zq9igl7dxl5g5qjbvv0mlac3w80djnkm0w8rxnaval3gmd"))))
5702 (build-system r-build-system)
5703 (inputs `(("python" ,python)))
5705 `(("r-jsonlite" ,r-jsonlite)
5706 ("r-matrix" ,r-matrix)
5707 ("r-rcpp" ,r-rcpp)))
5708 (home-page "https://github.com/rstudio/reticulate")
5709 (synopsis "R interface to Python")
5711 "This package provides an interface from R to Python modules, classes,
5712 and functions. When calling into Python, R data types are automatically
5713 converted to their equivalent Python types. When values are returned from
5714 Python to R they are converted back to R types.")
5715 (license license:asl2.0)))
5717 (define-public r-bibtex
5724 (uri (cran-uri "bibtex" version))
5727 "0wl3925ryd54g1nv3ncwllc493d39dpgy5md61940h69c0van1hz"))))
5728 (build-system r-build-system)
5729 (propagated-inputs `(("r-stringr" ,r-stringr)))
5730 (home-page "https://github.com/romainfrancois/bibtex")
5731 (synopsis "Bibtex parser")
5732 (description "This package provides a utility for R to parse a bibtex
5734 (license license:gpl2+)))
5736 (define-public r-ggseqlogo
5738 (name "r-ggseqlogo")
5743 (uri (cran-uri "ggseqlogo" version))
5746 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
5747 (build-system r-build-system)
5748 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
5749 (home-page "https://github.com/omarwagih/ggseqlogo")
5750 (synopsis "ggplot2 extension for drawing genetic sequence logos")
5752 "The range of functions provided by this package makes it possible to
5753 draw highly versatile genomic sequence logos. Features include, but are not
5754 limited to, modifying colour schemes and fonts used to draw the logo,
5755 generating multiple logo plots, and aiding the visualisation with annotations.
5756 Sequence logos can easily be combined with other ggplot2 plots.")
5757 ;; Unspecified version of the LGPL.
5758 (license license:lgpl3+)))
5760 (define-public r-ggsci
5767 (uri (cran-uri "ggsci" version))
5770 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
5771 (build-system r-build-system)
5773 `(("r-ggplot2" ,r-ggplot2)
5774 ("r-scales" ,r-scales)))
5775 (home-page "https://nanx.me/ggsci/")
5776 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
5778 "This package provides a collection of ggplot2 color palettes inspired by
5779 plots in scientific journals, data visualization libraries, science fiction
5780 movies, and TV shows.")
5781 (license license:gpl3)))
5783 (define-public r-ggsignif
5790 (uri (cran-uri "ggsignif" version))
5793 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
5794 (build-system r-build-system)
5796 `(("r-ggplot2" ,r-ggplot2)))
5797 (home-page "https://github.com/const-ae/ggsignif")
5798 (synopsis "Significance brackets for ggplot2")
5800 "Enrich your ggplots with group-wise comparisons. This package provides
5801 an easy way to indicate if two groups are significantly different. Commonly
5802 this is shown by a bracket on top connecting the groups of interest which
5803 itself is annotated with the level of significance. The package provides a
5804 single layer that takes the groups for comparison and the test as arguments
5805 and adds the annotation to the plot.")
5806 (license license:gpl3)))
5808 (define-public r-ggpubr
5815 (uri (cran-uri "ggpubr" version))
5818 "0ln1gh3zlfx5s7zqcpvfdiksq74v1pma5kwkhc6r0riqnjjd19pf"))))
5819 (build-system r-build-system)
5821 `(("r-cowplot" ,r-cowplot)
5822 ("r-dplyr" ,r-dplyr)
5823 ("r-ggplot2" ,r-ggplot2)
5824 ("r-ggrepel" ,r-ggrepel)
5825 ("r-ggsci" ,r-ggsci)
5826 ("r-ggsignif" ,r-ggsignif)
5828 ("r-gridextra" ,r-gridextra)
5829 ("r-magrittr" ,r-magrittr)
5830 ("r-polynom" ,r-polynom)
5831 ("r-purrr" ,r-purrr)
5832 ("r-rlang" ,r-rlang)
5833 ("r-scales" ,r-scales)
5834 ("r-tidyr" ,r-tidyr)))
5835 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
5836 (synopsis "ggplot2-based publication-ready plots")
5838 "The ggplot2 package is an excellent and flexible package for elegant
5839 data visualization in R. However the default generated plots require some
5840 formatting before we can send them for publication. The ggpubr package
5841 provides some easy-to-use functions for creating and customizing ggplot2-based
5842 publication-ready plots.")
5843 (license license:gpl2)))
5845 (define-public r-ellipse
5852 (uri (cran-uri "ellipse" version))
5855 "0g82vc51m3c1k0hnpp2zla6amxxgk2mmkl8ssnsc49jv3599r6hs"))))
5856 (build-system r-build-system)
5857 (home-page "https://cran.r-project.org/web/packages/ellipse/")
5858 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
5860 "This package contains various routines for drawing ellipses and
5861 ellipse-like confidence regions, implementing the plots described in Murdoch
5862 and Chow (1996), A graphical display of large correlation matrices, The
5863 American Statistician 50, 178-180. There are also routines implementing the
5864 profile plots described in Bates and Watts (1988), Nonlinear Regression
5865 Analysis and its Applications.")
5866 (license license:gpl2+)))
5868 (define-public r-flashclust
5870 (name "r-flashclust")
5875 (uri (cran-uri "flashClust" version))
5878 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
5879 (properties `((upstream-name . "flashClust")))
5880 (build-system r-build-system)
5881 (native-inputs `(("gfortran" ,gfortran)))
5882 (home-page "https://cran.r-project.org/web/packages/flashClust/")
5883 (synopsis "Implementation of optimal hierarchical clustering")
5885 "This package provides a fast implementation of hierarchical
5887 (license license:gpl2+)))
5889 (define-public r-factominer
5891 (name "r-factominer")
5896 (uri (cran-uri "FactoMineR" version))
5899 "0qiw60ypf3bf5xsqz2b9l82i4jvprjm8lzpp12lhl8d9j5s8m0j8"))))
5900 (properties `((upstream-name . "FactoMineR")))
5901 (build-system r-build-system)
5904 ("r-cluster" ,r-cluster)
5905 ("r-ellipse" ,r-ellipse)
5906 ("r-flashclust" ,r-flashclust)
5907 ("r-ggplot2" ,r-ggplot2)
5908 ("r-ggrepel" ,r-ggrepel)
5909 ("r-lattice" ,r-lattice)
5910 ("r-leaps" ,r-leaps)
5912 ("r-scatterplot3d" ,r-scatterplot3d)))
5913 (home-page "http://factominer.free.fr")
5914 (synopsis "Multivariate exploratory data analysis and data mining")
5916 "This package provides exploratory data analysis methods to summarize,
5917 visualize and describe datasets. The main principal component methods are
5918 available, those with the largest potential in terms of applications:
5919 principal component analysis (PCA) when variables are quantitative,
5920 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
5921 variables are categorical, Multiple Factor Analysis when variables are
5922 structured in groups, etc. and hierarchical cluster analysis.")
5923 (license license:gpl2+)))
5925 (define-public r-factoextra
5927 (name "r-factoextra")
5932 (uri (cran-uri "factoextra" version))
5935 "0bpsbcmp6jpa9qk53dhfzghrz98dh0h0n68brl7rjz724yjbvhn8"))))
5936 (build-system r-build-system)
5938 `(("r-abind" ,r-abind)
5939 ("r-cluster" ,r-cluster)
5940 ("r-dendextend" ,r-dendextend)
5941 ("r-factominer" ,r-factominer)
5942 ("r-ggplot2" ,r-ggplot2)
5943 ("r-ggpubr" ,r-ggpubr)
5944 ("r-ggrepel" ,r-ggrepel)
5945 ("r-reshape2" ,r-reshape2)
5946 ("r-tidyr" ,r-tidyr)))
5947 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
5948 (synopsis "Extract and visualize the results of multivariate data analyses")
5950 "This package provides some easy-to-use functions to extract and
5951 visualize the output of multivariate data analyses, including
5952 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
5953 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
5954 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
5955 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
5956 packages. It contains also functions for simplifying some clustering analysis
5957 steps and provides ggplot2-based elegant data visualization.")
5958 (license license:gpl2)))
5960 (define-public r-fansi
5967 (uri (cran-uri "fansi" version))
5970 "02f2rx7v7wz6w97m2slwky2i5y8f9iafycmkyr3siy3z3k8fj171"))))
5971 (build-system r-build-system)
5973 `(("r-knitr" ,r-knitr))) ; for vignettes
5974 (home-page "https://github.com/brodieG/fansi")
5975 (synopsis "ANSI control sequence aware string functions")
5977 "This package provides counterparts to R string manipulation functions
5978 that account for the effects of ANSI text formatting control sequences.")
5979 (license license:gpl2+)))
5981 (define-public r-nbclust
5988 (uri (cran-uri "NbClust" version))
5991 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
5992 (properties `((upstream-name . "NbClust")))
5993 (build-system r-build-system)
5994 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
5995 (synopsis "Determine the best number of clusters in a data set")
5997 "NbClust provides 30 indexes for determining the optimal number of
5998 clusters in a data set and offers the best clustering scheme from different
5999 results to the user.")
6000 (license license:gpl2)))
6002 (define-public r-hdf5r
6009 (uri (cran-uri "hdf5r" version))
6012 "1pq12vkfqxvcaznwaxvjdg3acimk5a20m8h18sixvxc34vnqxw8f"))))
6013 (build-system r-build-system)
6018 `(("r-bit64" ,r-bit64)
6020 (home-page "https://hhoeflin.github.io/hdf5r")
6021 (synopsis "Interface to the HDF5 binary data format")
6023 "HDF5 is a data model, library and file format for storing and managing
6024 large amounts of data. This package provides a nearly feature complete,
6025 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
6026 functionality is added so that HDF5 objects behave very similar to their
6027 corresponding R counterparts.")
6028 (license license:asl2.0)))
6030 (define-public r-itertools
6032 (name "r-itertools")
6037 (uri (cran-uri "itertools" version))
6040 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
6041 (build-system r-build-system)
6043 `(("r-iterators" ,r-iterators)))
6044 (home-page "https://cran.r-project.org/web/packages/itertools/")
6045 (synopsis "Iterator tools")
6047 "This package provides various tools for creating iterators, many
6048 patterned after functions in the Python @code{itertools} module, and others
6049 patterned after functions in the snow package.")
6050 (license license:gpl2)))
6052 (define-public r-polynom
6059 (uri (cran-uri "polynom" version))
6062 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
6063 (build-system r-build-system)
6064 (home-page "https://cran.r-project.org/web/packages/polynom/")
6065 (synopsis "Functions for univariate polynomial manipulations")
6067 "This package provides a collection of functions to implement a class for
6068 univariate polynomial manipulations.")
6069 (license license:gpl2)))
6071 (define-public r-gbrd
6078 (uri (cran-uri "gbRd" version))
6081 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
6082 (properties `((upstream-name . "gbRd")))
6083 (build-system r-build-system)
6084 (home-page "https://cran.r-project.org/web/packages/gbRd/")
6085 (synopsis "Utilities for processing Rd objects and files")
6087 "This package provides utilities for processing Rd objects and files.
6088 Extract argument descriptions and other parts of the help pages of
6090 (license license:gpl2+)))
6092 (define-public r-rjags
6099 (uri (cran-uri "rjags" version))
6102 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
6103 (build-system r-build-system)
6105 `(("r-coda" ,r-coda)))
6109 `(("pkg-config" ,pkg-config)))
6110 (home-page "http://mcmc-jags.sourceforge.net")
6111 (synopsis "Bayesian graphical models using MCMC")
6113 "This package provides an R interface to the JAGS MCMC library. JAGS is
6114 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
6115 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
6116 (license license:gpl2)))
6118 (define-public r-rdpack
6125 (uri (cran-uri "Rdpack" version))
6128 "11cd27s6zp5cxnwxcvz6rjf00y0r7aq8ywhzwpf1r4xy1z44kd4g"))))
6129 (properties `((upstream-name . "Rdpack")))
6130 (build-system r-build-system)
6132 `(("r-bibtex" ,r-bibtex)
6133 ("r-gbrd" ,r-gbrd)))
6134 (home-page "https://github.com/GeoBosh/Rdpack")
6135 (synopsis "Update and manipulate Rd documentation objects")
6137 "This package provides functions for manipulation of R documentation
6138 objects, including functions @code{reprompt()} and @code{ereprompt()} for
6139 updating Rd documentation for functions, methods and classes; it also includes
6140 Rd macros for citations and import of references from bibtex files for use in
6141 Rd files and roxygen2 comments, as well as many functions for manipulation of
6142 references and Rd files.")
6143 (license license:gpl2+)))
6145 (define-public r-officer
6152 (uri (cran-uri "officer" version))
6155 "1i6jmnbkx7gd0qyf6akhizmxp7y1dh3h7a886mcbmrzka9d60zh4"))))
6156 (build-system r-build-system)
6158 `(("r-base64enc" ,r-base64enc)
6159 ("r-digest" ,r-digest)
6160 ("r-htmltools" ,r-htmltools)
6161 ("r-magrittr" ,r-magrittr)
6164 ("r-rlang" ,r-rlang)
6168 (home-page "https://davidgohel.github.io/officer")
6169 (synopsis "Manipulation of Word and PowerPoint documents")
6171 "This package provides tools to access and manipulate Word and PowerPoint
6172 documents from R. The package focuses on tabular and graphical reporting from
6173 R; it also provides two functions that let users get document content into
6174 data objects. A set of functions lets add and remove images, tables and
6175 paragraphs of text in new or existing documents. When working with PowerPoint
6176 presentations, slides can be added or removed; shapes inside slides can also
6177 be added or removed. When working with Word documents, a cursor can be used
6178 to help insert or delete content at a specific location in the document.")
6179 (license license:gpl3)))
6181 (define-public r-abn
6188 (uri (cran-uri "abn" version))
6191 "19w6bdjyp4zwqs6p0flry4qxqynf9rh8ykdrfrp61wrdf7kysw0d"))))
6192 (build-system r-build-system)
6196 `(("r-lme4" ,r-lme4)
6200 ("r-rcpparmadillo" ,r-rcpparmadillo)
6201 ("r-rjags" ,r-rjags)))
6202 (home-page "http://www.r-bayesian-networks.org")
6203 (synopsis "Modelling multivariate data with additive bayesian networks")
6205 "Bayesian network analysis is a form of probabilistic graphical models
6206 which derives from empirical data a directed acyclic graph, DAG, describing
6207 the dependency structure between random variables. An additive Bayesian
6208 network model consists of a form of a DAG where each node comprises a
6209 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
6210 equivalent to Bayesian multivariate regression using graphical modelling, they
6211 generalises the usual multivariable regression, GLM, to multiple dependent
6212 variables. This package provides routines to help determine optimal Bayesian
6213 network models for a given data set, where these models are used to identify
6214 statistical dependencies in messy, complex data.")
6215 (license license:gpl2+)))
6217 (define-public r-acd
6224 (uri (cran-uri "ACD" version))
6227 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
6228 (properties `((upstream-name . "ACD")))
6229 (build-system r-build-system)
6230 (home-page "https://cran.r-project.org/web/packages/ACD/")
6231 (synopsis "Categorical data analysis with complete or missing responses")
6233 "This package provides tools for categorical data analysis with complete
6234 or missing responses.")
6235 (license license:gpl2+)))
6237 (define-public r-acdm
6244 (uri (cran-uri "ACDm" version))
6247 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
6248 (properties `((upstream-name . "ACDm")))
6249 (build-system r-build-system)
6251 `(("r-dplyr" ,r-dplyr)
6252 ("r-ggplot2" ,r-ggplot2)
6254 ("r-rsolnp" ,r-rsolnp)
6256 (home-page "https://cran.r-project.org/web/packages/ACDm/")
6257 (synopsis "Tools for Autoregressive Conditional Duration Models")
6259 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
6260 and Russell, 1998) models. It creates trade, price or volume durations from
6261 transactions (tic) data, performs diurnal adjustments, fits various ACD models
6263 (license license:gpl2+)))
6265 (define-public r-overlap
6272 (uri (cran-uri "overlap" version))
6275 "1j3m6ir1chdz0si2fhcw6gs7c9h09bv0chz18rpzxsywww6d4rzy"))))
6276 (build-system r-build-system)
6277 (home-page "https://cran.r-project.org/web/packages/overlap/")
6278 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
6280 "This package provides functions to fit kernel density functions to data
6281 on temporal activity patterns of animals; estimate coefficients of overlapping
6282 of densities for two species; and calculate bootstrap estimates of confidence
6284 (license license:gpl3+)))
6286 (define-public r-snakecase
6288 (name "r-snakecase")
6293 (uri (cran-uri "snakecase" version))
6296 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
6297 (build-system r-build-system)
6299 `(("r-stringi" ,r-stringi)
6300 ("r-stringr" ,r-stringr)))
6301 (home-page "https://github.com/Tazinho/snakecase")
6302 (synopsis "Convert strings into any case")
6304 "This package provides a consistent, flexible and easy to use tool to
6305 parse and convert strings into cases like snake or camel among others.")
6306 (license license:gpl3)))
6308 (define-public r-prediction
6310 (name "r-prediction")
6315 (uri (cran-uri "prediction" version))
6318 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
6319 (build-system r-build-system)
6321 `(("r-data-table" ,r-data-table)))
6322 (home-page "https://github.com/leeper/prediction")
6323 (synopsis "Tidy, type-safe prediction methods")
6325 "This package provides the @code{prediction()} function, a type-safe
6326 alternative to @code{predict()} that always returns a data frame. The package
6327 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
6328 from the @code{stats} package, as well as numerous other model classes from
6329 other add-on packages.")
6330 (license license:expat)))
6332 (define-public r-insight
6339 (uri (cran-uri "insight" version))
6342 "0scjmr8qvwaswb9wfq2lxp1v5fl72way8cid9agrf0z1agp0adad"))))
6343 (build-system r-build-system)
6344 (home-page "https://easystats.github.io/insight/")
6345 (synopsis "Easy access to model information for various model objects")
6347 "This package provides a tool to provide an easy, intuitive and
6348 consistent access to information contained in various R models, like model
6349 formulas, model terms, information about random effects, data that was used to
6350 fit the model or data from response variables. The package mainly revolves
6351 around two types of functions: Functions that find (the names of) information,
6352 starting with @code{find_}, and functions that get the underlying data,
6353 starting with @code{get_}. The package has a consistent syntax and works with
6354 many different model objects, where otherwise functions to access these
6355 information are missing.")
6356 (license license:gpl3)))
6358 (define-public r-sjlabelled
6360 (name "r-sjlabelled")
6365 (uri (cran-uri "sjlabelled" version))
6368 "0c9wy0gsr2sbkrv2638xbi7qm0gl6jyr6sfricavhkm7l4hljjkz"))))
6369 (build-system r-build-system)
6371 `(("r-haven" ,r-haven)
6372 ("r-insight" ,r-insight)
6373 ("r-magrittr" ,r-magrittr)
6374 ("r-purrr" ,r-purrr)
6375 ("r-rlang" ,r-rlang)
6376 ("r-tidyselect" ,r-tidyselect)))
6377 (home-page "https://github.com/strengejacke/sjlabelled")
6378 (synopsis "Labelled data utility functions")
6380 "This package provides a collection of functions dealing with labelled
6381 data, like reading and writing data between R and other statistical software
6382 packages. This includes easy ways to get, set or change value and variable
6383 label attributes, to convert labelled vectors into factors or numeric (and
6384 vice versa), or to deal with multiple declared missing values.")
6385 (license license:gpl3)))
6387 (define-public r-sjmisc
6394 (uri (cran-uri "sjmisc" version))
6397 "0rl0bmk91wc4dxdgy008fl0dwkx3ffvys30vgpnr78lb4pk45nb2"))))
6398 (build-system r-build-system)
6400 `(("r-dplyr" ,r-dplyr)
6401 ("r-insight" ,r-insight)
6402 ("r-magrittr" ,r-magrittr)
6403 ("r-purrr" ,r-purrr)
6404 ("r-rlang" ,r-rlang)
6405 ("r-sjlabelled" ,r-sjlabelled)
6406 ("r-tidyselect" ,r-tidyselect)))
6407 (home-page "https://github.com/strengejacke/sjmisc")
6408 (synopsis "Data and variable transformation functions")
6410 "This package is a collection of miscellaneous utility functions,
6411 supporting data transformation tasks like recoding, dichotomizing or grouping
6412 variables, setting and replacing missing values. The data transformation
6413 functions also support labelled data, and all integrate seamlessly into a
6414 tidyverse workflow.")
6415 (license license:gpl3)))
6417 (define-public r-nortest
6424 (uri (cran-uri "nortest" version))
6427 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
6428 (build-system r-build-system)
6429 (home-page "https://cran.r-project.org/web/packages/nortest/")
6430 (synopsis "Tests for normality")
6432 "This package provides five omnibus tests for testing the composite
6433 hypothesis of normality.")
6434 (license license:gpl2+)))
6436 (define-public r-moonbook
6443 (uri (cran-uri "moonBook" version))
6446 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
6447 (properties `((upstream-name . "moonBook")))
6448 (build-system r-build-system)
6450 `(("r-magrittr" ,r-magrittr)
6451 ("r-nortest" ,r-nortest)
6452 ("r-purrr" ,r-purrr)
6453 ("r-sjmisc" ,r-sjmisc)
6454 ("r-stringr" ,r-stringr)
6455 ("r-survival" ,r-survival)))
6456 (home-page "https://github.com/cardiomoon/moonBook")
6457 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
6459 "This package provides several analysis-related functions for the book
6460 entitled \"R statistics and graph for medical articles\" (written in Korean),
6461 version 1, by Keon-Woong Moon with Korean demographic data with several plot
6463 (license license:gpl2)))
6465 (define-public r-flextable
6467 (name "r-flextable")
6472 (uri (cran-uri "flextable" version))
6475 "1f869f2dfqkzhf6yix7xcbs8rn1nwq3sg623h74zg6h1pl6px66w"))))
6476 (build-system r-build-system)
6478 `(("r-base64enc" ,r-base64enc)
6479 ("r-data-table" ,r-data-table)
6480 ("r-gdtools" ,r-gdtools)
6481 ("r-htmltools" ,r-htmltools)
6482 ("r-knitr" ,r-knitr)
6483 ("r-officer" ,r-officer)
6484 ("r-rlang" ,r-rlang)
6485 ("r-rmarkdown" ,r-rmarkdown)
6486 ("r-xml2" ,r-xml2)))
6487 (home-page "https://davidgohel.github.io/flextable")
6488 (synopsis "Functions for tabular reporting")
6490 "This package provides tools to create pretty tables for HTML documents
6491 and other formats. Functions are provided to let users create tables, modify
6492 and format their content. It extends the @code{officer} package and can be
6493 used within R markdown documents when rendering to HTML and to Word
6495 (license license:gpl3)))
6497 (define-public r-writexl
6504 (uri (cran-uri "writexl" version))
6507 "09fhdip6igcg97fjx4c7727cx2lb49l4d74l4i8rg2bag2s5lrj3"))))
6508 (build-system r-build-system)
6509 (inputs `(("zlib" ,zlib)))
6510 (home-page "https://github.com/ropensci/writexl")
6511 (synopsis "Export data frames to xlsx format")
6513 "This package provides a data frame to xlsx exporter based on
6515 (license license:bsd-2)))
6517 (define-public r-biasedurn
6519 (name "r-biasedurn")
6524 (uri (cran-uri "BiasedUrn" version))
6527 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
6528 (properties `((upstream-name . "BiasedUrn")))
6529 (build-system r-build-system)
6530 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
6531 (synopsis "Biased Urn model distributions")
6533 "This package provides statistical models of biased sampling in the form
6534 of univariate and multivariate noncentral hypergeometric distributions,
6535 including Wallenius' noncentral hypergeometric distribution and Fisher's
6536 noncentral hypergeometric distribution (also called extended hypergeometric
6538 (license license:gpl3)))
6540 (define-public r-goplot
6547 (uri (cran-uri "GOplot" version))
6550 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
6551 (properties `((upstream-name . "GOplot")))
6552 (build-system r-build-system)
6554 `(("r-ggdendro" ,r-ggdendro)
6555 ("r-ggplot2" ,r-ggplot2)
6556 ("r-gridextra" ,r-gridextra)
6557 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6558 (home-page "https://github.com/wencke/wencke.github.io")
6559 (synopsis "Visualization of functional analysis data")
6561 "This package provides an implementation of multilayered visualizations
6562 for enhanced graphical representation of functional analysis data. It
6563 combines and integrates omics data derived from expression and functional
6564 annotation enrichment analyses. Its plotting functions have been developed
6565 with an hierarchical structure in mind: starting from a general overview to
6566 identify the most enriched categories (modified bar plot, bubble plot) to a
6567 more detailed one displaying different types of relevant information for the
6568 molecules in a given set of categories (circle plot, chord plot, cluster plot,
6569 Venn diagram, heatmap).")
6570 (license license:gpl2)))
6572 (define-public r-getopt
6579 (uri (cran-uri "getopt" version))
6582 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
6583 (build-system r-build-system)
6584 (home-page "https://github.com/trevorld/getopt")
6585 (synopsis "Command-line option processor for R")
6587 "This package is designed to be used with Rscript to write shebang
6588 scripts that accept short and long options. Many users will prefer to
6589 use the packages @code{optparse} or @code{argparse} which add extra
6590 features like automatically generated help options and usage texts,
6591 support for default values, positional argument support, etc.")
6592 (license license:gpl2+)))
6594 (define-public r-findpython
6596 (name "r-findpython")
6601 (uri (cran-uri "findpython" version))
6604 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
6605 (build-system r-build-system)
6606 (home-page "https://github.com/trevorld/findpython")
6607 (synopsis "Functions to find an acceptable Python binary")
6609 "This package was designed to find an acceptable Python binary that
6610 matches version and feature constraints.")
6611 (license license:expat)))
6613 ;; This in not the same as "r-argparser"
6614 (define-public r-argparse
6621 (uri (cran-uri "argparse" version))
6624 "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l"))))
6625 (build-system r-build-system)
6626 (inputs `(("python" ,python)))
6628 `(("r-findpython" ,r-findpython)
6629 ("r-jsonlite" ,r-jsonlite)
6631 (home-page "https://github.com/trevorld/argparse")
6632 (synopsis "Command line optional and positional argument parser")
6634 "This package provides a command line parser to be used with Rscript to
6635 write shebang scripts that gracefully accept positional and optional arguments
6636 and automatically generate usage notices.")
6637 (license license:gpl2+)))
6639 (define-public r-hash
6646 (uri (cran-uri "hash" version))
6649 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
6650 (build-system r-build-system)
6651 (home-page "https://cran.r-project.org/web/packages/hash/")
6652 (synopsis "Implementation of hash/associated arrays/dictionaries")
6654 "This package implements a data structure similar to hashes in Perl and
6655 dictionaries in Python but with a purposefully R flavor. For objects of
6656 appreciable size, access using hashes outperforms native named lists and
6658 (license license:gpl2+)))
6660 (define-public r-orddom
6667 (uri (cran-uri "orddom" version))
6670 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
6671 (build-system r-build-system)
6672 (propagated-inputs `(("r-psych" ,r-psych)))
6673 (home-page "https://cran.r-project.org/web/packages/orddom/")
6674 (synopsis "Ordinal dominance statistics")
6676 "This package provides tools to compute ordinal, statistics and effect
6677 sizes as an alternative to mean comparison: Cliff's delta or success rate
6678 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
6679 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
6680 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
6681 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
6682 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
6683 Group (Non-)Overlap considerations.")
6684 (license license:gpl2)))
6686 (define-public r-deriv
6693 (uri (cran-uri "Deriv" version))
6696 "0hlqm216bg3l79gq6m0am0xz6vd3l2hgjnjm6lym3mkmgkka4kxw"))))
6697 (properties `((upstream-name . "Deriv")))
6698 (build-system r-build-system)
6699 (home-page "https://cran.r-project.org/web/packages/Deriv")
6700 (synopsis "Symbolic differentiation")
6702 "This package provides an R-based solution for symbolic differentiation.
6703 It admits user-defined functions as well as function substitution in arguments
6704 of functions to be differentiated. Some symbolic simplification is part of
6706 (license license:gpl3+)))
6708 (define-public r-doby
6715 (uri (cran-uri "doBy" version))
6718 "1d0d6pwai1g4i5jls0jm9va29ci5hy92n5957608f3fzi1jwy635"))))
6719 (properties `((upstream-name . "doBy")))
6720 (build-system r-build-system)
6722 `(("r-broom" ,r-broom)
6723 ("r-deriv" ,r-deriv)
6724 ("r-dplyr" ,r-dplyr)
6725 ("r-magrittr" ,r-magrittr)
6727 ("r-matrix" ,r-matrix)
6729 ("r-pbkrtest" ,r-pbkrtest)
6730 ("r-tibble" ,r-tibble)))
6731 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
6732 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
6734 "This package contains:
6737 @item facilities for working with grouped data: @code{do}
6738 something to data stratified @code{by} some variables.
6739 @item implementations of least-squares means, general linear contrasts, and
6740 @item miscellaneous other utilities.
6742 (license license:gpl2+)))
6744 (define-public r-refgenome
6746 (name "r-refgenome")
6751 (uri (cran-uri "refGenome" version))
6754 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
6755 (properties `((upstream-name . "refGenome")))
6756 (build-system r-build-system)
6760 ("r-rsqlite" ,r-rsqlite)))
6761 (home-page "https://cran.r-project.org/web/packages/refGenome/")
6763 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
6765 "This package contains functionality for importing and managing of
6766 downloaded genome annotation data from the Ensembl genome browser (European
6767 Bioinformatics Institute) and from the UCSC genome browser (University of
6768 California, Santa Cruz) and annotation routines for genomic positions and
6769 splice site positions.")
6770 (license license:gpl2)))
6772 (define-public r-basix
6779 (uri (cran-uri "BASIX" version))
6782 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
6783 (properties `((upstream-name . "BASIX")))
6784 (build-system r-build-system)
6785 (home-page "https://cran.r-project.org/web/packages/BASIX/")
6786 (synopsis "Efficient C/C++ toolset for R")
6788 "BASIX provides some efficient C/C++ implementations of native R
6789 procedures to speed up calculations in R.")
6790 (license license:gpl2)))
6792 (define-public r-blockfest
6794 (name "r-blockfest")
6799 (uri (cran-uri "BlockFeST" version))
6802 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
6803 (properties `((upstream-name . "BlockFeST")))
6804 (build-system r-build-system)
6805 (propagated-inputs `(("r-basix" ,r-basix)))
6806 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
6807 (synopsis "Bayesian calculation of region-specific fixation index")
6809 "This package provides an R implementation of an extension of the
6810 BayeScan software for codominant markers, adding the option to group
6811 individual SNPs into pre-defined blocks. A typical application of this new
6812 approach is the identification of genomic regions, genes, or gene sets
6813 containing one or more SNPs that evolved under directional selection.")
6814 (license license:gpl2)))
6816 (define-public r-proc
6823 (uri (cran-uri "pROC" version))
6826 "1jx8af9p6sxbypqvj1cci7q9sbyaw310inbjxibjcr3acj59h45h"))))
6827 (properties `((upstream-name . "pROC")))
6828 (build-system r-build-system)
6830 `(("r-plyr" ,r-plyr)
6831 ("r-rcpp" ,r-rcpp)))
6832 (home-page "http://expasy.org/tools/pROC/")
6833 (synopsis "Display and analyze ROC curves")
6835 "This package provides tools for visualizing, smoothing and comparing
6836 receiver operating characteristic (ROC curves). The area under the
6837 curve (AUC) can be compared with statistical tests based on U-statistics or
6838 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
6839 (license license:gpl3+)))
6841 (define-public r-rootsolve
6843 (name "r-rootsolve")
6848 (uri (cran-uri "rootSolve" version))
6851 "0skrspq7sd7gaq73w91km14v8znc8chncgy64hvjgcng2xw15phx"))))
6852 (properties `((upstream-name . "rootSolve")))
6853 (build-system r-build-system)
6854 (native-inputs `(("gfortran" ,gfortran)))
6855 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
6856 (synopsis "Tools for the analysis of ordinary differential equations")
6858 "This package provides routines to find the root of nonlinear functions,
6859 and to perform steady-state and equilibrium analysis of @dfn{ordinary
6860 differential equations} (ODE). It includes routines that:
6863 @item generate gradient and jacobian matrices (full and banded),
6864 @item find roots of non-linear equations by the Newton-Raphson method,
6865 @item estimate steady-state conditions of a system of (differential) equations
6866 in full, banded or sparse form, using the Newton-Raphson method, or by
6867 dynamically running,
6868 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
6869 and 3-D partial differential equations, that have been converted to ordinary
6870 differential equations by numerical differencing (using the method-of-lines
6873 (license license:gpl2+)))
6875 (define-public r-abcanalysis
6877 (name "r-abcanalysis")
6882 (uri (cran-uri "ABCanalysis" version))
6884 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
6885 (properties `((upstream-name . "ABCanalysis")))
6886 (build-system r-build-system)
6887 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
6888 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
6889 (synopsis "Computed ABC Analysis")
6891 "Multivariate data sets often differ in several factors or derived statistical
6892 parameters, which have to be selected for a valid interpretation. Basing this
6893 selection on traditional statistical limits leads occasionally to the perception
6894 of losing information from a data set. This package provides tools to calculate
6895 these limits on the basis of the mathematical properties of the distribution of
6896 the analyzed items.")
6897 (license license:gpl3)))
6899 (define-public r-slam
6906 (uri (cran-uri "slam" version))
6908 (base32 "1ihhbx76miwys35gsbhijriadvrw4f51lc3v45pnn6cvcfd9hr0b"))))
6909 (build-system r-build-system)
6910 (home-page "https://cran.r-project.org/web/packages/slam/")
6911 (synopsis "Sparse lightweight arrays and matrices")
6913 "This package contains data structures and algorithms for sparse arrays and matrices,
6914 based on index arrays and simple triplet representations, respectively.")
6915 (license license:gpl2)))
6917 (define-public r-manipulatewidget
6919 (name "r-manipulatewidget")
6924 (uri (cran-uri "manipulateWidget" version))
6926 (base32 "1zagrbwkn2d50zzw8i2vyb1hsq4cydmfsqiy1a2qlp6zrv8a6q9x"))))
6928 `((upstream-name . "manipulateWidget")))
6929 (build-system r-build-system)
6931 `(("r-base64enc" ,r-base64enc)
6932 ("r-codetools" ,r-codetools)
6933 ("r-htmltools" ,r-htmltools)
6934 ("r-htmlwidgets" ,r-htmlwidgets)
6935 ("r-knitr" ,r-knitr)
6936 ("r-miniui" ,r-miniui)
6937 ("r-shiny" ,r-shiny)
6938 ("r-webshot" ,r-webshot)))
6939 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
6940 (synopsis "Add even more interactivity to interactive charts")
6942 "This package lets you create in just a few lines of R code a nice user interface to
6943 modify the data or the graphical parameters of one or multiple interactive
6944 charts. It is useful to quickly explore visually some data or for package
6945 developers to generate user interfaces easy to maintain.")
6946 (license license:gpl2+)))
6955 (uri (cran-uri "A3" version))
6957 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
6958 (properties `((upstream-name . "A3")))
6959 (build-system r-build-system)
6961 `(("r-pbapply" ,r-pbapply)
6962 ("r-xtable" ,r-xtable)))
6963 (home-page "https://cran.r-project.org/web/packages/A3/")
6964 (synopsis "Error metrics for predictive models")
6966 "This package supplies tools for tabulating and analyzing the results of predictive
6967 models. The methods employed are applicable to virtually any predictive model
6968 and make comparisons between different methodologies straightforward.")
6969 (license license:gpl2+)))
6971 (define-public r-infotheo
6978 (uri (cran-uri "infotheo" version))
6981 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
6982 (build-system r-build-system)
6983 (home-page "http://homepage.meyerp.com/software")
6984 (synopsis "Information-theoretic measures")
6986 "This package implements various measures of information theory based on
6987 several entropy estimators.")
6988 (license license:gpl3+)))
6990 (define-public r-abcoptim
6997 (uri (cran-uri "ABCoptim" version))
6999 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
7000 (properties `((upstream-name . "ABCoptim")))
7001 (build-system r-build-system)
7002 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
7003 (home-page "https://github.com/gvegayon/ABCoptim/")
7004 (synopsis "Optimization of Artificial Bee Colony algorithm")
7006 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
7007 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
7008 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
7009 algorithms, and uses only common control parameters such as colony size and
7010 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
7011 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
7012 This version is a work-in-progress and is written in R code.")
7013 (license license:expat)))
7015 (define-public r-abcp2
7022 (uri (cran-uri "ABCp2" version))
7024 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
7025 (properties `((upstream-name . "ABCp2")))
7026 (build-system r-build-system)
7027 (propagated-inputs `(("r-mass" ,r-mass)))
7028 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
7029 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
7031 "This package tests the goodness of fit of a distribution of offspring to the Normal,
7032 Poisson, and Gamma distribution and estimates the proportional paternity of the
7033 second male (P2) based on the best fit distribution.")
7034 (license license:gpl2)))
7036 (define-public r-abcrf
7043 (uri (cran-uri "abcrf" version))
7045 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
7046 (build-system r-build-system)
7048 `(("r-doparallel" ,r-doparallel)
7049 ("r-foreach" ,r-foreach)
7051 ("r-matrixstats" ,r-matrixstats)
7052 ("r-ranger" ,r-ranger)
7054 ("r-rcpparmadillo" ,r-rcpparmadillo)
7055 ("r-readr" ,r-readr)
7056 ("r-stringr" ,r-stringr)))
7057 (home-page "https://cran.r-project.org/web/packages/abcrf/")
7058 (synopsis "Approximate bayesian computation via random forests")
7060 "This package performs approximate bayesian computation (ABC) model choice and
7061 parameter inference via random forests. This machine learning tool named random
7062 forests (RF) can conduct selection among the highly complex models covered by
7064 (license license:gpl2+)))
7066 (define-public r-abctools
7073 (uri (cran-uri "abctools" version))
7075 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
7076 (build-system r-build-system)
7079 ("r-abind" ,r-abind)
7080 ("r-hmisc" ,r-hmisc)
7081 ("r-plyr" ,r-plyr)))
7082 (home-page "https://github.com/dennisprangle/abctools/")
7083 (synopsis "Tools for ABC analyses")
7085 "This @code{r-abctools} package provides tools for approximate Bayesian computation
7086 including summary statistic selection and assessing coverage. This includes
7087 recent dimension reduction algorithms to tune the choice of summary statistics,
7088 and coverage methods to tune the choice of threshold.")
7089 (license license:gpl2+)))
7091 (define-public r-ggstance
7098 (uri (cran-uri "ggstance" version))
7100 (base32 "0kdksay61hyb6612b07r84chh7a9aibjyclk3qcypvr9aang8hkh"))))
7101 (build-system r-build-system)
7103 `(("r-ggplot2" ,r-ggplot2)
7105 ("r-rlang" ,r-rlang)
7106 ("r-withr" ,r-withr)))
7107 (home-page "https://cran.r-project.org/web/packages/ggstance/")
7108 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
7110 "This package is a @code{r-ggplot2} extension that provides flipped components:
7112 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
7113 @item vertical versions of @code{r-ggplot2} positions.
7115 (license license:gpl3)))
7117 (define-public r-mosaiccore
7119 (name "r-mosaiccore")
7124 (uri (cran-uri "mosaicCore" version))
7126 (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
7127 (properties `((upstream-name . "mosaicCore")))
7128 (build-system r-build-system)
7130 `(("r-dplyr" ,r-dplyr)
7131 ("r-lazyeval" ,r-lazyeval)
7133 ("r-rlang" ,r-rlang)
7134 ("r-tidyr" ,r-tidyr)))
7135 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
7136 (synopsis "Common utilities for mosaic family packages")
7138 "Common utilities used in other Mosaic family packages are collected here.")
7139 (license license:gpl2+)))
7141 (define-public r-ggformula
7143 (name "r-ggformula")
7148 (uri (cran-uri "ggformula" version))
7150 (base32 "16ycabhnp78fsiv1dc63ccgh9gmpsy2683vbmq0fdzl6w3pd87sr"))))
7151 (build-system r-build-system)
7153 `(("r-ggplot2" ,r-ggplot2)
7154 ("r-ggstance" ,r-ggstance)
7155 ("r-magrittr" ,r-magrittr)
7156 ("r-mosaiccore" ,r-mosaiccore)
7157 ("r-rlang" ,r-rlang)
7158 ("r-stringr" ,r-stringr)
7159 ("r-tibble" ,r-tibble)
7160 ("r-tidyr" ,r-tidyr)))
7161 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
7162 (synopsis "Formula interface for the @code{r-ggplot2}")
7164 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
7165 gf_density(), and so on, bring the formula interface to ggplot(). This captures
7166 and extends the excellent simplicity of the lattice-graphics formula interface,
7167 while providing the intuitive capabilities of @code{r-ggplot2}.")
7168 (license license:expat)))
7170 (define-public r-mosaicdata
7172 (name "r-mosaicdata")
7177 (uri (cran-uri "mosaicData" version))
7179 (base32 "04z0mdm52mykqsxsinhmsihn181zf6cw321gayk2rjp7lj7mwdq9"))))
7180 (properties `((upstream-name . "mosaicData")))
7181 (build-system r-build-system)
7182 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
7183 (synopsis "Data sets for project Mosaic")
7185 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
7186 used to teach mathematics, statistics, computation and modeling.")
7187 (license license:gpl2+)))
7189 (define-public r-raster
7196 (uri (cran-uri "raster" version))
7199 "0faxv71hlxkblvbi3ps1vfzm3wwi0brwzmpsr5114bddcqyiqkvn"))))
7200 (build-system r-build-system)
7202 `(("r-rcpp" ,r-rcpp)
7204 (home-page "https://www.rspatial.org/")
7205 (synopsis "Geographic data analysis and modeling")
7207 "The package implements basic and high-level functions for reading,
7208 writing, manipulating, analyzing and modeling of gridded spatial data.
7209 Processing of very large files is supported.")
7210 (license license:gpl3+)))
7212 (define-public r-mosaic
7219 (uri (cran-uri "mosaic" version))
7221 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
7222 (build-system r-build-system)
7224 `(("r-broom" ,r-broom)
7225 ("r-dplyr" ,r-dplyr)
7226 ("r-ggdendro" ,r-ggdendro)
7227 ("r-ggformula" ,r-ggformula)
7228 ("r-ggplot2" ,r-ggplot2)
7229 ("r-ggrepel" ,r-ggrepel)
7231 ("r-gridextra" ,r-gridextra)
7232 ("r-lattice" ,r-lattice)
7233 ("r-latticeextra" ,r-latticeextra)
7234 ("r-lazyeval" ,r-lazyeval)
7236 ("r-matrix" ,r-matrix)
7237 ("r-mosaiccore" ,r-mosaiccore)
7238 ("r-mosaicdata" ,r-mosaicdata)
7239 ("r-readr" ,r-readr)
7240 ("r-tidyr" ,r-tidyr)))
7241 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
7242 (synopsis "Mathematics, statistics, and computation teaching utilities")
7244 "This package contain data sets and utilities from
7245 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
7246 statistics, computation and modeling. Project MOSAIC is a community of
7247 educators working to tie together aspects of quantitative work that students
7248 in science, technology, engineering and mathematics will need in their
7249 professional lives, but which are usually taught in isolation, if at all.")
7250 (license license:gpl2+)))
7252 (define-public r-abd
7259 (uri (cran-uri "abd" version))
7261 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
7262 (build-system r-build-system)
7264 `(("r-lattice" ,r-lattice)
7265 ("r-mosaic" ,r-mosaic)
7266 ("r-nlme" ,r-nlme)))
7267 (home-page "https://cran.r-project.org/web/packages/abd/")
7268 (synopsis "Analysis of biological data")
7270 "The @code{r-abd} package contains data sets and sample code for the Analysis of
7271 biological data by Michael Whitlock and Dolph Schluter.")
7272 (license license:gpl2)))
7274 (define-public r-svgui
7281 (uri (cran-uri "svGUI" version))
7283 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
7284 (properties `((upstream-name . "svGUI")))
7285 (build-system r-build-system)
7286 (home-page "https://github.com/SciViews/svGUI/")
7287 (synopsis "Functions for managing GUI clients in R")
7289 "The SciViews @code{svGUI} package eases the management of Graphical User
7290 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
7291 centralizes info about GUI elements currently used, and it dispatches GUI
7292 calls to the particular toolkits in use in function of the context.")
7293 (license license:gpl2)))
7295 (define-public r-svdialogs
7297 (name "r-svdialogs")
7302 (uri (cran-uri "svDialogs" version))
7304 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
7305 (properties `((upstream-name . "svDialogs")))
7306 (build-system r-build-system)
7309 ("zenity" ,zenity)))
7311 `(("r-rstudioapi" ,r-rstudioapi)
7312 ("r-svgui" ,r-svgui)))
7313 (home-page "https://github.com/SciViews/svDialogs/")
7314 (synopsis "Portable dialog boxes")
7316 "This package helps to construct standard dialog boxes for your GUI, including
7317 message boxes, input boxes, list, file or directory selection, and others. In
7318 case R cannot display GUI dialog boxes, a simpler command line version of these
7319 interactive elements is also provided as a fallback solution.")
7320 (license license:gpl2)))
7322 (define-public r-abe
7329 (uri (cran-uri "abe" version))
7332 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
7333 (build-system r-build-system)
7334 (home-page "https://cran.r-project.org/web/packages/abe/")
7335 (synopsis "Augmented backward elimination")
7337 "This package performs augmented backward elimination and checks the
7338 stability of the obtained model. Augmented backward elimination combines
7339 significance or information based criteria with the change in estimate to
7340 either select the optimal model for prediction purposes or to serve as a tool
7341 to obtain a practically sound, highly interpretable model.")
7342 (license license:gpl2+)))
7344 (define-public r-abf2
7351 (uri (cran-uri "abf2" version))
7353 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
7354 (build-system r-build-system)
7355 (home-page "https://cran.r-project.org/web/packages/abf2/")
7356 (synopsis "Load gap-free axon @code{r-abf2} files")
7358 "This package loads electrophysiology data from ABF2 files, as created by
7359 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
7360 mode are currently supported.")
7361 (license license:artistic2.0)))
7363 (define-public r-abhgenotyper
7365 (name "r-abhgenotyper")
7370 (uri (cran-uri "ABHgenotypeR" version))
7372 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
7373 (properties `((upstream-name . "ABHgenotypeR")))
7374 (build-system r-build-system)
7376 `(("r-ggplot2" ,r-ggplot2)
7377 ("r-reshape2" ,r-reshape2)))
7378 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
7379 (synopsis "Visualize and manipulate ABH genotypes")
7381 "The @code{r-abhgenotyper} package provides simple imputation,
7382 error-correction and plotting capacities for genotype data. The package is
7383 supposed to serve as an intermediate but independent analysis tool between the
7384 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
7385 not found in either TASSEL or @code{r-qtl} in addition to visualization of
7386 genotypes as \"graphical genotypes\".")
7387 (license license:gpl3)))
7389 (define-public r-furrr
7396 (uri (cran-uri "furrr" version))
7399 "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx"))))
7400 (build-system r-build-system)
7402 `(("r-future" ,r-future)
7403 ("r-globals" ,r-globals)
7404 ("r-purrr" ,r-purrr)
7405 ("r-rlang" ,r-rlang)))
7406 (home-page "https://github.com/DavisVaughan/furrr")
7407 (synopsis "Apply mapping functions in parallel using futures")
7409 "This package provides implementations of the family of @code{map()}
7410 functions from the @code{purrr} package that can be resolved using any
7411 @code{future}-supported backend, e.g. parallel on the local machine or
7412 distributed on a compute cluster.")
7413 (license license:lgpl2.1+)))
7415 (define-public r-abjutils
7422 (uri (cran-uri "abjutils" version))
7424 (base32 "0n4zps65y3zg0gfzlv97w91si52a9izkncirskbkj5x9hk0nhxcv"))))
7425 (build-system r-build-system)
7427 `(("r-devtools" ,r-devtools)
7428 ("r-dplyr" ,r-dplyr)
7429 ("r-furrr" ,r-furrr)
7430 ("r-future" ,r-future)
7433 ("r-magrittr" ,r-magrittr)
7434 ("r-progress" ,r-progress)
7435 ("r-purrr" ,r-purrr)
7436 ("r-readr" ,r-readr)
7437 ("r-rlang" ,r-rlang)
7438 ("r-rstudioapi" ,r-rstudioapi)
7439 ("r-scales" ,r-scales)
7440 ("r-stringi" ,r-stringi)
7441 ("r-stringr" ,r-stringr)
7442 ("r-tibble" ,r-tibble)
7443 ("r-tidyr" ,r-tidyr)))
7444 (home-page "https://github.com/abjur/abjutils/")
7445 (synopsis "Collection of tools for jurimetrical analysis")
7447 "This package implements general purpose tools, such as functions for
7448 sampling and basic manipulation of Brazilian lawsuits identification number.
7449 It also implements functions for text cleaning, such as accentuation
7451 (license license:expat)))
7453 (define-public r-abnormality
7455 (name "r-abnormality")
7460 (uri (cran-uri "abnormality" version))
7462 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
7463 (build-system r-build-system)
7465 `(("r-mass" ,r-mass)
7466 ("r-matrix" ,r-matrix)))
7467 (home-page "https://cran.r-project.org/web/packages/abnormality/")
7468 (synopsis "Measure a subject's abnormality with respect to a reference population")
7470 "This package contains functions to implement the methodology and
7471 considerations laid out by Marks et al. in the article \"Measuring abnormality
7472 in high dimensional spaces: applications in biomechanical gait analysis\".
7473 Using high-dimensional datasets to measure a subject's overall level of
7474 abnormality as compared to a reference population is often needed in outcomes
7476 (license license:expat)))
7478 (define-public r-abodoutlier
7480 (name "r-abodoutlier")
7485 (uri (cran-uri "abodOutlier" version))
7487 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
7488 (properties `((upstream-name . "abodOutlier")))
7489 (build-system r-build-system)
7491 `(("r-cluster" ,r-cluster)))
7492 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
7493 (synopsis "Angle-based outlier detection")
7495 "This package performs angle-based outlier detection on a given data
7496 frame. It offers three methods to process data:
7498 @item full but slow implementation using all the data that has cubic
7500 @item a fully randomized method;
7501 @item a method using k-nearest neighbours.
7503 These algorithms are well suited for high dimensional data outlier
7505 (license license:expat)))
7507 (define-public r-abps
7514 (uri (cran-uri "ABPS" version))
7516 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
7517 (properties `((upstream-name . "ABPS")))
7518 (build-system r-build-system)
7519 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
7520 (home-page "https://cran.r-project.org/web/packages/ABPS/")
7521 (synopsis "Abnormal blood profile score to detect blood doping")
7523 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
7524 The ABPS is a part of the Athlete biological passport program of the World
7525 anti-doping agency, which combines several blood parameters into a single
7526 score in order to detect blood doping. The package also contains functions to
7527 calculate other scores used in anti-doping programs, such as the ratio of
7528 hemoglobin to reticulocytes (OFF-score), as well as example data.")
7529 (license license:gpl2+)))
7531 (define-public r-parmigene
7533 (name "r-parmigene")
7538 (uri (cran-uri "parmigene" version))
7541 "1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d"))))
7542 (build-system r-build-system)
7543 (home-page "https://cran.r-project.org/web/packages/parmigene/")
7544 (synopsis "Mutual information estimation for gene network reconstruction")
7546 "This package provides a parallel estimation of the mutual information
7547 based on entropy estimates from k-nearest neighbors distances and algorithms
7548 for the reconstruction of gene regulatory networks.")
7549 (license license:agpl3+)))
7551 (define-public r-pscl
7558 (uri (cran-uri "pscl" version))
7560 (base32 "1phf3awsfr4ncqfqzin5m1pz0g7y1zhbcm2sz7358ssw914fd7rc"))))
7561 (build-system r-build-system)
7563 `(("r-mass" ,r-mass)))
7564 (home-page "https://github.com/atahk/pscl/")
7565 (synopsis "Political science computational laboratory")
7567 "The @code{pscl} is an R package providing classes and methods for:
7569 @item Bayesian analysis of roll call data (item-response models);
7570 @item elementary Bayesian statistics;
7571 @item maximum likelihood estimation of zero-inflated and hurdle models for count
7573 @item utility functions.
7575 (license license:gpl2)))
7577 (define-public r-accelmissing
7579 (name "r-accelmissing")
7584 (uri (cran-uri "accelmissing" version))
7586 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
7587 (build-system r-build-system)
7589 `(("r-mice" ,r-mice)
7590 ("r-pscl" ,r-pscl)))
7591 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
7592 (synopsis "Missing value imputation for accelerometer data")
7594 "This package provides a statistical method to impute the missing values in
7595 accelerometer data. The methodology includes both parametric and
7596 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
7597 model. It also provides multiple functions to preprocess the accelerometer data
7598 previous to the missing data imputation. These include detecting the wearing
7599 and the non-wearing time, selecting valid days and subjects, and creating plots.")
7600 (license license:gpl2+)))
7602 (define-public r-mhsmm
7609 (uri (cran-uri "mhsmm" version))
7611 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
7612 (build-system r-build-system)
7613 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
7614 (home-page "https://github.com/jaredo/mhsmm/")
7615 (synopsis "Inference for hidden Markov and semi-Markov models")
7617 "The @code{r-mhsmm} package implements estimation and prediction methods for
7618 hidden Markov and semi-Markov models for multiple observation sequences. Such
7619 techniques are of interest when observed data is thought to be dependent on some
7620 unobserved (or hidden) state. Also, this package is suitable for equidistant
7621 time series data, with multivariate and/or missing data. Allows user defined
7622 emission distributions.")
7623 (license license:gpl2+)))
7625 (define-public r-nleqslv
7632 (uri (cran-uri "nleqslv" version))
7634 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
7635 (build-system r-build-system)
7636 (native-inputs `(("gfortran" ,gfortran)))
7637 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
7638 (synopsis "Solve systems of nonlinear equations")
7640 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
7641 Broyden or a Newton method with a choice of global strategies such as line
7642 search and trust region. There are options for using a numerical or user
7643 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
7644 singular or ill-conditioned Jacobian.")
7645 (license license:gpl2+)))
7647 (define-public r-physicalactivity
7649 (name "r-physicalactivity")
7654 (uri (cran-uri "PhysicalActivity" version))
7656 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
7658 `((upstream-name . "PhysicalActivity")))
7659 (build-system r-build-system)
7660 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
7661 (synopsis "Procesing accelerometer data for physical activity measurement")
7663 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
7664 for classification of monitor wear and nonwear time intervals in accelerometer
7665 data collected to assess physical activity. The package also contains functions
7666 for making plots of accelerometer data and obtaining the summary of various
7667 information including daily monitor wear time and the mean monitor wear time
7668 during valid days. The revised package version 0.2-1 improved the functions
7669 regarding speed, robustness and add better support for time zones and daylight
7670 saving. In addition, several functions were added:
7672 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
7673 @item the @code{markPAI} can categorize physical activity intensity level based
7674 on user-defined cut-points of accelerometer counts.
7676 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
7677 @code{queryActigraph} functions.")
7678 (license license:gpl3+)))
7680 (define-public r-acc
7687 (uri (cran-uri "acc" version))
7689 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
7690 (build-system r-build-system)
7692 `(("r-circlize" ,r-circlize)
7694 ("r-ggplot2" ,r-ggplot2)
7695 ("r-iterators" ,r-iterators)
7696 ("r-mhsmm" ,r-mhsmm)
7697 ("r-nleqslv" ,r-nleqslv)
7698 ("r-physicalactivity" ,r-physicalactivity)
7700 ("r-r-utils" ,r-r-utils)
7702 ("r-rcpparmadillo" ,r-rcpparmadillo)
7703 ("r-rsqlite" ,r-rsqlite)
7705 (home-page "https://cran.r-project.org/web/packages/acc/")
7706 (synopsis "Exploring accelerometer data")
7708 "This package processes accelerometer data from uni-axial and tri-axial devices
7709 and generates data summaries. Also, includes functions to plot, analyze, and
7710 simulate accelerometer data.")
7711 (license license:gpl2+)))
7713 (define-public r-rbenchmark
7715 (name "r-rbenchmark")
7720 (uri (cran-uri "rbenchmark" version))
7722 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
7723 (build-system r-build-system)
7724 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
7725 (synopsis "Benchmarking routine for R")
7727 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
7728 and is intended to facilitate benchmarking of arbitrary R code. The library
7729 consists of just one function, benchmark, which is a simple wrapper around
7730 system.time. Given a specification of the benchmarking process (counts of
7731 replications, evaluation environment) and an arbitrary number of expressions,
7732 benchmark evaluates each of the expressions in the specified environment,
7733 replicating the evaluation as many times as specified, and returning the results
7734 conveniently wrapped into a data frame.")
7735 (license license:gpl2+)))
7737 (define-public r-mitools
7744 (uri (cran-uri "mitools" version))
7747 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
7748 (build-system r-build-system)
7749 (propagated-inputs `(("r-dbi" ,r-dbi)))
7750 (home-page "https://cran.r-project.org/web/packages/mitools/")
7751 (synopsis "Tools for multiple imputation of missing data")
7753 "This package provides tools to perform analyses and combine results from
7754 multiple-imputation datasets.")
7755 (license license:gpl2)))
7757 (define-public r-magick
7764 (uri (cran-uri "magick" version))
7767 "1xh5mhaks3wk1iwqs9d3lnbfv121lc1yz5fqdzk5il9ppr831l85"))))
7768 (build-system r-build-system)
7770 `(("imagemagick" ,imagemagick)
7773 `(("r-curl" ,r-curl)
7774 ("r-magrittr" ,r-magrittr)
7775 ("r-rcpp" ,r-rcpp)))
7777 `(("pkg-config" ,pkg-config)))
7778 (home-page "https://github.com/ropensci/magick")
7779 (synopsis "Advanced graphics and image-processing in R")
7781 "This package provides bindings to ImageMagick, a comprehensive image
7782 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
7783 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
7784 operations are vectorized via the Magick++ STL meaning they operate either on
7785 a single frame or a series of frames for working with layers, collages, or
7786 animation. In RStudio, images are automatically previewed when printed to the
7787 console, resulting in an interactive editing environment.")
7788 (license license:expat)))
7790 (define-public r-survey
7797 (uri (cran-uri "survey" version))
7800 "0xclsy4ram4k48vzh5m5bpmknnpwxnss85v73s4czsjj5ffjxwwh"))))
7801 (build-system r-build-system)
7803 `(("r-lattice" ,r-lattice)
7804 ("r-matrix" ,r-matrix)
7805 ("r-minqa" ,r-minqa)
7806 ("r-mitools" ,r-mitools)
7807 ("r-numderiv" ,r-numderiv)
7808 ("r-survival" ,r-survival)))
7809 (home-page "http://r-survey.r-forge.r-project.org/survey/")
7810 (synopsis "Analysis of complex survey samples")
7812 "This package provides tools for the analysis of complex survey samples.
7813 The provided features include: summary statistics, two-sample tests, rank
7814 tests, generalised linear models, cumulative link models, Cox models,
7815 loglinear models, and general maximum pseudolikelihood estimation for
7816 multistage stratified, cluster-sampled, unequally weighted survey samples;
7817 variances by Taylor series linearisation or replicate weights;
7818 post-stratification, calibration, and raking; two-phase subsampling designs;
7819 graphics; PPS sampling without replacement; principal components, and factor
7821 ;; Either version of the GPL.
7822 (license (list license:gpl2 license:gpl3))))
7824 (define-public r-dvmisc
7831 (uri (cran-uri "dvmisc" version))
7833 (base32 "0x391pxg5mqgp5xxc8qwhwxky8ds7d9gr9iwmsb12c92kxfk00bv"))))
7834 (build-system r-build-system)
7836 `(("r-cubature" ,r-cubature)
7837 ("r-data-table" ,r-data-table)
7838 ("r-dplyr" ,r-dplyr)
7839 ("r-ggplot2" ,r-ggplot2)
7841 ("r-mvtnorm" ,r-mvtnorm)
7842 ("r-pracma" ,r-pracma)
7843 ("r-purrr" ,r-purrr)
7844 ("r-rbenchmark" ,r-rbenchmark)
7846 ("r-survey" ,r-survey)))
7847 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
7848 (synopsis "Faster computation of common statistics and miscellaneous functions")
7850 "This package implements faster versions of base R functions (e.g. mean, standard
7851 deviation, covariance, weighted mean), mostly written in C++, along with
7852 miscellaneous functions for various purposes (e.g. create the histogram with
7853 fitted probability density function or probability mass function curve, create
7854 the body mass index groups, assess the linearity assumption in logistic
7856 (license license:gpl2)))
7858 (define-public r-accelerometry
7860 (name "r-accelerometry")
7865 (uri (cran-uri "accelerometry" version))
7867 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
7868 (build-system r-build-system)
7870 `(("r-dvmisc" ,r-dvmisc)
7871 ("r-rcpp" ,r-rcpp)))
7872 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
7873 (synopsis "Functions for processing accelerometer data")
7875 "This package provides a collection of functions that perform operations on
7876 time-series accelerometer data, such as identify the non-wear time, flag minutes
7877 that are part of an activity bout, and find the maximum 10-minute average count
7878 value. The functions are generally very flexible, allowing for a variety of
7879 algorithms to be implemented.")
7880 (license license:gpl3)))
7882 (define-public r-absim
7889 (uri (cran-uri "AbSim" version))
7891 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
7892 (properties `((upstream-name . "AbSim")))
7893 (build-system r-build-system)
7896 ("r-powerlaw" ,r-powerlaw)))
7897 (home-page "https://cran.r-project.org/web/packages/AbSim/")
7898 (synopsis "Time resolved simulations of antibody repertoires")
7900 "This package provides simulation methods for the evolution of antibody repertoires.
7901 The heavy and light chain variable region of both human and C57BL/6 mice can
7902 be simulated in a time-dependent fashion. Both single lineages using one set of
7903 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
7904 with an initial V-D-J recombination event, starting the first phylogenetic tree.
7905 Upon completion, the main loop of the algorithm begins, with each iteration
7906 representing one simulated time step. Various mutation events are possible at
7907 each time step, contributing to a diverse final repertoire.")
7908 (license license:gpl2)))
7910 (define-public r-quic
7917 (uri (cran-uri "QUIC" version))
7919 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
7920 (properties `((upstream-name . "QUIC")))
7921 (build-system r-build-system)
7922 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
7923 (synopsis "Regularized sparse inverse covariance matrix estimation")
7925 "This package implements the regularized Gaussian maximum likelihood
7926 estimation of the inverse of a covariance matrix. It uses Newton's method and
7927 coordinate descent to solve the regularized inverse covariance matrix
7928 estimation problem.")
7929 ;; The project home page states that the release is under GPLv3 or later.
7930 ;; The CRAN page only says GPL-3.
7931 (license license:gpl3+)))
7933 (define-public r-abundant
7940 (uri (cran-uri "abundant" version))
7942 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
7943 (build-system r-build-system)
7945 `(("r-quic" ,r-quic)))
7946 (home-page "https://cran.r-project.org/web/packages/abundant/")
7947 (synopsis "Abundant regression and high-dimensional principal fitted components")
7949 "This package provides tools to fit and predict with the high-dimensional
7950 principal fitted components model. This model is described by Cook, Forzani,
7951 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
7952 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
7953 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
7954 (license license:gpl2+)))
7956 (define-public r-ac3net
7963 (uri (cran-uri "Ac3net" version))
7965 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
7966 (properties `((upstream-name . "Ac3net")))
7967 (build-system r-build-system)
7969 `(("r-data-table" ,r-data-table)))
7970 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
7971 (synopsis "Inferring directional conservative causal core gene networks")
7972 (description "This package infers directional Conservative causal core
7973 (gene) networks (C3NET). This is a version of the algorithm C3NET with
7974 directional network.")
7975 (license license:gpl3+)))
7977 (define-public r-aca
7984 (uri (cran-uri "ACA" version))
7986 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
7987 (properties `((upstream-name . "ACA")))
7988 (build-system r-build-system)
7989 (home-page "https://cran.r-project.org/web/packages/ACA/")
7990 (synopsis "Abrupt change-point or aberration detection in point series")
7992 "This package offers an interactive function for the detection of breakpoints in
7994 ;; Any version of the GPL
7995 (license (list license:gpl2+ license:gpl3+))))
7997 (define-public r-acceptancesampling
7999 (name "r-acceptancesampling")
8004 (uri (cran-uri "AcceptanceSampling" version))
8006 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
8008 `((upstream-name . "AcceptanceSampling")))
8009 (build-system r-build-system)
8010 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
8011 (synopsis "Creation and evaluation of acceptance sampling plans")
8013 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
8014 acceptance sampling plans. Acceptance sampling is a methodology commonly used
8015 in quality control and improvement. International standards of acceptance
8016 sampling provide sampling plans for specific circumstances. The aim of this
8017 package is to provide an easy-to-use interface to visualize single, double or
8018 multiple sampling plans. In addition, methods have been provided to enable the
8019 user to assess sampling plans against pre-specified levels of performance, as
8020 measured by the probability of acceptance for a given level of quality in the
8022 (license license:gpl3+)))
8024 (define-public r-acclma
8031 (uri (cran-uri "ACCLMA" version))
8033 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
8034 (properties `((upstream-name . "ACCLMA")))
8035 (build-system r-build-system)
8036 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
8037 (synopsis "ACC & LMA graph plotting")
8039 "This package contains a function that imports data from a @acronym{CSV,
8040 Comma-Separated Values} file, or uses manually entered data from the format (x,
8041 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
8042 Curve} vs @acronym{LOI, Line of Independence} graph and
8043 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
8044 function is @code{plotLMA} (source file, header) that takes a data set and plots the
8045 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
8046 string) was passed, a manual data entry window is opened. The header parameter
8047 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
8048 a header row or not. The dataset should contain only one independent variable
8049 (x) and one dependent variable (y) and can contain a weight for each
8051 (license license:gpl2)))
8053 (define-public r-aspi
8060 (uri (cran-uri "aspi" version))
8062 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
8063 (build-system r-build-system)
8065 "https://cran.r-project.org/web/packages/aspi/")
8067 "Analysis of symmetry of parasitic infections")
8069 "This package provides tools for the analysis and visualization of bilateral
8070 asymmetry in parasitic infections.")
8071 (license license:gpl3+)))
8073 (define-public r-sandwich
8080 (uri (cran-uri "sandwich" version))
8083 "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv"))))
8084 (build-system r-build-system)
8086 `(("r-zoo" ,r-zoo)))
8087 (home-page "https://cran.r-project.org/web/packages/sandwich/")
8088 (synopsis "Robust Covariance Matrix Estimators")
8090 "This package provides model-robust standard error estimators for
8091 cross-sectional, time series, clustered, panel, and longitudinal data.")
8092 ;; Either version of the license.
8093 (license (list license:gpl2 license:gpl3))))
8095 (define-public r-th-data
8102 (uri (cran-uri "TH.data" version))
8105 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
8106 (properties `((upstream-name . "TH.data")))
8107 (build-system r-build-system)
8109 `(("r-mass" ,r-mass)
8110 ("r-survival" ,r-survival)))
8111 (home-page "https://cran.r-project.org/web/packages/TH.data/")
8112 (synopsis "Shared data sets")
8114 "This package contains supporting data sets that are used in other
8115 packages maintained by Torsten Hothorn.")
8116 (license license:gpl3)))
8118 (define-public r-multcomp
8125 (uri (cran-uri "multcomp" version))
8128 "1kzmdn9jmz5bmhf3wsfr12ljbasmwsgcsfdia52k0bi6q0swdg19"))))
8129 (build-system r-build-system)
8131 `(("r-codetools" ,r-codetools)
8132 ("r-mvtnorm" ,r-mvtnorm)
8133 ("r-sandwich" ,r-sandwich)
8134 ("r-survival" ,r-survival)
8135 ("r-th-data" ,r-th-data)))
8136 (home-page "https://cran.r-project.org/web/packages/multcomp/")
8137 (synopsis "Simultaneous inference in general parametric models")
8139 "Simultaneous tests and confidence intervals for general linear
8140 hypotheses in parametric models, including linear, generalized linear, linear
8141 mixed effects, and survival models. The package includes demos reproducing
8142 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
8143 Hothorn, Westfall, 2010, CRC Press).")
8144 (license license:gpl2)))
8146 (define-public r-emmeans
8149 (version "1.4.3.01")
8153 (uri (cran-uri "emmeans" version))
8156 "16v5j31516nbqnj2zhgqvyp5yxd4zcs5zi0aspa5plr2qikvrkmg"))))
8157 (build-system r-build-system)
8159 `(("r-estimability" ,r-estimability)
8160 ("r-mvtnorm" ,r-mvtnorm)
8161 ("r-numderiv" ,r-numderiv)
8163 ("r-xtable" ,r-xtable)))
8164 (home-page "https://github.com/rvlenth/emmeans")
8165 (synopsis "Estimated marginal means, aka least-squares means")
8167 "This package provides tools to obtain @dfn{estimated marginal
8168 means} (EMMs) for many linear, generalized linear, and mixed models. It can
8169 be used to compute contrasts or linear functions of EMMs, trends, and
8170 comparisons of slopes.")
8171 ;; Either version of the license.
8172 (license (list license:gpl2 license:gpl3))))
8174 (define-public r-pwr
8181 (uri (cran-uri "pwr" version))
8184 "0r5g781lr677vp3zyhgmi7r68c87l8gd05l1s3ffnxgn5wf043sm"))))
8185 (build-system r-build-system)
8187 `(("r-knitr" ,r-knitr)))
8188 (home-page "https://github.com/heliosdrm/pwr")
8189 (synopsis "Basic functions for power analysis")
8191 "This package provides power analysis functions along the lines of
8193 (license license:gpl3+)))
8195 (define-public r-libcoin
8202 (uri (cran-uri "libcoin" version))
8205 "1cm9x1dlg9f7fh7n5nw3x4a7rl88c7ylrlc8x3rx4mq5w1j42x0a"))))
8206 (build-system r-build-system)
8207 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8208 (home-page "https://cran.r-project.org/web/packages/libcoin")
8209 (synopsis "Linear test statistics for permutation inference")
8211 "This package provides basic infrastructure for linear test statistics
8212 and permutation inference in the framework of Strasser and Weber (1999).")
8213 (license license:gpl2)))
8215 (define-public r-coin
8222 (uri (cran-uri "coin" version))
8225 "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx"))))
8226 (build-system r-build-system)
8228 `(("r-libcoin" ,r-libcoin)
8229 ("r-matrixstats" ,r-matrixstats)
8230 ("r-modeltools" ,r-modeltools)
8231 ("r-multcomp" ,r-multcomp)
8232 ("r-mvtnorm" ,r-mvtnorm)
8233 ("r-survival" ,r-survival)))
8234 (home-page "http://coin.r-forge.r-project.org")
8235 (synopsis "Conditional inference procedures in a permutation test framework")
8237 "This package provides conditional inference procedures for the general
8238 independence problem including two-sample, K-sample (non-parametric ANOVA),
8239 correlation, censored, ordered and multivariate problems.")
8240 (license license:gpl2)))
8242 (define-public r-bayesplot
8244 (name "r-bayesplot")
8249 (uri (cran-uri "bayesplot" version))
8252 "0sq0ajnm96hmlqf1cv5n2gshh3qdij4n1zbm7qrniz2q6b5aj342"))))
8253 (build-system r-build-system)
8255 `(("pandoc" ,ghc-pandoc)
8256 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
8258 `(("r-dplyr" ,r-dplyr)
8259 ("r-ggplot2" ,r-ggplot2)
8260 ("r-ggridges" ,r-ggridges)
8262 ("r-reshape2" ,r-reshape2)
8263 ("r-rlang" ,r-rlang)
8264 ("r-tibble" ,r-tibble)
8265 ("r-tidyselect" ,r-tidyselect)))
8266 (home-page "http://mc-stan.org/bayesplot")
8267 (synopsis "Plotting for Bayesian models")
8269 "This package provides plotting functions for posterior analysis, model
8270 checking, and MCMC diagnostics. The package is designed not only to provide
8271 convenient functionality for users, but also a common set of functions that
8272 can be easily used by developers working on a variety of R packages for
8273 Bayesian modeling.")
8274 (license license:gpl3+)))
8276 (define-public r-tmb
8283 (uri (cran-uri "TMB" version))
8286 "1r2d8c5iazihba42sn33yarv0dcfiy989sx64zcf14zr8k6cgjzs"))))
8287 (properties `((upstream-name . "TMB")))
8288 (build-system r-build-system)
8290 `(("r-matrix" ,r-matrix)
8291 ("r-rcppeigen" ,r-rcppeigen)))
8292 (home-page "http://tmb-project.org")
8293 (synopsis "Template model builder: a general random effect tool")
8295 "With this tool, a user should be able to quickly implement complex
8296 random effect models through simple C++ templates. The package combines
8297 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
8298 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
8299 from R) to obtain an efficient implementation of the applied Laplace
8300 approximation with exact derivatives. Key features are: Automatic sparseness
8301 detection, parallelism through BLAS and parallel user templates.")
8302 (license license:gpl2)))
8304 (define-public r-sjstats
8311 (uri (cran-uri "sjstats" version))
8313 (base32 "029rl05p88bp01favz300m980r1khcx2a2kn88yqbnbgkjjgqqc6"))))
8314 (build-system r-build-system)
8316 `(("r-bayestestr" ,r-bayestestr)
8317 ("r-broom" ,r-broom)
8318 ("r-dplyr" ,r-dplyr)
8319 ("r-emmeans" ,r-emmeans)
8320 ("r-insight" ,r-insight)
8322 ("r-magrittr" ,r-magrittr)
8324 ("r-modelr" ,r-modelr)
8325 ("r-parameters" ,r-parameters)
8326 ("r-performance" ,r-performance)
8327 ("r-purrr" ,r-purrr)
8328 ("r-rlang" ,r-rlang)
8329 ("r-sjlabelled" ,r-sjlabelled)
8330 ("r-sjmisc" ,r-sjmisc)
8331 ("r-tidyr" ,r-tidyr)))
8332 (home-page "https://github.com/strengejacke/sjstats")
8333 (synopsis "Functions for common statistical computations")
8335 "This package provides a collection of convenient functions for common
8336 statistical computations, which are not directly provided by R's @code{base}
8337 or @code{stats} packages. This package aims at providing, first, shortcuts
8338 for statistical measures, which otherwise could only be calculated with
8339 additional effort. Second, these shortcut functions are generic, and can be
8340 applied not only to vectors, but also to other objects as well. The focus of
8341 most functions lies on summary statistics or fit measures for regression
8342 models, including generalized linear models, mixed effects models and Bayesian
8344 (license license:gpl3)))
8346 (define-public r-glmmtmb
8353 (uri (cran-uri "glmmTMB" version))
8356 "035hkywa37bz555fv6znxd4hfcs5w884365wfnwk4jx5vann4vvb"))))
8357 (properties `((upstream-name . "glmmTMB")))
8358 (build-system r-build-system)
8360 `(("r-lme4" ,r-lme4)
8361 ("r-matrix" ,r-matrix)
8363 ("r-rcppeigen" ,r-rcppeigen)
8366 `(("r-knitr" ,r-knitr))) ; for vignettes
8367 (home-page "https://github.com/glmmTMB")
8368 (synopsis "Generalized linear mixed models")
8370 "Fit linear and generalized linear mixed models with various extensions,
8371 including zero-inflation. The models are fitted using maximum likelihood
8372 estimation via the Template Model Builder. Random effects are assumed to be
8373 Gaussian on the scale of the linear predictor and are integrated out using the
8374 Laplace approximation. Gradients are calculated using automatic
8376 (license license:agpl3+)))
8378 (define-public r-bayestestr
8380 (name "r-bayestestr")
8385 (uri (cran-uri "bayestestR" version))
8388 "1d3f50rzjzgzclwd6j887dssyhv7hdq7pik9nnlr3w775v3f69zc"))))
8389 (properties `((upstream-name . "bayestestR")))
8390 (build-system r-build-system)
8392 `(("r-insight" ,r-insight)))
8393 (home-page "https://github.com/easystats/bayestestR")
8394 (synopsis "Describe Bayesian models and posterior distributions")
8396 "This package provides utilities to understand and describe posterior
8397 distributions and Bayesian models. It includes point-estimates such as
8398 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
8399 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
8400 ROPE percentage and pd).")
8401 (license license:gpl3)))
8403 (define-public r-performance
8405 (name "r-performance")
8410 (uri (cran-uri "performance" version))
8413 "0lxpmp9smn5r3xvfik36nr608wcpmmximjh0v2sckyvjf7hnb4s0"))))
8414 (build-system r-build-system)
8416 `(("r-bayestestr" ,r-bayestestr)
8417 ("r-insight" ,r-insight)))
8418 (home-page "https://easystats.github.io/performance/")
8419 (synopsis "Assessment of regression models performance")
8421 "This package provides utilities for computing measures to assess model
8422 quality, which are not directly provided by R's @code{base} or @code{stats}
8423 packages. These include e.g. measures like r-squared, intraclass correlation
8424 coefficient, root mean squared error or functions to check models for
8425 overdispersion, singularity or zero-inflation and more. Functions apply to a
8426 large variety of regression models, including generalized linear models, mixed
8427 effects models and Bayesian models.")
8428 (license license:gpl3)))
8430 (define-public r-ggeffects
8432 (name "r-ggeffects")
8437 (uri (cran-uri "ggeffects" version))
8440 "0ryfbaav0k874kbwmhbiv7fan93dmkpaimm1iw5kryjhhs3917lb"))))
8441 (build-system r-build-system)
8443 `(("r-dplyr" ,r-dplyr)
8444 ("r-insight" ,r-insight)
8445 ("r-magrittr" ,r-magrittr)
8447 ("r-purrr" ,r-purrr)
8448 ("r-rlang" ,r-rlang)
8449 ("r-sjlabelled" ,r-sjlabelled)
8450 ("r-sjmisc" ,r-sjmisc)))
8451 (home-page "https://github.com/strengejacke/ggeffects")
8452 (synopsis "Create tidy data frames of marginal effects for ggplot")
8454 "This package provides tools to compute marginal effects from statistical
8455 models and return the result as tidy data frames. These data frames are ready
8456 to use with the @code{ggplot2} package. Marginal effects can be calculated
8457 for many different models. Interaction terms, splines and polynomial terms
8458 are also supported. The two main functions are @code{ggpredict()} and
8459 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
8460 results using @code{ggplot2}.")
8461 (license license:gpl3)))
8463 (define-public r-effectsize
8465 (name "r-effectsize")
8470 (uri (cran-uri "effectsize" version))
8473 "07vgmxdl75798hgdh90zysafjh97rmmj2wjjyr6xff4fbhi8rlkb"))))
8474 (properties `((upstream-name . "effectsize")))
8475 (build-system r-build-system)
8477 `(("r-bayestestr" ,r-bayestestr)
8478 ("r-insight" ,r-insight)
8479 ("r-parameters" ,r-parameters)))
8480 (home-page "https://github.com/easystats/effectsize")
8481 (synopsis "Indices of effect size and standardized parameters")
8483 "This package provides utilities to work with indices of effect size and
8484 standardized parameters for a wide variety of models, allowing computation and
8485 conversion of indices such as Cohen's d, r, odds, etc.")
8486 (license license:gpl3)))
8488 (define-public r-sjplot
8495 (uri (cran-uri "sjPlot" version))
8497 (base32 "0rmfc2pq80w0kxh6icljhqm31q580s0czvllsfxk6crmpyfgxkp7"))))
8498 (properties `((upstream-name . "sjPlot")))
8499 (build-system r-build-system)
8501 `(("r-bayestestr" ,r-bayestestr)
8502 ("r-dplyr" ,r-dplyr)
8503 ("r-effectsize" ,r-effectsize)
8504 ("r-forcats" ,r-forcats)
8505 ("r-ggeffects" ,r-ggeffects)
8506 ("r-ggplot2" ,r-ggplot2)
8507 ("r-ggrepel" ,r-ggrepel)
8508 ("r-glmmtmb" ,r-glmmtmb)
8509 ("r-insight" ,r-insight)
8510 ("r-knitr" ,r-knitr)
8512 ("r-magrittr" ,r-magrittr)
8514 ("r-modelr" ,r-modelr)
8515 ("r-parameters" ,r-parameters)
8516 ("r-performance" ,r-performance)
8517 ("r-psych" ,r-psych)
8518 ("r-purrr" ,r-purrr)
8519 ("r-rlang" ,r-rlang)
8520 ("r-scales" ,r-scales)
8521 ("r-sjlabelled" ,r-sjlabelled)
8522 ("r-sjmisc" ,r-sjmisc)
8523 ("r-sjstats" ,r-sjstats)
8524 ("r-tidyr" ,r-tidyr)))
8525 (home-page "https://strengejacke.github.io/sjPlot/")
8526 (synopsis "Data visualization for statistics in social science")
8528 "This package represents a collection of plotting and table output
8529 functions for data visualization. Results of various statistical
8530 analyses (that are commonly used in social sciences) can be visualized using
8531 this package, including simple and cross tabulated frequencies, histograms,
8532 box plots, (generalized) linear models, mixed effects models, principal
8533 component analysis and correlation matrices, cluster analyses, scatter plots,
8534 stacked scales, effects plots of regression models (including interaction
8535 terms) and much more. This package supports labelled data.")
8536 (license license:gpl3)))
8538 (define-public r-ini
8545 (uri (cran-uri "ini" version))
8548 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
8549 (build-system r-build-system)
8550 (home-page "https://github.com/dvdscripter/ini")
8551 (synopsis "Read and write configuration files")
8553 "This package provides tools to parse simple @code{.ini} configuration
8554 files to an structured list. Users can manipulate this resulting list with
8555 @code{lapply()} functions. This same structured list can be used to write
8556 back to file after modifications.")
8557 (license license:gpl3)))
8566 (uri (cran-uri "gh" version))
8569 "1llinfajb0g7006jd2w1hpskxpmkjhnqarcjb71r1qvsccb2ph7k"))))
8570 (build-system r-build-system)
8572 `(("r-httr" ,r-httr)
8574 ("r-jsonlite" ,r-jsonlite)))
8575 (home-page "https://github.com/r-lib/gh#readme")
8576 (synopsis "Access the GitHub API via R")
8578 "This package provides a minimal R client to access the GitHub API.")
8579 (license license:expat)))
8588 (uri (cran-uri "fs" version))
8591 "1g26rgx13dzigp2vrlld6h28q33lwbax97zvwdrq2pc3iz54v4yn"))))
8592 (build-system r-build-system)
8594 `(("r-rcpp" ,r-rcpp)))
8596 `(("pkg-config" ,pkg-config)))
8597 (home-page "http://fs.r-lib.org")
8598 (synopsis "Cross-platform file system operations based on libuv")
8600 "This package provides a cross-platform interface to file system
8601 operations, built on top of the libuv C library.")
8602 (license license:gpl3)))
8604 (define-public r-clisymbols
8606 (name "r-clisymbols")
8611 (uri (cran-uri "clisymbols" version))
8614 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
8615 (build-system r-build-system)
8616 (home-page "https://github.com/gaborcsardi/clisymbols")
8617 (synopsis "Unicode symbols at the R prompt")
8619 "This package provides a small subset of Unicode symbols, that are useful
8620 when building command line applications. They fall back to alternatives on
8621 terminals that do not support Unicode.")
8622 (license license:expat)))
8624 (define-public r-usethis
8631 (uri (cran-uri "usethis" version))
8634 "07an5wbikilg7cb3q6x5aykw8dfqnjrc3wpfb7gjmy0d9fh20fcy"))))
8635 (build-system r-build-system)
8637 `(("r-clipr" ,r-clipr)
8638 ("r-clisymbols" ,r-clisymbols)
8639 ("r-crayon" ,r-crayon)
8644 ("r-git2r" ,r-git2r)
8646 ("r-purrr" ,r-purrr)
8647 ("r-rlang" ,r-rlang)
8648 ("r-rprojroot" ,r-rprojroot)
8649 ("r-rstudioapi" ,r-rstudioapi)
8650 ("r-whisker" ,r-whisker)
8651 ("r-withr" ,r-withr)
8652 ("r-yaml" ,r-yaml)))
8653 (home-page "https://github.com/r-lib/usethis")
8654 (synopsis "Automate R package and project setup")
8656 "This package helps you to automate R package and project setup tasks
8657 that are otherwise performed manually. This includes setting up unit testing,
8658 test coverage, continuous integration, Git, GitHub integration, licenses,
8659 Rcpp, RStudio projects, and more.")
8660 (license license:gpl3)))
8662 (define-public r-sessioninfo
8664 (name "r-sessioninfo")
8669 (uri (cran-uri "sessioninfo" version))
8672 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
8673 (build-system r-build-system)
8676 ("r-withr" ,r-withr)))
8677 (home-page "https://github.com/r-lib/sessioninfo#readme")
8678 (synopsis "R session information")
8680 "This package provides tools to query and print information about the
8681 current R session. It is similar to @code{utils::sessionInfo()}, but includes
8682 more information about packages, and where they were installed from.")
8683 (license license:gpl2)))
8685 (define-public r-remotes
8692 (uri (cran-uri "remotes" version))
8695 "19v8dmnk9l4i9m64p7zgmj7y1vhnnwhi5kyn0k5d034zzkvchi49"))))
8696 (build-system r-build-system)
8697 (home-page "https://github.com/r-lib/remotes#readme")
8698 (synopsis "R package installation from remote repositories")
8700 "Download and install R packages stored in GitHub, BitBucket, or plain
8701 subversion or git repositories. This package is a lightweight replacement of
8702 the @code{install_*} functions in the @code{devtools} package. Indeed most of
8703 the code was copied over from @code{devtools}.")
8704 (license license:gpl2+)))
8706 (define-public r-xopen
8713 (uri (cran-uri "xopen" version))
8716 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
8717 (build-system r-build-system)
8719 `(("r-processx" ,r-processx)))
8720 (home-page "https://github.com/r-lib/xopen#readme")
8721 (synopsis "Open system files, URLs, anything")
8723 "This package provides a cross-platform solution to open files,
8724 directories or URLs with their associated programs.")
8725 (license license:expat)))
8727 (define-public r-rcmdcheck
8729 (name "r-rcmdcheck")
8734 (uri (cran-uri "rcmdcheck" version))
8737 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
8738 (build-system r-build-system)
8740 `(("r-callr" ,r-callr)
8742 ("r-crayon" ,r-crayon)
8744 ("r-digest" ,r-digest)
8745 ("r-pkgbuild" ,r-pkgbuild)
8746 ("r-prettyunits" ,r-prettyunits)
8748 ("r-rprojroot" ,r-rprojroot)
8749 ("r-sessioninfo" ,r-sessioninfo)
8750 ("r-withr" ,r-withr)
8751 ("r-xopen" ,r-xopen)))
8752 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
8753 (synopsis "Run R CMD check from R and capture results")
8755 "Run @code{R CMD check} from R programmatically, and capture the results
8756 of the individual checks.")
8757 (license license:expat)))
8759 (define-public r-rapportools
8761 (name "r-rapportools")
8766 (uri (cran-uri "rapportools" version))
8769 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
8770 (build-system r-build-system)
8772 `(("r-pander" ,r-pander)
8774 ("r-reshape" ,r-reshape)))
8775 (home-page "https://cran.r-project.org/web/packages/rapportools/")
8776 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
8778 "This package provides helper functions that act as wrappers to more
8779 advanced statistical methods with the advantage of having sane defaults for
8781 (license license:agpl3+)))
8783 (define-public r-pander
8790 (uri (cran-uri "pander" version))
8793 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
8794 (build-system r-build-system)
8796 `(("r-digest" ,r-digest)
8797 ("r-rcpp" ,r-rcpp)))
8798 (home-page "https://rapporter.github.io/pander")
8799 (synopsis "Render R objects into Pandoc's markdown")
8801 "The main aim of the pander R package is to provide a minimal and easy
8802 tool for rendering R objects into Pandoc's markdown. The package is also
8803 capable of exporting/converting complex Pandoc documents (reports) in various
8805 ;; This package is licensed under either the AGPLv3+ or the very rarely
8807 (license license:agpl3+)))
8809 (define-public r-summarytools
8811 (name "r-summarytools")
8816 (uri (cran-uri "summarytools" version))
8819 "1n695baz56mg4f13xjjadfq0xalw5xsn6xicil0yap5hgi8fsr3a"))))
8820 (build-system r-build-system)
8822 `(("r-checkmate" ,r-checkmate)
8823 ("r-dplyr" ,r-dplyr)
8824 ("r-htmltools" ,r-htmltools)
8825 ("r-lubridate" ,r-lubridate)
8826 ("r-magick" ,r-magick)
8827 ("r-matrixstats" ,r-matrixstats)
8828 ("r-pander" ,r-pander)
8830 ("r-rapportools" ,r-rapportools)
8831 ("r-rcurl" ,r-rcurl)
8832 ("r-tibble" ,r-tibble)
8833 ("r-tidyr" ,r-tidyr)))
8834 (home-page "https://github.com/dcomtois/summarytools")
8835 (synopsis "Tools to quickly and neatly summarize data")
8837 "This package provides tools for data frame summaries, cross-tabulations,
8838 weight-enabled frequency tables and common univariate statistics in concise
8839 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
8840 good point-of-entry for exploring data, both for experienced and new R
8842 (license license:gpl2)))
8844 (define-public r-lsei
8851 (uri (cran-uri "lsei" version))
8854 "1xl06fb3is744pxlh42wx5hn1h0ab1k31wnmsmh0524kxzcyp0a7"))))
8855 (build-system r-build-system)
8857 `(("gfortran" ,gfortran)))
8858 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
8859 (synopsis "Solve regression problems under equality/inequality constraints")
8861 "It contains functions that solve least squares linear regression
8862 problems under linear equality/inequality constraints. Functions for solving
8863 quadratic programming problems are also available, which transform such
8864 problems into least squares ones first.")
8865 (license license:gpl2+)))
8867 (define-public r-npsurv
8874 (uri (cran-uri "npsurv" version))
8877 "1wq4c9yfha5azjhrn40iiqkshmvh611sa90jp3lh82n4bl9zfk20"))))
8878 (build-system r-build-system)
8880 `(("r-lsei" ,r-lsei)))
8881 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
8882 (synopsis "Nonparametric survival analysis")
8884 "This package contains functions for non-parametric survival analysis of
8885 exact and interval-censored observations.")
8886 (license license:gpl2+)))
8888 (define-public r-clusteval
8890 (name "r-clusteval")
8895 (uri (cran-uri "clusteval" version))
8898 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
8899 (build-system r-build-system)
8901 `(("r-mvtnorm" ,r-mvtnorm)
8902 ("r-rcpp" ,r-rcpp)))
8903 (home-page "https://cran.r-project.org/web/packages/clusteval/")
8904 (synopsis "Evaluation of clustering algorithms")
8906 "This R package provides a suite of tools to evaluate clustering
8907 algorithms, clusterings, and individual clusters.")
8908 (license license:expat)))
8910 (define-public r-tweedie
8917 (uri (cran-uri "tweedie" version))
8920 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
8921 (build-system r-build-system)
8922 (native-inputs `(("gfortran" ,gfortran)))
8923 (home-page "https://cran.r-project.org/web/packages/tweedie/")
8924 (synopsis "Evaluation of Tweedie exponential family models")
8926 "Maximum likelihood computations for Tweedie families, including the
8927 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
8928 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
8929 and related methods.")
8930 (license license:gpl2+)))
8932 (define-public r-rcppgsl
8939 (uri (cran-uri "RcppGSL" version))
8941 (base32 "0cnw2k7cfqrm79r6j283aybflxig80x4n4rjkfp2317wf10mrsa5"))))
8942 (properties `((upstream-name . "RcppGSL")))
8943 (build-system r-build-system)
8945 `(("r-rcpp" ,r-rcpp)
8948 `(("r-knitr" ,r-knitr))) ; for vignettes
8949 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
8950 (synopsis "Rcpp integration for GSL vectors and matrices")
8952 "The GNU Scientific Library (or GSL) is a collection of numerical
8953 routines for scientific computing. It is particularly useful for C and C++
8954 programs as it provides a standard C interface to a wide range of mathematical
8955 routines. There are over 1000 functions in total with an extensive test
8956 suite. The RcppGSL package provides an easy-to-use interface between GSL data
8957 structures and R using concepts from Rcpp which is itself a package that eases
8958 the interfaces between R and C++.")
8959 (license license:gpl2+)))
8961 (define-public r-mvabund
8968 (uri (cran-uri "mvabund" version))
8971 "0la935gsiryfc0zixxr1dqj0av271x96pqxbi3bp6dksbw5gm68k"))))
8972 (build-system r-build-system)
8974 `(("r-mass" ,r-mass)
8976 ("r-rcppgsl" ,r-rcppgsl)
8977 ("r-statmod" ,r-statmod)
8978 ("r-tweedie" ,r-tweedie)))
8979 (home-page "https://cran.r-project.org/web/packages/mvabund/")
8980 (synopsis "Statistical methods for analysing multivariate abundance data")
8982 "This package provides a set of tools for displaying, modeling and
8983 analysing multivariate abundance data in community ecology.")
8984 (license license:lgpl2.1+)))
8986 (define-public r-afex
8993 (uri (cran-uri "afex" version))
8996 "12n020y7rjm7402940gkqxa5j901p093f381i23p66fa3fyrshkf"))))
8997 (build-system r-build-system)
9001 ("r-lmertest" ,r-lmertest)
9002 ("r-pbkrtest" ,r-pbkrtest)
9003 ("r-reshape2" ,r-reshape2)))
9004 (home-page "https://afex.singmann.science/")
9005 (synopsis "Analysis of factorial experiments")
9007 "This package provides convenience functions for analyzing factorial
9008 experiments using ANOVA or mixed models.")
9009 (license license:gpl2+)))
9011 (define-public r-lmertest
9018 (uri (cran-uri "lmerTest" version))
9021 "1nkz8cmxa5yb8q4i65bmhnn5pd4bhwcyjplyscynb24z3f64xp9b"))))
9022 (properties `((upstream-name . "lmerTest")))
9023 (build-system r-build-system)
9025 `(("r-ggplot2" ,r-ggplot2)
9028 ("r-numderiv" ,r-numderiv)))
9029 (home-page "https://github.com/runehaubo/lmerTestR")
9030 (synopsis "Tests in linear mixed effects models")
9032 "This package provides p-values in type I, II or III anova and summary
9033 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
9034 method. A Kenward-Roger method is also available via the @code{pbkrtest}
9035 package. Model selection methods include step, drop1 and anova-like tables
9036 for random effects (ranova). Methods for Least-Square means (LS-means) and
9037 tests of linear contrasts of fixed effects are also available.")
9038 (license license:gpl2+)))
9040 (define-public r-r2glmm
9047 (uri (cran-uri "r2glmm" version))
9050 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
9051 (build-system r-build-system)
9053 `(("r-afex" ,r-afex)
9054 ("r-data-table" ,r-data-table)
9055 ("r-dplyr" ,r-dplyr)
9056 ("r-ggplot2" ,r-ggplot2)
9057 ("r-gridextra" ,r-gridextra)
9058 ("r-lmertest" ,r-lmertest)
9060 ("r-matrix" ,r-matrix)
9062 ("r-pbkrtest" ,r-pbkrtest)))
9063 (home-page "https://github.com/bcjaeger/r2glmm")
9064 (synopsis "Compute R squared for mixed (multilevel) models")
9066 "This package computes model and semi partial R squared with confidence
9067 limits for the linear and generalized linear mixed model (LMM and GLMM). The
9068 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
9069 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
9071 (license license:gpl2)))
9073 (define-public r-weights
9080 (uri (cran-uri "weights" version))
9083 "0186bfpkhxngrshac6bpg37alp6slwhwd43inrm8hqg0vhpfgc4c"))))
9084 (build-system r-build-system)
9086 `(("r-gdata" ,r-gdata)
9087 ("r-hmisc" ,r-hmisc)
9088 ("r-mice" ,r-mice)))
9090 "https://cran.r-project.org/web/packages/weights/")
9091 (synopsis "Weighting and weighted statistics")
9092 (description "This package Provides a variety of functions for producing
9093 simple weighted statistics, such as weighted Pearson's correlations, partial
9094 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
9095 includes some software for quickly recoding survey data and plotting point
9096 estimates from interaction terms in regressions (and multiply imputed
9097 regressions). NOTE: Weighted partial correlation calculations pulled to
9099 (license license:gpl2+)))
9101 (define-public r-rcppannoy
9103 (name "r-rcppannoy")
9108 (uri (cran-uri "RcppAnnoy" version))
9111 "1wiigx5g5788j6lyc3f6bs1rsvc4alyc3052g35hxl1giinxmhn4"))))
9112 (properties `((upstream-name . "RcppAnnoy")))
9113 (build-system r-build-system)
9115 `(("r-rcpp" ,r-rcpp)))
9117 `(("r-knitr" ,r-knitr))) ; for vignettes
9118 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
9119 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
9121 "Annoy is a small C++ library for Approximate Nearest Neighbors written
9122 for efficient memory usage as well an ability to load from and save to disk.
9123 This package provides an R interface.")
9124 ;; Annoy is released under ASL 2.0, but this wrapper is released under
9126 (license (list license:gpl2+ license:asl2.0))))
9128 (define-public r-rcpphnsw
9135 (uri (cran-uri "RcppHNSW" version))
9138 "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv"))))
9139 (properties `((upstream-name . "RcppHNSW")))
9140 (build-system r-build-system)
9141 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9142 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
9143 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
9145 "Hnswlib is a C++ library for approximate nearest neighbors. This
9146 package provides a minimal R interface by relying on the Rcpp package.")
9147 ;; hnswlib is released under Version 2.0 of the Apache License.
9148 (license (list license:gpl3 license:asl2.0))))
9150 (define-public r-rcppparallel
9152 (name "r-rcppparallel")
9157 (uri (cran-uri "RcppParallel" version))
9160 "0p13f2mywjr7gmskf8ri4y8p5yr1bvr4xrpw2w11vdvafwz1vcia"))))
9161 (properties `((upstream-name . "RcppParallel")))
9162 (build-system r-build-system)
9163 (home-page "http://rcppcore.github.io/RcppParallel")
9164 (synopsis "Parallel programming tools for Rcpp")
9166 "This package provides high level functions for parallel programming with
9167 Rcpp. For example, the @code{parallelFor()} function can be used to convert
9168 the work of a standard serial @code{for} loop into a parallel one and the
9169 @code{parallelReduce()} function can be used for accumulating aggregates or
9171 (license license:gpl2)))
9173 (define-public r-ncdf4
9180 (uri (cran-uri "ncdf4" version))
9183 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
9184 (build-system r-build-system)
9186 `(("netcdf" ,netcdf)
9188 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
9189 (synopsis "R interface to Unidata netCDF format data files")
9191 "This package provides a high-level R interface to data files written
9192 using Unidata's netCDF library (version 4 or earlier), which are binary data
9193 files that are portable across platforms and include metadata information in
9194 addition to the data sets. Using this package, netCDF files can be opened and
9195 data sets read in easily. It is also easy to create new netCDF dimensions,
9196 variables, and files, in either version 3 or 4 format, and manipulate existing
9198 (license license:gpl3+)))
9200 (define-public r-biocmanager
9202 (name "r-biocmanager")
9207 (uri (cran-uri "BiocManager" version))
9209 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
9210 (properties `((upstream-name . "BiocManager")))
9211 (build-system r-build-system)
9212 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
9213 (synopsis "Access the Bioconductor project package repository")
9215 "This package provides a convenient tool to install and update
9216 Bioconductor packages.")
9217 (license license:artistic2.0)))
9219 (define-public r-rgl
9222 (version "0.100.30")
9226 (uri (cran-uri "rgl" version))
9229 "0rzqzskcwf2ah4yr62x5rjwf7yh90d43h39gk7jmfc5lc08zaxc5"))))
9230 (build-system r-build-system)
9232 `(("pkg-config" ,pkg-config)))
9234 `(("freetype" ,freetype)
9238 ("ghc-pandoc" ,ghc-pandoc)
9241 `(("r-crosstalk" ,r-crosstalk)
9242 ("r-htmltools" ,r-htmltools)
9243 ("r-htmlwidgets" ,r-htmlwidgets)
9244 ("r-jsonlite" ,r-jsonlite)
9245 ("r-knitr" ,r-knitr)
9246 ("r-magrittr" ,r-magrittr)
9247 ("r-manipulatewidget" ,r-manipulatewidget)
9248 ("r-shiny" ,r-shiny)))
9249 (home-page "https://r-forge.r-project.org/projects/rgl/")
9250 (synopsis "3D visualization using OpenGL")
9252 "This package provides medium to high level functions for 3D interactive graphics,
9253 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
9254 as functions for constructing representations of geometric
9255 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
9256 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
9257 image formats, including PNG, Postscript, SVG, PGF.")
9258 ;; Any version of the GPL.
9259 (license (list license:gpl2+ license:gpl3+))))
9261 (define-public r-multicool
9263 (name "r-multicool")
9268 (uri (cran-uri "multicool" version))
9271 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
9272 (build-system r-build-system)
9273 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9274 (home-page "https://cran.r-project.org/web/packages/multicool/")
9275 (synopsis "Permutations of multisets in cool-lex order")
9277 "This package provides a set of tools to permute multisets without loops
9278 or hash tables and to generate integer partitions. Cool-lex order is similar
9279 to colexicographical order.")
9280 (license license:gpl2)))
9282 (define-public r-misc3d
9289 (uri (cran-uri "misc3d" version))
9292 "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
9293 (build-system r-build-system)
9294 (home-page "https://cran.r-project.org/web/packages/misc3d/")
9295 (synopsis "Miscellaneous 3D Plots")
9297 "This package provides a collection of miscellaneous 3d plots, including
9299 ;; Any version of the GPL.
9300 (license (list license:gpl2+ license:gpl3+))))
9309 (uri (cran-uri "ks" version))
9311 (base32 "0hcccjfqnzdxkmnfzq8c5a7yhc138azwyl7rp29d1vl1jawwrwfq"))))
9312 (build-system r-build-system)
9315 ("r-kernlab" ,r-kernlab)
9316 ("r-kernsmooth" ,r-kernsmooth)
9317 ("r-matrix" ,r-matrix)
9318 ("r-mclust" ,r-mclust)
9320 ("r-multicool" ,r-multicool)
9321 ("r-mvtnorm" ,r-mvtnorm)))
9322 (home-page "http://www.mvstat.net/tduong/")
9323 (synopsis "Kernel smoothing")
9325 "This package provides kernel smoothers for univariate and multivariate
9326 data, including density functions, density derivatives, cumulative
9327 distributions, modal clustering, discriminant analysis, and two-sample
9328 hypothesis testing.")
9329 ;; Either version of the GPL.
9330 (license (list license:gpl2 license:gpl3))))
9332 (define-public r-feature
9339 (uri (cran-uri "feature" version))
9342 "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
9343 (build-system r-build-system)
9346 ("r-misc3d" ,r-misc3d)
9348 (home-page "http://www.mvstat.net/tduong/")
9349 (synopsis "Inferential feature significance for kernel density estimation")
9351 "The feature package contains functions to display and compute kernel
9352 density estimates, significant gradient and significant curvature regions.
9353 Significant gradient and/or curvature regions often correspond to significant
9354 features (e.g. local modes).")
9355 ;; Either version of the GPL.
9356 (license (list license:gpl2 license:gpl3))))
9358 (define-public r-arm
9365 (uri (cran-uri "arm" version))
9368 "0vvp90jygajd6ydky57z66wqjq9msfbl88irj5jbsray574mh4bg"))))
9369 (build-system r-build-system)
9371 `(("r-abind" ,r-abind)
9375 ("r-matrix" ,r-matrix)
9376 ("r-nlme" ,r-nlme)))
9377 (home-page "https://cran.r-project.org/web/packages/arm/")
9378 (synopsis "Data analysis using regression and multilevel/hierarchical models")
9380 "This package provides functions to accompany A. Gelman and J. Hill,
9381 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
9382 University Press, 2007.")
9383 (license license:gpl3+)))
9385 (define-public r-circular
9392 (uri (cran-uri "circular" version))
9395 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
9396 (build-system r-build-system)
9398 `(("r-boot" ,r-boot)
9399 ("r-mvtnorm" ,r-mvtnorm)))
9401 `(("gfortran" ,gfortran)))
9402 (home-page "https://cran.r-project.org/web/packages/circular/")
9403 (synopsis "Circular statistics")
9405 "This package provides tools for circular statistics, from \"Topics in
9406 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
9408 (license license:gpl2+)))
9410 (define-public r-activity
9417 (uri (cran-uri "activity" version))
9420 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
9421 (build-system r-build-system)
9423 `(("r-circular" ,r-circular)
9424 ("r-insol" ,r-insol)
9425 ("r-pbapply" ,r-pbapply)))
9426 (home-page "https://cran.r-project.org/web/packages/activity/")
9427 (synopsis "Animal activity statistics")
9429 "This package provides functions to fit kernel density functions to
9430 animal activity time data; plot activity distributions; quantify overall
9431 levels of activity; statistically compare activity metrics through
9432 bootstrapping; and evaluate variation in linear variables with time (or other
9433 circular variables).")
9434 (license license:gpl3)))
9436 (define-public r-ouch
9443 (uri (cran-uri "ouch" version))
9446 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
9447 (build-system r-build-system)
9448 (propagated-inputs `(("r-subplex" ,r-subplex)))
9449 (home-page "http://kingaa.github.io/ouch/")
9450 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
9452 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
9453 for evolution along a phylogenetic tree.")
9454 (license license:gpl2+)))
9456 (define-public r-fmsb
9463 (uri (cran-uri "fmsb" version))
9466 "1n29bnyp20pvpk2lsa9fblsj5w7amp14snc74pk5w3yr5y6rj0s5"))))
9467 (build-system r-build-system)
9468 (home-page "http://minato.sip21c.org/msb/")
9469 (synopsis "Functions for medical statistics book with demographic data")
9471 "This package provides several utility functions for the book entitled
9472 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
9473 Japan, 2007) with Japanese demographic data and some demographic analysis
9474 related functions.")
9475 (license license:gpl2+)))
9477 (define-public r-stabledist
9479 (name "r-stabledist")
9484 (uri (cran-uri "stabledist" version))
9487 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
9488 (build-system r-build-system)
9489 (home-page "http://www.rmetrics.org")
9490 (synopsis "Stable distribution functions")
9492 "This package provides density, probability and quantile functions, and
9493 random number generation for (skew) stable distributions, using the
9494 parametrizations of Nolan.")
9495 (license license:gpl2+)))
9497 (define-public r-gsl
9504 (uri (cran-uri "gsl" version))
9507 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
9508 (build-system r-build-system)
9511 (home-page "https://cran.r-project.org/web/packages/gsl")
9512 (synopsis "Wrapper for the GNU Scientific Library")
9514 "This package provides an R wrapper for the special functions and quasi
9515 random number generators of the GNU Scientific Library.")
9516 (license license:gpl2+)))
9518 (define-public r-adgoftest
9520 (name "r-adgoftest")
9525 (uri (cran-uri "ADGofTest" version))
9528 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
9529 (properties `((upstream-name . "ADGofTest")))
9530 (build-system r-build-system)
9531 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
9532 (synopsis "Anderson-Darling GoF test")
9534 "This package provides an implementation of the Anderson-Darling GoF test
9535 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
9536 Anderson-Darling Distribution\".")
9537 ;; Any version of the GPL.
9538 (license license:gpl3+)))
9540 (define-public r-softimpute
9542 (name "r-softimpute")
9547 (uri (cran-uri "softImpute" version))
9550 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
9551 (properties `((upstream-name . "softImpute")))
9552 (build-system r-build-system)
9554 `(("r-matrix" ,r-matrix)))
9556 `(("gfortran" ,gfortran)))
9557 (home-page "https://cran.r-project.org/web/packages/softImpute")
9558 (synopsis "Matrix completion via iterative soft-thresholded SVD")
9560 "This package provides iterative methods for matrix completion that use
9561 nuclear-norm regularization. The package includes procedures for centering
9562 and scaling rows, columns or both, and for computing low-rank @dfn{single
9563 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
9565 (license license:gpl2)))
9567 (define-public r-fftwtools
9569 (name "r-fftwtools")
9574 (uri (cran-uri "fftwtools" version))
9577 "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6"))))
9578 (build-system r-build-system)
9579 (inputs `(("fftw" ,fftw)))
9580 (home-page "https://github.com/krahim/fftwtools")
9581 (synopsis "Wrapper for FFTW3")
9583 "This package provides a wrapper for several FFTW functions. It provides
9584 access to the two-dimensional FFT, the multivariate FFT, and the
9585 one-dimensional real to complex FFT using the FFTW3 library. The package
9586 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
9587 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
9588 The FFT functions have a parameter that allows them to not return the
9589 redundant complex conjugate when the input is real data.")
9590 (license license:gpl2+)))
9592 (define-public r-tiff
9599 (uri (cran-uri "tiff" version))
9602 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
9603 (build-system r-build-system)
9605 `(("libtiff" ,libtiff)
9606 ("libjpeg" ,libjpeg)
9608 (home-page "http://www.rforge.net/tiff/")
9609 (synopsis "Read and write TIFF images")
9611 "This package provides an easy and simple way to read, write and display
9612 bitmap images stored in the TIFF format. It can read and write both files and
9613 in-memory raw vectors.")
9614 ;; Either of these two license versions.
9615 (license (list license:gpl2 license:gpl3))))
9617 (define-public r-nlp
9624 (uri (cran-uri "NLP" version))
9627 "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w"))))
9628 (properties `((upstream-name . "NLP")))
9629 (build-system r-build-system)
9630 (home-page "https://cran.r-project.org/web/packages/NLP/")
9631 (synopsis "Natural language processing infrastructure")
9633 "This package provides basic classes and methods for Natural Language
9635 (license license:gpl3)))
9644 (uri (cran-uri "tm" version))
9647 "0spv43kjbpxq3rdxx8ysgrncjyc35ydiwk7gp8n4sig45iqyz59r"))))
9648 (properties `((upstream-name . "tm")))
9649 (build-system r-build-system)
9655 ("r-xml2" ,r-xml2)))
9656 (home-page "http://tm.r-forge.r-project.org/")
9657 (synopsis "Text mining package")
9659 "This package provides a framework for text mining applications within R.")
9660 (license license:gpl3)))
9662 (define-public r-waveslim
9669 (uri (cran-uri "waveslim" version))
9672 "0mky0nb4xxp8rybp87mxw2f1q6k400wpxv01zr4injv7ja6028xk"))))
9673 (build-system r-build-system)
9675 `(("gfortran" ,gfortran)))
9676 (home-page "http://waveslim.blogspot.com")
9677 (synopsis "Basic wavelet routines for signal processing")
9679 "This package provides basic wavelet routines for time series (1D),
9680 image (2D) and array (3D) analysis. The code provided here is based on
9681 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
9682 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
9683 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
9684 pairs (Selesnick 2001, 2002).")
9685 (license license:bsd-3)))
9687 (define-public r-wordcloud
9689 (name "r-wordcloud")
9694 (uri (cran-uri "wordcloud" version))
9697 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
9698 (build-system r-build-system)
9700 `(("r-rcolorbrewer" ,r-rcolorbrewer)
9702 ;; The "tm" package is only "suggested" according to CRAN, but the
9703 ;; wordcloud package cannot be loaded without it.
9705 (home-page "https://cran.r-project.org/web/packages/wordcloud")
9706 (synopsis "Word clouds")
9708 "This package provides functionality to create pretty word clouds,
9709 visualize differences and similarity between documents, and avoid
9710 over-plotting in scatter plots with text.")
9711 (license license:lgpl2.1)))
9713 (define-public r-colorramps
9715 (name "r-colorramps")
9720 (uri (cran-uri "colorRamps" version))
9723 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
9724 (properties `((upstream-name . "colorRamps")))
9725 (build-system r-build-system)
9726 (home-page "https://cran.r-project.org/web/packages/colorRamps")
9727 (synopsis "Build color tables")
9728 (description "This package provides features to build gradient color
9730 ;; Any version of the GPL
9731 (license license:gpl3+)))
9733 (define-public r-tidytree
9740 (uri (cran-uri "tidytree" version))
9742 (base32 "1sbfwcxf9v1lhpa0392b49b6qfjrq7nlqz2djqzk5aknj9j64zvy"))))
9743 (build-system r-build-system)
9746 ("r-dplyr" ,r-dplyr)
9747 ("r-lazyeval" ,r-lazyeval)
9748 ("r-magrittr" ,r-magrittr)
9749 ("r-rlang" ,r-rlang)
9750 ("r-tibble" ,r-tibble)))
9751 (home-page "https://github.com/GuangchuangYu/tidytree")
9752 (synopsis "Tidy tool for phylogenetic tree data manipulation")
9754 "Phylogenetic trees generally contain multiple components including nodes,
9755 edges, branches and associated data. This package provides an approach to
9756 convert tree objects to tidy data frames. It also provides tidy interfaces to
9757 manipulate tree data.")
9758 (license license:artistic2.0)))
9760 (define-public r-rvcheck
9767 (uri (cran-uri "rvcheck" version))
9769 (base32 "1a3xlzi4n1rqiapfa180aif7n7nws8pbg8k3nk7ccaczvmni38aw"))))
9770 (build-system r-build-system)
9772 `(("r-biocmanager" ,r-biocmanager)
9773 ("r-rlang" ,r-rlang)))
9774 (home-page "https://cran.r-project.org/web/packages/rvcheck")
9775 (synopsis "R package version check")
9777 "This package provides tools to check the latest release version of R and
9778 R packages (on CRAN, Bioconductor or Github).")
9779 (license license:artistic2.0)))
9781 (define-public r-docopt
9788 (uri (cran-uri "docopt" version))
9791 "06zknnd0c5s2y0hbddzdlr3m63ib783izpck6pgz7sjbab5pd068"))))
9792 (build-system r-build-system)
9793 (home-page "https://github.com/docopt/docopt.R")
9794 (synopsis "Command-line interface specification language")
9796 "This package enables you to define a command-line interface by just
9797 giving it a description in the specific format.")
9798 (license license:expat)))
9800 (define-public r-sparsesvd
9802 (name "r-sparsesvd")
9807 (uri (cran-uri "sparsesvd" version))
9810 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
9811 (build-system r-build-system)
9812 (propagated-inputs `(("r-matrix" ,r-matrix)))
9813 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
9814 (synopsis "Sparse truncated singular value decomposition")
9816 "This package provides a Wrapper around the SVDLIBC library
9817 for (truncated) singular value decomposition of a sparse matrix. Currently,
9818 only sparse real matrices in Matrix package format are supported.")
9819 ;; SVDLIBC is released under BSD-2. The R interface is released under
9821 (license (list license:bsd-3 license:bsd-2))))
9823 (define-public r-speedglm
9830 (uri (cran-uri "speedglm" version))
9833 "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz"))))
9834 (build-system r-build-system)
9836 `(("r-mass" ,r-mass)
9837 ("r-matrix" ,r-matrix)))
9838 (home-page "https://cran.r-project.org/web/packages/speedglm")
9839 (synopsis "Fit linear and generalized linear models to large data sets")
9841 "This package provides tools for fitting linear models and generalized
9842 linear models to large data sets by updating algorithms.")
9843 ;; Any version of the GPL
9844 (license license:gpl2+)))
9846 (define-public r-densityclust
9848 (name "r-densityclust")
9853 (uri (cran-uri "densityClust" version))
9856 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
9857 (properties `((upstream-name . "densityClust")))
9858 (build-system r-build-system)
9861 ("r-ggplot2" ,r-ggplot2)
9862 ("r-ggrepel" ,r-ggrepel)
9863 ("r-gridextra" ,r-gridextra)
9864 ("r-rcolorbrewer" ,r-rcolorbrewer)
9866 ("r-rtsne" ,r-rtsne)))
9867 (home-page "https://cran.r-project.org/web/packages/densityClust")
9868 (synopsis "Clustering by fast search and find of density peaks")
9870 "This package provides an improved implementation (based on k-nearest
9871 neighbors) of the density peak clustering algorithm, originally described by
9872 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
9873 large datasets (> 100,000 samples) very efficiently.")
9874 (license license:gpl2+)))
9876 (define-public r-combinat
9883 (uri (cran-uri "combinat" version))
9886 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
9887 (build-system r-build-system)
9888 (home-page "https://cran.r-project.org/web/packages/combinat")
9889 (synopsis "Combinatorics utilities")
9890 (description "This package provides assorted routines for combinatorics.")
9891 (license license:gpl2)))
9893 (define-public r-qlcmatrix
9895 (name "r-qlcmatrix")
9900 (uri (cran-uri "qlcMatrix" version))
9903 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
9904 (properties `((upstream-name . "qlcMatrix")))
9905 (build-system r-build-system)
9907 `(("r-docopt" ,r-docopt)
9908 ("r-matrix" ,r-matrix)
9910 ("r-sparsesvd" ,r-sparsesvd)))
9911 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
9912 (synopsis "Sparse matrix functions for quantitative language comparison")
9914 "This package provides an extension of the functionality of the Matrix
9915 package for using sparse matrices. Some of the functions are very general,
9916 while other are highly specific for the special data format used for
9917 @dfn{quantitative language comparison} (QLC).")
9918 (license license:gpl3)))
9920 (define-public r-ddrtree
9927 (uri (cran-uri "DDRTree" version))
9930 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
9931 (properties `((upstream-name . "DDRTree")))
9932 (build-system r-build-system)
9935 ("r-irlba" ,r-irlba)
9937 ("r-rcppeigen" ,r-rcppeigen)))
9938 (home-page "https://cran.r-project.org/web/packages/DDRTree")
9939 (synopsis "Learning principal graphs with DDRTree")
9941 "This package provides an implementation of the framework of
9942 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
9943 dimensional space while constructs a principal tree which passes through the
9944 middle of the data simultaneously. DDRTree shows superiority to
9945 alternatives (Wishbone, DPT) for inferring the ordering as well as the
9946 intrinsic structure of single cell genomics data. In general, it could be
9947 used to reconstruct the temporal progression as well as the bifurcation
9948 structure of any data type.")
9949 (license license:asl2.0)))
9951 (define-public r-corpcor
9958 (uri (cran-uri "corpcor" version))
9961 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
9962 (build-system r-build-system)
9963 (home-page "http://strimmerlab.org/software/corpcor/")
9964 (synopsis "Efficient estimation of covariance and (partial) correlation")
9966 "This package implements a James-Stein-type shrinkage estimator for the
9967 covariance matrix, with separate shrinkage for variances and correlations.
9968 Furthermore, functions are available for fast singular value decomposition,
9969 for computing the pseudoinverse, and for checking the rank and positive
9970 definiteness of a matrix.")
9971 (license license:gpl3+)))
9973 (define-public r-rspectra
9980 (uri (cran-uri "RSpectra" version))
9983 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
9984 (properties `((upstream-name . "RSpectra")))
9985 (build-system r-build-system)
9987 `(("r-matrix" ,r-matrix)
9989 ("r-rcppeigen" ,r-rcppeigen)))
9990 (home-page "https://github.com/yixuan/RSpectra")
9991 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
9993 "This package provides an R interface to the Spectra library for
9994 large-scale eigenvalue and SVD problems. It is typically used to compute a
9995 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
9996 which is usually more efficient than @code{eigen()} if k << n.")
9998 (license license:mpl2.0)))
10000 (define-public r-vbsr
10007 (uri (cran-uri "vbsr" version))
10010 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
10011 (build-system r-build-system)
10012 (home-page "https://cran.r-project.org/web/packages/vbsr")
10013 (synopsis "Variational Bayes spike regression regularized linear models")
10015 "This package provides an efficient algorithm for solving ultra-sparse
10016 regularized regression models using a variational Bayes algorithm with a spike
10017 prior. The algorithm is solved on a path, with coordinate updates, and is
10018 capable of generating very sparse models. Very general model
10019 diagnostics for controlling type-1 errors are also provided.")
10020 (license license:gpl2)))
10022 (define-public r-flare
10025 (version "1.6.0.2")
10029 (uri (cran-uri "flare" version))
10032 "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
10033 (build-system r-build-system)
10035 `(("r-igraph" ,r-igraph)
10036 ("r-lattice" ,r-lattice)
10038 ("r-matrix" ,r-matrix)))
10039 (home-page "https://cran.r-project.org/web/packages/flare")
10040 (synopsis "Family of Lasso regression implementations")
10042 "This package provides implementations of a family of Lasso variants
10043 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
10044 high dimensional sparse linear models.")
10045 (license license:gpl2)))
10047 (define-public r-lassopv
10054 (uri (cran-uri "lassopv" version))
10057 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
10058 (build-system r-build-system)
10059 (propagated-inputs `(("r-lars" ,r-lars)))
10060 (home-page "https://github.com/lingfeiwang/lassopv")
10061 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
10063 "This package enables you to estimate the p-values for predictors x
10064 against target variable y in Lasso regression, using the regularization
10065 strength when each predictor enters the active set of regularization path for
10066 the first time as the statistic.")
10067 (license license:gpl3)))
10069 (define-public r-splitstackshape
10071 (name "r-splitstackshape")
10076 (uri (cran-uri "splitstackshape" version))
10079 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
10080 (build-system r-build-system)
10082 `(("r-data-table" ,r-data-table)))
10083 (home-page "https://github.com/mrdwab/splitstackshape")
10084 (synopsis "Stack and reshape datasets after splitting concatenated values")
10086 "Online data collection tools like Google Forms often export
10087 multiple-response questions with data concatenated in cells. The
10088 @code{concat.split} (cSplit) family of functions provided by this package
10089 splits such data into separate cells. This package also includes functions to
10090 stack groups of columns and to reshape wide data, even when the data are
10091 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
10092 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
10094 (license license:gpl3)))
10096 (define-public r-tfmpvalue
10098 (name "r-tfmpvalue")
10103 (uri (cran-uri "TFMPvalue" version))
10106 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
10107 (properties `((upstream-name . "TFMPvalue")))
10108 (build-system r-build-system)
10109 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10110 (home-page "https://github.com/ge11232002/TFMPvalue")
10111 (synopsis "P-value computation for position weight matrices")
10113 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
10114 identification from sequence/alignments, we are interested in the significance
10115 of certain match scores. TFMPvalue provides the accurate calculation of a
10116 p-value with a score threshold for position weight matrices, or the score with
10117 a given p-value. It is an interface to code originally made available by
10118 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
10119 Touzet and Varre (2007).")
10120 (license license:gpl2)))
10122 (define-public r-rnifti
10129 (uri (cran-uri "RNifti" version))
10132 "0hfid40pgfi1ykqka8y3v0m7h0iyd6fbvycvqlad3ibmbg621f0w"))))
10133 (properties `((upstream-name . "RNifti")))
10134 (build-system r-build-system)
10135 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10136 (home-page "https://github.com/jonclayden/RNifti")
10137 (synopsis "Fast R and C++ access to NIfTI images")
10139 "This package provides very fast read and write access to images stored
10140 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
10141 compiled C and interpreted R code. It also provides a C/C++ API that can be
10142 used by other packages.")
10143 (license license:gpl2)))
10145 (define-public r-shades
10152 (uri (cran-uri "shades" version))
10155 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
10156 (build-system r-build-system)
10157 (home-page "https://github.com/jonclayden/shades")
10158 (synopsis "Simple color manipulation")
10160 "This package provides functions for easily manipulating colors,
10161 creating color scales and calculating color distances.")
10162 (license license:bsd-3)))
10164 (define-public r-ore
10171 (uri (cran-uri "ore" version))
10173 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
10174 (build-system r-build-system)
10175 (home-page "https://github.com/jonclayden/ore")
10176 (synopsis "R interface to the Onigmo regular expression library")
10178 "This package provides an alternative to R's built-in functionality for
10179 handling regular expressions, based on the Onigmo library. It offers
10180 first-class compiled regex objects, partial matching and function-based
10181 substitutions, amongst other features.")
10182 (license license:bsd-3)))
10184 (define-public r-reportr
10191 (uri (cran-uri "reportr" version))
10194 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
10195 (build-system r-build-system)
10196 (propagated-inputs `(("r-ore" ,r-ore)))
10197 (home-page "https://github.com/jonclayden/reportr")
10198 (synopsis "General message and error reporting system")
10200 "This package provides a system for reporting messages, which offers
10201 certain useful features over the standard R system, such as the incorporation
10202 of output consolidation, message filtering, assertions, expression
10203 substitution, automatic generation of stack traces for debugging, and
10204 conditional reporting based on the current \"output level\".")
10205 (license license:gpl2)))
10207 (define-public r-tractor-base
10209 (name "r-tractor-base")
10214 (uri (cran-uri "tractor.base" version))
10217 "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i"))))
10218 (properties `((upstream-name . "tractor.base")))
10219 (build-system r-build-system)
10222 ("r-reportr" ,r-reportr)
10223 ("r-rnifti" ,r-rnifti)
10224 ("r-shades" ,r-shades)))
10225 (home-page "http://www.tractor-mri.org.uk")
10226 (synopsis "Read, manipulate and visualize magnetic resonance images")
10228 "This package provides functions for working with magnetic resonance
10229 images. It supports reading and writing of popular file formats (DICOM,
10230 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
10231 visualization; flexible image manipulation; metadata and sparse image
10233 (license license:gpl2)))
10235 (define-public r-grimport
10237 (name "r-grimport")
10242 (uri (cran-uri "grImport" version))
10245 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
10246 (properties `((upstream-name . "grImport")))
10247 (build-system r-build-system)
10249 `(("ghostscript" ,ghostscript)))
10251 `(("r-xml" ,r-xml)))
10252 (home-page "https://cran.r-project.org/web/packages/grImport")
10253 (synopsis "Convert, import, and draw PostScript pictures")
10255 "This package provides functions for converting, importing, and drawing
10256 PostScript pictures in R plots.")
10257 (license license:gpl2+)))
10259 (define-public r-grimport2
10261 (name "r-grimport2")
10266 (uri (cran-uri "grImport2" version))
10269 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
10270 (properties `((upstream-name . "grImport2")))
10271 (build-system r-build-system)
10273 `(("r-base64enc" ,r-base64enc)
10277 (home-page "https://cran.r-project.org/web/packages/grImport2/")
10278 (synopsis "Import SVG graphics")
10280 "This package provides functions for importing external vector images and
10281 drawing them as part of R plots. This package is different from the
10282 @code{grImport} package because, where that package imports PostScript format
10283 images, this package imports SVG format images. Furthermore, this package
10284 imports a specific subset of SVG, so external images must be preprocessed
10285 using a package like @code{rsvg} to produce SVG that this package can import.
10286 SVG features that are not supported by R graphics, such as gradient fills, can
10287 be imported and then exported via the @code{gridSVG} package.")
10288 (license license:gpl2+)))
10290 (define-public r-kohonen
10297 (uri (cran-uri "kohonen" version))
10300 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
10301 (build-system r-build-system)
10303 `(("r-rcpp" ,r-rcpp)))
10304 (home-page "https://cran.r-project.org/web/packages/kohonen")
10305 (synopsis "Supervised and unsupervised self-organising maps")
10307 "This package provides functions to train @dfn{self-organising
10308 maps} (SOMs). Also interrogation of the maps and prediction using trained
10309 maps are supported. The name of the package refers to Teuvo Kohonen, the
10310 inventor of the SOM.")
10311 (license license:gpl2+)))
10313 (define-public r-nnls
10320 (uri (cran-uri "nnls" version))
10323 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
10324 (build-system r-build-system)
10325 (native-inputs `(("gfortran" ,gfortran)))
10326 (home-page "https://cran.r-project.org/web/packages/nnls")
10327 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
10329 "This package provides an R interface to the Lawson-Hanson implementation
10330 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
10331 the combination of non-negative and non-positive constraints.")
10332 (license license:gpl2+)))
10334 (define-public r-iso
10341 (uri (cran-uri "Iso" version))
10344 "014mm5b1f7i6nwlz3kyg1biph0y542kcx5bd13p68cv5a928qzid"))))
10345 (properties `((upstream-name . "Iso")))
10346 (build-system r-build-system)
10347 (native-inputs `(("gfortran" ,gfortran)))
10348 (home-page "http://www.stat.auckland.ac.nz/~rolf/")
10349 (synopsis "Functions to perform isotonic regression")
10351 "This package provides support for linear order and unimodal
10352 order (univariate) isotonic regression and bivariate isotonic regression with
10353 linear order on both variables.")
10354 (license license:gpl2+)))
10356 (define-public r-chemometricswithr
10358 (name "r-chemometricswithr")
10363 (uri (cran-uri "ChemometricsWithR" version))
10366 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
10368 `((upstream-name . "ChemometricsWithR")))
10369 (build-system r-build-system)
10371 `(("r-devtools" ,r-devtools)
10372 ("r-kohonen" ,r-kohonen)
10375 (home-page "https://github.com/rwehrens/CWR")
10376 (synopsis "Chemometrics with R")
10378 "This package provides functions and scripts used in the book
10379 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
10380 Life Sciences\" by Ron Wehrens, Springer (2011).")
10381 (license license:gpl2+)))
10383 (define-public r-als
10390 (uri (cran-uri "ALS" version))
10393 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
10394 (properties `((upstream-name . "ALS")))
10395 (build-system r-build-system)
10398 ("r-nnls" ,r-nnls)))
10399 (home-page "https://cran.r-project.org/web/packages/ALS")
10400 (synopsis "Multivariate curve resolution alternating least squares")
10402 "Alternating least squares is often used to resolve components
10403 contributing to data with a bilinear structure; the basic technique may be
10404 extended to alternating constrained least squares. This package provides an
10405 implementation of @dfn{multivariate curve resolution alternating least
10406 squares} (MCR-ALS).
10408 Commonly applied constraints include unimodality, non-negativity, and
10409 normalization of components. Several data matrices may be decomposed
10410 simultaneously by assuming that one of the two matrices in the bilinear
10411 decomposition is shared between datasets.")
10412 (license license:gpl2+)))
10414 (define-public r-strucchange
10416 (name "r-strucchange")
10421 (uri (cran-uri "strucchange" version))
10424 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
10425 (build-system r-build-system)
10427 `(("r-sandwich" ,r-sandwich)
10429 (home-page "https://cran.r-project.org/web/packages/strucchange")
10430 (synopsis "Testing, monitoring, and dating structural changes")
10432 "This package provides tools for testing, monitoring and dating
10433 structural changes in (linear) regression models. It features tests/methods
10434 from the generalized fluctuation test framework as well as from the F
10435 test (Chow test) framework. This includes methods to fit, plot and test
10436 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
10437 statistics, respectively. It is possible to monitor incoming data online
10438 using fluctuation processes. Finally, the breakpoints in regression models
10439 with structural changes can be estimated together with confidence intervals.
10440 Emphasis is always given to methods for visualizing the data.")
10441 ;; Either of these two GPL versions
10442 (license (list license:gpl2 license:gpl3))))
10444 (define-public r-pixmap
10451 (uri (cran-uri "pixmap" version))
10454 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
10455 (build-system r-build-system)
10456 (home-page "https://cran.r-project.org/web/packages/pixmap")
10457 (synopsis "Tools for bitmap images")
10459 "This package provides functions for importing, exporting, plotting and
10460 other manipulations of bitmapped images.")
10461 (license license:gpl2)))
10463 (define-public r-rapidjsonr
10465 (name "r-rapidjsonr")
10470 (uri (cran-uri "rapidjsonr" version))
10473 "0h4phjjhykbb45rg5b1xn48vqxdcvcngbm0416ds8in7j469wbwd"))))
10474 (build-system r-build-system)
10475 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
10476 (synopsis "JSON parser")
10478 "This package provides JSON parsing capability through the Rapidjson
10480 (license license:expat)))
10482 (define-public r-ontologyindex
10484 (name "r-ontologyindex")
10489 (uri (cran-uri "ontologyIndex" version))
10492 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
10493 (properties `((upstream-name . "ontologyIndex")))
10494 (build-system r-build-system)
10495 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
10496 (synopsis "Functions for processing ontologies in R")
10498 "This package provides functions for reading ontologies into R as lists
10499 and manipulating sets of ontological terms.")
10500 (license license:gpl2+)))
10502 (define-public r-gargle
10509 (uri (cran-uri "gargle" version))
10512 "08zhfk2sl342w35i5n2c93ayypg3z0kbl0020l3y9adqka1vazgx"))))
10513 (build-system r-build-system)
10518 ("r-jsonlite" ,r-jsonlite)
10519 ("r-rlang" ,r-rlang)
10520 ("r-withr" ,r-withr)))
10521 (home-page "https://gargle.r-lib.org")
10522 (synopsis "Utilities for working with Google APIs")
10524 "This package provides utilities for working with Google APIs. This
10525 includes functions and classes for handling common credential types and for
10526 preparing, executing, and processing HTTP requests.")
10527 (license license:expat)))
10529 (define-public r-bigrquery
10531 (name "r-bigrquery")
10536 (uri (cran-uri "bigrquery" version))
10539 "1ggh2gngr5x0g6y7d55y6kvn94anf7qi1bkc28cjmw61hxjq38fb"))))
10540 (build-system r-build-system)
10542 `(("r-assertthat" ,r-assertthat)
10543 ("r-bit64" ,r-bit64)
10546 ("r-gargle" ,r-gargle)
10549 ("r-jsonlite" ,r-jsonlite)
10550 ("r-prettyunits" ,r-prettyunits)
10551 ("r-progress" ,r-progress)
10552 ("r-rapidjsonr" ,r-rapidjsonr)
10554 ("r-rlang" ,r-rlang)
10555 ("r-tibble" ,r-tibble)))
10556 (home-page "https://github.com/rstats-db/bigrquery")
10557 (synopsis "R interface to Google's BigQuery API")
10559 "This package provides an R interface to Google's BigQuery database.")
10560 (license license:gpl3)))
10562 (define-public r-gmp
10565 (version "0.5-13.5")
10569 (uri (cran-uri "gmp" version))
10572 "042mzsl6z6s61fy5m21yf9q83l08vnyqljn4iax7kqyiycpsp0gn"))))
10573 (build-system r-build-system)
10576 (modify-phases %standard-phases
10577 (add-after 'unpack 'set-CC
10578 (lambda _ (setenv "CC" "gcc") #t)))))
10579 (inputs `(("gmp" ,gmp)))
10580 (home-page "https://cran.r-project.org/web/packages/gmp")
10581 (synopsis "Multiple precision arithmetic")
10583 "This package supports multiple precision arithmetic (big integers and
10584 rationals, prime number tests, matrix computation), \"arithmetic without
10585 limitations\" using the GNU Multiple Precision library.")
10586 ;; Any version of the GPL.
10587 (license license:gpl3+)))
10589 (define-public r-rmpfr
10596 (uri (cran-uri "Rmpfr" version))
10599 "1zq3as34r27v2yc729731997wdhxb6cs5ilmak4nmsljabnac7gc"))))
10600 (properties `((upstream-name . "Rmpfr")))
10601 (build-system r-build-system)
10605 `(("r-gmp" ,r-gmp)))
10606 (home-page "http://rmpfr.r-forge.r-project.org/")
10607 (synopsis "R bindings to the MPFR library")
10609 "This package supports arithmetic (via S4 classes and methods) for
10610 arbitrary precision floating point numbers, including transcendental
10611 functions. To this end, the package interfaces with the @dfn{Multiple
10612 Precision Floating-Point Reliable} (MPFR) library.")
10613 (license license:gpl2+)))
10615 (define-public r-assertive-base
10617 (name "r-assertive-base")
10622 (uri (cran-uri "assertive.base" version))
10625 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
10627 `((upstream-name . "assertive.base")))
10628 (build-system r-build-system)
10629 (home-page "https://bitbucket.org/richierocks/assertive.base")
10630 (synopsis "Core of the assertive package")
10632 "This package provides a minimal set of predicates and assertions used by
10633 the assertive package. This is mainly for use by other package developers who
10634 want to include run-time testing features in their own packages.")
10635 (license license:gpl3+)))
10637 (define-public r-assertive-properties
10639 (name "r-assertive-properties")
10644 (uri (cran-uri "assertive.properties" version))
10647 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
10649 `((upstream-name . "assertive.properties")))
10650 (build-system r-build-system)
10652 `(("r-assertive-base" ,r-assertive-base)))
10653 (home-page "https://bitbucket.org/richierocks/assertive.properties")
10654 (synopsis "Assertions to check properties of variables")
10656 "This package provides a set of predicates and assertions for checking
10657 the properties of variables, such as length, names and attributes. This is
10658 mainly for use by other package developers who want to include run-time
10659 testing features in their own packages.")
10660 (license license:gpl3+)))
10662 (define-public r-assertive-numbers
10664 (name "r-assertive-numbers")
10669 (uri (cran-uri "assertive.numbers" version))
10672 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
10674 `((upstream-name . "assertive.numbers")))
10675 (build-system r-build-system)
10677 `(("r-assertive-base" ,r-assertive-base)))
10678 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
10679 (synopsis "Assertions to check properties of numbers")
10681 "This package provides a set of predicates and assertions for checking
10682 the properties of numbers. This is mainly for use by other package developers
10683 who want to include run-time testing features in their own packages.")
10684 (license license:gpl3+)))
10686 (define-public r-assertive-sets
10688 (name "r-assertive-sets")
10693 (uri (cran-uri "assertive.sets" version))
10696 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
10698 `((upstream-name . "assertive.sets")))
10699 (build-system r-build-system)
10701 `(("r-assertive-base" ,r-assertive-base)))
10702 (home-page "https://bitbucket.org/richierocks/assertive.sets")
10703 (synopsis "Assertions to check properties of sets")
10705 "This package provides a set of predicates and assertions for checking
10706 the properties of sets. This is mainly for use by other package developers
10707 who want to include run-time testing features in their own packages.")
10708 (license license:gpl3+)))
10710 (define-public r-assertive-matrices
10712 (name "r-assertive-matrices")
10717 (uri (cran-uri "assertive.matrices" version))
10720 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
10722 `((upstream-name . "assertive.matrices")))
10723 (build-system r-build-system)
10725 `(("r-assertive-base" ,r-assertive-base)))
10726 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
10727 (synopsis "Assertions to check properties of matrices")
10729 "This package provides a set of predicates and assertions for checking
10730 the properties of matrices. This is mainly for use by other package
10731 developers who want to include run-time testing features in their own
10733 (license license:gpl3+)))
10735 (define-public r-assertive-models
10737 (name "r-assertive-models")
10742 (uri (cran-uri "assertive.models" version))
10745 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
10747 `((upstream-name . "assertive.models")))
10748 (build-system r-build-system)
10750 `(("r-assertive-base" ,r-assertive-base)))
10751 (home-page "https://bitbucket.org/richierocks/assertive.models")
10752 (synopsis "Assertions to check properties of models")
10754 "This package provides a set of predicates and assertions for checking
10755 the properties of models. This is mainly for use by other package developers
10756 who want to include run-time testing features in their own packages.")
10757 (license license:gpl3+)))
10759 (define-public r-assertive-reflection
10761 (name "r-assertive-reflection")
10766 (uri (cran-uri "assertive.reflection" version))
10769 "19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj"))))
10771 `((upstream-name . "assertive.reflection")))
10772 (build-system r-build-system)
10774 `(("r-assertive-base" ,r-assertive-base)))
10775 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
10776 (synopsis "Assertions for checking the state of R")
10778 "This package provides a set of predicates and assertions for checking
10779 the state and capabilities of R, the operating system it is running on, and
10780 the IDE being used. This is mainly for use by other package developers who
10781 want to include run-time testing features in their own packages.")
10782 (license license:gpl3+)))
10784 (define-public r-assertive-types
10786 (name "r-assertive-types")
10791 (uri (cran-uri "assertive.types" version))
10794 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
10796 `((upstream-name . "assertive.types")))
10797 (build-system r-build-system)
10799 `(("r-assertive-base" ,r-assertive-base)
10800 ("r-assertive-properties" ,r-assertive-properties)
10801 ("r-codetools" ,r-codetools)))
10802 (home-page "https://bitbucket.org/richierocks/assertive.types")
10803 (synopsis "Assertions to check types of variables")
10805 "This package provides a set of predicates and assertions for checking
10806 the types of variables. This is mainly for use by other package developers
10807 who want to include run-time testing features in their own packages.")
10808 (license license:gpl3+)))
10810 (define-public r-assertive-files
10812 (name "r-assertive-files")
10817 (uri (cran-uri "assertive.files" version))
10820 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
10822 `((upstream-name . "assertive.files")))
10823 (build-system r-build-system)
10825 `(("r-assertive-base" ,r-assertive-base)
10826 ("r-assertive-numbers" ,r-assertive-numbers)))
10827 (home-page "https://bitbucket.org/richierocks/assertive.files")
10828 (synopsis "Assertions to check properties of files")
10830 "This package provides a set of predicates and assertions for checking
10831 the properties of files and connections. This is mainly for use by other
10832 package developers who want to include run-time testing features in their own
10834 (license license:gpl3+)))
10836 (define-public r-assertive-code
10838 (name "r-assertive-code")
10843 (uri (cran-uri "assertive.code" version))
10846 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
10848 `((upstream-name . "assertive.code")))
10849 (build-system r-build-system)
10851 `(("r-assertive-base" ,r-assertive-base)
10852 ("r-assertive-properties" ,r-assertive-properties)
10853 ("r-assertive-types" ,r-assertive-types)))
10854 (home-page "https://bitbucket.org/richierocks/assertive.code")
10855 (synopsis "Assertions to check properties of code")
10857 "This package provides a set of predicates and assertions for checking
10858 the properties of code. This is mainly for use by other package developers
10859 who want to include run-time testing features in their own packages.")
10860 (license license:gpl3+)))
10862 (define-public r-assertive-datetimes
10864 (name "r-assertive-datetimes")
10869 (uri (cran-uri "assertive.datetimes" version))
10872 "00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78"))))
10874 `((upstream-name . "assertive.datetimes")))
10875 (build-system r-build-system)
10877 `(("r-assertive-base" ,r-assertive-base)
10878 ("r-assertive-types" ,r-assertive-types)))
10879 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
10880 (synopsis "Assertions to check properties of dates and times")
10882 "This package provides a set of predicates and assertions for checking
10883 the properties of dates and times. This is mainly for use by other package
10884 developers who want to include run-time testing features in their own
10886 (license license:gpl3+)))
10888 (define-public r-assertive-strings
10890 (name "r-assertive-strings")
10895 (uri (cran-uri "assertive.strings" version))
10898 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
10900 `((upstream-name . "assertive.strings")))
10901 (build-system r-build-system)
10903 `(("r-assertive-base" ,r-assertive-base)
10904 ("r-assertive-types" ,r-assertive-types)
10905 ("r-stringi" ,r-stringi)))
10906 (home-page "https://bitbucket.org/richierocks/assertive.strings")
10907 (synopsis "Assertions to check properties of strings")
10909 "This package provides a set of predicates and assertions for checking
10910 the properties of strings. This is mainly for use by other package developers
10911 who want to include run-time testing features in their own packages.")
10912 (license license:gpl3+)))
10914 (define-public r-assertive-data-us
10916 (name "r-assertive-data-us")
10921 (uri (cran-uri "assertive.data.us" version))
10924 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
10926 `((upstream-name . "assertive.data.us")))
10927 (build-system r-build-system)
10929 `(("r-assertive-base" ,r-assertive-base)
10930 ("r-assertive-strings" ,r-assertive-strings)))
10931 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
10932 (synopsis "Assertions to check properties of strings")
10934 "This package provides a set of predicates and assertions for checking
10935 the properties of US-specific complex data types. This is mainly for use by
10936 other package developers who want to include run-time testing features in
10937 their own packages.")
10938 (license license:gpl3+)))
10940 (define-public r-assertive-data-uk
10942 (name "r-assertive-data-uk")
10947 (uri (cran-uri "assertive.data.uk" version))
10950 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
10952 `((upstream-name . "assertive.data.uk")))
10953 (build-system r-build-system)
10955 `(("r-assertive-base" ,r-assertive-base)
10956 ("r-assertive-strings" ,r-assertive-strings)))
10957 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
10958 (synopsis "Assertions to check properties of strings")
10960 "This package provides a set of predicates and assertions for checking
10961 the properties of UK-specific complex data types. This is mainly for use by
10962 other package developers who want to include run-time testing features in
10963 their own packages.")
10964 (license license:gpl3+)))
10966 (define-public r-assertive-data
10968 (name "r-assertive-data")
10973 (uri (cran-uri "assertive.data" version))
10976 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
10978 `((upstream-name . "assertive.data")))
10979 (build-system r-build-system)
10981 `(("r-assertive-base" ,r-assertive-base)
10982 ("r-assertive-strings" ,r-assertive-strings)))
10983 (home-page "https://bitbucket.org/richierocks/assertive.data")
10984 (synopsis "Assertions to check properties of data")
10986 "This package provides a set of predicates and assertions for checking
10987 the properties of (country independent) complex data types. This is mainly
10988 for use by other package developers who want to include run-time testing
10989 features in their own packages.")
10990 (license license:gpl3+)))
10992 (define-public r-assertive
10994 (name "r-assertive")
10999 (uri (cran-uri "assertive" version))
11002 "0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3"))))
11003 (build-system r-build-system)
11005 `(("r-assertive-base" ,r-assertive-base)
11006 ("r-assertive-code" ,r-assertive-code)
11007 ("r-assertive-data" ,r-assertive-data)
11008 ("r-assertive-data-uk" ,r-assertive-data-uk)
11009 ("r-assertive-data-us" ,r-assertive-data-us)
11010 ("r-assertive-datetimes" ,r-assertive-datetimes)
11011 ("r-assertive-files" ,r-assertive-files)
11012 ("r-assertive-matrices" ,r-assertive-matrices)
11013 ("r-assertive-models" ,r-assertive-models)
11014 ("r-assertive-numbers" ,r-assertive-numbers)
11015 ("r-assertive-properties" ,r-assertive-properties)
11016 ("r-assertive-reflection" ,r-assertive-reflection)
11017 ("r-assertive-sets" ,r-assertive-sets)
11018 ("r-assertive-strings" ,r-assertive-strings)
11019 ("r-assertive-types" ,r-assertive-types)
11020 ("r-knitr" ,r-knitr)))
11021 (home-page "https://bitbucket.org/richierocks/assertive")
11022 (synopsis "Readable check functions to ensure code integrity")
11024 "This package provides lots of predicates (@code{is_*} functions) to
11025 check the state of your variables, and assertions (@code{assert_*} functions)
11026 to throw errors if they aren't in the right form.")
11027 (license license:gpl3+)))
11029 (define-public r-dotcall64
11031 (name "r-dotcall64")
11036 (uri (cran-uri "dotCall64" version))
11039 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
11040 (properties `((upstream-name . "dotCall64")))
11041 (build-system r-build-system)
11042 (native-inputs `(("gfortran" ,gfortran)))
11043 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
11044 (synopsis "Enhanced foreign function interface supporting long vectors")
11046 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
11047 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
11048 supports long vectors, arguments of type 64-bit integer, and provides a
11049 mechanism to avoid unnecessary copies of read-only and write-only arguments.
11050 This makes it a convenient and fast interface to C/C++ and Fortran code.")
11051 (license license:gpl2+)))
11053 (define-public r-spam
11060 (uri (cran-uri "spam" version))
11062 (base32 "1wfv45jq8zy8kyjr308zicc1461y1777qll1cy6lw4071f9rvba2"))))
11063 (build-system r-build-system)
11065 `(("r-dotcall64" ,r-dotcall64)))
11066 (native-inputs `(("gfortran" ,gfortran)))
11067 (home-page "https://www.math.uzh.ch/pages/spam/")
11068 (synopsis "Sparse matrix algebra")
11070 "This package provides a set of functions for sparse matrix algebra.
11071 Differences with other sparse matrix packages are:
11074 @item it only supports (essentially) one sparse matrix format;
11075 @item it is based on transparent and simple structure(s);
11076 @item it is tailored for MCMC calculations within G(M)RF;
11077 @item and it is fast and scalable (with the extension package @code{spam64}).
11079 ;; Either of these licenses
11080 (license (list license:bsd-3 license:lgpl2.0))))
11082 (define-public r-fields
11089 (uri (cran-uri "fields" version))
11091 (base32 "173zm5vr236ydiq0v27qy0l3x7h9fc7jly38iakg77j26i0a01il"))))
11092 (build-system r-build-system)
11094 `(("r-maps" ,r-maps)
11095 ("r-spam" ,r-spam)))
11097 `(("gfortran" ,gfortran)))
11098 (home-page "https://www.image.ucar.edu/fields")
11099 (synopsis "Tools for spatial data")
11101 "This is a package for curve, surface and function fitting with an
11102 emphasis on splines, spatial data and spatial statistics. The major methods
11103 include cubic, and thin plate splines, Kriging, and compactly supported
11104 covariance functions for large data sets.")
11105 (license license:gpl2+)))
11107 (define-public r-spatialextremes
11109 (name "r-spatialextremes")
11110 (version "2.0-7.2")
11114 (uri (cran-uri "SpatialExtremes" version))
11117 "0aqq9ryxi4xsdqjhc1lhb7ai8szs7m2vys6nn0ygps1w3pm4xwj8"))))
11119 `((upstream-name . "SpatialExtremes")))
11120 (build-system r-build-system)
11122 `(("r-fields" ,r-fields)
11123 ("r-maps" ,r-maps)))
11124 (home-page "http://spatialextremes.r-forge.r-project.org/")
11125 (synopsis "Modelling spatial extremes")
11127 "This package provides tools for the statistical modelling of spatial
11128 extremes using max-stable processes, copula or Bayesian hierarchical models.
11129 More precisely, this package allows (conditional) simulations from various
11130 parametric max-stable models, analysis of the extremal spatial dependence, the
11131 fitting of such processes using composite likelihoods or least square (simple
11132 max-stable processes only), model checking and selection and prediction.")
11133 (license license:gpl2+)))
11135 (define-public r-drc
11142 (uri (cran-uri "drc" version))
11145 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
11146 (build-system r-build-system)
11149 ("r-gtools" ,r-gtools)
11151 ("r-multcomp" ,r-multcomp)
11152 ("r-plotrix" ,r-plotrix)
11153 ("r-scales" ,r-scales)))
11154 (home-page "https://cran.r-project.org/web/packages/drc")
11155 (synopsis "Analysis of dose-response curves")
11157 "This package provides a suite of flexible and versatile model fitting
11158 and after-fitting functions for the analysis of dose-response data.")
11159 (license license:gpl2+)))
11161 (define-public r-rmeta
11168 (uri (cran-uri "rmeta" version))
11171 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
11172 (build-system r-build-system)
11173 (home-page "https://cran.r-project.org/web/packages/rmeta")
11174 (synopsis "Tools for meta-analysis")
11176 "This package provides functions for simple fixed and random effects
11177 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
11178 draws standard summary plots, funnel plots, and computes summaries and tests
11179 for association and heterogeneity.")
11180 (license license:gpl2)))
11182 (define-public r-bootstrap
11184 (name "r-bootstrap")
11189 (uri (cran-uri "bootstrap" version))
11192 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
11193 (build-system r-build-system)
11194 (native-inputs `(("gfortran" ,gfortran)))
11195 (home-page "https://cran.r-project.org/web/packages/bootstrap")
11196 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
11198 "This package provides software and data for the book \"An Introduction
11199 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
11200 This package is primarily provided for projects already based on it, and for
11201 support of the book. New projects should preferentially use the recommended
11202 package \"boot\".")
11203 (license license:bsd-3)))
11205 (define-public r-survivalroc
11207 (name "r-survivalroc")
11212 (uri (cran-uri "survivalROC" version))
11215 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
11216 (properties `((upstream-name . "survivalROC")))
11217 (build-system r-build-system)
11218 (home-page "https://cran.r-project.org/web/packages/survivalROC")
11219 (synopsis "Time-dependent ROC curve estimation from censored survival data")
11221 "Compute time-dependent ROC curve from censored survival data using
11222 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
11223 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
11224 (license license:gpl2+)))
11226 (define-public r-longitudinal
11228 (name "r-longitudinal")
11233 (uri (cran-uri "longitudinal" version))
11236 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
11237 (build-system r-build-system)
11238 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
11239 (home-page "http://strimmerlab.org/software/longitudinal/")
11240 (synopsis "Analysis of multiple time course data")
11242 "This package contains general data structures and functions for
11243 longitudinal data with multiple variables, repeated measurements, and
11244 irregularly spaced time points. It also implements a shrinkage estimator of
11245 dynamical correlation and dynamical covariance.")
11246 (license license:gpl3+)))
11248 (define-public r-genenet
11255 (uri (cran-uri "GeneNet" version))
11258 "0w52apk0nnr8nsskf26ff7ana8xiksr8wqmkjxzwhzgg7fncm61p"))))
11259 (properties `((upstream-name . "GeneNet")))
11260 (build-system r-build-system)
11262 `(("r-corpcor" ,r-corpcor)
11263 ("r-fdrtool" ,r-fdrtool)
11264 ("r-longitudinal" ,r-longitudinal)))
11265 (home-page "http://strimmerlab.org/software/genenet/")
11266 (synopsis "Modeling and inferring gene networks")
11268 "This package analyzes gene expression (time series) data with focus on
11269 the inference of gene networks. In particular, GeneNet implements the methods
11270 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
11271 for learning large-scale gene association networks (including assignment of
11272 putative directions).")
11273 (license license:gpl3+)))
11275 (define-public r-rbamtools
11277 (name "r-rbamtools")
11278 (version "2.16.17")
11282 (uri (cran-uri "rbamtools" version))
11285 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
11286 (build-system r-build-system)
11287 (inputs `(("zlib" ,zlib)))
11289 `(("r-refgenome" ,r-refgenome)))
11290 (home-page "https://cran.r-project.org/web/packages/rbamtools")
11291 (synopsis "Read and write BAM (binary alignment) files")
11293 "This package provides an R interface to functions of the SAMtools
11295 (license license:artistic2.0)))
11297 (define-public r-protviz
11304 (uri (cran-uri "protViz" version))
11307 "0cznzm1ijlq33yd5wsa61prav77y2vi698w0n2fx1xcv504c4bjv"))))
11308 (properties `((upstream-name . "protViz")))
11309 (build-system r-build-system)
11310 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11311 (home-page "https://github.com/protViz/protViz/")
11312 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
11314 "This package helps with quality checks, visualizations and analysis of
11315 mass spectrometry data, coming from proteomics experiments. The package is
11316 developed, tested and used at the Functional Genomics Center Zurich, where it
11317 is used mainly for prototyping, teaching, and having fun with proteomics data.
11318 But it can also be used to do data analysis for small scale data sets.")
11319 (license license:gpl3)))
11321 (define-public r-cmprsk
11328 (uri (cran-uri "cmprsk" version))
11330 (base32 "0xhgfg5b4i9skkaxp7gzkafgg5bqs5q1rp4hpw2jjmykg2nifn99"))))
11331 (build-system r-build-system)
11333 `(("r-survival" ,r-survival)))
11335 `(("gfortran" ,gfortran)))
11336 (home-page "https://cran.r-project.org/web/packages/cmprsk")
11337 (synopsis "Subdistribution analysis of competing risks")
11339 "This package provides tool for estimation, testing and regression
11340 modeling of subdistribution functions in competing risks, as described in
11341 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
11342 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
11343 A proportional hazards model for the subdistribution of a competing risk,
11344 JASA, 94:496-509.")
11345 (license license:gpl2+)))
11347 (define-public r-etm
11354 (uri (cran-uri "etm" version))
11357 "1yivbq8y0ijcl1m4nir4q9hp4pi6iphwxgjprygsdf7vp98wq677"))))
11358 (build-system r-build-system)
11360 `(("r-data-table" ,r-data-table)
11361 ("r-lattice" ,r-lattice)
11363 ("r-rcpparmadillo" ,r-rcpparmadillo)
11364 ("r-survival" ,r-survival)))
11365 (home-page "https://cran.r-project.org/web/packages/etm")
11366 (synopsis "Empirical transition matrix")
11368 "The @dfn{empirical transition matrix} (etm) package permits to estimate
11369 the matrix of transition probabilities for any time-inhomogeneous multistate
11370 model with finite state space using the Aalen-Johansen estimator.")
11371 (license license:expat)))
11373 (define-public r-epi
11380 (uri (cran-uri "Epi" version))
11383 "046y10vwks5y84pzccmrn6d4pd6qz70imvp1hw5ywp8fnwzfh4g5"))))
11384 (properties `((upstream-name . "Epi")))
11385 (build-system r-build-system)
11387 `(("r-cmprsk" ,r-cmprsk)
11388 ("r-data-table" ,r-data-table)
11391 ("r-matrix" ,r-matrix)
11393 ("r-numderiv" ,r-numderiv)
11395 ("r-survival" ,r-survival)
11397 (home-page "http://BendixCarstensen.com/Epi/")
11398 (synopsis "Statistical analysis in epidemiology")
11400 "This package provides functions for demographic and epidemiological
11401 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
11402 particular representation, manipulation and simulation of multistate data -
11403 the Lexis suite of functions, which includes interfaces to the @code{mstate},
11404 @code{etm} and @code{cmprsk} packages. It also contains functions for
11405 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
11406 data and some useful functions for tabulation and plotting, as well as a
11407 number of epidemiological data sets.")
11408 (license license:gpl2)))
11410 (define-public r-ppls
11413 (version "1.6-1.1")
11417 (uri (cran-uri "ppls" version))
11420 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
11421 (build-system r-build-system)
11422 (propagated-inputs `(("r-mass" ,r-mass)))
11423 (home-page "https://cran.r-project.org/web/packages/ppls")
11424 (synopsis "Penalized partial least squares")
11426 "This package contains linear and nonlinear regression methods based on
11427 partial least squares and penalization techniques. Model parameters are
11428 selected via cross-validation, and confidence intervals ans tests for the
11429 regression coefficients can be conducted via jackknifing.")
11430 (license license:gpl2+)))
11432 (define-public r-huge
11439 (uri (cran-uri "huge" version))
11441 (base32 "07n3j1va2z4v30rj22cww72khgzbz2xsp0yc0qswlrwyxi4my5i3"))))
11442 (build-system r-build-system)
11444 `(("r-igraph" ,r-igraph)
11446 ("r-matrix" ,r-matrix)
11448 ("r-rcppeigen" ,r-rcppeigen)))
11449 (home-page "https://cran.r-project.org/web/packages/huge")
11450 (synopsis "High-dimensional undirected graph estimation")
11452 "This package provides a general framework for high-dimensional
11453 undirected graph estimation. It integrates data preprocessing, neighborhood
11454 screening, graph estimation, and model selection techniques into a pipeline.")
11455 (license license:gpl2)))
11457 (define-public r-parcor
11464 (uri (cran-uri "parcor" version))
11467 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
11468 (build-system r-build-system)
11471 ("r-genenet" ,r-genenet)
11472 ("r-glmnet" ,r-glmnet)
11474 ("r-ppls" ,r-ppls)))
11475 (home-page "https://cran.r-project.org/web/packages/parcor")
11476 (synopsis "Regularized estimation of partial correlation matrices")
11478 "This package estimates the matrix of partial correlations based on
11479 different regularized regression methods: lasso, adaptive lasso, PLS, and
11480 Ridge Regression. In addition, the package provides model selection for
11481 lasso, adaptive lasso and Ridge regression based on cross-validation.")
11482 (license license:gpl2+)))
11484 (define-public r-mcmc
11491 (uri (cran-uri "mcmc" version))
11494 "1fc6a6asn53lx7x7pnlb5mb716nv4pcmbp99f1i30y4hzygihfj4"))))
11495 (build-system r-build-system)
11496 (home-page "http://www.stat.umn.edu/geyer/mcmc/")
11497 (synopsis "Markov chain Monte Carlo")
11499 "This package simulates continuous distributions of random vectors using
11500 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
11501 function that evaluates the log unnormalized density. Algorithms are random
11502 walk Metropolis algorithm (function @code{metrop}), simulated
11503 tempering (function @code{temper}), and morphometric random walk
11504 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
11505 by change of variable.")
11506 (license license:expat)))
11508 (define-public r-listenv
11515 (uri (cran-uri "listenv" version))
11518 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
11519 (build-system r-build-system)
11521 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11522 (home-page "https://github.com/HenrikBengtsson/listenv")
11523 (synopsis "Environments behaving (almost) as lists")
11525 "This package implements list environments. List environments are
11526 environments that have list-like properties. For instance, the elements of a
11527 list environment are ordered and can be accessed and iterated over using index
11529 (license license:lgpl2.1+)))
11531 (define-public r-globals
11538 (uri (cran-uri "globals" version))
11541 "1ha8iasgijp4q3v2b0b17y1wh7cd3nvzd9b03w49qm2bidkaf68m"))))
11542 (build-system r-build-system)
11544 `(("r-codetools" ,r-codetools)))
11545 (home-page "https://github.com/HenrikBengtsson/globals")
11546 (synopsis "Identify global objects in R expressions")
11548 "This package provides tools to identify global (\"unknown\" or \"free\")
11549 objects in R expressions by code inspection using various strategies, e.g.
11550 conservative or liberal. The objective of this package is to make it as
11551 simple as possible to identify global objects for the purpose of exporting
11552 them in distributed compute environments.")
11553 (license license:lgpl2.1+)))
11555 (define-public r-future
11562 (uri (cran-uri "future" version))
11565 "101hi8warqa0py9l6c5p98f7i9xjhx01w655z6a35jx1dhspykzd"))))
11566 (build-system r-build-system)
11568 `(("r-digest" ,r-digest)
11569 ("r-globals" ,r-globals)
11570 ("r-listenv" ,r-listenv)))
11572 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11573 (home-page "https://github.com/HenrikBengtsson/future")
11574 (synopsis "Unified parallel and distributed processing in R")
11576 "The purpose of this package is to provide a lightweight and unified
11577 Future API for sequential and parallel processing of R expression via futures.
11578 This package implements sequential, multicore, multisession, and cluster
11579 futures. With these, R expressions can be evaluated on the local machine, in
11580 parallel a set of local machines, or distributed on a mix of local and remote
11581 machines. Extensions to this package implement additional backends for
11582 processing futures via compute cluster schedulers etc. Because of its unified
11583 API, there is no need to modify any code in order to switch from sequential on
11584 the local machine to, say, distributed processing on a remote compute cluster.")
11585 (license license:lgpl2.1+)))
11587 (define-public r-future-apply
11589 (name "r-future-apply")
11594 (uri (cran-uri "future.apply" version))
11597 "0wd3bh114zkvrqlpn8gqz4ix1igr9hr8x72h2g00a7mqkfjfqx33"))))
11598 (properties `((upstream-name . "future.apply")))
11599 (build-system r-build-system)
11601 `(("r-future" ,r-future)
11602 ("r-globals" ,r-globals)))
11604 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11605 (home-page "https://github.com/HenrikBengtsson/future.apply")
11606 (synopsis "Apply function to elements in parallel using futures")
11608 "This package provides implementations of @code{apply()},
11609 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
11610 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
11611 can be resolved using any future-supported backend, e.g. parallel on the local
11612 machine or distributed on a compute cluster.")
11613 (license license:gpl2+)))
11615 (define-public r-rsvd
11622 (uri (cran-uri "rsvd" version))
11625 "0fia77y5fxnhwkcxlgp98ygb8fdfraky75x80hkf7kvvpwc5rzn8"))))
11626 (build-system r-build-system)
11628 `(("r-matrix" ,r-matrix)))
11629 (home-page "https://github.com/erichson/rSVD")
11630 (synopsis "Randomized singular value decomposition")
11632 "Low-rank matrix decompositions are fundamental tools and widely used for
11633 data analysis, dimension reduction, and data compression. Classically, highly
11634 accurate deterministic matrix algorithms are used for this task. However, the
11635 emergence of large-scale data has severely challenged our computational
11636 ability to analyze big data. The concept of randomness has been demonstrated
11637 as an effective strategy to quickly produce approximate answers to familiar
11638 problems such as the @dfn{singular value decomposition} (SVD). This package
11639 provides several randomized matrix algorithms such as the randomized singular
11640 value decomposition (@code{rsvd}), randomized principal component
11641 analysis (@code{rpca}), randomized robust principal component
11642 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
11643 and the randomized CUR decomposition (@code{rcur}). In addition several plot
11644 functions are provided.")
11645 (license license:gpl3+)))
11647 (define-public r-sloop
11654 (uri (cran-uri "sloop" version))
11657 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
11658 (build-system r-build-system)
11660 `(("r-codetools" ,r-codetools)
11661 ("r-crayon" ,r-crayon)
11662 ("r-purrr" ,r-purrr)
11663 ("r-rlang" ,r-rlang)
11664 ("r-tibble" ,r-tibble)))
11665 (home-page "https://github.com/r-lib/sloop")
11666 (synopsis "Helpers for object-oriented programming in R")
11668 "This package provides a collection of helper functions designed to
11669 help you to better understand object oriented programming in R, particularly
11671 (license license:gpl3)))
11673 (define-public r-capushe
11680 (uri (cran-uri "capushe" version))
11683 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
11684 (build-system r-build-system)
11685 (propagated-inputs `(("r-mass" ,r-mass)))
11686 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
11687 (synopsis "Calibrating penalties using slope heuristics")
11689 "This package provides tools for the calibration of penalized criteria
11690 for model selection. The calibration methods available are based on the slope
11692 (license license:gpl2+)))
11694 (define-public r-dorng
11701 (uri (cran-uri "doRNG" version))
11704 "1sb75aqkliprglfxc4x4wds6alqgzhvl2n812g1d32a88ra3slr7"))))
11705 (properties `((upstream-name . "doRNG")))
11706 (build-system r-build-system)
11708 `(("r-foreach" ,r-foreach)
11709 ("r-iterators" ,r-iterators)
11710 ("r-pkgmaker" ,r-pkgmaker)
11711 ("r-rngtools" ,r-rngtools)))
11712 (home-page "https://renozao.github.io/doRNG/")
11713 (synopsis "Generic reproducible parallel backend for foreach loops")
11715 "This package provides functions to perform reproducible parallel
11716 @code{foreach} loops, using independent random streams as generated by
11717 L'Ecuyer's combined multiple-recursive generator. It enables to easily
11718 convert standard @code{%dopar%} loops into fully reproducible loops,
11719 independently of the number of workers, the task scheduling strategy, or the
11720 chosen parallel environment and associated foreach backend.")
11721 (license license:gpl2+)))
11723 (define-public r-blockmodeling
11725 (name "r-blockmodeling")
11730 (uri (cran-uri "blockmodeling" version))
11733 "11v9903y9dwlzaqp8sx0fsibcg82phvappddy37r8lnxd4vchsd2"))))
11734 (build-system r-build-system)
11736 `(("r-doparallel" ,r-doparallel)
11737 ("r-dorng" ,r-dorng)
11738 ("r-foreach" ,r-foreach)
11739 ("r-matrix" ,r-matrix)))
11740 (native-inputs `(("gfortran" ,gfortran)))
11741 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
11742 (synopsis "Generalized and classical blockmodeling of valued networks")
11744 "This package is primarily meant as an implementation of generalized
11745 blockmodeling for valued networks. In addition, measures of similarity or
11746 dissimilarity based on structural equivalence and regular equivalence (REGE
11747 algorithms) can be computed and partitioned matrices can be plotted.")
11748 (license license:gpl2+)))
11750 (define-public r-upsetr
11757 (uri (cran-uri "UpSetR" version))
11760 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
11761 (properties `((upstream-name . "UpSetR")))
11762 (build-system r-build-system)
11764 `(("r-ggplot2" ,r-ggplot2)
11765 ("r-gridextra" ,r-gridextra)
11767 ("r-scales" ,r-scales)))
11768 (home-page "https://github.com/hms-dbmi/UpSetR")
11769 (synopsis "Visualize intersecting sets")
11771 "This package provides a more scalable alternative to Venn and Euler
11772 diagrams for visualizing intersecting sets. Create visualizations of
11773 intersecting sets using a novel matrix design, along with visualizations of
11774 several common set, element and attribute related tasks.")
11775 (license license:expat)))
11777 ;; This package includes a JavaScript file, which is not minified. When
11778 ;; upgrading please check that there are no new minified JavaScript files.
11779 (define-public r-shinybs
11786 (uri (cran-uri "shinyBS" version))
11789 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
11790 (properties `((upstream-name . "shinyBS")))
11791 (build-system r-build-system)
11792 ;; The tests spawn Shiny browser apps. They cannot be run
11793 ;; non-interactively.
11794 (arguments '(#:tests? #f))
11796 `(("r-htmltools" ,r-htmltools)
11797 ("r-shiny" ,r-shiny)))
11798 (home-page "https://ebailey78.github.io/shinyBS/")
11799 (synopsis "Twitter Bootstrap components for Shiny")
11801 "This package adds additional Twitter Bootstrap components to Shiny.")
11802 (license license:gpl3)))
11804 (define-public r-outliers
11806 (name "r-outliers")
11811 (uri (cran-uri "outliers" version))
11814 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
11815 (build-system r-build-system)
11816 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
11817 (synopsis "Tests for outliers")
11819 "This package provides a collection of some tests commonly used for
11820 identifying outliers.")
11821 (license license:gpl2+)))
11823 (define-public r-bayesm
11830 (uri (cran-uri "bayesm" version))
11832 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
11833 (build-system r-build-system)
11835 `(("r-rcpp" ,r-rcpp)
11836 ("r-rcpparmadillo" ,r-rcpparmadillo)))
11837 (home-page "http://www.perossi.org/home/bsm-1")
11838 (synopsis "Bayesian inference for marketing/micro-econometrics")
11840 "This package covers many important models used in marketing and
11841 micro-econometrics applications, including Bayes Regression (univariate or
11842 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
11843 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
11844 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
11845 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
11846 Estimation with normal base, Hierarchical Linear Models with normal prior and
11847 covariates, Hierarchical Linear Models with a mixture of normals prior and
11848 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
11849 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
11850 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
11851 analysis of choice-based conjoint data, Bayesian treatment of linear
11852 instrumental variables models, Analysis of Multivariate Ordinal survey data
11853 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
11854 Coefficient Logit Models.")
11855 (license license:gpl2+)))
11857 (define-public r-tensora
11864 (uri (cran-uri "tensorA" version))
11867 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
11868 (properties `((upstream-name . "tensorA")))
11869 (build-system r-build-system)
11870 (home-page "http://www.stat.boogaart.de/tensorA")
11871 (synopsis "Advanced tensor arithmetic with named indices")
11873 "This package provides convenience functions for advanced linear algebra
11874 with tensors and computation with datasets of tensors on a higher level
11875 abstraction. It includes Einstein and Riemann summing conventions, dragging,
11876 co- and contravariate indices, and parallel computations on sequences of
11878 (license license:gpl2+)))
11880 (define-public r-rarpack
11887 (uri (cran-uri "rARPACK" version))
11890 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
11891 (properties `((upstream-name . "rARPACK")))
11892 (build-system r-build-system)
11893 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
11894 (home-page "https://github.com/yixuan/rARPACK")
11895 (synopsis "Solvers for large scale eigenvalue and SVD problems")
11897 "This package was previously an R wrapper of the ARPACK library, and now
11898 a shell of the R package RSpectra, an R interface to the Spectra library for
11899 solving large scale eigenvalue/vector problems. The current version of
11900 rARPACK simply imports and exports the functions provided by RSpectra. New
11901 users of rARPACK are advised to switch to the RSpectra package.")
11902 (license license:bsd-3)))
11904 (define-public r-compositions
11906 (name "r-compositions")
11911 (uri (cran-uri "compositions" version))
11914 "103hbmibrf1n333pn4xpll1gqqsv4szms0n5gdq7zak31aar0bg4"))))
11915 (build-system r-build-system)
11917 `(("r-bayesm" ,r-bayesm)
11918 ("r-robustbase" ,r-robustbase)
11919 ("r-tensora" ,r-tensora)))
11920 (home-page "http://www.stat.boogaart.de/compositions")
11921 (synopsis "Compositional data analysis")
11923 "This package provides functions for the consistent analysis of
11924 compositional data (e.g. portions of substances) and positive
11925 numbers (e.g. concentrations).")
11926 (license license:gpl2+)))
11928 (define-public r-cobs
11935 (uri (cran-uri "cobs" version))
11938 "1pqvz7czcchri4x79g78hbwyagb3bqzdqb047zkbdinyz067c7kb"))))
11939 (build-system r-build-system)
11941 `(("r-quantreg" ,r-quantreg)
11942 ("r-sparsem" ,r-sparsem)))
11943 (home-page "https://cran.r-project.org/web/packages/cobs")
11944 (synopsis "Constrained B-Splines (sparse matrix based)")
11946 "This package provides qualitatively constrained (regression) smoothing
11947 splines via linear programming and sparse matrices.")
11948 (license license:gpl2+)))
11950 (define-public r-drimpute
11952 (name "r-drimpute")
11957 (uri (cran-uri "DrImpute" version))
11960 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
11961 (properties `((upstream-name . "DrImpute")))
11962 (build-system r-build-system)
11964 `(("r-rcpp" ,r-rcpp)
11965 ("r-rcpparmadillo" ,r-rcpparmadillo)))
11966 (home-page "https://github.com/ikwak2/DrImpute")
11967 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
11969 "This is an R package for imputing dropout events. Many statistical
11970 methods in cell type identification, visualization and lineage reconstruction
11971 do not account for dropout events. DrImpute can improve the performance of
11972 such software by imputing dropout events.")
11973 (license license:gpl3)))
11975 (define-public r-gamlss-dist
11977 (name "r-gamlss-dist")
11982 (uri (cran-uri "gamlss.dist" version))
11984 (base32 "1rl7hzdg5xpvaq3yyzwxhsaqzzs0qidi3ibv454fisijgv8l4vqw"))))
11985 (properties `((upstream-name . "gamlss.dist")))
11986 (build-system r-build-system)
11987 (propagated-inputs `(("r-mass" ,r-mass)))
11988 (home-page "http://www.gamlss.org/")
11989 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
11991 "This package provides a set of distributions which can be used for
11992 modelling the response variables in Generalized Additive Models for Location
11993 Scale and Shape. The distributions can be continuous, discrete or mixed
11994 distributions. Extra distributions can be created, by transforming, any
11995 continuous distribution defined on the real line, to a distribution defined on
11996 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
11997 transformation, respectively.")
11998 ;; Either version of the GPL.
11999 (license (list license:gpl2 license:gpl3))))
12001 ;; This package includes JavaScript files, which are not minified. When
12002 ;; upgrading please check that there are no new minified JavaScript files.
12003 (define-public r-shinyjs
12010 (uri (cran-uri "shinyjs" version))
12013 "113zpijri0l80rlgrvqn6bxk0sdqgl79h7yhja2p76f9dc9i2sr8"))))
12014 (build-system r-build-system)
12016 `(("r-digest" ,r-digest)
12017 ("r-htmltools" ,r-htmltools)
12018 ("r-jsonlite" ,r-jsonlite)
12019 ("r-shiny" ,r-shiny)))
12020 (home-page "https://deanattali.com/shinyjs")
12021 (synopsis "Improve the user experience of your Shiny apps")
12023 "Perform common useful JavaScript operations in Shiny apps that will
12024 greatly improve your apps without having to know any JavaScript. Examples
12025 include: hiding an element, disabling an input, resetting an input back to its
12026 original value, delaying code execution by a few seconds, and many more useful
12027 functions for both the end user and the developer. Shinyjs can also be used
12028 to easily call your own custom JavaScript functions from R.")
12029 (license license:agpl3+)))
12031 ;; This package includes minified JavaScript files. When upgrading please
12032 ;; check that there are no new minified JavaScript files.
12033 (define-public r-colourpicker
12035 (name "r-colourpicker")
12040 (uri (cran-uri "colourpicker" version))
12043 "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
12044 (build-system r-build-system)
12046 `(#:modules ((guix build utils)
12047 (guix build r-build-system)
12051 (modify-phases %standard-phases
12052 (add-after 'unpack 'process-javascript
12053 (lambda* (#:key inputs #:allow-other-keys)
12054 (with-directory-excursion "inst"
12058 `((,(assoc-ref inputs "js-salvattore")
12059 "examples/colourInput/www/salvattore.min.js")
12060 (,(assoc-ref inputs "js-jquery")
12061 "htmlwidgets/lib/jquery/jquery.min.js")
12062 ("www/shared/colourpicker/js/colourpicker.js"
12063 "www/shared/colourpicker/js/colourpicker.min.js"))))
12064 (lambda (sources targets)
12065 (for-each (lambda (source target)
12066 (format #t "Processing ~a --> ~a~%"
12068 (delete-file target)
12069 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
12070 (call-with-output-file target
12072 (dump-port minified port)))))
12073 sources targets))))
12076 `(("r-ggplot2" ,r-ggplot2)
12077 ("r-htmltools" ,r-htmltools)
12078 ("r-htmlwidgets" ,r-htmlwidgets)
12079 ("r-jsonlite" ,r-jsonlite)
12080 ("r-miniui" ,r-miniui)
12081 ("r-shiny" ,r-shiny)
12082 ("r-shinyjs" ,r-shinyjs)))
12084 `(("uglify-js" ,uglify-js)
12088 (uri "https://code.jquery.com/jquery-3.3.1.js")
12091 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
12095 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
12098 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
12099 (home-page "https://github.com/daattali/colourpicker")
12100 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
12102 "This package provides a color picker that can be used as an input in
12103 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
12104 custom color palettes, and many more options. A plot color helper tool is
12105 available as an RStudio Addin, which helps you pick colors to use in your
12106 plots. A more generic color picker RStudio Addin is also provided to let you
12107 select colors to use in your R code.")
12108 (license license:expat)))
12110 (define-public r-ggextra
12117 (uri (cran-uri "ggExtra" version))
12120 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
12121 (properties `((upstream-name . "ggExtra")))
12122 (build-system r-build-system)
12124 `(("r-colourpicker" ,r-colourpicker)
12125 ("r-ggplot2" ,r-ggplot2)
12126 ("r-gtable" ,r-gtable)
12127 ("r-miniui" ,r-miniui)
12129 ("r-scales" ,r-scales)
12130 ("r-shiny" ,r-shiny)
12131 ("r-shinyjs" ,r-shinyjs)))
12132 (home-page "https://github.com/daattali/ggExtra")
12133 (synopsis "Marginal histograms for ggplot2 and other enhancements")
12135 "This package is a collection of functions and layers to enhance ggplot2.
12136 The flagship function is @code{ggMarginal()}, which can be used to add
12137 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
12138 (license license:expat)))
12140 (define-public r-minpack-lm
12142 (name "r-minpack-lm")
12147 (uri (cran-uri "minpack.lm" version))
12150 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
12151 (properties `((upstream-name . "minpack.lm")))
12152 (build-system r-build-system)
12153 (native-inputs `(("gfortran" ,gfortran)))
12154 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
12155 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
12157 "The @code{nls.lm} function provides an R interface to @code{lmder} and
12158 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
12159 problems by a modification of the Levenberg-Marquardt algorithm, with support
12160 for lower and upper parameter bounds. The implementation can be used via
12161 @code{nls}-like calls using the @code{nlsLM} function.")
12162 (license license:gpl3)))
12164 (define-public r-moments
12171 (uri (cran-uri "moments" version))
12174 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
12175 (build-system r-build-system)
12176 (home-page "https://cran.r-project.org/web/packages/moments")
12177 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
12179 "This package provides functions to calculate: moments, Pearson's
12180 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
12181 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
12182 (license license:gpl2+)))
12184 (define-public r-msir
12191 (uri (cran-uri "msir" version))
12194 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
12195 (build-system r-build-system)
12197 `(("r-mclust" ,r-mclust)))
12198 (home-page "https://cran.r-project.org/web/packages/msir")
12199 (synopsis "Model-based sliced inverse regression")
12201 "This is an R package for dimension reduction based on finite Gaussian
12202 mixture modeling of inverse regression.")
12203 (license license:gpl2+)))
12205 (define-public r-pbivnorm
12207 (name "r-pbivnorm")
12212 (uri (cran-uri "pbivnorm" version))
12215 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
12216 (build-system r-build-system)
12217 (native-inputs `(("gfortran" ,gfortran)))
12218 (home-page "https://github.com/brentonk/pbivnorm")
12219 (synopsis "Vectorized bivariate normal CDF")
12221 "This package provides a vectorized R function for calculating
12222 probabilities from a standard bivariate normal CDF.")
12223 (license license:gpl2+)))
12225 (define-public r-lavaan
12232 (uri (cran-uri "lavaan" version))
12235 "04kvsh2m6mnzlhv83phr3hjzy4sx1ck6f7dgsm7xb8cs84dnxszy"))))
12236 (build-system r-build-system)
12238 `(("r-mass" ,r-mass)
12239 ("r-mnormt" ,r-mnormt)
12240 ("r-numderiv" ,r-numderiv)
12241 ("r-pbivnorm" ,r-pbivnorm)))
12242 (home-page "http://lavaan.ugent.be")
12243 (synopsis "Latent variable analysis")
12245 "This package provides tools to fit a variety of latent variable models,
12246 including confirmatory factor analysis, structural equation modeling and
12247 latent growth curve models.")
12248 (license license:gpl2+)))
12250 (define-public r-nonnest2
12252 (name "r-nonnest2")
12257 (uri (cran-uri "nonnest2" version))
12260 "1bq44qqmm59j91m0sny4xnqmxqlga4cm48qdsw8xfs3x19xwmxk6"))))
12261 (build-system r-build-system)
12263 `(("r-compquadform" ,r-compquadform)
12264 ("r-lavaan" ,r-lavaan)
12265 ("r-mvtnorm" ,r-mvtnorm)
12266 ("r-sandwich" ,r-sandwich)))
12267 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
12268 (synopsis "Tests of non-nested models")
12270 "This package allows for testing of non-nested models. It includes tests
12271 of model distinguishability and of model fit that can be applied to both
12272 nested and non-nested models. The package also includes functionality to
12273 obtain confidence intervals associated with AIC and BIC.")
12274 ;; Either version of the GPL.
12275 (license (list license:gpl2 license:gpl3))))
12277 (define-public r-penalized
12279 (name "r-penalized")
12284 (uri (cran-uri "penalized" version))
12287 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
12288 (build-system r-build-system)
12290 `(("r-rcpp" ,r-rcpp)
12291 ("r-rcpparmadillo" ,r-rcpparmadillo)
12292 ("r-survival" ,r-survival)))
12293 (home-page "https://cran.r-project.org/web/packages/penalized/")
12294 (synopsis "Penalized estimation in GLMs and in the Cox model")
12296 "This package provides tools for fitting possibly high dimensional
12297 penalized regression models. The penalty structure can be any combination of
12298 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
12299 constraint on the regression coefficients. The supported regression models
12300 are linear, logistic and Poisson regression and the Cox Proportional Hazards
12301 model. Cross-validation routines allow optimization of the tuning
12303 (license license:gpl2+)))
12305 (define-public r-zim
12312 (uri (cran-uri "ZIM" version))
12315 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
12316 (properties `((upstream-name . "ZIM")))
12317 (build-system r-build-system)
12318 (propagated-inputs `(("r-mass" ,r-mass)))
12319 (home-page "https://github.com/biostatstudio/ZIM")
12320 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
12322 "Analyze count time series with excess zeros. Two types of statistical
12323 models are supported: Markov regression and state-space models. They are also
12324 known as observation-driven and parameter-driven models respectively in the
12325 time series literature. The functions used for Markov regression or
12326 observation-driven models can also be used to fit ordinary regression models
12327 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
12328 negative binomial (ZINB) assumption. The package also contains miscellaneous
12329 functions to compute density, distribution, quantile, and generate random
12330 numbers from ZIP and ZINB distributions.")
12331 (license license:gpl3)))
12333 (define-public r-nor1mix
12340 (uri (cran-uri "nor1mix" version))
12343 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
12344 (build-system r-build-system)
12345 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
12346 (synopsis "Normal (1-d) mixture models")
12348 "This package provides S3 classes and methods for one-dimensional normal
12349 mixture models, for, e.g., density estimation or clustering algorithms
12350 research and teaching; it provides the widely used Marron-Wand densities. It
12351 also provides tools for efficient random number generation and graphics.")
12352 (license license:gpl2+)))
12354 (define-public r-beanplot
12356 (name "r-beanplot")
12361 (uri (cran-uri "beanplot" version))
12364 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
12365 (build-system r-build-system)
12366 (home-page "https://cran.r-project.org/web/packages/beanplot/")
12367 (synopsis "Visualization via beanplots")
12369 "This package provides beanplots, an alternative to
12370 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
12372 (license license:gpl2)))
12374 (define-public r-pbdzmq
12381 (uri (cran-uri "pbdZMQ" version))
12384 "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
12385 (properties `((upstream-name . "pbdZMQ")))
12386 (build-system r-build-system)
12388 `(("zeromq" ,zeromq)
12391 `(("pkg-config" ,pkg-config)))
12392 (home-page "https://pbdr.org/")
12393 (synopsis "R interface to ZeroMQ")
12395 "ZeroMQ is a well-known library for high-performance asynchronous
12396 messaging in scalable, distributed applications. This package provides high
12397 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
12398 interactive client/server programming frameworks. A few wrapper functions
12399 compatible with @code{rzmq} are also provided.")
12400 (license license:gpl3)))
12402 (define-public r-repr
12409 (uri (cran-uri "repr" version))
12412 "0jy43g34r38fqprcdys0p9pliahrj5l64a9bbkzy206qgz0j5ppc"))))
12413 (build-system r-build-system)
12415 `(("r-base64enc" ,r-base64enc)
12416 ("r-htmltools" ,r-htmltools)
12417 ("r-jsonlite" ,r-jsonlite)
12418 ("r-pillar" ,r-pillar)))
12419 (home-page "https://cran.r-project.org/web/packages/repr/")
12420 (synopsis "Serializable representations")
12422 "This package provides string and binary representations of objects for
12423 several formats and MIME types.")
12424 (license license:gpl3)))
12426 (define-public r-irdisplay
12428 (name "r-irdisplay")
12433 (uri (cran-uri "IRdisplay" version))
12436 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
12437 (properties `((upstream-name . "IRdisplay")))
12438 (build-system r-build-system)
12440 `(("r-repr" ,r-repr)))
12441 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
12442 (synopsis "Jupyter display machinery")
12444 "This package provides an interface to the rich display capabilities of
12445 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
12446 running IRkernel session.")
12447 (license license:expat)))
12449 (define-public r-irkernel
12451 (name "r-irkernel")
12456 (uri (cran-uri "IRkernel" version))
12459 "1viqxs91dys1z4cf7gb59rmqvzb8lc7jdp4azrpmhgwa8qf46s94"))))
12460 (properties `((upstream-name . "IRkernel")))
12461 (build-system r-build-system)
12464 (modify-phases %standard-phases
12465 (add-after 'install 'install-kernelspec
12466 (lambda* (#:key outputs #:allow-other-keys)
12467 (let ((out (assoc-ref outputs "out")))
12468 (setenv "HOME" "/tmp")
12469 (invoke "jupyter" "kernelspec" "install"
12472 (string-append out "/site-library/IRkernel/kernelspec"))
12475 `(("jupyter" ,jupyter)))
12477 `(("r-crayon" ,r-crayon)
12478 ("r-digest" ,r-digest)
12479 ("r-evaluate" ,r-evaluate)
12480 ("r-irdisplay" ,r-irdisplay)
12481 ("r-jsonlite" ,r-jsonlite)
12482 ("r-pbdzmq" ,r-pbdzmq)
12484 ("r-uuid" ,r-uuid)))
12485 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
12486 (synopsis "Native R kernel for Jupyter")
12488 "The R kernel for the Jupyter environment executes R code which the
12489 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
12491 (license license:expat)))
12493 (define-public r-gmodels
12500 (uri (cran-uri "gmodels" version))
12503 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
12504 (build-system r-build-system)
12506 `(("r-gdata" ,r-gdata)
12507 ("r-mass" ,r-mass)))
12508 (home-page "https://cran.r-project.org/web/packages/gmodels/")
12509 (synopsis "Various R programming tools for model fitting")
12511 "This package provides various R programming tools for model fitting.")
12512 (license license:gpl2)))
12514 (define-public r-apcluster
12516 (name "r-apcluster")
12521 (uri (cran-uri "apcluster" version))
12524 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
12525 (build-system r-build-system)
12527 `(("r-matrix" ,r-matrix)
12528 ("r-rcpp" ,r-rcpp)))
12529 (home-page "https://cran.r-project.org/web/packages/apcluster/")
12530 (synopsis "Affinity propagation clustering")
12532 "This package implements affinity propagation clustering introduced by
12533 Frey and Dueck (2007). The package further provides leveraged affinity
12534 propagation and an algorithm for exemplar-based agglomerative clustering that
12535 can also be used to join clusters obtained from affinity propagation. Various
12536 plotting functions are available for analyzing clustering results.")
12537 (license license:gpl2+)))
12539 (define-public r-valr
12546 (uri (cran-uri "valr" version))
12549 "14jhrwkiwmha3vlmm7b50n2xxyizj6ddmy89gb20mpzq7qhz1ika"))))
12550 (build-system r-build-system)
12552 `(("r-broom" ,r-broom)
12553 ("r-dplyr" ,r-dplyr)
12554 ("r-ggplot2" ,r-ggplot2)
12556 ("r-readr" ,r-readr)
12557 ("r-rlang" ,r-rlang)
12558 ("r-stringr" ,r-stringr)
12559 ("r-tibble" ,r-tibble)))
12560 (home-page "http://github.com/rnabioco/valr")
12561 (synopsis "Genome interval arithmetic in R")
12563 "This package enables you to read and manipulate genome intervals and
12564 signals. It provides functionality similar to command-line tool suites within
12565 R, enabling interactive analysis and visualization of genome-scale data.")
12566 (license license:expat)))
12568 (define-public r-rematch2
12570 (name "r-rematch2")
12575 (uri (cran-uri "rematch2" version))
12578 "00cznm6rk33b53w7zybkz7549bnydc66znpi5mb0xd24pmqp0rvq"))))
12579 (build-system r-build-system)
12581 `(("r-tibble" ,r-tibble)))
12582 (home-page "https://github.com/r-lib/rematch2")
12583 (synopsis "Tidy output from regular expression matching")
12585 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
12586 return the match results in tidy data frames.")
12587 (license license:expat)))
12589 (define-public r-picante
12596 (uri (cran-uri "picante" version))
12599 "1bcq2j7fs89c2jib68qq6la67rxyg9raryf162mwvjakpf6k19l1"))))
12600 (build-system r-build-system)
12604 ("r-vegan" ,r-vegan)))
12605 (home-page "https://cran.r-project.org/web/packages/picante/")
12606 (synopsis "Integrating phylogenies and ecology")
12608 "This package provides functions for phylocom integration, community
12609 analyses, null-models, traits and evolution. It implements numerous
12610 ecophylogenetic approaches including measures of community phylogenetic and
12611 trait diversity, phylogenetic signal, estimation of trait values for
12612 unobserved taxa, null models for community and phylogeny randomizations, and
12613 utility functions for data input/output and phylogeny plotting. A full
12614 description of package functionality and methods are provided by Kembel et
12616 (license license:gpl2)))
12618 (define-public r-reinforcelearn
12620 (name "r-reinforcelearn")
12625 (uri (cran-uri "reinforcelearn" version))
12628 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
12629 (build-system r-build-system)
12631 `(("r-checkmate" ,r-checkmate)
12633 ("r-purrr" ,r-purrr)
12635 (home-page "https://markusdumke.github.io/reinforcelearn")
12636 (synopsis "Reinforcement learning")
12638 "This package implements reinforcement learning environments and
12639 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
12640 can be used with function approximation, eligibility traces (Singh & Sutton,
12641 1996) and experience replay (Mnih et al., 2013).")
12642 (license license:expat)))
12644 (define-public r-lemon
12651 (uri (cran-uri "lemon" version))
12654 "0wsn5bfg10wq4dnrgpyraz2bzx9p19c7hf1pwj3h4zmpqfgsdbpw"))))
12655 (build-system r-build-system)
12657 `(("r-ggplot2" ,r-ggplot2)
12658 ("r-gridextra" ,r-gridextra)
12659 ("r-gtable" ,r-gtable)
12660 ("r-knitr" ,r-knitr)
12661 ("r-lattice" ,r-lattice)
12663 ("r-scales" ,r-scales)))
12664 (home-page "https://github.com/stefanedwards/lemon")
12665 (synopsis "Freshen up your ggplot2 plots")
12667 "This package provides functions for working with legends and axis lines
12668 of ggplot2, facets that repeat axis lines on all panels, and some knitr
12670 (license license:gpl3)))
12672 (define-public r-wgaim
12679 (uri (cran-uri "wgaim" version))
12681 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
12682 (build-system r-build-system)
12684 `(("r-ggplot2" ,r-ggplot2)
12686 (home-page "https://cran.r-project.org/web/packages/wgaim")
12687 (synopsis "Whole genome average interval mapping for QTL detection")
12689 "This package integrates sophisticated mixed modelling methods with a
12690 whole genome approach to detecting significant QTL in linkage maps.")
12691 (license license:gpl2+)))
12693 (define-public r-bedr
12700 (uri (cran-uri "bedr" version))
12703 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
12704 (build-system r-build-system)
12706 `(("r-data-table" ,r-data-table)
12707 ("r-r-utils" ,r-r-utils)
12708 ("r-testthat" ,r-testthat)
12709 ("r-venndiagram" ,r-venndiagram)
12712 ("bedtools" ,bedtools)
12713 ("htslib" ,htslib))) ; for tabix
12715 `(("r-knitr" ,r-knitr))) ; for vignettes
12716 (home-page "https://cran.r-project.org/web/packages/bedr")
12717 (synopsis "Genomic region processing")
12719 "This package is for genomic regions processing using command line tools
12720 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
12721 utilities to perform genome arithmetic e.g indexing, formatting and merging.
12722 The bedr package's API enhances access to these tools as well as offers
12723 additional utilities for genomic regions processing.")
12724 (license license:gpl2)))
12726 (define-public r-sets
12733 (uri (cran-uri "sets" version))
12736 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
12737 (properties `((upstream-name . "sets")))
12738 (build-system r-build-system)
12739 (home-page "https://cran.r-project.org/web/packages/sets")
12740 (synopsis "Sets, generalized sets, customizable sets and intervals")
12742 "This package provides data structures and basic operations for ordinary
12743 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
12744 customizable sets, and intervals.")
12745 (license license:gpl2)))
12747 (define-public r-partitions
12749 (name "r-partitions")
12754 (uri (cran-uri "partitions" version))
12757 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
12758 (build-system r-build-system)
12761 ("r-polynom" ,r-polynom)
12762 ("r-sets" ,r-sets)))
12763 (home-page "https://cran.r-project.org/web/packages/partitions")
12764 (synopsis "Additive partitions of integers")
12766 "This package provides tools to enumerates the partitions, unequal
12767 partitions, and restricted partitions of an integer; the three corresponding
12768 partition functions are also given.")
12769 ;; Any version of the GPL
12770 (license license:gpl2+)))
12772 (define-public r-brobdingnag
12774 (name "r-brobdingnag")
12779 (uri (cran-uri "Brobdingnag" version))
12782 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
12783 (properties `((upstream-name . "Brobdingnag")))
12784 (build-system r-build-system)
12785 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
12786 (synopsis "Very large numbers in R")
12788 "This package handles very large numbers in R. Real numbers are held
12789 using their natural logarithms, plus a logical flag indicating sign. The
12790 package includes a vignette that gives a step-by-step introduction to using S4
12792 ;; Any version of the GPL
12793 (license license:gpl2+)))
12795 (define-public r-untb
12802 (uri (cran-uri "untb" version))
12805 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
12806 (build-system r-build-system)
12808 `(("r-brobdingnag" ,r-brobdingnag)
12809 ("r-partitions" ,r-partitions)
12810 ("r-polynom" ,r-polynom)))
12811 (home-page "https://github.com/RobinHankin/untb.git")
12812 (synopsis "Ecological drift under the UNTB")
12814 "This package provides numerical simulations, and visualizations, of
12815 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
12816 (license license:gpl2+)))
12818 (define-public r-stepwise
12820 (name "r-stepwise")
12825 (uri (cran-uri "stepwise" version))
12828 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
12829 (build-system r-build-system)
12830 (home-page "http://stat.sfu.ca/statgen/research/stepwise.html")
12831 (synopsis "Stepwise detection of recombination breakpoints")
12833 "This package provides a stepwise approach to identifying recombination
12834 breakpoints in a genomic sequence alignment.")
12835 (license license:gpl2+)))
12837 (define-public r-snpmaxsel
12839 (name "r-snpmaxsel")
12844 (uri (cran-uri "SNPmaxsel" version))
12847 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
12848 (properties `((upstream-name . "SNPmaxsel")))
12849 (build-system r-build-system)
12851 `(("r-combinat" ,r-combinat)
12852 ("r-mvtnorm" ,r-mvtnorm)))
12853 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
12854 (synopsis "Maximally selected statistics for SNP data")
12856 "This package implements asymptotic methods related to maximally selected
12857 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
12859 (license license:gpl2+)))
12861 (define-public r-acsnminer
12863 (name "r-acsnminer")
12864 (version "0.16.8.25")
12867 (uri (cran-uri "ACSNMineR" version))
12870 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
12871 (properties `((upstream-name . "ACSNMineR")))
12872 (build-system r-build-system)
12874 `(("r-ggplot2" ,r-ggplot2)
12875 ("r-gridextra" ,r-gridextra)))
12876 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
12877 (synopsis "Gene enrichment analysis")
12879 "This package provides tools to compute and represent gene set enrichment
12880 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
12881 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
12882 enrichment can be run with hypergeometric test or Fisher exact test, and can
12883 use multiple corrections. Visualization of data can be done either by
12884 barplots or heatmaps.")
12885 (license license:gpl2+)))
12887 (define-public r-seqinr
12894 (uri (cran-uri "seqinr" version))
12897 "0j30za6kji6y3v09cvcydiacnp65pv6ig8aw7cydl47l5s9chky4"))))
12898 (build-system r-build-system)
12900 `(("r-ade4" ,r-ade4)
12901 ("r-segmented" ,r-segmented)))
12904 (home-page "http://seqinr.r-forge.r-project.org/")
12905 (synopsis "Biological sequences retrieval and analysis")
12907 "This package provides tools for exploratory data analysis and data
12908 visualization of biological sequence (DNA and protein) data. It also includes
12909 utilities for sequence data management under the ACNUC system.")
12910 (license license:gpl2+)))
12912 (define-public r-units
12919 (uri (cran-uri "units" version))
12922 "02nls8m0r1r7kljs4x35naz3szq62hyqyd5vracf1xwi1kz5kdsh"))))
12923 (build-system r-build-system)
12925 `(("udunits" ,udunits)))
12927 `(("r-rcpp" ,r-rcpp)))
12928 (home-page "https://github.com/r-quantities/units/")
12929 (synopsis "Measurement Units for R Vectors")
12931 "This package provides support for measurement units in R vectors,
12932 matrices and arrays: automatic propagation, conversion, derivation and
12933 simplification of units; raising errors in case of unit incompatibility. It
12934 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
12936 (license license:gpl2)))
12938 (define-public r-classint
12940 (name "r-classint")
12945 (uri (cran-uri "classInt" version))
12948 "0w980hrw8sgfdfyd5dsimalq7gwhvqm7507abk7k363pvgks23dv"))))
12949 (properties `((upstream-name . "classInt")))
12950 (build-system r-build-system)
12952 `(("r-class" ,r-class)
12953 ("r-e1071" ,r-e1071)
12954 ("r-kernsmooth" ,r-kernsmooth)))
12955 (native-inputs `(("gfortran" ,gfortran)))
12956 (home-page "https://github.com/r-spatial/classInt/")
12957 (synopsis "Choose univariate class intervals")
12959 "This package provides selected commonly used methods for choosing
12960 univariate class intervals for mapping or other graphics purposes.")
12961 (license license:gpl2+)))
12963 (define-public r-spdata
12970 (uri (cran-uri "spData" version))
12973 "190msrrpn226x27pcnck4ac34f9k4xcn26cyz2apdri2nzkr6zbw"))))
12974 (properties `((upstream-name . "spData")))
12975 (build-system r-build-system)
12976 (home-page "https://github.com/Nowosad/spData")
12977 (synopsis "Datasets for spatial analysis")
12979 "This a package containing diverse spatial datasets for demonstrating,
12980 benchmarking and teaching spatial data analysis. It includes R data of class
12981 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
12982 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
12983 of the datasets are designed to illustrate specific analysis techniques.
12984 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
12985 illustrate point pattern analysis techniques.")
12986 (license license:cc0)))
12988 (define-public r-learnbayes
12990 (name "r-learnbayes")
12995 (uri (cran-uri "LearnBayes" version))
12998 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
12999 (properties `((upstream-name . "LearnBayes")))
13000 (build-system r-build-system)
13001 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
13002 (synopsis "Functions for learning Bayesian inference")
13004 "This package provides a collection of functions helpful in learning the
13005 basic tenets of Bayesian statistical inference. It contains functions for
13006 summarizing basic one and two parameter posterior distributions and predictive
13007 distributions. It contains MCMC algorithms for summarizing posterior
13008 distributions defined by the user. It also contains functions for regression
13009 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
13011 (license license:gpl2+)))
13013 (define-public r-deldir
13020 (uri (cran-uri "deldir" version))
13023 "0790dwxb2mz1ffz8gd5vwdr0if2q76dzy3vab5rsykf9kz72n4g0"))))
13024 (build-system r-build-system)
13025 (native-inputs `(("gfortran" ,gfortran)))
13026 (home-page "https://cran.r-project.org/web/packages/deldir")
13027 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
13029 "This package provides tools for calculating the Delaunay triangulation
13030 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
13031 of a planar point set. It plots triangulations and tessellations in various
13032 ways, clips tessellations to sub-windows, calculates perimeters of
13033 tessellations, and summarizes information about the tiles of the
13035 (license license:gpl2+)))
13037 (define-public r-sf
13044 (uri (cran-uri "sf" version))
13047 "05dyq0vcz2f1fl03hk3v1a4nz4s84yyqw4rc9w9cwfq71gvm9qwf"))))
13048 (build-system r-build-system)
13055 `(("r-classint" ,r-classint)
13057 ("r-magrittr" ,r-magrittr)
13059 ("r-units" ,r-units)))
13060 (native-inputs `(("pkg-config" ,pkg-config)))
13061 (home-page "https://github.com/r-spatial/sf/")
13062 (synopsis "Simple features for R")
13064 "This package provides support for simple features, a standardized way to
13065 encode spatial vector data. It binds to GDAL for reading and writing data, to
13066 GEOS for geometrical operations, and to PROJ for projection conversions and
13067 datum transformations.")
13068 ;; Either of these licenses
13069 (license (list license:gpl2 license:expat))))
13071 (define-public r-spdep
13078 (uri (cran-uri "spdep" version))
13081 "1f8cjffqqc6rnb3n4qym70ca6nz2kvrsd3g587wrqdr79nnbwnrk"))))
13082 (build-system r-build-system)
13084 `(("r-boot" ,r-boot)
13086 ("r-deldir" ,r-deldir)
13088 ("r-gmodels" ,r-gmodels)
13089 ("r-learnbayes" ,r-learnbayes)
13091 ("r-matrix" ,r-matrix)
13095 ("r-spdata" ,r-spdata)))
13096 (home-page "https://github.com/r-spatial/spdep/")
13097 (synopsis "Spatial dependence: weighting schemes, statistics and models")
13099 "This package provides a collection of functions to create spatial
13100 weights matrix objects from polygon contiguities, from point patterns by
13101 distance and tessellations, for summarizing these objects, and for permitting
13102 their use in spatial data analysis, including regional aggregation by minimum
13104 (license license:gpl2+)))
13106 (define-public r-adegenet
13108 (name "r-adegenet")
13113 (uri (cran-uri "adegenet" version))
13116 "0ynfblp0hbd3dp3k86fn1wyhqr28lk6hs2bg4q7gyf0sfdfzwhrh"))))
13117 (build-system r-build-system)
13119 `(("r-ade4" ,r-ade4)
13122 ("r-dplyr" ,r-dplyr)
13123 ("r-ggplot2" ,r-ggplot2)
13124 ("r-igraph" ,r-igraph)
13126 ("r-reshape2" ,r-reshape2)
13127 ("r-seqinr" ,r-seqinr)
13128 ("r-shiny" ,r-shiny)
13129 ("r-spdep" ,r-spdep)
13130 ("r-vegan" ,r-vegan)))
13131 (home-page "https://github.com/thibautjombart/adegenet")
13132 (synopsis "Exploratory analysis of genetic and genomic data")
13134 "This package provides a toolset for the exploration of genetic and
13135 genomic data. Adegenet provides formal (S4) classes for storing and handling
13136 various genetic data, including genetic markers with varying ploidy and
13137 hierarchical population structure (@code{genind} class), alleles counts by
13138 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
13139 also implements original multivariate methods (DAPC, sPCA), graphics,
13140 statistical tests, simulation tools, distance and similarity measures, and
13141 several spatial methods. A range of both empirical and simulated datasets is
13142 also provided to illustrate various methods.")
13143 (license license:gpl2+)))
13145 (define-public r-pegas
13152 (uri (cran-uri "pegas" version))
13154 (base32 "0sb8cmz4d238mcb56hv9fa0cagm00k82r7aj4cj4lxa1flxlpy8p"))))
13155 (build-system r-build-system)
13157 `(("r-adegenet" ,r-adegenet)
13159 (home-page "http://ape-package.ird.fr/pegas.html")
13160 (synopsis "Population and evolutionary genetics analysis system")
13162 "This package provides functions for reading, writing, plotting,
13163 analysing, and manipulating allelic and haplotypic data, including from VCF
13164 files, and for the analysis of population nucleotide sequences and
13165 micro-satellites including coalescent analyses, linkage disequilibrium,
13166 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
13167 minimum spanning tree and network, and median-joining networks.")
13168 (license license:gpl2+)))
13170 (define-public r-rmetasim
13172 (name "r-rmetasim")
13177 (uri (cran-uri "rmetasim" version))
13180 "0sz4mdprdi6sgkfwfdvh2hr9nxiwq17sw0vggq3cvs7lzb0i6m9r"))))
13181 (build-system r-build-system)
13183 `(("r-ade4" ,r-ade4)
13184 ("r-adegenet" ,r-adegenet)
13185 ("r-gtools" ,r-gtools)
13186 ("r-pegas" ,r-pegas)))
13187 (home-page "https://cran.r-project.org/web/packages/rmetasim")
13188 (synopsis "Individual-based population genetic simulation environment")
13190 "This package provides an interface between R and the metasim simulation
13191 engine. The simulation environment is documented in: Strand, A.(2002),
13192 Metasim 1.0: an individual-based environment for simulating population
13193 genetics of complex population dynamics.")
13195 (license license:gpl2+)))
13197 (define-public r-genetics
13199 (name "r-genetics")
13200 (version "1.3.8.1.2")
13204 (uri (cran-uri "genetics" version))
13207 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
13208 (build-system r-build-system)
13210 `(("r-combinat" ,r-combinat)
13211 ("r-gdata" ,r-gdata)
13212 ("r-gtools" ,r-gtools)
13214 ("r-mvtnorm" ,r-mvtnorm)))
13215 (home-page "https://cran.r-project.org/web/packages/genetics/")
13216 (synopsis "Population genetics")
13218 "This package provides classes and methods for handling genetic data.
13219 It includes classes to represent genotypes and haplotypes at single markers up
13220 to multiple markers on multiple chromosomes. Function include allele
13221 frequencies, flagging homo/heterozygotes, flagging carriers of certain
13222 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
13223 and testing for linkage disequilibrium, ...")
13224 ;; Any GPL version.
13225 (license license:gpl2+)))
13227 (define-public r-snp-plotter
13229 (name "r-snp-plotter")
13234 (uri (cran-uri "snp.plotter" version))
13237 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
13238 (properties `((upstream-name . "snp.plotter")))
13239 (build-system r-build-system)
13240 (propagated-inputs `(("r-genetics" ,r-genetics)))
13241 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
13242 (synopsis "Plot p-values using single SNP and/or haplotype data")
13244 "This package helps you create plots of p-values using single SNP and/or
13245 haplotype data. Main features of the package include options to display a
13246 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
13247 datasets simultaneously. Plots can be created using global and/or individual
13248 haplotype p-values along with single SNP p-values. Images are created as
13249 either PDF/EPS files.")
13250 (license license:gpl2+)))
13252 (define-public r-polspline
13254 (name "r-polspline")
13259 (uri (cran-uri "polspline" version))
13261 (base32 "0c7fnxpqpy3hibiim4yib6l6bq363s97wwvllxp4lp8h06fjcyyn"))))
13262 (build-system r-build-system)
13263 (native-inputs `(("gfortran" ,gfortran)))
13264 (home-page "https://cran.r-project.org/web/packages/polspline/")
13265 (synopsis "Polynomial spline routines")
13267 "This package provides routines for the polynomial spline fitting
13268 routines hazard regression, hazard estimation with flexible tails, logspline,
13269 lspec, polyclass, and polymars.")
13270 (license license:gpl2+)))
13272 (define-public r-rms
13279 (uri (cran-uri "rms" version))
13281 (base32 "19knh1sw0icw6jh9wfb2hq5jf49i2qfvp9myvqm5paa495689x9q"))))
13282 (build-system r-build-system)
13284 `(("r-ggplot2" ,r-ggplot2)
13285 ("r-hmisc" ,r-hmisc)
13286 ("r-htmltable" ,r-htmltable)
13287 ("r-htmltools" ,r-htmltools)
13288 ("r-lattice" ,r-lattice)
13289 ("r-multcomp" ,r-multcomp)
13291 ("r-polspline" ,r-polspline)
13292 ("r-quantreg" ,r-quantreg)
13293 ("r-rpart" ,r-rpart)
13294 ("r-sparsem" ,r-sparsem)
13295 ("r-survival" ,r-survival)))
13296 (native-inputs `(("gfortran" ,gfortran)))
13297 (home-page "http://biostat.mc.vanderbilt.edu/rms")
13298 (synopsis "Regression modeling strategies")
13300 "This is a package for regression modeling, testing, estimation,
13301 validation, graphics, prediction, and typesetting by storing enhanced model
13302 design attributes in the fit. The rms package is a collection of functions
13303 that assist with and streamline modeling. It also contains functions for
13304 binary and ordinal logistic regression models, ordinal models for continuous Y
13305 with a variety of distribution families, and the Buckley-James multiple
13306 regression model for right-censored responses, and implements penalized
13307 maximum likelihood estimation for logistic and ordinary linear models. The
13308 package works with almost any regression model, but it was especially written
13309 to work with binary or ordinal regression models, Cox regression, accelerated
13310 failure time models, ordinary linear models, the Buckley-James model,
13311 generalized least squares for serially or spatially correlated observations,
13312 generalized linear models, and quantile regression.")
13313 (license license:gpl2+)))
13315 (define-public r-haplo-stats
13317 (name "r-haplo-stats")
13322 (uri (cran-uri "haplo.stats" version))
13325 "19kxascqq5qz0zdxx0w837ji207y1z2ggxkl4vmlbay03k2dw2mx"))))
13326 (properties `((upstream-name . "haplo.stats")))
13327 (build-system r-build-system)
13329 `(("r-rms" ,r-rms)))
13331 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
13332 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
13333 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
13335 "This package provides routines for the analysis of indirectly measured
13336 haplotypes. The statistical methods assume that all subjects are unrelated
13337 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
13338 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
13339 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
13340 examples in the vignette.")
13341 (license license:gpl2+)))
13343 (define-public r-bqtl
13350 (uri (cran-uri "bqtl" version))
13353 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
13354 (build-system r-build-system)
13355 (native-inputs `(("gfortran" ,gfortran)))
13356 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
13357 (synopsis "Bayesian QTL mapping toolkit")
13359 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
13360 lines. It includes maximum likelihood and Bayesian tools.")
13361 (license license:gpl2+)))
13363 (define-public r-ibdreg
13370 (uri (cran-uri "ibdreg" version))
13373 "1kaa5q1byi30wzr0mw4w2cv1ssxprzcwf91wrpqwkgcsdy7dkh2g"))))
13374 (build-system r-build-system)
13375 (home-page "https://www.mayo.edu/research/labs/\
13376 statistical-genetics-genetic-epidemiology/software")
13377 (synopsis "Regression methods for IBD linkage with covariates")
13379 "This package provides a method to test genetic linkage with covariates
13380 by regression methods with response IBD sharing for relative pairs. Account
13381 for correlations of IBD statistics and covariates for relative pairs within
13382 the same pedigree.")
13383 (license license:gpl2+)))
13385 (define-public r-dlmap
13392 (uri (cran-uri "dlmap" version))
13395 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
13396 (build-system r-build-system)
13398 `(("r-ibdreg" ,r-ibdreg)
13402 ("r-wgaim" ,r-wgaim)))
13403 (home-page "https://cran.r-project.org/web/packages/dlmap/")
13404 (synopsis "Detection localization mapping for QTL")
13406 "This is package for QTL mapping in a mixed model framework with separate
13407 detection and localization stages. The first stage detects the number of QTL
13408 on each chromosome based on the genetic variation due to grouped markers on
13409 the chromosome; the second stage uses this information to determine the most
13410 likely QTL positions. The mixed model can accommodate general fixed and
13411 random effects, including spatial effects in field trials and pedigree
13412 effects. It is applicable to backcrosses, doubled haploids, recombinant
13413 inbred lines, F2 intercrosses, and association mapping populations.")
13414 (license license:gpl2)))
13416 (define-public r-ldheatmap
13418 (name "r-ldheatmap")
13423 (uri (cran-uri "LDheatmap" version))
13426 "1r0j8bihi5z1x0sgaf7dwzpsw9i0nc1vylvipvc0cia2ka1lr9dc"))))
13427 (properties `((upstream-name . "LDheatmap")))
13428 (build-system r-build-system)
13430 `(("r-genetics" ,r-genetics)
13432 ("r-snpstats" ,r-snpstats)))
13433 (home-page "http://stat.sfu.ca/statgen/research/ldheatmap.html")
13434 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
13436 "This package provides tools to produce a graphical display, as a heat
13437 map, of measures of pairwise linkage disequilibria between SNPs. Users may
13438 optionally include the physical locations or genetic map distances of each SNP
13440 (license license:gpl3)))
13442 (define-public r-hwde
13449 (uri (cran-uri "hwde" version))
13452 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
13453 (build-system r-build-system)
13454 (home-page "https://cran.r-project.org/web/packages/hwde/")
13455 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
13457 "This package fits models for genotypic disequilibria, as described in
13458 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
13459 terms are available that account for first order interactions between loci.
13460 It also implements, for a single locus in a single population, a conditional
13461 exact test for Hardy-Weinberg equilibrium.")
13462 (license license:gpl2+)))
13464 (define-public r-tdthap
13471 (uri (cran-uri "tdthap" version))
13474 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
13475 (build-system r-build-system)
13476 (home-page "https://cran.r-project.org/web/packages/tdthap/")
13477 (synopsis "TDT tests for extended haplotypes")
13479 "Functions and examples are provided for transmission/disequilibrium
13480 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
13481 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
13482 (license license:artistic2.0)))
13484 (define-public r-sparql
13490 (uri (cran-uri "SPARQL" version))
13493 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
13494 (properties `((upstream-name . "SPARQL")))
13495 (build-system r-build-system)
13497 `(("r-rcurl" ,r-rcurl)
13499 (home-page "https://cran.r-project.org/web/packages/SPARQL")
13500 (synopsis "SPARQL client for R")
13501 (description "This package provides an interface to use SPARQL to pose
13502 SELECT or UPDATE queries to an end-point.")
13503 ;; The only license indication is found in the DESCRIPTION file,
13504 ;; which states GPL-3. So we cannot assume GPLv3+.
13505 (license license:gpl3)))
13507 (define-public r-bookdown
13509 (name "r-bookdown")
13513 (uri (cran-uri "bookdown" version))
13516 "1gwgvx1yg6q3wccnhidr3gshdvlgr42i4pvlg4h29kpsa7smjiv1"))))
13517 (build-system r-build-system)
13519 `(("r-htmltools" ,r-htmltools)
13520 ("r-knitr" ,r-knitr)
13521 ("r-rmarkdown" ,r-rmarkdown)
13522 ("r-tinytex" ,r-tinytex)
13524 ("pandoc" ,ghc-pandoc)))
13525 (home-page "https://github.com/rstudio/bookdown")
13526 (synopsis "Authoring books and technical documents with R markdown")
13527 (description "This package provides output formats and utilities for
13528 authoring books and technical documents with R Markdown.")
13529 (license license:gpl3)))
13531 (define-public r-optparse
13533 (name "r-optparse")
13538 (uri (cran-uri "optparse" version))
13541 "0wyrc42ja3ab5szx46zmz8lm7vzfqxkjca0m0sms8g9hqbmmay6d"))))
13542 (build-system r-build-system)
13544 `(("r-getopt" ,r-getopt)))
13545 (home-page "https://github.com/trevorld/optparse")
13546 (synopsis "Command line option parser")
13548 "This package provides a command line parser inspired by Python's
13549 @code{optparse} library to be used with Rscript to write shebang scripts
13550 that accept short and long options.")
13551 (license license:gpl2+)))
13553 (define-public r-wgcna
13560 (uri (cran-uri "WGCNA" version))
13563 "1s7gy5vd7x67hpgli8r7ba2z99w3psiyv5hqmrh94zw141dg210a"))))
13564 (properties `((upstream-name . "WGCNA")))
13565 (build-system r-build-system)
13567 `(("r-annotationdbi" ,r-annotationdbi)
13568 ("r-doparallel" ,r-doparallel)
13569 ("r-dynamictreecut" ,r-dynamictreecut)
13570 ("r-fastcluster" ,r-fastcluster)
13571 ("r-foreach" ,r-foreach)
13572 ("r-go-db" ,r-go-db)
13573 ("r-hmisc" ,r-hmisc)
13574 ("r-impute" ,r-impute)
13576 ("r-robust" ,r-robust)
13577 ("r-survival" ,r-survival)
13578 ("r-matrixstats" ,r-matrixstats)
13579 ("r-preprocesscore" ,r-preprocesscore)))
13581 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
13582 (synopsis "Weighted correlation network analysis")
13584 "This package provides functions necessary to perform Weighted
13585 Correlation Network Analysis on high-dimensional data. It includes functions
13586 for rudimentary data cleaning, construction and summarization of correlation
13587 networks, module identification and functions for relating both variables and
13588 modules to sample traits. It also includes a number of utility functions for
13589 data manipulation and visualization.")
13590 (license license:gpl2+)))
13592 (define-public r-kernlab
13599 (uri (cran-uri "kernlab" version))
13601 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
13602 (build-system r-build-system)
13603 (home-page "https://cran.r-project.org/web/packages/kernlab")
13604 (synopsis "Kernel-based machine learning tools")
13606 "This package provides kernel-based machine learning methods for
13607 classification, regression, clustering, novelty detection, quantile regression
13608 and dimensionality reduction. Among other methods @code{kernlab} includes
13609 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
13611 (license license:gpl2)))
13613 (define-public r-hierfstat
13615 (name "r-hierfstat")
13616 (version "0.04-22")
13620 (uri (cran-uri "hierfstat" version))
13623 "1fav2v2996v5kb1ffa6v5wxfm921syxg6as034vd3j4jfhdibyfx"))))
13624 (build-system r-build-system)
13626 `(("r-ade4" ,r-ade4)
13627 ("r-adegenet" ,r-adegenet)
13628 ("r-gtools" ,r-gtools)))
13629 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
13630 (synopsis "Estimation and tests of hierarchical F-statistics")
13632 "This package allows the estimation of hierarchical F-statistics from
13633 haploid or diploid genetic data with any numbers of levels in the hierarchy,
13634 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
13635 are also given to test via randomisations the significance of each F and
13636 variance components, using the likelihood-ratio statistics G.")
13637 (license license:gpl2+)))
13639 (define-public r-hapassoc
13641 (name "r-hapassoc")
13646 (uri (cran-uri "hapassoc" version))
13649 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
13650 (build-system r-build-system)
13651 (home-page "http://stat.sfu.ca/statgen/research/hapassoc.html")
13652 (synopsis "Inference of trait associations with SNP haplotypes")
13654 "Hapassoc performs likelihood inference of trait associations with
13655 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
13656 functions are developed primarily for data collected in cohort or
13657 cross-sectional studies. They can accommodate uncertain haplotype phase and
13658 handle missing genotypes at some SNPs.")
13659 (license license:gpl2)))
13661 (define-public r-sampling
13663 (name "r-sampling")
13668 (uri (cran-uri "sampling" version))
13671 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
13672 (build-system r-build-system)
13674 `(("r-lpsolve" ,r-lpsolve)
13675 ("r-mass" ,r-mass)))
13676 (home-page "https://cran.r-project.org/web/packages/sampling/")
13677 (synopsis "Survey sampling")
13679 "This package provides functions for drawing and calibrating samples.")
13680 (license license:gpl2+)))
13682 (define-public r-r2html
13689 (uri (cran-uri "R2HTML" version))
13692 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
13693 (properties `((upstream-name . "R2HTML")))
13694 (build-system r-build-system)
13695 (home-page "https://github.com/nalimilan/R2HTML")
13696 (synopsis "HTML export for R objects")
13698 "This package includes HTML functions and methods to write in an HTML
13699 file. Thus, making HTML reports is easy. It includes a function that allows
13700 redirection on the fly, which appears to be very useful for teaching purposes,
13701 as the student can keep a copy of the produced output to keep all that they
13702 did during the course. The package comes with a vignette describing how to
13703 write HTML reports for statistical analysis. Finally, a driver for Sweave
13704 allows to parse HTML flat files containing R code and to automatically write
13705 the corresponding outputs (tables and graphs).")
13706 (license license:gpl2+)))
13708 (define-public r-rjava
13715 (uri (cran-uri "rJava" version))
13718 "0s9cjy1wh7snmbqwznh8f1r4ipylr7mgda4a979z963a8lqy32n2"))))
13719 (properties `((upstream-name . "rJava")))
13720 (build-system r-build-system)
13722 `(#:modules ((guix build utils)
13723 (guix build r-build-system)
13726 (modify-phases %standard-phases
13727 (add-after 'unpack 'set-JAVA_HOME
13728 (lambda* (#:key inputs #:allow-other-keys)
13729 (let ((jdk (assoc-ref inputs "jdk")))
13730 (setenv "JAVA_HOME" jdk)
13731 (setenv "JAVA" (which "java"))
13732 (setenv "JAR" (which "jar"))
13733 (setenv "JAVAC" (which "javac"))
13734 (setenv "JAVAH" (which "javah"))
13735 (setenv "JAVA_CPPFLAGS"
13736 (string-append "-I" jdk "/include "
13737 "-I" jdk "/include/linux"))
13738 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
13739 ((lib) (setenv "JAVA_LIBS" lib))
13740 (_ (error "Could not find libjvm.so"))))
13744 ("jdk" ,icedtea-8 "jdk")
13747 (home-page "http://www.rforge.net/rJava/")
13748 (synopsis "Low-Level R to Java interface")
13750 "This package provides a low-level interface to the Java VM very much
13751 like .C/.Call and friends. It allows the creation of objects, calling methods
13752 and accessing fields.")
13753 (license license:gpl2)))
13755 (define-public r-svmisc
13762 (uri (cran-uri "svMisc" version))
13765 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
13766 (properties `((upstream-name . "svMisc")))
13767 (build-system r-build-system)
13768 (home-page "https://github.com/SciViews/svMisc")
13769 (synopsis "Miscellaneous functions for SciViews")
13771 "This package provides miscellaneous functions for SciViews or general
13772 use, including tools to manage a temporary environment attached to the search
13773 path for temporary variables you do not want to @code{save()} or
13774 @code{load()}; test the current platform; showing progress bars, etc.")
13775 (license license:gpl2)))
13777 (define-public r-xyz
13784 (uri (cran-uri "xyz" version))
13787 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
13788 (build-system r-build-system)
13790 `(("r-rcpp" ,r-rcpp)))
13791 (home-page "https://cran.r-project.org/web/packages/xyz/")
13792 (synopsis "Algorithm for fast interaction search in high-dimensional data")
13794 "High dimensional interaction search by brute force requires a quadratic
13795 computational cost in the number of variables. The xyz algorithm provably
13796 finds strong interactions in almost linear time. For details of the algorithm
13797 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
13798 interaction search in high-dimensional data.")
13799 ;; Any version of the GPL.
13800 (license license:gpl2+)))
13802 (define-public r-rttf2pt1
13804 (name "r-rttf2pt1")
13809 (uri (cran-uri "Rttf2pt1" version))
13812 "12hf9r3mhjr9sawdvf7qhjf1zph2q64f77i81jwvy7awidbm0kja"))))
13813 (properties `((upstream-name . "Rttf2pt1")))
13814 (build-system r-build-system)
13815 (home-page "https://github.com/wch/Rttf2pt1")
13816 (synopsis "Font conversion utility")
13818 "This package contains the program @code{ttf2pt1}, for use with the
13819 @code{extrafont} package.")
13820 ;; Most of the files are covered under the Expat license. Some files are
13821 ;; covered under BSD-3. Deviations for individual files are recorded in
13822 ;; the LICENSE file.
13823 (license (list license:bsd-3 license:expat
13824 (license:non-copyleft "file://LICENSE")))))
13826 (define-public r-extrafontdb
13828 (name "r-extrafontdb")
13833 (uri (cran-uri "extrafontdb" version))
13836 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
13837 (build-system r-build-system)
13838 (home-page "https://github.com/wch/extrafontdb")
13839 (synopsis "Database for the extrafont package")
13841 "This package holds the database for the @code{extrafont} package.")
13842 (license license:gpl2)))
13844 (define-public r-extrafont
13846 (name "r-extrafont")
13851 (uri (cran-uri "extrafont" version))
13854 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
13855 (build-system r-build-system)
13857 `(("r-extrafontdb" ,r-extrafontdb)
13858 ("r-rttf2pt1" ,r-rttf2pt1)))
13859 (home-page "https://github.com/wch/extrafont")
13860 (synopsis "Tools for using fonts in R")
13862 "The extrafont package makes it easier to use fonts other than the basic
13863 PostScript fonts that R uses. Fonts that are imported into extrafont can be
13864 used with PDF or PostScript output files. There are two hurdles for using
13865 fonts in PDF (or Postscript) output files:
13868 @item Making R aware of the font and the dimensions of the characters.
13869 @item Embedding the fonts in the PDF file so that the PDF can be displayed
13870 properly on a device that doesn't have the font. This is usually needed if
13871 you want to print the PDF file or share it with others.
13874 The extrafont package makes both of these things easier.")
13875 (license license:gpl2)))
13877 (define-public r-xkcd
13884 (uri (cran-uri "xkcd" version))
13887 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
13888 (build-system r-build-system)
13890 `(("r-extrafont" ,r-extrafont)
13891 ("r-ggplot2" ,r-ggplot2)
13892 ("r-hmisc" ,r-hmisc)))
13893 (home-page "https://cran.r-project.org/web/packages/xkcd/")
13894 (synopsis "Plot ggplot2 graphics in the XKCD style")
13896 "This package provides the means to plot ggplot2 graphs in the style of
13897 the XKCD web comic.")
13898 (license license:gpl3)))
13900 (define-public r-msigdbr
13907 (uri (cran-uri "msigdbr" version))
13910 "19p8z617m3my8la7n1qgb1s2msf940r372im3q30qkbcx3qxg3sd"))))
13911 (build-system r-build-system)
13913 `(("r-dplyr" ,r-dplyr)
13914 ("r-magrittr" ,r-magrittr)
13915 ("r-rlang" ,r-rlang)
13916 ("r-tibble" ,r-tibble)))
13917 (home-page "https://github.com/igordot/msigdbr")
13918 (synopsis "MSigDB gene sets for multiple organisms")
13920 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
13921 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
13922 software in a standard R data frame with key-value pairs. Included are the
13923 original human gene symbols and Entrez IDs as well as the equivalents for
13924 various frequently studied model organisms such as mouse, rat, pig, fly, and
13926 ;; The package is covered under the Expat license, but the upstream MSigDB
13927 ;; files are made available under the Creative Commons Attribution 4.0
13928 ;; International license.
13929 (license (list license:expat license:cc-by4.0))))
13931 (define-public r-gridgraphics
13933 (name "r-gridgraphics")
13938 (uri (cran-uri "gridGraphics" version))
13941 "1kr3p54bkv2q7agxrva30y9bkwkiq1k2cfl5z1kvyjv6f5xi4w5p"))))
13942 (properties `((upstream-name . "gridGraphics")))
13943 (build-system r-build-system)
13944 (home-page "https://github.com/pmur002/gridgraphics")
13945 (synopsis "Redraw base graphics using @code{grid} graphics")
13947 "This package provides functions to convert a page of plots drawn with
13948 the @code{graphics} package into identical output drawn with the @code{grid}
13949 package. The result looks like the original @code{graphics}-based plot, but
13950 consists of @code{grid} grobs and viewports that can then be manipulated with
13951 @code{grid} functions (e.g., edit grobs and revisit viewports).")
13952 (license license:gpl2+)))
13954 (define-public r-farver
13961 (uri (cran-uri "farver" version))
13964 "0aq1hk561pz3s3lpay1adwsihha6mxp7zbj4n1m6307g34awlhhn"))))
13965 (build-system r-build-system)
13966 (home-page "https://github.com/thomasp85/farver")
13967 (synopsis "Vectorized color conversion and comparison")
13969 "The encoding of color can be handled in many different ways, using
13970 different color spaces. As different color spaces have different uses,
13971 efficient conversion between these representations are important. This
13972 package provides a set of functions that gives access to very fast color space
13973 conversion and comparisons implemented in C++, and offers 100-fold speed
13974 improvements over the @code{convertColor} function in the @code{grDevices}
13976 (license license:expat)))
13978 (define-public r-ggplotify
13980 (name "r-ggplotify")
13985 (uri (cran-uri "ggplotify" version))
13988 "0nv3wdmxnc5ww9m3xlgnb0jp30j45dg33nqc6gg3y36svg8anjcg"))))
13989 (build-system r-build-system)
13991 `(("r-ggplot2" ,r-ggplot2)
13992 ("r-gridgraphics" ,r-gridgraphics)
13993 ("r-rvcheck" ,r-rvcheck)))
13994 (home-page "https://github.com/GuangchuangYu/ggplotify")
13995 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
13997 "This package provides tools to convert plot function calls (using
13998 expression or formula) to @code{grob} or @code{ggplot} objects that are
13999 compatible with the @code{grid} and @code{ggplot2} environment. With this
14000 package, we are able to e.g. use @code{cowplot} to align plots produced by
14001 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
14002 converting them to @code{ggplot} objects.")
14003 (license license:artistic2.0)))
14005 (define-public r-triebeard
14007 (name "r-triebeard")
14012 (uri (cran-uri "triebeard" version))
14015 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
14016 (build-system r-build-system)
14017 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
14018 (home-page "https://github.com/Ironholds/triebeard/")
14019 (synopsis "Radix trees in Rcpp")
14021 "Radix trees, or tries, are key-value data structures optimized for
14022 efficient lookups, similar in purpose to hash tables. This package provides
14023 an implementation of radix trees for use in R programming and in developing
14024 packages with Rcpp.")
14025 (license license:expat)))
14027 (define-public r-tweenr
14034 (uri (cran-uri "tweenr" version))
14037 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
14038 (build-system r-build-system)
14040 `(("r-farver" ,r-farver)
14041 ("r-magrittr" ,r-magrittr)
14043 ("r-rlang" ,r-rlang)))
14044 (home-page "https://github.com/thomasp85/tweenr")
14045 (synopsis "Interpolate data for smooth animations")
14047 "In order to create smooth animation between states of data, tweening is
14048 necessary. This package provides a range of functions for creating tweened
14049 data that can be used as basis for animation. Furthermore it adds a number of
14050 vectorized interpolaters for common R data types such as numeric, date and
14052 (license license:expat)))
14054 (define-public r-polyclip
14056 (name "r-polyclip")
14061 (uri (cran-uri "polyclip" version))
14064 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
14065 (build-system r-build-system)
14066 (native-inputs `(("pkg-config" ,pkg-config)))
14067 (home-page "http://www.angusj.com/delphi/clipper.php")
14068 (synopsis "Polygon clipping")
14070 "This package provides an R port of the library Clipper. It performs
14071 polygon clipping operations (intersection, union, set minus, set difference)
14072 for polygonal regions of arbitrary complexity, including holes. It computes
14073 offset polygons (spatial buffer zones, morphological dilations, Minkowski
14074 dilations) for polygonal regions and polygonal lines. It computes the
14075 Minkowski Sum of general polygons. There is a function for removing
14076 self-intersections from polygon data.")
14077 (license license:boost1.0)))
14079 (define-public r-urltools
14081 (name "r-urltools")
14086 (uri (cran-uri "urltools" version))
14089 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
14090 (build-system r-build-system)
14092 `(("r-rcpp" ,r-rcpp)
14093 ("r-triebeard" ,r-triebeard)))
14094 (home-page "https://github.com/Ironholds/urltools/")
14095 (synopsis "Vectorized tools for URL handling and parsing")
14097 "This package provides a toolkit for all URL-handling needs, including
14098 encoding and decoding, parsing, parameter extraction and modification. All
14099 functions are designed to be both fast and entirely vectorized. It is
14100 intended to be useful for people dealing with web-related datasets, such as
14101 server-side logs, although may be useful for other situations involving large
14103 (license license:expat)))
14105 (define-public r-ggforce
14112 (uri (cran-uri "ggforce" version))
14115 "04926cqrda6psvy2nzkkw4czwyxdp7fnxg76byp14v12kgd72lm0"))))
14116 (build-system r-build-system)
14118 `(("r-ggplot2" ,r-ggplot2)
14119 ("r-gtable" ,r-gtable)
14121 ("r-polyclip" ,r-polyclip)
14123 ("r-rcppeigen" ,r-rcppeigen)
14124 ("r-rlang" ,r-rlang)
14125 ("r-scales" ,r-scales)
14126 ("r-tidyselect" ,r-tidyselect)
14127 ("r-tweenr" ,r-tweenr)
14128 ("r-withr" ,r-withr)))
14129 (home-page "https://ggforce.data-imaginist.com")
14130 (synopsis "Accelerating ggplot2")
14132 "The aim of the ggplot2 package is to aid in visual data investigations.
14133 This focus has led to a lack of facilities for composing specialized plots.
14134 Thi package aims to be a collection of mainly new statistics and geometries
14135 that fills this gap.")
14136 (license license:expat)))
14138 (define-public r-europepmc
14140 (name "r-europepmc")
14145 (uri (cran-uri "europepmc" version))
14148 "1ngqs1sqzkbwv98dd5z4cxj8bnz41wyd0g060a2vpqi3s99s4i2h"))))
14149 (build-system r-build-system)
14151 `(("r-dplyr" ,r-dplyr)
14153 ("r-jsonlite" ,r-jsonlite)
14155 ("r-progress" ,r-progress)
14156 ("r-purrr" ,r-purrr)
14157 ("r-urltools" ,r-urltools)
14158 ("r-xml2" ,r-xml2)))
14159 (home-page "https://github.com/ropensci/europepmc/")
14160 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
14162 "This package provides an R Client for the
14163 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
14164 Service}. It gives access to both metadata on life science literature and
14165 open access full texts. Europe PMC indexes all PubMed content and other
14166 literature sources including Agricola, a bibliographic database of citations
14167 to the agricultural literature, or Biological Patents. In addition to
14168 bibliographic metadata, the client allows users to fetch citations and
14169 reference lists. Links between life-science literature and other EBI
14170 databases, including ENA, PDB or ChEMBL are also accessible.")
14171 (license license:gpl3)))
14173 (define-public r-ggraph
14180 (uri (cran-uri "ggraph" version))
14183 "0qj7w3af0pgmd9mil6y571jikfkln7b8csvzg6b08spwbglfy1s3"))))
14184 (build-system r-build-system)
14186 `(("r-digest" ,r-digest)
14187 ("r-dplyr" ,r-dplyr)
14188 ("r-ggforce" ,r-ggforce)
14189 ("r-ggplot2" ,r-ggplot2)
14190 ("r-ggrepel" ,r-ggrepel)
14191 ("r-graphlayouts" ,r-graphlayouts)
14192 ("r-gtable" ,r-gtable)
14193 ("r-igraph" ,r-igraph)
14196 ("r-rlang" ,r-rlang)
14197 ("r-scales" ,r-scales)
14198 ("r-tidygraph" ,r-tidygraph)
14199 ("r-viridis" ,r-viridis)))
14200 (home-page "https://cran.r-project.org/web/packages/ggraph/")
14201 (synopsis "Implementation of grammar of graphics for graphs and networks")
14203 "The grammar of graphics as implemented in ggplot2 is a poor fit for
14204 graph and network visualizations due to its reliance on tabular data input.
14205 The ggraph package is an extension of the ggplot2 API tailored to graph
14206 visualizations and provides the same flexible approach to building up plots
14208 (license license:gpl3)))
14210 (define-public r-varselrf
14212 (name "r-varselrf")
14217 (uri (cran-uri "varSelRF" version))
14220 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
14221 (properties `((upstream-name . "varSelRF")))
14222 (build-system r-build-system)
14224 `(("r-randomforest" ,r-randomforest)))
14225 (home-page "http://ligarto.org/rdiaz/Software/Software.html")
14226 (synopsis "Variable selection using random forests")
14228 "This package provides tools for the variable selection from random
14229 forests using both backwards variable elimination (for the selection of small
14230 sets of non-redundant variables) and selection based on the importance
14231 spectrum (somewhat similar to scree plots; for the selection of large,
14232 potentially highly-correlated variables). The main applications are in
14233 high-dimensional data (e.g., microarray data, and other genomics and
14234 proteomics applications).")
14235 (license license:gpl2+)))
14237 (define-public r-pamr
14244 (uri (cran-uri "pamr" version))
14247 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
14248 (build-system r-build-system)
14250 `(("r-cluster" ,r-cluster)
14251 ("r-survival" ,r-survival)))
14252 (native-inputs `(("gfortran" ,gfortran)))
14253 (home-page "https://cran.r-project.org/web/packages/pamr/")
14254 (synopsis "Prediction Analysis for Microarrays")
14256 "This package provides some functions for sample classification in
14258 (license license:gpl2)))
14260 (define-public r-rda
14263 (version "1.0.2-2.1")
14267 (uri (cran-uri "rda" version))
14270 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
14271 (build-system r-build-system)
14272 (home-page "https://cran.r-project.org/web/packages/rda/")
14273 (synopsis "Shrunken centroids regularized discriminant analysis")
14275 "This package provides tools for shrunken centroids regularized
14276 discriminant analysis for the purpose of classifying high dimensional data.")
14277 (license license:gpl2+)))
14279 (define-public r-ggvis
14286 (uri (cran-uri "ggvis" version))
14289 "091i9f17912j8qcyxppjgwzjnyqj7769ixs9d2gjg6f2clskqdw2"))))
14290 (build-system r-build-system)
14292 `(("r-assertthat" ,r-assertthat)
14293 ("r-dplyr" ,r-dplyr)
14294 ("r-htmltools" ,r-htmltools)
14295 ("r-jsonlite" ,r-jsonlite)
14296 ("r-lazyeval" ,r-lazyeval)
14297 ("r-magrittr" ,r-magrittr)
14298 ("r-shiny" ,r-shiny)))
14299 (home-page "https://ggvis.rstudio.com/")
14300 (synopsis "Interactive grammar of graphics")
14302 "This package is a data visualization package for R providing an
14303 implementation of an interactive grammar of graphics, taking the best parts of
14304 ggplot2, combining them with the reactive framework of Shiny and drawing web
14305 graphics using Vega.")
14306 (license license:gpl2)))
14308 (define-public r-gbm
14315 (uri (cran-uri "gbm" version))
14318 "0vs6ljaqhwwpgr8wlbhmm4v147rd82kl16rpaijqiylxcc8dxyq6"))))
14319 (build-system r-build-system)
14321 `(("r-gridextra" ,r-gridextra)
14322 ("r-lattice" ,r-lattice)
14323 ("r-survival" ,r-survival)))
14324 (home-page "https://github.com/gbm-developers/gbm")
14325 (synopsis "Generalized boosted regression models")
14327 "This package is an implementation of extensions to Freund and Schapire's
14328 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
14329 regression methods for least squares, absolute loss, t-distribution loss,
14330 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
14331 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
14332 and Learning to Rank measures (LambdaMart).")
14333 (license license:gpl2+)))
14335 (define-public r-threejs
14342 (uri (cran-uri "threejs" version))
14345 "1s3rdlzy7man6177ycayg6xsh6k8y1r9rdj9yzn3b93j2rs0nxbi"))))
14346 (build-system r-build-system)
14348 `(#:modules ((guix build utils)
14349 (guix build r-build-system)
14353 (modify-phases %standard-phases
14354 (add-after 'unpack 'process-javascript
14355 (lambda* (#:key inputs #:allow-other-keys)
14356 (with-directory-excursion "inst"
14360 `((,(assoc-ref inputs "js-jquery")
14361 "htmlwidgets/lib/jquery/jquery.min.js")
14362 (,(assoc-ref inputs "js-threejs-85")
14363 "htmlwidgets/lib/threejs-85/three.min.js"))))
14364 (lambda (sources targets)
14365 (for-each (lambda (source target)
14366 (format #t "Processing ~a --> ~a~%"
14368 (delete-file target)
14369 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14370 (call-with-output-file target
14372 (dump-port minified port)))))
14373 sources targets))))
14376 `(("r-base64enc" ,r-base64enc)
14377 ("r-crosstalk" ,r-crosstalk)
14378 ("r-htmlwidgets" ,r-htmlwidgets)
14379 ("r-igraph" ,r-igraph)))
14381 `(("uglify-js" ,uglify-js)
14385 (uri "https://code.jquery.com/jquery-3.3.1.js")
14388 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
14392 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r85/build/three.js")
14395 "17khh3dmijdjw4qb9qih1rqhxgrmm3pc6w8lzdx6rf6a3mrc9xnl"))))))
14396 (home-page "https://bwlewis.github.io/rthreejs")
14397 (synopsis "Interactive 3D scatter plots, networks and globes")
14399 "Create interactive 3D scatter plots, network plots, and globes in R
14400 using the three.js visualization library.")
14401 (license license:expat)))
14403 (define-public r-mlbench
14410 (uri (cran-uri "mlbench" version))
14413 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
14414 (build-system r-build-system)
14415 (home-page "https://cran.r-project.org/web/packages/mlbench/")
14416 (synopsis "Machine learning benchmark problems")
14418 "This package provides a collection of artificial and real-world machine
14419 learning benchmark problems, including, e.g., several data sets from the UCI
14421 (license license:gpl2)))
14423 (define-public r-mpm
14430 (uri (cran-uri "mpm" version))
14433 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
14434 (build-system r-build-system)
14436 `(("r-kernsmooth" ,r-kernsmooth)
14437 ("r-mass" ,r-mass)))
14438 (home-page "http://mpm.r-forge.r-project.org")
14439 (synopsis "Multivariate projection methods")
14441 "This is a package for exploratory graphical analysis of multivariate
14442 data, specifically gene expression data with different projection methods:
14443 principal component analysis, correspondence analysis, spectral map
14445 (license license:gpl2+)))
14447 (define-public r-png
14453 (uri (cran-uri "png" version))
14456 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
14457 (build-system r-build-system)
14459 `(("libpng" ,libpng)
14461 (home-page "http://www.rforge.net/png/")
14462 (synopsis "Read and write PNG images")
14464 "This package provides an easy and simple way to read, write and display
14465 bitmap images stored in the PNG format. It can read and write both files and
14466 in-memory raw vectors.")
14467 ;; Any of these GPL versions.
14468 (license (list license:gpl2 license:gpl3))))
14470 (define-public r-ggcorrplot
14472 (name "r-ggcorrplot")
14477 (uri (cran-uri "ggcorrplot" version))
14480 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
14481 (build-system r-build-system)
14483 `(("r-ggplot2" ,r-ggplot2)
14484 ("r-reshape2" ,r-reshape2)))
14485 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
14486 (synopsis "Visualization of a correlation matrix using ggplot2")
14488 "The ggcorrplot package can be used to visualize easily a correlation
14489 matrix using ggplot2. It provides a solution for reordering the correlation
14490 matrix and displays the significance level on the plot. It also includes a
14491 function for computing a matrix of correlation p-values.")
14492 (license license:gpl2)))
14494 (define-public r-flexdashboard
14496 (name "r-flexdashboard")
14497 (version "0.5.1.1")
14501 (uri (cran-uri "flexdashboard" version))
14504 "0fy3nbrr67zqgd44r2mc850s5sp0hzfcw3zqs15m8kxzj1aw067x"))))
14505 (build-system r-build-system)
14507 `(#:modules ((guix build utils)
14508 (guix build r-build-system)
14512 (ice-9 textual-ports))
14514 (modify-phases %standard-phases
14515 (add-after 'unpack 'process-javascript
14516 (lambda* (#:key inputs #:allow-other-keys)
14517 (with-directory-excursion "inst"
14518 ;; Concatenate all components of prism.js
14519 (let ((contents (string-join
14520 (map (lambda (name)
14521 (call-with-input-file
14522 (assoc-ref inputs name)
14526 "js-prism-line-numbers"))
14528 (call-with-output-file "prism-src.js"
14529 (cut display contents <>)))
14533 `(("www/stickytableheaders/jquery.stickytableheaders.js"
14534 "www/stickytableheaders/jquery.stickytableheaders.min.js")
14536 "www/sly/sly.min.js")
14538 "www/prism/prism.js")
14539 (,(assoc-ref inputs "js-raphael")
14540 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
14541 (,(assoc-ref inputs "js-featherlight")
14542 "www/featherlight/featherlight.min.js"))))
14543 (lambda (sources targets)
14544 (for-each (lambda (source target)
14545 (format #t "Processing ~a --> ~a~%"
14547 (delete-file target)
14548 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14549 (call-with-output-file target
14551 (dump-port minified port)))))
14552 sources targets))))
14555 `(("r-htmltools" ,r-htmltools)
14556 ("r-htmlwidgets" ,r-htmlwidgets)
14557 ("r-jsonlite" ,r-jsonlite)
14558 ("r-knitr" ,r-knitr)
14559 ("r-rmarkdown" ,r-rmarkdown)
14560 ("r-shiny" ,r-shiny)))
14562 `(("uglify-js" ,uglify-js)
14566 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
14569 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
14573 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
14576 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
14580 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
14583 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
14584 ("js-prism-line-numbers"
14587 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
14590 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
14594 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
14597 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
14598 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
14599 (synopsis "R Markdown format for flexible dashboards")
14601 "This package provides an R Markdown format for converting an R Markdown
14602 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
14603 of its components to the containing web page.")
14604 (license license:expat)))
14606 (define-public r-preseqr
14613 (uri (cran-uri "preseqR" version))
14616 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
14617 (properties `((upstream-name . "preseqR")))
14618 (build-system r-build-system)
14620 `(("r-polynom" ,r-polynom)))
14621 (home-page "https://cran.r-project.org/web/packages/preseqR/")
14622 (synopsis "Predicting species accumulation curves")
14624 "This package can be used to predict the r-species accumulation
14625 curve (r-SAC), which is the number of species represented at least r times as
14626 a function of the sampling effort. When r = 1, the curve is known as the
14627 species accumulation curve, or the library complexity curve in high-throughput
14628 genomic sequencing. The package includes both parametric and nonparametric
14629 methods, as described by Deng C, et al. (2018).")
14630 (license license:gpl3)))
14632 (define-public r-mapplots
14634 (name "r-mapplots")
14639 (uri (cran-uri "mapplots" version))
14642 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
14643 (build-system r-build-system)
14644 (home-page "https://cran.r-project.org/web/packages/mapplots/")
14645 (synopsis "Data visualization on maps")
14647 "This package helps you create simple maps; add sub-plots like pie plots
14648 to a map or any other plot; format, plot and export gridded data. The package
14649 was developed for displaying fisheries data but most functions can be used for
14650 more generic data visualisation.")
14651 (license license:gpl2+)))
14653 (define-public r-pmcmr
14660 (uri (cran-uri "PMCMR" version))
14663 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
14664 (properties `((upstream-name . "PMCMR")))
14665 (build-system r-build-system)
14666 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
14667 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
14669 "This is a deprecated package for calculating pairwise multiple
14670 comparisons of mean rank sums. This package is superseded by the novel
14671 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
14672 compatibility of dependent packages for some time.")
14673 (license license:gpl3+)))
14675 (define-public r-downloader
14677 (name "r-downloader")
14682 (uri (cran-uri "downloader" version))
14685 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
14686 (build-system r-build-system)
14688 `(("r-digest" ,r-digest)))
14689 (home-page "https://github.com/wch/downloader")
14690 (synopsis "Download files over HTTP and HTTPS")
14692 "This package provides a wrapper for the @code{download.file} function,
14693 making it possible to download files over HTTPS across platforms. The
14694 @code{RCurl} package provides this functionality (and much more) but has
14695 external dependencies. This package has is implemented purely in R.")
14696 (license license:gpl2)))
14698 (define-public r-rex
14705 (uri (cran-uri "rex" version))
14708 "0alsadgjgass3wr8y5d247j12qqzg454sc84vpskclrkmz778g5x"))))
14709 (build-system r-build-system)
14711 `(("r-lazyeval" ,r-lazyeval)
14712 ("r-magrittr" ,r-magrittr)))
14713 (home-page "https://github.com/kevinushey/rex")
14714 (synopsis "Friendly regular expressions")
14716 "This package provides a friendly interface for the construction of
14717 regular expressions. Regular expressions are a very powerful feature, however
14718 they are often difficult to interpret. Rex allows you to build complex
14719 regular expressions from human readable expressions")
14720 (license license:expat)))
14722 (define-public r-xmlparsedata
14724 (name "r-xmlparsedata")
14729 (uri (cran-uri "xmlparsedata" version))
14732 "0gjr3l5z5dp276lchr2649as1rkj56d2mlvbr66yg393zzw50lsh"))))
14733 (properties `((upstream-name . "xmlparsedata")))
14734 (build-system r-build-system)
14735 (home-page "https://github.com/r-lib/xmlparsedata#readme")
14736 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
14738 "This package provides tools to convert the output of
14739 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
14740 @code{XPath}, and is easier to manipulate in general.")
14741 (license license:expat)))
14743 (define-public r-cyclocomp
14745 (name "r-cyclocomp")
14750 (uri (cran-uri "cyclocomp" version))
14753 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
14754 (properties `((upstream-name . "cyclocomp")))
14755 (build-system r-build-system)
14757 `(("r-callr" ,r-callr)
14758 ("r-crayon" ,r-crayon)
14760 ("r-remotes" ,r-remotes)
14761 ("r-withr" ,r-withr)))
14762 (home-page "https://github.com/MangoTheCat/cyclocomp")
14763 (synopsis "Cyclomatic complexity of R code")
14765 "Cyclomatic complexity is a software metric, used to indicate the
14766 complexity of a program. It is a quantitative measure of the number of
14767 linearly independent paths through a program's source code. This package
14768 provides tools to compute this metric.")
14769 (license license:expat)))
14771 (define-public r-lintr
14778 (uri (cran-uri "lintr" version))
14781 "09gbci4v5n4gsfzminly8332fw7faxdi1kkyvpa10dydx02sjcwb"))))
14782 (properties `((upstream-name . "lintr")))
14783 (build-system r-build-system)
14785 `(("r-codetools" ,r-codetools)
14786 ("r-crayon" ,r-crayon)
14787 ("r-cyclocomp" ,r-cyclocomp)
14788 ("r-digest" ,r-digest)
14790 ("r-jsonlite" ,r-jsonlite)
14791 ("r-knitr" ,r-knitr)
14793 ("r-rstudioapi" ,r-rstudioapi)
14794 ("r-stringdist" ,r-stringdist)
14795 ("r-testthat" ,r-testthat)
14797 ("r-xmlparsedata" ,r-xmlparsedata)))
14798 (home-page "https://github.com/jimhester/lintr")
14799 (synopsis "Linter for R code")
14800 (description "This package checks adherence to a given style, syntax
14801 errors and possible semantic issues. It supports on the fly checking of R
14802 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
14803 (license license:expat)))
14805 (define-public r-sctransform
14807 (name "r-sctransform")
14812 (uri (cran-uri "sctransform" version))
14815 "1r5kiqqs318q59h2i8m7c6nhghp9w6q26ss2y5a390lkhsawgx6p"))))
14816 (build-system r-build-system)
14818 `(("r-future" ,r-future)
14819 ("r-future-apply" ,r-future-apply)
14820 ("r-ggplot2" ,r-ggplot2)
14821 ("r-gridextra" ,r-gridextra)
14823 ("r-matrix" ,r-matrix)
14825 ("r-rcppeigen" ,r-rcppeigen)
14826 ("r-reshape2" ,r-reshape2)))
14827 (home-page "https://github.com/ChristophH/sctransform")
14828 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
14830 "This package provides a normalization method for single-cell UMI count
14831 data using a variance stabilizing transformation. The transformation is based
14832 on a negative binomial regression model with regularized parameters. As part
14833 of the same regression framework, this package also provides functions for
14834 batch correction, and data correction.")
14835 (license license:gpl3)))
14837 (define-public r-styler
14844 (uri (cran-uri "styler" version))
14847 "0rdbz60x8bymis6r6188ia1y0ip3nhf5y363i4cmakr618irjab9"))))
14848 (build-system r-build-system)
14850 `(("r-backports" ,r-backports)
14852 ("r-magrittr" ,r-magrittr)
14853 ("r-purrr" ,r-purrr)
14854 ("r-rematch2" ,r-rematch2)
14855 ("r-rlang" ,r-rlang)
14856 ("r-rprojroot" ,r-rprojroot)
14857 ("r-tibble" ,r-tibble)
14858 ("r-withr" ,r-withr)
14859 ("r-xfun" ,r-xfun)))
14860 (home-page "https://github.com/r-lib/styler")
14861 (synopsis "Non-invasive pretty printing of R code")
14863 "This is a package for pretty-printing R code without changing the user's
14864 formatting intent.")
14865 (license license:gpl3)))
14867 (define-public r-scrime
14874 (uri (cran-uri "scrime" version))
14877 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
14878 (build-system r-build-system)
14879 (home-page "https://cran.r-project.org/web/packages/scrime/")
14880 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
14882 "This package provides tools for the analysis of high-dimensional data
14883 developed/implemented at the group \"Statistical Complexity Reduction In
14884 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
14885 the functions can also be applied to other types of categorical data.")
14886 (license license:gpl2)))
14888 (define-public r-pbmcapply
14890 (name "r-pbmcapply")
14895 (uri (cran-uri "pbmcapply" version))
14898 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
14899 (build-system r-build-system)
14900 (home-page "https://github.com/kvnkuang/pbmcapply")
14901 (synopsis "Track the progress of apply procedures with a progress bar")
14903 "This light-weight package helps you track and visualize the progress of
14904 parallel versions of vectorized R functions of the @code{mc*apply} family.")
14905 (license license:expat)))
14907 (define-public r-blme
14914 (uri (cran-uri "blme" version))
14917 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
14918 (build-system r-build-system)
14919 (propagated-inputs `(("r-lme4" ,r-lme4)))
14920 (home-page "https://github.com/vdorie/blme")
14921 (synopsis "Bayesian linear mixed-effects models")
14923 "This package provides tools for maximum a posteriori estimation for
14924 linear and generalized linear mixed-effects models in a Bayesian setting. It
14925 extends the lme4 package.")
14926 (license license:gpl2+)))
14928 (define-public r-batchtools
14930 (name "r-batchtools")
14935 (uri (cran-uri "batchtools" version))
14938 "02mj21ypcjv5fs7ajf63p6bq0cyvihdl55hlpqx6kmsfjin1cr0v"))))
14939 (build-system r-build-system)
14941 `(("r-backports" ,r-backports)
14942 ("r-base64url" ,r-base64url)
14944 ("r-checkmate" ,r-checkmate)
14945 ("r-data-table" ,r-data-table)
14946 ("r-digest" ,r-digest)
14948 ("r-progress" ,r-progress)
14950 ("r-rappdirs" ,r-rappdirs)
14951 ("r-stringi" ,r-stringi)
14952 ("r-withr" ,r-withr)))
14953 (home-page "https://github.com/mllg/batchtools")
14954 (synopsis "Tools for computation on batch systems")
14956 "As a successor of the packages BatchJobs and BatchExperiments, this
14957 package provides a parallel implementation of the Map function for high
14958 performance computing systems managed by various schedulers. A multicore and
14959 socket mode allow the parallelization on a local machines, and multiple
14960 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
14961 the package provides an abstraction mechanism to define large-scale computer
14962 experiments in a well-organized and reproducible way.")
14963 (license license:lgpl3)))
14965 (define-public r-clue
14972 (uri (cran-uri "clue" version))
14975 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
14976 (build-system r-build-system)
14977 (propagated-inputs `(("r-cluster" ,r-cluster)))
14978 (home-page "https://cran.r-project.org/web/packages/clue/")
14979 (synopsis "Tools for analyzing cluster ensembles")
14980 (description "Cluster ensembles are collections of individual solutions to
14981 a given clustering problem which are useful or necessary to consider in a wide
14982 range of applications. This R package provides an extensible computational
14983 environment for creating and analyzing cluster ensembles, with basic data
14984 structures for representing partitions and hierarchies, and facilities for
14985 computing on them, including methods for measuring proximity and obtaining
14986 consensus and secondary clusterings.")
14987 (license license:gpl2)))
14989 (define-public r-sitmo
14996 (uri (cran-uri "sitmo" version))
14999 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
15000 (build-system r-build-system)
15001 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
15002 (home-page "https://github.com/coatless/sitmo/")
15003 (synopsis "Parallel pseudo random number generator header files")
15005 "This package provides two high quality and fast PPRNGs that may be used
15006 in an OpenMP parallel environment. In addition, there is a generator for one
15007 dimensional low-discrepancy sequence.")
15008 (license license:expat)))
15010 (define-public r-dqrng
15017 (uri (cran-uri "dqrng" version))
15020 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
15021 (build-system r-build-system)
15025 ("r-sitmo" ,r-sitmo)))
15026 (home-page "https://www.daqana.org/dqrng")
15027 (synopsis "Fast pseudo random number generators")
15029 "Several fast random number generators are provided as C++ header-only
15030 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
15031 Additionally, fast functions for generating random numbers according to a
15032 uniform, normal and exponential distribution are included. The latter two use
15033 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
15034 functions are exported to R and as a C++ interface and are enabled for use
15035 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
15036 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
15037 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
15038 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
15039 ;; whole is distributed under the terms of the AGPL 3.
15040 (license license:agpl3)))
15042 (define-public r-dalex
15049 (uri (cran-uri "DALEX" version))
15052 "1zviaf7530v8w996lbma0vplabrapgwldi7h70pr0439sxaqd421"))))
15053 (properties `((upstream-name . "DALEX")))
15054 (build-system r-build-system)
15055 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
15056 (home-page "https://pbiecek.github.io/DALEX/")
15057 (synopsis "Descriptive machine learning explanations")
15059 "Machine Learning models are widely used and have various applications in
15060 classification or regression. Models created with boosting, bagging, stacking
15061 or similar techniques are often used due to their high performance, but such
15062 black-box models usually lack interpretability. The DALEX package contains
15063 various explainers that help to understand the link between input variables
15064 and model output.")
15065 ;; Any version of the GPL
15066 (license license:gpl3+)))
15068 (define-public r-enrichr
15075 (uri (cran-uri "enrichR" version))
15078 "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
15079 (properties `((upstream-name . "enrichR")))
15080 (build-system r-build-system)
15082 `(("r-httr" ,r-httr)
15083 ("r-rjson" ,r-rjson)))
15084 (home-page "https://cran.r-project.org/web/packages/enrichR/")
15085 (synopsis "R Interface to Enrichr database for analyzing gene sets")
15087 "This package provides an R interface to all Enrichr databases, a
15088 web-based tool for analyzing gene sets and returns any enrichment of common
15089 annotated biological functions.")
15090 (license license:gpl2+)))
15092 (define-public r-plot3d
15099 (uri (cran-uri "plot3D" version))
15102 "0chn70fqwyca8lbnjnpbcj08ni0dfbax2gjmzhk2c4w72c04mzpn"))))
15103 (properties `((upstream-name . "plot3D")))
15104 (build-system r-build-system)
15105 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
15106 (home-page "https://cran.r-project.org/web/packages/plot3D")
15107 (synopsis "Plot multi-dimensional data")
15109 "This package provides functions for viewing 2D and 3D data, including
15110 perspective plots, slice plots, surface plots, scatter plots, etc. It
15111 includes data sets from oceanography.")
15112 (license license:gpl3+)))
15114 (define-public r-ggfortify
15116 (name "r-ggfortify")
15121 (uri (cran-uri "ggfortify" version))
15124 "191q2z7w0l4v7swjlxs2hjgbjngw2838688s7ygnj0kigsm310f3"))))
15125 (build-system r-build-system)
15127 `(("r-dplyr" ,r-dplyr)
15128 ("r-ggplot2" ,r-ggplot2)
15129 ("r-gridextra" ,r-gridextra)
15130 ("r-scales" ,r-scales)
15131 ("r-stringr" ,r-stringr)
15132 ("r-tibble" ,r-tibble)
15133 ("r-tidyr" ,r-tidyr)))
15134 (home-page "https://github.com/sinhrks/ggfortify")
15135 (synopsis "Data visualization tools for statistical analysis results")
15137 "This package provides unified plotting tools for statistics commonly
15138 used, such as GLM, time series, PCA families, clustering and survival
15139 analysis. The package offers a single plotting interface for these analysis
15140 results and plots in a unified style using the @code{ggplot2} package.")
15141 (license license:gpl2)))
15143 (define-public r-refmanager
15145 (name "r-refmanager")
15150 (uri (cran-uri "RefManageR" version))
15153 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
15154 (properties `((upstream-name . "RefManageR")))
15155 (build-system r-build-system)
15157 `(("r-bibtex" ,r-bibtex)
15159 ("r-jsonlite" ,r-jsonlite)
15160 ("r-lubridate" ,r-lubridate)
15162 ("r-stringr" ,r-stringr)
15163 ("r-xml2" ,r-xml2)))
15164 (home-page "https://github.com/ropensci/RefManageR/")
15165 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
15167 "This package provides tools for importing and working with bibliographic
15168 references. It greatly enhances the @code{bibentry} class by providing a
15169 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
15170 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
15171 by various formats for name lists (author by last names, translator by full
15172 names, etc.). Entries can be updated, combined, sorted, printed in a number
15173 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
15174 into R and converted to @code{BibEntry} objects.")
15175 ;; Any of these licenses may be picked.
15176 (license (list license:gpl2 license:gpl3 license:bsd-3))))
15178 (define-public r-citr
15185 (uri (cran-uri "citr" version))
15188 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
15189 (build-system r-build-system)
15191 `(("r-assertthat" ,r-assertthat)
15194 ("r-miniui" ,r-miniui)
15195 ("r-refmanager" ,r-refmanager)
15196 ("r-rstudioapi" ,r-rstudioapi)
15197 ("r-shiny" ,r-shiny)
15198 ("r-shinyjs" ,r-shinyjs)
15199 ("r-yaml" ,r-yaml)))
15200 (home-page "https://github.com/crsh/citr")
15201 (synopsis "RStudio add-in to insert Markdown citations")
15203 "This package provides functions and an RStudio add-in that search a
15204 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
15205 the current document.")
15206 (license license:expat)))
15208 (define-public r-xgboost
15211 (version "0.90.0.2")
15215 (uri (cran-uri "xgboost" version))
15218 "1gy9rzg43mjpfis893vf15drmbigfn0481zrzss9ajnmnk0q8194"))))
15219 (build-system r-build-system)
15221 `(("r-data-table" ,r-data-table)
15222 ("r-magrittr" ,r-magrittr)
15223 ("r-matrix" ,r-matrix)
15224 ("r-stringi" ,r-stringi)))
15225 (home-page "https://github.com/dmlc/xgboost")
15226 (synopsis "Extreme gradient boosting")
15228 "This package provides an R interface to Extreme Gradient Boosting, which
15229 is an efficient implementation of the gradient boosting framework from Chen
15230 and Guestrin (2016). The package includes efficient linear model solver and
15231 tree learning algorithms. The package can automatically do parallel
15232 computation on a single machine. It supports various objective functions,
15233 including regression, classification and ranking. The package is made to be
15234 extensible, so that users are also allowed to define their own objectives
15236 (license license:asl2.0)))
15238 (define-public r-umap
15241 (version "0.2.4.0")
15245 (uri (cran-uri "umap" version))
15248 "1dzbwq96k5vqr64wk6s26ks4311h570xg6gf0prr4vnn033pqnch"))))
15249 (build-system r-build-system)
15251 `(("r-openssl" ,r-openssl)
15253 ("r-reticulate" ,r-reticulate)
15254 ("r-rspectra" ,r-rspectra)))
15255 (home-page "https://github.com/tkonopka/umap")
15256 (synopsis "Uniform manifold approximation and projection")
15258 "Uniform manifold approximation and projection is a technique for
15259 dimension reduction. This package provides an interface to the UMAP algorithm
15260 in R, including a translation of the original algorithm into R.")
15261 (license license:expat)))
15263 (define-public r-uwot
15270 (uri (cran-uri "uwot" version))
15273 "0pz9wa89xq4d119q86lskrznf979m0r1db8iaprcz7kxbi6b8lrj"))))
15274 (build-system r-build-system)
15276 `(("r-dqrng" ,r-dqrng)
15278 ("r-irlba" ,r-irlba)
15279 ("r-matrix" ,r-matrix)
15281 ("r-rcppannoy" ,r-rcppannoy)
15282 ("r-rcppparallel" ,r-rcppparallel)
15283 ("r-rcppprogress" ,r-rcppprogress)
15284 ("r-rspectra" ,r-rspectra)))
15285 (home-page "https://github.com/jlmelville/uwot")
15286 (synopsis "Uniform manifold approximation and projection")
15288 "This package provides an implementation of the Uniform Manifold
15289 Approximation and Projection dimensionality reduction by McInnes et
15290 al. (2018). It also provides means to transform new data and to carry out
15291 supervised dimensionality reduction. An implementation of the related
15292 LargeVis method of Tang et al. (2016) is also provided.")
15293 (license license:gpl3)))
15295 (define-public r-kableextra
15297 (name "r-kableextra")
15302 (uri (cran-uri "kableExtra" version))
15305 "1nicvw06xsf3a1f5c10mih07b76m2v5s5h165vmz0qx6n1a3492i"))))
15306 (properties `((upstream-name . "kableExtra")))
15307 (build-system r-build-system)
15309 `(("r-digest" ,r-digest)
15311 ("r-htmltools" ,r-htmltools)
15312 ("r-knitr" ,r-knitr)
15313 ("r-magrittr" ,r-magrittr)
15314 ("r-readr" ,r-readr)
15315 ("r-rmarkdown" ,r-rmarkdown)
15316 ("r-rstudioapi" ,r-rstudioapi)
15317 ("r-rvest" ,r-rvest)
15318 ("r-scales" ,r-scales)
15319 ("r-stringr" ,r-stringr)
15320 ("r-viridislite" ,r-viridislite)
15321 ("r-webshot" ,r-webshot)
15322 ("r-xml2" ,r-xml2)))
15323 (home-page "https://haozhu233.github.io/kableExtra/")
15324 (synopsis "Construct complex tables with pipe syntax")
15326 "Build complex HTML or LaTeX tables using @code{kable()} from
15327 @code{knitr} and the piping syntax from @code{magrittr}. The function
15328 @code{kable()} is a light weight table generator coming from @code{knitr}.
15329 This package simplifies the way to manipulate the HTML or LaTeX codes
15330 generated by @code{kable()} and allows users to construct complex tables and
15331 customize styles using a readable syntax.")
15332 (license license:expat)))
15334 (define-public r-glasso
15341 (uri (cran-uri "glasso" version))
15343 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
15344 (build-system r-build-system)
15345 (native-inputs `(("gfortran" ,gfortran)))
15346 (home-page "http://www-stat.stanford.edu/~tibs/glasso")
15347 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
15349 "This is a package for estimation of a sparse inverse covariance matrix
15350 using a lasso (L1) penalty. Facilities are provided for estimates along a
15351 path of values for the regularization parameter.")
15352 (license license:gpl2)))
15354 (define-public r-rhpcblasctl
15356 (name "r-rhpcblasctl")
15357 (version "0.18-205")
15361 (uri (cran-uri "RhpcBLASctl" version))
15364 "1ls2286fvrp1g7p8v4l6axznychh3qndranfpzqz806cm9ml1cdp"))))
15365 (properties `((upstream-name . "RhpcBLASctl")))
15366 (build-system r-build-system)
15367 (home-page "http://prs.ism.ac.jp/~nakama/Rhpc/")
15368 (synopsis "Control the number of threads on BLAS")
15370 "This package allows you to control the number of threads the BLAS
15371 library uses. It is also possible to control the number of threads in
15373 (license license:agpl3+)))
15375 (define-public r-lda
15382 (uri (cran-uri "lda" version))
15385 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
15386 (build-system r-build-system)
15387 (home-page "https://cran.r-project.org/web/packages/lda/")
15388 (synopsis "Collapsed Gibbs sampling methods for topic models")
15390 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
15391 related models. This includes (but is not limited to) sLDA, corrLDA, and the
15392 mixed-membership stochastic blockmodel. Inference for all of these models is
15393 implemented via a fast collapsed Gibbs sampler written in C. Utility
15394 functions for reading/writing data typically used in topic models, as well as
15395 tools for examining posterior distributions are also included.")
15396 ;; Any version of the LGPL
15397 (license license:lgpl3+)))
15399 (define-public r-rann-l1
15406 (uri (cran-uri "RANN.L1" version))
15409 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
15410 (properties `((upstream-name . "RANN.L1")))
15411 (build-system r-build-system)
15412 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
15413 (synopsis "Fast nearest neighbour search using L1 metric")
15415 "This package provides tools to find the k nearest neighbours for every
15416 point in a given dataset in O(N log N) time using Arya and Mount's ANN
15417 library. There is support for approximate as well as exact searches, fixed
15418 radius searches and @code{bd} as well as @code{kd} trees. The distance is
15419 computed using the L1 (Manhattan, taxicab) metric.")
15420 (license license:gpl3+)))
15422 (define-public r-leiden
15429 (uri (cran-uri "leiden" version))
15432 "19gq27zin4gf4sh7h24gyq3f8jjir20n2l36a7pk1pbzcr4ixyhp"))))
15433 (properties `((upstream-name . "leiden")))
15434 (build-system r-build-system)
15436 `(("r-igraph" ,r-igraph)
15437 ("r-matrix" ,r-matrix)
15438 ("r-reticulate" ,r-reticulate)))
15439 (home-page "https://github.com/TomKellyGenetics/leiden")
15440 (synopsis "R implementation of Leiden clustering algorithm")
15442 "This package implements the Python @code{leidenalg} module to be called
15443 in R. It enables clustering using the Leiden algorithm for partitioning a
15444 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
15445 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
15446 (license license:gpl3)))
15448 (define-public r-patchwork
15449 ;; There has been no public release yet.
15450 (let ((commit "fd7958bae3e7a1e30237c751952e412a0a1d1242")
15453 (name "r-patchwork")
15454 (version (git-version "0.0.1" revision commit))
15458 (uri (git-reference
15459 (url "https://github.com/thomasp85/patchwork.git")
15461 (file-name (git-file-name name version))
15464 "00fq520xwy1ysg4k8x48x9b0yy9wyi8y8zj6dvxjg4bwx0yyp6s4"))))
15465 (build-system r-build-system)
15467 `(("r-ggplot2" ,r-ggplot2)
15468 ("r-gtable" ,r-gtable)))
15469 (home-page "https://github.com/thomasp85/patchwork")
15470 (synopsis "Compose ggplot2 plots")
15472 "The @code{ggplot2} package provides a strong API for sequentially
15473 building up a plot, but does not concern itself with composition of multiple
15474 plots. Patchwork is a package that expands the API to allow for arbitrarily
15475 complex composition of plots by providing mathmatical operators for combining
15477 (license license:expat))))
15479 (define-public r-liger
15486 (uri (git-reference
15487 (url "https://github.com/MacoskoLab/liger.git")
15488 (commit (string-append "v" version))))
15489 (file-name (git-file-name name version))
15492 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
15493 (modules '((guix build utils)))
15496 (delete-file "inst/java/ModularityOptimizer.jar")
15498 (build-system r-build-system)
15501 (modify-phases %standard-phases
15502 (add-after 'unpack 'build-java-part
15503 (lambda* (#:key inputs #:allow-other-keys)
15504 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
15505 (for-each (lambda (file) (invoke "javac" file))
15506 (find-files "." "\\.java$"))
15507 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
15508 (find-files "." "\\.class$"))
15511 `(("r-cowplot" ,r-cowplot)
15512 ("r-dosnow" ,r-dosnow)
15513 ("r-dplyr" ,r-dplyr)
15515 ("r-foreach" ,r-foreach)
15516 ("r-ggplot2" ,r-ggplot2)
15517 ("r-ggrepel" ,r-ggrepel)
15518 ("r-hmisc" ,r-hmisc)
15520 ("r-irlba" ,r-irlba)
15521 ("r-matrix" ,r-matrix)
15522 ("r-mclust" ,r-mclust)
15523 ("r-patchwork" ,r-patchwork)
15525 ("r-rann-l1" ,r-rann-l1)
15527 ("r-rcpparmadillo" ,r-rcpparmadillo)
15528 ("r-riverplot" ,r-riverplot)
15529 ("r-rtsne" ,r-rtsne)
15530 ("r-snow" ,r-snow)))
15532 `(("jdk" ,icedtea "jdk")
15533 ;; See https://github.com/MacoskoLab/liger/issues/96
15534 ;; The optimizer is released under the Expat license.
15538 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
15541 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
15543 ("r-knitr" ,r-knitr))) ; for vignettes
15544 (home-page "https://github.com/MacoskoLab/liger")
15545 (synopsis "Integrate and analyze multiple single-cell datasets")
15547 "LIGER is a package for integrating and analyzing multiple single-cell
15548 datasets, developed and maintained by the Macosko lab. It relies on
15549 integrative non-negative matrix factorization to identify shared and
15550 dataset-specific factors.")
15551 (license license:gpl3)))
15553 (define-public r-harmony
15554 ;; There are no tagged commits
15555 (let ((commit "4d1653870d4dd70fff1807c182882db1fbf9af5a")
15559 (version (git-version "1.0" revision commit))
15563 (uri (git-reference
15564 (url "https://github.com/immunogenomics/harmony")
15566 (file-name (git-file-name name version))
15569 "1gasdldr4aalr9h2q9kmm3y4i7azkgnhdn4bmvsszs7lg9xacw85"))))
15570 (build-system r-build-system)
15572 `(("r-cowplot" ,r-cowplot)
15573 ("r-dplyr" ,r-dplyr)
15574 ("r-ggplot2" ,r-ggplot2)
15575 ("r-irlba" ,r-irlba)
15576 ("r-matrix" ,r-matrix)
15578 ("r-rcpparmadillo" ,r-rcpparmadillo)
15579 ("r-rcppprogress" ,r-rcppprogress)
15580 ("r-rlang" ,r-rlang)
15581 ("r-tibble" ,r-tibble)
15582 ("r-tidyr" ,r-tidyr)))
15583 (home-page "https://github.com/immunogenomics/harmony")
15584 (synopsis "Integration of single cell sequencing data")
15586 "This package provides an implementation of the Harmony algorithm for
15587 single cell integration, described in Korsunsky et al
15588 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
15589 function and interfaces to external frameworks.")
15590 (license license:gpl3))))
15592 (define-public r-covr
15599 (uri (cran-uri "covr" version))
15601 (base32 "0p44kr6yz5sqza5zvq6divqglzkpv0if9pjpjmzhmdaaddjrqzg5"))))
15602 (properties `((upstream-name . "covr")))
15603 (build-system r-build-system)
15605 `(("r-crayon" ,r-crayon)
15606 ("r-digest" ,r-digest)
15608 ("r-jsonlite" ,r-jsonlite)
15610 ("r-withr" ,r-withr)
15611 ("r-yaml" ,r-yaml)))
15612 (home-page "https://github.com/r-lib/covr")
15613 (synopsis "Test coverage for R packages")
15615 "Thisp package enables you to track and report code coverage for your
15616 package and (optionally) upload the results to a coverage service. Code
15617 coverage is a measure of the amount of code being exercised by a set of tests.
15618 It is an indirect measure of test quality and completeness. This package is
15619 compatible with any testing methodology or framework and tracks coverage of
15620 both R code and compiled C/C++/FORTRAN code.")
15621 (license license:gpl3)))
15623 (define-public r-systemfonts
15625 (name "r-systemfonts")
15630 (uri (cran-uri "systemfonts" version))
15633 "0m0ljid683xcam2f14x7k2zv1yx4npac38a3gfv11vhxfbnpgp0z"))))
15634 (properties `((upstream-name . "systemfonts")))
15635 (build-system r-build-system)
15637 `(("fontconfig" ,fontconfig)
15638 ("freetype" ,freetype)
15641 `(("pkg-config" ,pkg-config)))
15642 (home-page "https://github.com/r-lib/systemfonts")
15643 (synopsis "System native font finding")
15645 "This package provides system native access to the font catalogue. As
15646 font handling varies between systems it is difficult to correctly locate
15647 installed fonts across different operating systems. The 'systemfonts' package
15648 provides bindings to the native libraries for finding font files that can then
15649 be used further by e.g. graphic devices.")
15650 (license license:expat)))
15652 (define-public r-graphlayouts
15654 (name "r-graphlayouts")
15659 (uri (cran-uri "graphlayouts" version))
15662 "03dizbhhdhnzbj2i5zvqgs617kwcv4h2pha4f16adic0fph1rxl3"))))
15663 (properties `((upstream-name . "graphlayouts")))
15664 (build-system r-build-system)
15666 `(("r-igraph" ,r-igraph)
15668 ("r-rcpparmadillo" ,r-rcpparmadillo)))
15669 (home-page "https://github.com/schochastics/graphlayouts")
15670 (synopsis "Additional layout algorithms for network visualizations")
15672 "This package provides several layout algorithms to visualize networks
15673 which are not part of the igraph library. Most are based on the concept of
15674 stress majorization by Gansner et al. (2004)
15675 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms allow to
15676 emphasize hidden group structures in networks or focus on specific nodes.")
15677 (license license:expat)))
15679 (define-public r-tidygraph
15681 (name "r-tidygraph")
15686 (uri (cran-uri "tidygraph" version))
15689 "1zpsarm74afbc7p5dlyb0whc09670qdcddw1ckb25cfc9hfh0hjn"))))
15690 (properties `((upstream-name . "tidygraph")))
15691 (build-system r-build-system)
15693 `(("r-dplyr" ,r-dplyr)
15694 ("r-igraph" ,r-igraph)
15695 ("r-magrittr" ,r-magrittr)
15696 ("r-pillar" ,r-pillar)
15699 ("r-rlang" ,r-rlang)
15700 ("r-tibble" ,r-tibble)
15701 ("r-tidyr" ,r-tidyr)))
15702 (home-page "https://github.com/thomasp85/tidygraph")
15703 (synopsis "Tidy API for graph manipulation")
15705 "This package provides a graph implementation that can be thought of as
15706 two tidy data frames describing node and edge data respectively. It provides
15707 an approach to manipulate these two virtual data frames using the API defined
15708 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
15709 common graph algorithms.")
15710 (license license:expat)))
15712 (define-public r-soupx
15713 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
15717 (version (git-version "0.3.1" revision commit))
15721 (uri (git-reference
15722 (url "https://github.com/constantAmateur/SoupX")
15724 (file-name (git-file-name name version))
15727 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
15728 (properties `((upstream-name . "SoupX")))
15729 (build-system r-build-system)
15731 `(("r-ggplot2" ,r-ggplot2)
15732 ("r-matrix" ,r-matrix)
15733 ("r-seurat" ,r-seurat)))
15734 (home-page "https://github.com/constantAmateur/SoupX")
15735 (synopsis "Single cell mRNA Soup eXterminator")
15737 "This package provides a package for quantifying, profiling and
15738 removing cell free mRNA contamination (the \"soup\") from droplet based single
15739 cell RNA-seq experiments.")
15740 (license license:gpl2))))
15742 (define-public r-assertr
15749 (uri (cran-uri "assertr" version))
15752 "0g4ii6vhp0155a29ljhs64a09x0nzy5ybvwwchhk4mkcgsvnvfkj"))))
15753 (build-system r-build-system)
15755 `(("r-dplyr" ,r-dplyr)
15757 ("r-rlang" ,r-rlang)))
15759 `(("r-knitr" ,r-knitr))) ; needed for vignette
15760 (home-page "https://github.com/ropensci/assertr")
15761 (synopsis "Assertive programming for R analysis pipelines")
15763 "This package provides functionality to assert conditions that have to be
15764 met so that errors in data used in analysis pipelines can fail quickly. It is
15765 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
15767 (license license:expat)))
15769 (define-public r-parameters
15771 (name "r-parameters")
15776 (uri (cran-uri "parameters" version))
15779 "0ifb9g1h8sn661q7jf9d8glk58gxdcym5ywbmx7phwn0y3is5wdv"))))
15780 (properties `((upstream-name . "parameters")))
15781 (build-system r-build-system)
15783 `(("r-bayestestr" ,r-bayestestr)
15784 ("r-insight" ,r-insight)))
15785 (home-page "https://cran.r-project.org/web/packages/parameters")
15786 (synopsis "Processing of model parameters")
15788 "This package provides utilities for processing the parameters of various
15789 statistical models. Beyond computing p values, CIs, and other indices for a
15790 wide variety of models, this package implements features like standardization
15791 or bootstrapping of parameters and models, feature reduction (feature
15792 extraction and variable selection) as well as conversion between indices of
15794 (license license:gpl3)))
15796 (define-public r-rgdal
15803 (uri (cran-uri "rgdal" version))
15805 (base32 "1jd691amf3ghznq5im15gvhl6v6k25klpl75m4ngrqf9xlxaa3as"))))
15806 (properties `((upstream-name . "rgdal")))
15807 (build-system r-build-system)
15815 `(("pkg-config" ,pkg-config)))
15816 (home-page "http://rgdal.r-forge.r-project.org")
15817 (synopsis "Bindings for the Geospatial Data Abstraction Library")
15819 "This package provides bindings to the Geospatial Data Abstraction
15820 Library (GDAL) and access to projection/transformation operations from the
15822 (license license:gpl2+)))
15824 (define-public r-insol
15831 (uri (cran-uri "insol" version))
15834 "14ikz05375pjn9hby7kwkhcnykjilbnkdy5i8lsl7c5qdbhmqcm5"))))
15835 (properties `((upstream-name . "insol")))
15836 (build-system r-build-system)
15838 `(("r-raster" ,r-raster)
15839 ("r-rgdal" ,r-rgdal)))
15841 `(("gfortran" ,gfortran)))
15842 (home-page "https://meteoexploration.com/R/insol/index.html")
15843 (synopsis "Tools for calculating solar radiation")
15845 "This package provides functions to compute insolation on tilted
15846 surfaces, computes atmospheric transmittance and related parameters such as:
15847 Earth radius vector, declination, sunset and sunrise, daylength, equation of
15848 time, vector in the direction of the sun, vector normal to surface, and some
15849 atmospheric physics.")
15850 (license license:gpl2+)))
15852 (define-public r-lifecycle
15854 (name "r-lifecycle")
15859 (uri (cran-uri "lifecycle" version))
15862 "11rk7hkw63rfrf4aqmb4xrb88kg95xh8hajpjvjfwjym2v02h74n"))))
15863 (properties `((upstream-name . "lifecycle")))
15864 (build-system r-build-system)
15866 `(("r-glue" ,r-glue)
15867 ("r-rlang" ,r-rlang)))
15868 (home-page "https://github.com/r-lib/lifecycle")
15869 (synopsis "Manage the life cycle of your package functions")
15871 "Manage the life cycle of your exported functions with shared
15872 conventions, documentation badges, and non-invasive deprecation warnings. The
15873 lifecycle package defines four development stages (experimental, maturing,
15874 stable, and questioning) and three deprecation stages (soft-deprecated,
15875 deprecated, and defunct). It makes it easy to insert badges corresponding to
15876 these stages in your documentation. Usage of deprecated functions are
15877 signalled with increasing levels of non-invasive verbosity.")
15878 (license license:gpl3)))
15880 (define-public r-assertable
15882 (name "r-assertable")
15887 (uri (cran-uri "assertable" version))
15890 "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
15891 (build-system r-build-system)
15893 `(("r-data-table" ,r-data-table)))
15894 (home-page "https://cran.r-project.org/web/packages/assertable/")
15895 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
15896 (description "This package provides simple, flexible assertions on
15897 data.frame or data.table objects with verbose output for vetting. While other
15898 assertion packages apply towards more general use-cases, @code{assertable} is
15899 tailored towards tabular data. It includes functions to check variable names
15900 and values, whether the dataset contains all combinations of a given set of
15901 unique identifiers, and whether it is a certain length. In addition,
15902 @code{assertable} includes utility functions to check the existence of target
15903 files and to efficiently import multiple tabular data files into one
15905 (license license:gpl3)))
15907 (define-public r-quadprog
15909 (name "r-quadprog")
15914 (uri (cran-uri "quadprog" version))
15916 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
15917 (build-system r-build-system)
15919 `(("gfortran" ,gfortran)))
15920 (home-page "https://cran.r-project.org/web/packages/quadprog")
15921 (synopsis "Functions to solve quadratic programming problems")
15923 "This package contains routines and documentation for solving quadratic
15924 programming problems.")
15925 (license license:gpl3+)))
15927 (define-public r-desolve
15934 (uri (cran-uri "deSolve" version))
15936 (base32 "0735y3p5glhqx69rzrc8qgmvs7p7w0p98qxmvylb6bgqp6kp0cbp"))))
15937 (properties `((upstream-name . "deSolve")))
15938 (build-system r-build-system)
15940 `(("gfortran" ,gfortran)))
15941 (home-page "https://desolve.r-forge.r-project.org/")
15942 (synopsis "Solvers for initial value problems of differential equations")
15943 (description "This package provides functions that solve initial
15944 value problems of a system of first-order ordinary differential equations (ODE),
15945 of partial differential equations (PDE), of differential algebraic equations
15946 (DAE), and of delay differential equations. The functions provide an interface
15947 to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection,
15948 to the FORTRAN functions dvode and daspk and a C-implementation of solvers of
15949 the Runge-Kutta family with fixed or variable time steps. The package contains
15950 routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial
15951 differential equations (PDE) that have been converted to ODEs by numerical
15953 (license license:gpl2+)))
15955 (define-public r-pracma
15961 (uri (cran-uri "pracma" version))
15963 (base32 "0isd3s0i4mzmva8lkh0j76hwjy1w50q7d1n9lhxsnnkgalx3xs1g"))))
15964 (build-system r-build-system)
15965 (home-page "https://cran.r-project.org/web/packages/pracma/")
15966 (synopsis "Practical numerical math functions")
15967 (description "This package provides functions for numerical analysis and
15968 linear algebra, numerical optimization, differential equations, plus some
15969 special functions. It uses Matlab function names where appropriate to simplify
15971 (license license:gpl3+)))
15973 (define-public r-subplex
15980 (uri (cran-uri "subplex" version))
15983 "10cbgbx1bgsax5z7gz6716g360xpq4mvq19cf4qqrxv02mmwz57z"))))
15984 (build-system r-build-system)
15986 `(("gfortran" ,gfortran)))
15987 (home-page "https://cran.r-project.org/web/packages/subplex")
15988 (synopsis "Unconstrained optimization using the subplex algorithm")
15990 "This package implements the Subplex optimization algorithm.
15991 It solves unconstrained optimization problems using a simplex method on
15992 subspaces. The method is well suited for optimizing objective functions that
15993 are noisy or are discontinuous at the solution.")
15994 (license license:gpl3+)))
15996 (define-public r-txtplot
16003 (uri (cran-uri "txtplot" version))
16006 "1949ab1bzvysdb79g8x1gaknj0ih3d6g63pv9512h5m5l3a6c31h"))))
16007 (build-system r-build-system)
16008 (home-page "https://cran.r-project.org/web/packages/txtplot/")
16009 (synopsis "Text-based plotting")
16010 (description "This package provides functions to produce rudimentary ASCII
16011 graphics directly in the terminal window. This package provides a basic
16012 plotting function (and equivalents of curve, density, acf and barplot) as well
16013 as a boxplot function.")
16014 (license license:lgpl3+)))