1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
4 ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
5 ;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
6 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
7 ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
8 ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
9 ;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net>
10 ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
11 ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
12 ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
13 ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
14 ;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com>
15 ;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
16 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
17 ;;; Copyright © 2018 Eric Brown <brown@fastmail.com>
18 ;;; Copyright © 2018, 2019 Brett Gilio <brettg@gnu.org>
19 ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
20 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
22 ;;; This file is part of GNU Guix.
24 ;;; GNU Guix is free software; you can redistribute it and/or modify it
25 ;;; under the terms of the GNU General Public License as published by
26 ;;; the Free Software Foundation; either version 3 of the License, or (at
27 ;;; your option) any later version.
29 ;;; GNU Guix is distributed in the hope that it will be useful, but
30 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
31 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
32 ;;; GNU General Public License for more details.
34 ;;; You should have received a copy of the GNU General Public License
35 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
37 (define-module (gnu packages cran)
38 #:use-module ((guix licenses) #:prefix license:)
39 #:use-module (guix packages)
40 #:use-module (guix download)
41 #:use-module (guix git-download)
42 #:use-module (guix utils)
43 #:use-module (guix build-system r)
44 #:use-module (gnu packages algebra)
45 #:use-module (gnu packages base)
46 #:use-module (gnu packages bioinformatics)
47 #:use-module (gnu packages c)
48 #:use-module (gnu packages compression)
49 #:use-module (gnu packages curl)
50 #:use-module (gnu packages databases)
51 #:use-module (gnu packages fontutils)
52 #:use-module (gnu packages gcc)
53 #:use-module (gnu packages geo)
54 #:use-module (gnu packages ghostscript)
55 #:use-module (gnu packages gl)
56 #:use-module (gnu packages gnome)
57 #:use-module (gnu packages graph)
58 #:use-module (gnu packages gtk)
59 #:use-module (gnu packages haskell-xyz)
60 #:use-module (gnu packages icu4c)
61 #:use-module (gnu packages image)
62 #:use-module (gnu packages imagemagick)
63 #:use-module (gnu packages java)
64 #:use-module (gnu packages javascript)
65 #:use-module (gnu packages lisp-xyz)
66 #:use-module (gnu packages machine-learning)
67 #:use-module (gnu packages maths)
68 #:use-module (gnu packages mpi)
69 #:use-module (gnu packages multiprecision)
70 #:use-module (gnu packages networking)
71 #:use-module (gnu packages pcre)
72 #:use-module (gnu packages perl)
73 #:use-module (gnu packages pkg-config)
74 #:use-module (gnu packages python)
75 #:use-module (gnu packages python-xyz)
76 #:use-module (gnu packages statistics)
77 #:use-module (gnu packages tcl)
78 #:use-module (gnu packages tls)
79 #:use-module (gnu packages web)
80 #:use-module (gnu packages xorg))
82 (define-public r-clipr
89 (uri (cran-uri "clipr" version))
92 "1qn2p13d0c1bpqss6mv9hk60980rzhznfqpyaf5x0fy65svy9903"))))
93 (build-system r-build-system)
94 (home-page "https://github.com/mdlincoln/clipr")
95 (synopsis "Read and write from the system clipboard")
97 "This package provides simple utility functions to read from and write to
98 the system clipboards.")
99 (license license:gpl3)))
101 (define-public r-scales
108 (uri (cran-uri "scales" version))
110 (base32 "00rdbfj5mwc3kr8pskidn3n2zkp4ms6cx36xazz54pxw3pysdr0y"))))
111 (build-system r-build-system)
113 `(("r-farver" ,r-farver)
114 ("r-labeling" ,r-labeling)
115 ("r-lifecycle" ,r-lifecycle)
116 ("r-munsell" ,r-munsell)
117 ("r-rcolorbrewer" ,r-rcolorbrewer)
119 ("r-viridislite" ,r-viridislite)))
120 (home-page "https://github.com/hadley/scales")
121 (synopsis "Scale functions for visualization")
123 "This package provides graphical scales that map data to aesthetics, and
124 provides methods for automatically determining breaks and labels for axes and
126 (license license:expat)))
128 (define-public r-pheatmap
135 (uri (cran-uri "pheatmap" version))
138 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
139 (build-system r-build-system)
141 `(("r-gtable" ,r-gtable)
142 ("r-rcolorbrewer" ,r-rcolorbrewer)
143 ("r-scales" ,r-scales)))
144 (home-page "https://cran.r-project.org/web/packages/pheatmap")
145 (synopsis "Pretty heatmaps")
147 "This package provides an implementation of heatmaps that offers more
148 control over dimensions and appearance.")
149 (license license:gpl2+)))
151 (define-public r-ellipsis
158 (uri (cran-uri "ellipsis" version))
161 "01z9gq311nzwv3a0sa49jhm5ylqd59srip4vjkrf23hzgb5i9y0b"))))
162 (build-system r-build-system)
164 `(("r-rlang" ,r-rlang)))
165 (home-page "https://github.com/hadley/ellipsis")
166 (synopsis "Tools for working with additional arguments")
168 "In S3 generics, it's useful to take @code{...} so that methods can have
169 additional arguments. But this flexibility comes at a cost: misspelled
170 arguments will be silently ignored. The @code{ellipsis} package is an
171 experiment that allows a generic to warn if any arguments passed in @code{...}
173 (license license:gpl3)))
182 (uri (cran-uri "grr" version))
185 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
186 (build-system r-build-system)
187 (home-page "https://cran.r-project.org/web/packages/grr")
188 (synopsis "Alternative implementations of base R functions")
190 "This package provides alternative implementations of some base R
191 functions, including @code{sort}, @code{order}, and @code{match}. The
192 functions are simplified but can be faster or have other advantages.")
193 (license license:gpl3)))
195 (define-public r-matrix-utils
197 (name "r-matrix-utils")
202 (uri (cran-uri "Matrix.utils" version))
205 "1x64r4aj3gy1dzjjysyrk1j9jq3qsnyrqws8i6bs7q8pf6gvr7va"))))
206 (properties `((upstream-name . "Matrix.utils")))
207 (build-system r-build-system)
210 ("r-matrix" ,r-matrix)))
211 (home-page "https://github.com/cvarrichio/Matrix.utils")
213 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
215 "This package implements data manipulation methods such as @code{cast},
216 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
218 (license license:gpl3)))
227 (uri (cran-uri "sys" version))
230 "14wvy46i2iz9jn7lj3cvifmps932s3395wq681hniva0f8m7q8d6"))))
231 (build-system r-build-system)
232 (home-page "https://github.com/jeroen/sys")
233 (synopsis "Powerful and reliable tools for running system commands in R")
235 "This package provides drop-in replacements for the base @code{system2()}
236 function with fine control and consistent behavior across platforms. It
237 supports clean interruption, timeout, background tasks, and streaming STDIN /
238 STDOUT / STDERR over binary or text connections. The package also provides
239 functions for evaluating expressions inside a temporary fork. Such
240 evaluations have no side effects on the main R process, and support reliable
241 interrupts and timeouts. This provides the basis for a sandboxing
243 (license license:expat)))
245 (define-public r-askpass
252 (uri (cran-uri "askpass" version))
255 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
256 (build-system r-build-system)
257 (propagated-inputs `(("r-sys" ,r-sys)))
258 (home-page "https://github.com/jeroen/askpass")
259 (synopsis "Safe password entry for R")
261 "This package provides cross-platform utilities for prompting the user
262 for credentials or a passphrase, for example to authenticate with a server or
263 read a protected key.")
264 (license license:expat)))
266 (define-public r-vegan
273 (uri (cran-uri "vegan" version))
276 "0g60rgn1i7wqf9pf5m1yki1m45gcp7i5hmjic0ci0f6vng70mh5k"))))
277 (build-system r-build-system)
279 `(("gfortran" ,gfortran)))
281 `(("r-cluster" ,r-cluster)
282 ("r-knitr" ,r-knitr) ; needed for vignettes
283 ("r-lattice" ,r-lattice)
286 ("r-permute" ,r-permute)))
287 (home-page "https://cran.r-project.org/web/packages/vegan")
288 (synopsis "Functions for community ecology")
290 "The vegan package provides tools for descriptive community ecology. It
291 has most basic functions of diversity analysis, community ordination and
292 dissimilarity analysis. Most of its multivariate tools can be used for other
293 data types as well.")
294 (license license:gpl2+)))
296 (define-public r-tidyverse
303 (uri (cran-uri "tidyverse" version))
306 "02gyys08qv2v4cl2d66gml4d31ipxay0iyfwwksvxyclx60wp2kd"))))
307 (build-system r-build-system)
309 `(("r-broom" ,r-broom)
311 ("r-crayon" ,r-crayon)
312 ("r-dbplyr" ,r-dbplyr)
314 ("r-forcats" ,r-forcats)
315 ("r-ggplot2" ,r-ggplot2)
319 ("r-jsonlite" ,r-jsonlite)
320 ("r-lubridate" ,r-lubridate)
321 ("r-magrittr" ,r-magrittr)
322 ("r-modelr" ,r-modelr)
323 ("r-pillar" ,r-pillar)
326 ("r-readxl" ,r-readxl)
327 ("r-reprex" ,r-reprex)
329 ("r-rstudioapi" ,r-rstudioapi)
331 ("r-stringr" ,r-stringr)
332 ("r-tibble" ,r-tibble)
335 (home-page "https://tidyverse.tidyverse.org")
336 (synopsis "Install and load packages from the \"Tidyverse\"")
338 "The @code{tidyverse} is a set of packages that work in harmony because
339 they share common data representations and API design. This package is
340 designed to make it easy to install and load multiple tidyverse packages in a
342 (license license:gpl3)))
344 (define-public r-rvest
351 (uri (cran-uri "rvest" version))
353 (base32 "0r0a5jic09xw5pk0x42pr99r3zab5m9s4x85ymx1sl769jz42zqf"))))
354 (build-system r-build-system)
357 ("r-magrittr" ,r-magrittr)
358 ("r-selectr" ,r-selectr)
360 (home-page "https://github.com/hadley/rvest")
361 (synopsis "Simple web scraping for R")
363 "@code{r-rvest} helps you scrape information from web pages. It is
364 designed to work with @code{magrittr} to make it easy to express common web
365 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
366 (license license:gpl3)))
368 (define-public r-selectr
375 (uri (cran-uri "selectr" version))
377 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
378 (build-system r-build-system)
380 `(("r-stringr" ,r-stringr)
382 (home-page "https://sjp.co.nz/projects/selectr/")
383 (synopsis "Translate CSS selectors to XPath expressions")
385 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
386 expression. This allows you to use CSS selectors when working with the XML
387 package as it can only evaluate XPath expressions. Also provided are
388 convenience functions useful for using CSS selectors on XML nodes. This
389 package is a port of the Python package @code{cssselect}.")
390 (license license:bsd-3)))
392 (define-public r-reprex
399 (uri (cran-uri "reprex" version))
402 "0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10"))))
403 (build-system r-build-system)
405 `(("r-callr" ,r-callr)
409 ("r-rmarkdown" ,r-rmarkdown)
410 ("r-whisker" ,r-whisker)
411 ("r-withr" ,r-withr)))
412 (home-page "https://github.com/tidyverse/reprex")
413 (synopsis "Prepare reproducible R code examples for sharing")
415 "This package provides a convenience wrapper that uses the
416 @code{rmarkdown} package to render small snippets of code to target formats
417 that include both code and output. The goal is to encourage the sharing of
418 small, reproducible, and runnable examples on code-oriented websites or email.
419 @code{reprex} also extracts clean, runnable R code from various common formats,
420 such as copy/paste from an R session.")
421 (license license:expat)))
423 (define-public r-callr
430 (uri (cran-uri "callr" version))
433 "0bdlp0labwyfl36jqslj2g7zmw7zwr58v9gam435kiblhjimb8fc"))))
434 (build-system r-build-system)
437 ("r-processx" ,r-processx)))
438 (home-page "https://github.com/r-lib/callr#readme")
439 (synopsis "Call R from R")
441 "It is sometimes useful to perform a computation in a separate R process,
442 without affecting the current R process at all. This package does exactly
444 (license license:expat)))
446 (define-public r-readxl
453 (uri (cran-uri "readxl" version))
456 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
457 (build-system r-build-system)
459 `(("r-cellranger" ,r-cellranger)
460 ("r-progress" ,r-progress)
462 ("r-tibble" ,r-tibble)))
463 (home-page "https://readxl.tidyverse.org")
464 (synopsis "Read Excel files")
466 "This package lets you import Excel files into R. It supports
467 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
468 the embedded @code{RapidXML} C++ library.")
469 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
470 ;; 'rapidxml' which is Boost.
471 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
473 (define-public r-modelr
480 (uri (cran-uri "modelr" version))
483 "0nnfhlzz75ihs8azy963cc4cwg1kx81rybk4z3wm98bbghwfxfs5"))))
484 (build-system r-build-system)
486 `(("r-broom" ,r-broom)
488 ("r-magrittr" ,r-magrittr)
491 ("r-tibble" ,r-tibble)
492 ("r-tidyr" ,r-tidyr)))
493 (home-page "https://github.com/tidyverse/modelr")
494 (synopsis "Helper functions for modelling in pipelines")
496 "Functions for modelling that help you seamlessly integrate modelling
497 into a pipeline of data manipulation and visualisation.")
498 (license license:gpl3)))
500 (define-public r-httpuv
506 (uri (cran-uri "httpuv" version))
509 "13ax0hs2lc39ilznh1zarwqdzahcbhb8adilrfik3xg0fkljpcwk"))))
510 (build-system r-build-system)
514 ("r-promises" ,r-promises)
517 (home-page "https://github.com/rstudio/httpuv")
518 (synopsis "HTTP and WebSocket server library for R")
520 "The httpuv package provides low-level socket and protocol support for
521 handling HTTP and WebSocket requests directly from within R. It is primarily
522 intended as a building block for other packages, rather than making it
523 particularly easy to create complete web applications using httpuv alone.")
524 ;; This package includes third-party code that was originally released
525 ;; under various non-copyleft licenses. Full licensing information can be
526 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
527 (license license:gpl3+)))
529 (define-public r-jsonlite
535 (uri (cran-uri "jsonlite" version))
538 "0xrki07wc17bkmhz0h7jay784j1sls2i9bf1mfpj6yl59791v4kl"))))
539 (build-system r-build-system)
540 (home-page "https://arxiv.org/abs/1403.2805")
541 (synopsis "Robust, high performance JSON parser and generator for R")
543 "The jsonlite package provides a fast JSON parser and generator optimized
544 for statistical data and the web. It offers flexible, robust, high
545 performance tools for working with JSON in R and is particularly powerful for
546 building pipelines and interacting with a web API. In addition to converting
547 JSON data from/to R objects, jsonlite contains functions to stream, validate,
548 and prettify JSON data. The unit tests included with the package verify that
549 all edge cases are encoded and decoded consistently for use with dynamic data
550 in systems and applications.")
551 (license license:expat)))
553 (define-public r-servr
559 (uri (cran-uri "servr" version))
562 "199k9aghwk9rf1rm8pjg60xacqww25cza259h5dfj1ixil0m6dxi"))))
563 (build-system r-build-system)
565 `(("r-httpuv" ,r-httpuv)
566 ("r-jsonlite" ,r-jsonlite)
569 (home-page "https://github.com/yihui/servr")
570 (synopsis "Simple HTTP server to serve static files or dynamic documents")
572 "Servr provides an HTTP server in R to serve static files, or dynamic
573 documents that can be converted to HTML files (e.g., R Markdown) under a given
575 (license license:expat)))
577 (define-public r-htmltools
583 (uri (cran-uri "htmltools" version))
586 "06l17d8jkf438yk2mchpsp4j90bynnapz3nabh5vkcc324p5a62v"))))
587 (build-system r-build-system)
589 `(("r-digest" ,r-digest)
591 ("r-rlang" ,r-rlang)))
592 (home-page "https://cran.r-project.org/web/packages/htmltools")
593 (synopsis "R tools for HTML")
595 "This package provides tools for HTML generation and output in R.")
596 (license license:expat)))
598 (define-public r-htmlwidgets
600 (name "r-htmlwidgets")
604 (uri (cran-uri "htmlwidgets" version))
607 "10fp306l1nybkah6jrlrqwwdb6zvklbddp8i3w9v9naj8la5jbnl"))))
608 (build-system r-build-system)
610 `(("r-htmltools" ,r-htmltools)
611 ("r-jsonlite" ,r-jsonlite)
613 (home-page "https://github.com/ramnathv/htmlwidgets")
614 (synopsis "HTML Widgets for R")
616 "HTML widgets is a framework for creating HTML widgets that render in
617 various contexts including the R console, R Markdown documents, and Shiny web
619 (license license:expat)))
621 (define-public r-htmltable
628 (uri (cran-uri "htmlTable" version))
631 "0g9r156k9yl1f092hfw3b9wjx11akf0shbi3x0d0mvpnflvc8nfl"))))
632 (properties `((upstream-name . "htmlTable")))
633 (build-system r-build-system)
635 `(("r-checkmate" ,r-checkmate)
636 ("r-htmltools" ,r-htmltools)
637 ("r-htmlwidgets" ,r-htmlwidgets)
639 ("r-magrittr" ,r-magrittr)
640 ("r-rstudioapi" ,r-rstudioapi)
641 ("r-stringr" ,r-stringr)))
642 (home-page "http://gforge.se/packages/")
643 (synopsis "Advanced tables for Markdown/HTML")
645 "This package provides functions to build tables with advanced layout
646 elements such as row spanners, column spanners, table spanners, zebra
647 striping, and more. While allowing advanced layout, the underlying
648 CSS-structure is simple in order to maximize compatibility with word
649 processors such as LibreOffice. The package also contains a few text
650 formatting functions that help outputting text compatible with HTML or
652 (license license:gpl3+)))
654 (define-public r-curl
660 (uri (cran-uri "curl" version))
663 "1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl"))))
664 (build-system r-build-system)
667 (modify-phases %standard-phases
668 ;; The environment variable CURL_CA_BUNDLE is only respected when
669 ;; running Windows, so we disable the platform checks.
670 ;; This can be removed once the libcurl has been patched.
671 (add-after 'unpack 'allow-CURL_CA_BUNDLE
673 (substitute* "R/onload.R"
674 (("if \\(!grepl\\(\"mingw\".*")
676 (substitute* "src/handle.c"
677 (("#ifdef _WIN32") "#if 1"))
683 `(("pkg-config" ,pkg-config)))
684 (home-page "https://github.com/jeroenooms/curl")
685 (synopsis "HTTP client for R")
687 "The @code{curl()} and @code{curl_download()} functions provide highly
688 configurable drop-in replacements for base @code{url()} and
689 @code{download.file()} with better performance, support for encryption, gzip
690 compression, authentication, and other @code{libcurl} goodies. The core of
691 the package implements a framework for performing fully customized requests
692 where data can be processed either in memory, on disk, or streaming via the
693 callback or connection interfaces.")
694 (license license:expat)))
696 (define-public r-hwriter
703 (uri (cran-uri "hwriter" version))
706 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
707 (build-system r-build-system)
708 (home-page "https://cran.r-project.org/web/packages/hwriter")
709 (synopsis "Output R objects in HTML format")
711 "This package provides easy-to-use and versatile functions to output R
712 objects in HTML format.")
713 (license license:lgpl2.1+)))
715 (define-public r-rjson
722 (uri (cran-uri "rjson" version))
725 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
726 (build-system r-build-system)
727 (home-page "https://cran.r-project.org/web/packages/rjson")
728 (synopsis "JSON library for R")
730 "This package provides functions to convert R objects into JSON objects
732 (license license:gpl2+)))
734 (define-public r-fastmap
741 (uri (cran-uri "fastmap" version))
744 "1v7sp56xiha0bh78g3w92k52p9vkp7ryzpw0z66nyddxzrfv0y27"))))
745 (properties `((upstream-name . "fastmap")))
746 (build-system r-build-system)
747 (home-page "https://r-lib.github.io/fastmap/")
748 (synopsis "Fast implementation of a key-value store")
750 "This package provides a fast implementation of a key-value store.
751 Environments are commonly used as key-value stores, but every time a new key
752 is used, it is added to R's global symbol table, causing a small amount of
753 memory leakage. This can be problematic in cases where many different keys
754 are used. Fastmap avoids this memory leak issue by implementing the map using
755 data structures in C++.")
756 (license license:expat)))
758 (define-public r-shiny
766 (url "https://github.com/rstudio/shiny.git")
767 (commit (string-append "v" version))))
768 (file-name (git-file-name name version))
771 "17ac48g414h9dhi0k4wrah4gyik0q5r0xw3kc01c02qfjwimqsx7"))))
772 (build-system r-build-system)
774 `(#:modules ((guix build r-build-system)
775 (guix build minify-build-system)
778 #:imported-modules (,@%r-build-system-modules
779 (guix build minify-build-system))
781 (modify-phases (@ (guix build r-build-system) %standard-phases)
782 (add-after 'unpack 'replace-bundled-minified-JavaScript
783 (lambda* (#:key inputs #:allow-other-keys)
784 (let ((replace-file (lambda (old new)
785 (format #t "replacing ~a with ~a\n" old new)
788 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
789 ;; contain just data. They are not minified code, so we don't
791 (with-directory-excursion "inst/www/shared"
792 (replace-file "bootstrap/shim/respond.min.js"
793 (string-append (assoc-ref inputs "js-respond")
794 "/share/javascript/respond.min.js"))
795 (replace-file "bootstrap/shim/html5shiv.min.js"
796 (string-append (assoc-ref inputs "js-html5shiv")
797 "/share/javascript/html5shiv.min.js"))
798 (replace-file "json2-min.js"
799 (string-append (assoc-ref inputs "js-json2")
800 "/share/javascript/json2-min.js"))
801 (replace-file "strftime/strftime-min.js"
802 (string-append (assoc-ref inputs "js-strftime")
803 "/share/javascript/strftime.min.js"))
804 (replace-file "highlight/highlight.pack.js"
805 (string-append (assoc-ref inputs "js-highlight")
806 "/share/javascript/highlight.min.js"))
807 (replace-file "datatables/js/jquery.dataTables.min.js"
808 (string-append (assoc-ref inputs "js-datatables")
809 "/share/javascript/jquery.dataTables.min.js"))
810 (replace-file "selectize/js/selectize.min.js"
811 (string-append (assoc-ref inputs "js-selectize")
812 "/share/javascript/selectize.min.js"))
813 (replace-file "selectize/js/es5-shim.min.js"
814 (string-append (assoc-ref inputs "js-es5-shim")
815 "/share/javascript/es5-shim.min.js"))
816 (for-each (match-lambda
819 (minify source #:target target)))
820 '(("jqueryui/jquery-ui.js" .
821 "jqueryui/jquery-ui.min.js")
822 ("datepicker/js/bootstrap-datepicker.js" .
823 "datepicker/js/bootstrap-datepicker.min.js")
824 ("ionrangeslider/js/ion.rangeSlider.js" .
825 "ionrangeslider/js/ion.rangeSlider.min.js")
826 ("bootstrap/js/bootstrap.js" .
827 "bootstrap/js/bootstrap.min.js")
832 ("legacy/jquery.js" .
833 "legacy/jquery.min.js")
834 ("showdown/src/showdown.js" .
835 "showdown/compressed/showdown.js")))))
838 `(("r-crayon" ,r-crayon)
839 ("r-fastmap" ,r-fastmap)
840 ("r-httpuv" ,r-httpuv)
842 ("r-jsonlite" ,r-jsonlite)
843 ("r-xtable" ,r-xtable)
844 ("r-digest" ,r-digest)
845 ("r-htmltools" ,r-htmltools)
847 ("r-sourcetools" ,r-sourcetools)))
849 `(("js-datatables" ,js-datatables)
850 ("js-html5shiv" ,js-html5shiv)
851 ("js-json2" ,js-json2)
852 ("js-respond" ,js-respond)
853 ("js-selectize" ,js-selectize)
854 ("js-strftime" ,js-strftime)
855 ("js-highlight" ,js-highlight)
856 ("js-es5-shim" ,js-es5-shim)))
858 `(("uglify-js" ,uglify-js)))
859 (home-page "http://shiny.rstudio.com")
860 (synopsis "Easy interactive web applications with R")
862 "Makes it incredibly easy to build interactive web applications
863 with R. Automatic \"reactive\" binding between inputs and outputs and
864 extensive prebuilt widgets make it possible to build beautiful,
865 responsive, and powerful applications with minimal effort.")
866 (license license:artistic2.0)))
868 ;; This package includes minified JavaScript files. When upgrading please
869 ;; check that there are no new minified JavaScript files.
870 (define-public r-shinytree
877 (uri (cran-uri "shinyTree" version))
880 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
881 (modules '((guix build utils)))
884 ;; Delete minified JavaScript
885 (for-each delete-file
886 '("inst/www/jsTree-3.3.7/libs/require.js"
887 "inst/www/jsTree-3.3.7/libs/jquery.js"
888 "inst/www/jsTree-3.3.7/jstree.min.js"))
890 (properties `((upstream-name . "shinyTree")))
891 (build-system r-build-system)
893 `(#:modules ((guix build utils)
894 (guix build r-build-system)
898 (modify-phases %standard-phases
899 (add-after 'unpack 'replace-minified-javascript
900 (lambda* (#:key inputs #:allow-other-keys)
901 (with-directory-excursion "inst/www/jsTree-3.3.7/"
902 (symlink (string-append (assoc-ref inputs "js-requirejs")
903 "/share/javascript/require.min.js")
908 `((,(assoc-ref inputs "js-jquery")
912 (lambda (sources targets)
913 (for-each (lambda (source target)
914 (format #t "Processing ~a --> ~a~%"
916 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
917 (call-with-output-file target
919 (dump-port minified port)))))
923 `(("r-htmlwidgets" ,r-htmlwidgets)
924 ("r-jsonlite" ,r-jsonlite)
925 ("r-promises" ,r-promises)
927 ("r-stringr" ,r-stringr)))
929 `(("js-requirejs" ,js-requirejs)))
931 `(("uglify-js" ,uglify-js)
935 (uri "https://code.jquery.com/jquery-3.3.1.js")
938 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
939 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
940 (synopsis "jsTree bindings for Shiny")
942 "This package exposes R bindings to jsTree, a JavaScript library that
943 supports interactive trees, to enable rich, editable trees in Shiny.")
944 (license license:expat)))
946 (define-public r-shinydashboard
948 (name "r-shinydashboard")
952 (uri (cran-uri "shinydashboard" version))
955 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
956 (build-system r-build-system)
957 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
958 ;; Regenerate it from the included sources.
960 `(#:modules ((guix build utils)
961 (guix build r-build-system)
964 (modify-phases %standard-phases
965 (add-after 'unpack 'generate-minified-javascript
967 (with-directory-excursion "inst/AdminLTE"
968 (delete-file "app.min.js")
969 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
970 (call-with-output-file "app.min.js"
972 (dump-port minified port))))))))))
974 `(("r-htmltools" ,r-htmltools)
975 ("r-promises" ,r-promises)
976 ("r-shiny" ,r-shiny)))
978 `(("uglify-js" ,uglify-js)))
979 (home-page "http://rstudio.github.io/shinydashboard/")
980 (synopsis "Create dashboards with shiny")
981 (description "This package provides an extension to the Shiny web
982 application framework for R, making it easy to create attractive dashboards.")
983 ;; This package includes software that was released under the Expat
984 ;; license, but the whole package is released under GPL version 2 or
986 (license license:gpl2+)))
988 (define-public r-shinyfiles
990 (name "r-shinyfiles")
995 (uri (cran-uri "shinyFiles" version))
997 (base32 "1143m941hma9hc77c3xcw26c0ygfhn9ii2sbp9wrydxv4gc7mr8a"))))
998 (properties `((upstream-name . "shinyFiles")))
999 (build-system r-build-system)
1002 ("r-htmltools" ,r-htmltools)
1003 ("r-jsonlite" ,r-jsonlite)
1004 ("r-shiny" ,r-shiny)
1005 ("r-tibble" ,r-tibble)))
1006 (home-page "https://github.com/thomasp85/shinyFiles")
1007 (synopsis "Server-side file system viewer for Shiny")
1009 "This package provides functionality for client-side navigation of the
1010 server side file system in shiny apps. In case the app is running locally
1011 this gives the user direct access to the file system without the need to
1012 \"download\" files to a temporary location. Both file and folder selection as
1013 well as file saving is available.")
1014 (license license:gpl2+)))
1016 (define-public r-shinythemes
1018 (name "r-shinythemes")
1023 (uri (cran-uri "shinythemes" version))
1026 "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf"))))
1027 (properties `((upstream-name . "shinythemes")))
1028 (build-system r-build-system)
1029 (propagated-inputs `(("r-shiny" ,r-shiny)))
1030 (home-page "http://rstudio.github.io/shinythemes/")
1031 (synopsis "Themes for Shiny")
1033 "This package provides themes for use with Shiny. It includes several
1034 Bootstrap themes, which are packaged for use with Shiny applications.")
1035 ;; The package is released under version 3 of the GPL, but it includes
1036 ;; source files that are covered by the Expat license. It also includes
1037 ;; fonts under SIL or the ASL.
1038 (license (list license:gpl3 license:expat
1039 license:silofl1.1 license:asl2.0))))
1041 ;; The package sources include minified variants of d3.js and non-minified
1042 ;; source code of d3-jetpack.
1043 (define-public r-d3r
1050 (uri (cran-uri "d3r" version))
1053 "0xl3im76lp7pd5lhp8jfyqdm4j4zvjrx5a5fl81xv2cf7x3n4f2a"))))
1054 (build-system r-build-system)
1056 `(#:modules ((guix build utils)
1057 (guix build r-build-system)
1061 (modify-phases %standard-phases
1062 (add-after 'unpack 'process-javascript
1063 (lambda* (#:key inputs #:allow-other-keys)
1064 (with-directory-excursion "inst/www/d3/"
1068 `((,(assoc-ref inputs "d3.v3.js")
1069 "v3/dist/d3.min.js")
1070 (,(assoc-ref inputs "d3.v4.js")
1071 "v4/dist/d3.min.js")
1072 (,(assoc-ref inputs "d3.v5.js")
1073 "v5/dist/d3.min.js"))))
1074 (lambda (sources targets)
1075 (for-each (lambda (source target)
1076 (format #t "Processing ~a --> ~a~%"
1078 (delete-file target)
1079 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1080 (call-with-output-file target
1082 (dump-port minified port)))))
1086 `(("r-dplyr" ,r-dplyr)
1087 ("r-htmltools" ,r-htmltools)
1088 ("r-tidyr" ,r-tidyr)))
1090 `(("uglify-js" ,uglify-js)
1094 (uri "https://d3js.org/d3.v3.js")
1097 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
1101 (uri "https://d3js.org/d3.v4.js")
1104 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
1108 (uri "https://d3js.org/d3.v5.js")
1111 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))))
1112 (home-page "https://github.com/timelyportfolio/d3r")
1113 (synopsis "d3.js utilities for R")
1115 "This package provides a suite of functions to help ease the use of the
1116 d3.js visualization library in R. These helpers include
1117 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
1118 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
1119 R objects into the JSON format that the d3.js library expects.")
1120 (license license:bsd-3)))
1122 ;; We use the latest commit here because the last release was in 2016 while
1123 ;; the latest commit was in 2018.
1124 (define-public r-sankeyd3
1125 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
1129 (version (git-version "0.3.2" revision commit))
1134 (url "https://github.com/fbreitwieser/sankeyD3.git")
1136 (file-name (git-file-name name version))
1139 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
1140 (build-system r-build-system)
1143 ("r-htmlwidgets" ,r-htmlwidgets)
1144 ("r-shiny" ,r-shiny)
1145 ("r-magrittr" ,r-magrittr)))
1146 (home-page "https://github.com/fbreitwieser/sankeyD3")
1147 (synopsis "Sankey network graphs from R")
1149 "This package provides an R library to generate Sankey network graphs
1150 in R and Shiny via the D3 visualization library.")
1151 ;; The R code is licensed under GPLv3+. It includes the non-minified
1152 ;; JavaScript source code of d3-sankey, which is released under the
1153 ;; 3-clause BSD license.
1154 (license (list license:gpl3+ license:bsd-3)))))
1156 (define-public r-crosstalk
1158 (name "r-crosstalk")
1163 (uri (cran-uri "crosstalk" version))
1166 "0lfa89vhrzi7a1rghmygcjr8gzddw35sinb3jx6g49mc9jias7mk"))))
1167 (build-system r-build-system)
1169 `(("r-ggplot2" ,r-ggplot2)
1170 ("r-htmltools" ,r-htmltools)
1171 ("r-jsonlite" ,r-jsonlite)
1172 ("r-lazyeval" ,r-lazyeval)
1174 ("r-shiny" ,r-shiny)))
1175 (home-page "https://rstudio.github.io/crosstalk/")
1176 (synopsis "Inter-widget interactivity for HTML widgets")
1178 "This package provides building blocks for allowing HTML widgets to
1179 communicate with each other, with Shiny or without (i.e. static @code{.html}
1180 files). It currently supports linked brushing and filtering.")
1181 (license license:expat)))
1183 (define-public r-rook
1190 (uri (cran-uri "Rook" version))
1193 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
1194 (properties `((upstream-name . "Rook")))
1195 (build-system r-build-system)
1196 (propagated-inputs `(("r-brew" ,r-brew)))
1197 (home-page "https://cran.r-project.org/web/packages/Rook")
1198 (synopsis "Web server interface for R")
1200 "This package contains the Rook specification and convenience software
1201 for building and running Rook applications. A Rook application is an R
1202 reference class object that implements a @code{call} method or an R closure
1203 that takes exactly one argument, an environment, and returns a list with three
1204 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
1205 (license license:gpl2)))
1207 (define-public r-miniui
1214 (uri (cran-uri "miniUI" version))
1217 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
1218 (properties `((upstream-name . "miniUI")))
1219 (build-system r-build-system)
1221 `(("r-htmltools" ,r-htmltools)
1222 ("r-shiny" ,r-shiny)))
1223 (home-page "https://cran.r-project.org/web/packages/miniUI/")
1224 (synopsis "Shiny UI widgets for small screens")
1226 "This package provides UI widget and layout functions for writing Shiny apps that
1227 work well on small screens.")
1228 (license license:gpl3)))
1230 (define-public r-feather
1237 (uri (cran-uri "feather" version))
1240 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
1241 (build-system r-build-system)
1245 ("r-tibble" ,r-tibble)))
1246 (home-page "https://github.com/wesm/feather")
1247 (synopsis "R Bindings to the Feather API")
1248 (description "Read and write feather files, a lightweight binary columnar
1249 data store designed for maximum speed.")
1250 (license license:asl2.0)))
1252 (define-public r-maps
1259 (uri (cran-uri "maps" version))
1262 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
1263 (build-system r-build-system)
1264 (home-page "https://cran.r-project.org/web/packages/maps")
1265 (synopsis "Draw geographical maps")
1266 (description "This package provides an R module for display of maps.
1267 Projection code and larger maps are in separate packages (@code{mapproj} and
1269 (license license:gpl2)))
1271 (define-public r-mapproj
1278 (uri (cran-uri "mapproj" version))
1281 "0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h"))))
1282 (build-system r-build-system)
1283 (propagated-inputs `(("r-maps" ,r-maps)))
1284 (home-page "https://cran.r-project.org/web/packages/mapproj")
1285 (synopsis "Map projection in R")
1286 (description "This package converts latitude/longitude into projected
1288 (license (list license:gpl2 ; The R interface
1289 (license:non-copyleft ; The C code
1290 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
1291 "Lucent Public License Version 1.02")))))
1293 (define-public r-rgooglemaps
1295 (name "r-rgooglemaps")
1300 (uri (cran-uri "RgoogleMaps" version))
1303 "1y2dinxmzx6mg6ynpk2q7f4k4rxjm66my185gafdcvpc4rl7svs7"))))
1304 (properties `((upstream-name . "RgoogleMaps")))
1305 (build-system r-build-system)
1306 (propagated-inputs `(("r-png" ,r-png)))
1307 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
1308 (synopsis "Use Google Maps in R")
1309 (description "This package serves two purposes:
1311 @item Provide a comfortable R interface to query the Google server for static
1313 @item Use the map as a background image to overlay plots within R. This
1314 requires proper coordinate scaling.
1316 (license license:gpl2+)))
1318 (define-public r-geosphere
1320 (name "r-geosphere")
1325 (uri (cran-uri "geosphere" version))
1328 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
1329 (build-system r-build-system)
1330 (propagated-inputs `(("r-sp" ,r-sp)))
1331 (home-page "https://cran.r-project.org/web/packages/geosphere")
1332 (synopsis "Spherical trigonometry")
1333 (description "This package computes spherical trigonometry for geographic
1334 applications. That is, compute distances and related measures for angular
1335 (longitude/latitude) locations.")
1336 (license license:gpl3+)))
1338 (define-public r-jpeg
1345 (uri (cran-uri "jpeg" version))
1348 "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
1349 (build-system r-build-system)
1350 (inputs `(("libjpeg" ,libjpeg)))
1351 (home-page "http://www.rforge.net/jpeg/")
1352 (synopsis "Read and write JPEG images with R")
1353 (description "This package provides a way to read, write and display
1354 bitmap images stored in the JPEG format with R. It can read and write both
1355 files and in-memory raw vectors.")
1356 (license license:gpl2+)))
1358 (define-public r-ggmap
1365 (uri (cran-uri "ggmap" version))
1368 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
1369 (build-system r-build-system)
1371 `(("r-bitops" ,r-bitops)
1372 ("r-digest" ,r-digest)
1373 ("r-dplyr" ,r-dplyr)
1374 ("r-ggplot2" ,r-ggplot2)
1378 ("r-magrittr" ,r-magrittr)
1381 ("r-purrr" ,r-purrr)
1382 ("r-rgooglemaps" ,r-rgooglemaps)
1383 ("r-rjson" ,r-rjson)
1384 ("r-scales" ,r-scales)
1385 ("r-stringr" ,r-stringr)
1386 ("r-tibble" ,r-tibble)
1387 ("r-tidyr" ,r-tidyr)))
1388 (home-page "https://github.com/dkahle/ggmap")
1389 (synopsis "Spatial visualization with ggplot2")
1390 (description "This package provides a collection of functions to visualize
1391 spatial data and models on top of static maps from various online sources (e.g
1392 Google Maps and Stamen Maps). It includes tools common to those tasks,
1393 including functions for geolocation and routing.")
1394 (license license:gpl2)))
1396 (define-public r-haven
1403 (uri (cran-uri "haven" version))
1406 "0g9d6mxqmrw2zdms78jpx2sx73pczlyy771v1h5hmxqz9sqyk7hr"))))
1407 (build-system r-build-system)
1411 `(("r-forcats" ,r-forcats)
1414 ("r-rlang" ,r-rlang)
1415 ("r-readr" ,r-readr)
1416 ("r-tibble" ,r-tibble)
1417 ("r-tidyselect" ,r-tidyselect)))
1418 (home-page "https://haven.tidyverse.org")
1419 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
1421 "This package lets you mport foreign statistical formats into R via the
1422 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
1423 (license license:expat)))
1425 (define-public r-amap
1431 (uri (cran-uri "amap" version))
1434 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
1435 (build-system r-build-system)
1437 `(("gfortran" ,gfortran)))
1438 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
1439 (synopsis "Another multidimensional analysis package")
1440 (description "This package provides tools for clustering and principal
1441 component analysis (with robust methods, and parallelized functions).")
1442 (license license:gpl2+)))
1444 (define-public r-ape
1451 (uri (cran-uri "ape" version))
1454 "08wbk1kxhs32bmmvqlqanbdg1w235amd35k8m00fngsj9h9xzc08"))))
1455 (build-system r-build-system)
1457 `(("r-lattice" ,r-lattice)
1459 ("r-rcpp" ,r-rcpp)))
1460 (home-page "http://ape-package.ird.fr/")
1461 (synopsis "Analyses of phylogenetics and evolution")
1463 "This package provides functions for reading, writing, plotting, and
1464 manipulating phylogenetic trees, analyses of comparative data in a
1465 phylogenetic framework, ancestral character analyses, analyses of
1466 diversification and macroevolution, computing distances from DNA sequences,
1467 and several other tools.")
1468 (license license:gpl2+)))
1470 (define-public r-abbyyr
1477 (uri (cran-uri "abbyyR" version))
1480 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
1481 (properties `((upstream-name . "abbyyR")))
1482 (build-system r-build-system)
1484 `(("r-curl" ,r-curl)
1487 ("r-progress" ,r-progress)
1488 ("r-readr" ,r-readr)
1490 (home-page "https://github.com/soodoku/abbyyR")
1491 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
1493 "This package provides tools to get text from images of text using Abbyy
1494 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
1495 OCR images, barcodes, forms, documents with machine readable zones, e.g.
1496 passports and get the results in a variety of formats including plain text and
1497 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
1498 (license license:expat)))
1500 (define-public r-colorspace
1502 (name "r-colorspace")
1507 (uri (cran-uri "colorspace" version))
1509 (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9"))))
1510 (build-system r-build-system)
1511 (home-page "https://cran.r-project.org/web/packages/colorspace")
1512 (synopsis "Color space manipulation")
1514 "This package carries out a mapping between assorted color spaces
1515 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
1516 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
1517 colors are provided.")
1518 (license license:bsd-3)))
1520 (define-public r-glue
1527 (uri (cran-uri "glue" version))
1530 "1a1ycg9r3gd91visp49q49rsrdgyf8kr9dxdy3hk99kikn4z5hag"))))
1531 (build-system r-build-system)
1532 (home-page "https://github.com/tidyverse/glue")
1533 (synopsis "Interpreted string literals")
1535 "This package provides an implementation of interpreted string literals,
1536 inspired by Python's Literal String Interpolation (PEP-0498) and
1537 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
1538 (license license:expat)))
1540 (define-public r-pastecs
1546 (uri (cran-uri "pastecs" version))
1549 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
1550 (build-system r-build-system)
1552 `(("r-boot" ,r-boot)))
1553 (home-page "http://www.sciviews.org/pastecs")
1554 (synopsis "Analysis of space-time ecological series")
1556 "This package provides functions for regulation, decomposition and analysis
1557 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
1558 initiative to bring PASSTEC 2000 functionalities to R.")
1559 (license license:gpl2+)))
1561 (define-public r-plogr
1568 (uri (cran-uri "plogr" version))
1571 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
1572 (build-system r-build-system)
1573 (home-page "https://github.com/krlmlr/plogr")
1574 (synopsis "R bindings for the plog C++ logging library")
1576 "This package provides the header files for a stripped-down version of
1577 the plog header-only C++ logging library, and a method to log to R's standard
1579 (license license:expat)))
1581 (define-public r-pls
1588 (uri (cran-uri "pls" version))
1590 (base32 "121byimd6bg7jbrq5wz5fpi0vxq0vh8g724vkhnjzszbvcv1xsb7"))))
1591 (build-system r-build-system)
1592 (home-page "http://mevik.net/work/software/pls.html")
1593 (synopsis "Partial Least Squares and Principal Component Regression")
1595 "The pls package implements multivariate regression methods: Partial Least
1596 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
1597 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
1600 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
1601 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
1602 @item multi-response models (or @dfn{PLS2})
1603 @item flexible cross-validation
1604 @item Jackknife variance estimates of regression coefficients
1605 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
1606 (R)MSEP, R², and correlation loadings
1607 @item formula interface, modelled after @code{lm()}, with methods for predict,
1608 print, summary, plot, update, etc.
1609 @item extraction functions for coefficients, scores, and loadings
1610 @item MSEP, RMSEP, and R² estimates
1611 @item multiplicative scatter correction (@dfn{MSC})
1613 (license license:gpl2)))
1622 (uri (cran-uri "ps" version))
1624 (base32 "1lcq7r0q4jb8x6k023zr2ydj2dg925bqqbkhx1phpnyjrk897498"))))
1625 (build-system r-build-system)
1626 (home-page "https://ps.r-lib.org")
1627 (synopsis "List, query, and manipulate system processes")
1629 "The ps package implements an API to list, query, and manipulate system
1630 processes. Most of its code is based on the @code{psutil} Python package.")
1631 (license license:bsd-3)))
1633 (define-public r-pkgbuild
1640 (uri (cran-uri "pkgbuild" version))
1642 (base32 "0xnlz6ivhkbmncg9hfw5p69lm4rjy3wn5lyxmygxyf4rrfnnqwxx"))))
1643 (build-system r-build-system)
1645 `(("r-callr" ,r-callr)
1647 ("r-crayon" ,r-crayon)
1649 ("r-prettyunits" ,r-prettyunits)
1651 ("r-rprojroot" ,r-rprojroot)
1652 ("r-withr" ,r-withr)))
1653 (home-page "https://github.com/r-pkgs/pkgbuild")
1654 (synopsis "Find tools needed to build R packages")
1656 "This package provides functions used to build R packages. It locates
1657 compilers needed to build R packages on various platforms and ensures the PATH
1658 is configured appropriately so R can use them.")
1659 (license license:gpl3)))
1661 (define-public r-pkgload
1668 (uri (cran-uri "pkgload" version))
1671 "0z7jvharafahi2gv5547mk1n499isjzw06kfwymmxc0gd575d1ii"))))
1672 (build-system r-build-system)
1674 `(("r-desc" ,r-desc)
1675 ("r-pkgbuild" ,r-pkgbuild)
1676 ("r-rlang" ,r-rlang)
1677 ("r-rprojroot" ,r-rprojroot)
1678 ("r-rstudioapi" ,r-rstudioapi)
1679 ("r-withr" ,r-withr)))
1680 (home-page "https://github.com/r-lib/pkgload")
1681 (synopsis "Simulate package installation and attach")
1683 "This package simulates the process of installing a package and then
1684 attaching it. This is a key part of the @code{devtools} package as it allows
1685 you to rapidly iterate while developing a package.")
1686 (license license:gpl3)))
1688 (define-public r-rcpp
1695 (uri (cran-uri "Rcpp" version))
1697 (base32 "03h3zyjq948y0hrrs95lfk4zgx6wfrg64hjlrfrzf5na7bfh0d9b"))))
1698 (build-system r-build-system)
1700 `(("r-knitr" ,r-knitr))) ; for vignettes
1701 (home-page "http://www.rcpp.org")
1702 (synopsis "Seamless R and C++ integration")
1704 "The Rcpp package provides R functions as well as C++ classes which offer
1705 a seamless integration of R and C++. Many R data types and objects can be
1706 mapped back and forth to C++ equivalents which facilitates both writing of new
1707 code as well as easier integration of third-party libraries. Documentation
1708 about Rcpp is provided by several vignettes included in this package, via the
1709 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
1710 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
1711 @code{citation(\"Rcpp\")} for details on these last two.")
1712 (license license:gpl2+)))
1714 (define-public r-bindr
1721 (uri (cran-uri "bindr" version))
1724 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
1725 (build-system r-build-system)
1726 (home-page "https://github.com/krlmlr/bindr")
1727 (synopsis "Parametrized active bindings")
1729 "This package provides a simple interface for creating active bindings
1730 where the bound function accepts additional arguments.")
1731 (license license:expat)))
1733 (define-public r-bindrcpp
1740 (uri (cran-uri "bindrcpp" version))
1743 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
1744 (build-system r-build-system)
1746 `(("r-bindr" ,r-bindr)
1747 ("r-plogr" ,r-plogr)
1748 ("r-rcpp" ,r-rcpp)))
1749 (home-page "https://github.com/krlmlr/bindrcpp")
1750 (synopsis "Rcpp interface to active bindings")
1752 "This package provides an easy way to fill an environment with active
1753 bindings that call a C++ function.")
1754 (license license:expat)))
1756 (define-public r-auc
1763 (uri (cran-uri "AUC" version))
1766 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
1767 (properties `((upstream-name . "AUC")))
1768 (build-system r-build-system)
1769 (home-page "https://cran.r-project.org/web/packages/AUC")
1770 (synopsis "Compute the area under the curve of selected measures")
1772 "This package includes functions to compute the area under the curve of
1773 selected measures: the area under the sensitivity curve (AUSEC), the area
1774 under the specificity curve (AUSPC), the area under the accuracy
1775 curve (AUACC), and the area under the receiver operating characteristic
1776 curve (AUROC). The curves can also be visualized. Support for partial areas
1778 (license license:gpl2+)))
1780 (define-public r-calibrate
1782 (name "r-calibrate")
1787 (uri (cran-uri "calibrate" version))
1789 (base32 "1s423nr176l2sc66wp7hzgqkv7c2bq8d2bjrrvrrm5qa9y3zdx1k"))))
1790 (build-system r-build-system)
1792 `(("r-mass" ,r-mass)))
1793 (home-page "https://cran.r-project.org/web/packages/calibrate")
1794 (synopsis "Calibration of scatterplot and biplot axes")
1796 "This is a package for drawing calibrated scales with tick marks
1797 on (non-orthogonal) variable vectors in scatterplots and biplots.")
1798 (license license:gpl2)))
1800 (define-public r-shape
1807 (uri (cran-uri "shape" version))
1810 "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
1811 (build-system r-build-system)
1812 (home-page "https://cran.r-project.org/web/packages/shape")
1813 (synopsis "Functions for plotting graphical shapes")
1815 "This package provides functions for plotting graphical shapes such as
1816 ellipses, circles, cylinders, arrows, ...")
1817 (license license:gpl3+)))
1819 (define-public r-globaloptions
1821 (name "r-globaloptions")
1826 (uri (cran-uri "GlobalOptions" version))
1828 (base32 "0x89hfz80avq4zcskxl71i4zi0mgniqqxfrvz050aa2189wfyja2"))))
1829 (properties `((upstream-name . "GlobalOptions")))
1830 (build-system r-build-system)
1831 (home-page "https://github.com/jokergoo/GlobalOptions")
1832 (synopsis "Generate functions to get or set global options")
1834 "This package provides more controls on the option values such as
1835 validation and filtering on the values, making options invisible or private.")
1836 (license license:gpl2+)))
1838 (define-public r-circlize
1845 (uri (cran-uri "circlize" version))
1848 "0jvr9hmxyhg0zx101iiqkrg8wfaj86kp62xpv42n2j9fkn5r1mi2"))))
1849 (build-system r-build-system)
1851 `(("r-colorspace" ,r-colorspace)
1852 ("r-globaloptions" ,r-globaloptions)
1853 ("r-shape" ,r-shape)))
1854 (home-page "https://github.com/jokergoo/circlize")
1855 (synopsis "Circular visualization")
1857 "Circular layout is an efficient way to visualise huge amounts of
1858 information. This package provides an implementation of circular layout
1859 generation in R as well as an enhancement of available software. Its
1860 flexibility is based on the usage of low-level graphics functions such that
1861 self-defined high-level graphics can be easily implemented by users for
1862 specific purposes. Together with the seamless connection between the powerful
1863 computational and visual environment in R, it gives users more convenience and
1864 freedom to design figures for better understanding complex patterns behind
1865 multi-dimensional data.")
1866 (license license:gpl2+)))
1868 (define-public r-powerlaw
1875 (uri (cran-uri "poweRlaw" version))
1878 "1asr6ikr7hmj78jyg8r1gwvcjg14addkxdiz92nh06lv71a183r4"))))
1879 (properties `((upstream-name . "poweRlaw")))
1880 (build-system r-build-system)
1882 `(("r-vgam" ,r-vgam)))
1883 (home-page "https://github.com/csgillespie/poweRlaw")
1884 (synopsis "Tools for the analysis of heavy tailed distributions")
1886 "This package provides an implementation of maximum likelihood estimators
1887 for a variety of heavy tailed distributions, including both the discrete and
1888 continuous power law distributions. Additionally, a goodness-of-fit based
1889 approach is used to estimate the lower cut-off for the scaling region.")
1890 ;; Any of these GPL versions.
1891 (license (list license:gpl2 license:gpl3))))
1893 (define-public r-compare
1900 (uri (cran-uri "compare" version))
1903 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
1904 (build-system r-build-system)
1905 (home-page "https://cran.r-project.org/web/packages/compare")
1906 (synopsis "Comparing objects for differences")
1908 "This package provides functions to compare a model object to a
1909 comparison object. If the objects are not identical, the functions can be
1910 instructed to explore various modifications of the objects (e.g., sorting
1911 rows, dropping names) to see if the modified versions are identical.")
1912 (license license:gpl2+)))
1914 (define-public r-dendextend
1916 (name "r-dendextend")
1921 (uri (cran-uri "dendextend" version))
1924 "1iclvd9cyckd4djpa87ynm05fk6zl4b4m735za1w4irimc130m3r"))))
1925 (build-system r-build-system)
1927 `(("r-ggplot2" ,r-ggplot2)
1928 ("r-magrittr" ,r-magrittr)
1929 ("r-viridis" ,r-viridis)))
1930 (home-page "https://cran.r-project.org/web/packages/dendextend")
1931 (synopsis "Extending 'dendrogram' functionality in R")
1933 "This package offers a set of functions for extending @code{dendrogram}
1934 objects in R, letting you visualize and compare trees of hierarchical
1935 clusterings. You can adjust a tree's graphical parameters (the color, size,
1936 type, etc of its branches, nodes and labels) and visually and statistically
1937 compare different dendrograms to one another.")
1938 ;; Any of these versions
1939 (license (list license:gpl2 license:gpl3))))
1941 (define-public r-getoptlong
1943 (name "r-getoptlong")
1948 (uri (cran-uri "GetoptLong" version))
1951 "1l8xkvyl152bsyvxazsvx2sm1vkygn75x0lsg3sbg7xp6drdn3kc"))))
1952 (properties `((upstream-name . "GetoptLong")))
1953 (build-system r-build-system)
1957 `(("r-globaloptions" ,r-globaloptions)
1958 ("r-rjson" ,r-rjson)))
1959 (home-page "https://github.com/jokergoo/GetoptLong")
1960 (synopsis "Parsing command-line arguments and variable interpolation")
1962 "This is yet another command-line argument parser which wraps the
1963 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
1964 use in R. It also provides a simple way for variable interpolation in R.")
1965 (license license:gpl2+)))
1967 (define-public r-fastmatch
1969 (name "r-fastmatch")
1974 (uri (cran-uri "fastmatch" version))
1977 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
1978 (build-system r-build-system)
1979 (home-page "http://www.rforge.net/fastmatch")
1980 (synopsis "Fast match function")
1982 "This package provides a fast @code{match} replacement for cases that
1983 require repeated look-ups. It is slightly faster that R's built-in
1984 @code{match} function on first match against a table, but extremely fast on
1985 any subsequent lookup as it keeps the hash table in memory.")
1986 (license license:gpl2)))
1995 (uri (cran-uri "ff" version))
1998 "1w724q4jpzbvzpilb2ifviaxkjgk9lzwxz9gksnvicbmfa20fqqw"))))
1999 (build-system r-build-system)
2000 (propagated-inputs `(("r-bit" ,r-bit)))
2001 (home-page "http://ff.r-forge.r-project.org/")
2002 (synopsis "Memory-efficient storage of large data on disk and access functions")
2004 "This package provides data structures that are stored on disk but
2005 behave (almost) as if they were in RAM by transparently mapping only a section
2007 ;; error Architecture not supported.
2008 (supported-systems (delete "aarch64-linux" %supported-systems))
2009 (license license:gpl2)))
2011 (define-public r-ffbase
2018 (uri (cran-uri "ffbase" version))
2021 "04kxx2f3f0743c5nvpb7x1x0pcd220dazpd5ag1pidxbz3xa85nw"))))
2022 (build-system r-build-system)
2025 ("r-fastmatch" ,r-fastmatch)
2027 (home-page "http://github.com/edwindj/ffbase")
2028 (synopsis "Basic statistical functions for package 'ff'")
2030 "This package extends the out of memory vectors of @code{ff} with
2031 statistical functions and other utilities to ease their usage.")
2032 (license license:gpl3)))
2034 (define-public r-prettyunits
2036 (name "r-prettyunits")
2041 (uri (cran-uri "prettyunits" version))
2044 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
2045 (build-system r-build-system)
2046 (home-page "https://github.com/gaborcsardi/prettyunits")
2047 (synopsis "Pretty, human readable formatting of quantities")
2049 "This package provides tools for pretty, human readable formatting of
2051 (license license:expat)))
2053 (define-public r-reshape
2060 (uri (cran-uri "reshape" version))
2063 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
2064 (build-system r-build-system)
2066 `(("r-plyr" ,r-plyr)
2067 ("r-rcpp" ,r-rcpp)))
2068 (home-page "http://had.co.nz/reshape")
2069 (synopsis "Flexibly reshape data")
2071 "Flexibly restructure and aggregate data using just two functions:
2072 @code{melt} and @code{cast}. This package provides them.")
2073 (license license:expat)))
2075 (define-public r-progress
2082 (uri (cran-uri "progress" version))
2085 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
2086 (build-system r-build-system)
2088 `(("r-crayon" ,r-crayon)
2090 ("r-prettyunits" ,r-prettyunits)
2092 (home-page "https://github.com/gaborcsardi/progress")
2093 (synopsis "Terminal progress bars")
2095 "This package provides configurable progress bars. They may include
2096 percentage, elapsed time, and/or the estimated completion time. They work in
2097 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
2098 package also provides a C++ API, that works with or without Rcpp.")
2099 (license license:expat)))
2101 (define-public r-ggally
2108 (uri (cran-uri "GGally" version))
2111 "1zjmcc5bzagvy7c5cmdcl39xmx07fwi98yrj4i05w7y40kqcsiws"))))
2112 (properties `((upstream-name . "GGally")))
2113 (build-system r-build-system)
2115 `(("libressl" ,libressl)))
2117 `(("r-ggplot2" ,r-ggplot2)
2118 ("r-gtable" ,r-gtable)
2120 ("r-progress" ,r-progress)
2121 ("r-rcolorbrewer" ,r-rcolorbrewer)
2122 ("r-reshape" ,r-reshape)
2123 ("r-rlang" ,r-rlang)))
2124 (home-page "https://ggobi.github.io/ggally")
2125 (synopsis "Extension to ggplot2")
2127 "The R package ggplot2 is a plotting system based on the grammar of
2128 graphics. GGally extends ggplot2 by adding several functions to reduce the
2129 complexity of combining geometric objects with transformed data. Some of
2130 these functions include a pairwise plot matrix, a two group pairwise plot
2131 matrix, a parallel coordinates plot, a survival plot, and several functions to
2133 (license license:gpl2+)))
2135 (define-public r-proxy
2142 (uri (cran-uri "proxy" version))
2145 "17b6qfllqrhzrxqgx7dccffgybnkcria5a68ap5ly3plg04ypm4x"))))
2146 (build-system r-build-system)
2147 (home-page "https://cran.r-project.org/web/packages/proxy")
2148 (synopsis "Distance and similarity measures")
2150 "This package provides an extensible framework for the efficient
2151 calculation of auto- and cross-proximities, along with implementations of the
2152 most popular ones.")
2153 (license license:gpl2)))
2162 (uri (cran-uri "sp" version))
2164 (base32 "0kpjsqh3lzqp1m0avsvm54lazlgwfx3hyf0av3mvbyslsanj42ll"))))
2165 (build-system r-build-system)
2167 `(("r-lattice" ,r-lattice)))
2168 (home-page "https://cran.r-project.org/web/packages/sp")
2169 (synopsis "Classes and methods for spatial data")
2171 "This package provides classes and methods for spatial data; the classes
2172 document where the spatial location information resides, for 2D or 3D data.
2173 Utility functions are provided, e.g. for plotting data as maps, spatial
2174 selection, as well as methods for retrieving coordinates, for subsetting,
2175 print, summary, etc.")
2176 (license license:gpl2+)))
2178 (define-public r-rmtstat
2185 (uri (cran-uri "RMTstat" version))
2188 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
2189 (properties `((upstream-name . "RMTstat")))
2190 (build-system r-build-system)
2191 (home-page "https://cran.r-project.org/web/packages/RMTstat")
2192 (synopsis "Distributions, statistics and tests derived from random matrix theory")
2194 "This package provides functions for working with the Tracy-Widom laws
2195 and other distributions related to the eigenvalues of large Wishart
2197 (license license:bsd-3)))
2199 (define-public r-rmpi
2205 (uri (cran-uri "Rmpi" version))
2208 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
2209 (properties `((upstream-name . "Rmpi")))
2210 (build-system r-build-system)
2212 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
2213 #:phases (modify-phases %standard-phases
2214 (add-before 'install 'mpi-setup
2217 `(("openmpi" ,openmpi)))
2219 `(("pkg-config" ,pkg-config)))
2220 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
2221 (synopsis "R interface to message-passing interface (MPI)")
2223 "This package provides an interface (wrapper) to MPI APIs. It also
2224 provides an interactive R manager and worker environment.")
2225 (license license:gpl2+)))
2227 (define-public r-lmoments
2234 (uri (cran-uri "Lmoments" version))
2237 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
2238 (properties `((upstream-name . "Lmoments")))
2239 (build-system r-build-system)
2241 `(("r-rcpp" ,r-rcpp)
2242 ("r-rcpparmadillo" ,r-rcpparmadillo)))
2243 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
2244 (synopsis "L-moments and quantile mixtures")
2246 "This package contains functions to estimate L-moments and trimmed
2247 L-moments from the data. It also contains functions to estimate the
2248 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
2249 quantile mixture from L-moments and trimmed L-moments.")
2250 (license license:gpl2)))
2252 (define-public r-distillery
2254 (name "r-distillery")
2259 (uri (cran-uri "distillery" version))
2262 "1mi3ig9jq0kd7yrwc5m37lmrw04p1b4lirnbsxi10z3n5yay4429"))))
2263 (build-system r-build-system)
2264 (home-page "https://ral.ucar.edu/staff/ericg/")
2265 (synopsis "Functions for confidence intervals and object information")
2267 "This package provides some very simple method functions for confidence
2268 interval calculation and to distill pertinent information from a potentially
2269 complex object; primarily used in common with the packages extRemes and
2271 (license license:gpl2+)))
2273 (define-public r-extremes
2280 (uri (cran-uri "extRemes" version))
2283 "0hmgynxhzswqnhwb2sxrkczgam8c17s3vpxqc5bcz0bwczpxxyvm"))))
2284 (properties `((upstream-name . "extRemes")))
2285 (build-system r-build-system)
2287 `(("r-distillery" ,r-distillery)
2288 ("r-lmoments" ,r-lmoments)))
2289 (home-page "https://www.assessment.ucar.edu/toolkit/")
2290 (synopsis "Extreme value analysis")
2292 "ExtRemes is a suite of functions for carrying out analyses on the
2293 extreme values of a process of interest; be they block maxima over long blocks
2294 or excesses over a high threshold.")
2295 (license license:gpl2+)))
2297 (define-public r-lmtest
2304 (uri (cran-uri "lmtest" version))
2307 "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx"))))
2308 (build-system r-build-system)
2310 `(("r-zoo" ,r-zoo)))
2312 `(("gfortran" ,gfortran)))
2313 (home-page "https://cran.r-project.org/web/packages/lmtest")
2314 (synopsis "Testing linear regression models")
2316 "This package provides a collection of tests, data sets, and examples for
2317 diagnostic checking in linear regression models. Furthermore, some generic
2318 tools for inference in parametric models are provided.")
2319 ;; Either version is okay
2320 (license (list license:gpl2 license:gpl3))))
2322 (define-public r-idr
2328 (uri (cran-uri "idr" version))
2331 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
2332 (build-system r-build-system)
2333 (home-page "https://cran.r-project.org/web/packages/idr/")
2334 (synopsis "Irreproducible discovery rate")
2336 "This is a package for estimating the copula mixture model and plotting
2337 correspondence curves in \"Measuring reproducibility of high-throughput
2338 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
2339 by Li, Brown, Huang, and Bickel")
2340 (license license:gpl2+)))
2342 (define-public r-inline
2348 (uri (cran-uri "inline" version))
2351 "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
2352 (build-system r-build-system)
2353 (home-page "https://cran.r-project.org/web/packages/inline")
2354 (synopsis "Functions to inline C, C++, Fortran function calls from R")
2356 "This package provides functionality to dynamically define R functions
2357 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
2358 @code{.Call} calling conventions.")
2359 ;; Any version of the LGPL.
2360 (license license:lgpl3+)))
2362 (define-public r-bdsmatrix
2364 (name "r-bdsmatrix")
2369 (uri (cran-uri "bdsmatrix" version))
2372 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
2373 (properties `((upstream-name . "bdsmatrix")))
2374 (build-system r-build-system)
2375 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
2376 (synopsis "Routines for block diagonal symmetric matrices")
2378 "This package provides procedures to work with block diagonal symmetric
2379 matrices, a special case of sparse matrices.")
2380 (license license:lgpl2.0)))
2382 (define-public r-bbmle
2389 (uri (cran-uri "bbmle" version))
2392 "1idn55w5f3iw4r0ydyww8xyinninw07sxlwfqb565vmdrs87dwl4"))))
2393 (build-system r-build-system)
2395 `(("r-bdsmatrix" ,r-bdsmatrix)
2396 ("r-lattice" ,r-lattice)
2398 ("r-matrix" ,r-matrix)
2399 ("r-mvtnorm" ,r-mvtnorm)
2400 ("r-numderiv" ,r-numderiv)))
2401 (home-page "https://cran.r-project.org/web/packages/bbmle")
2402 (synopsis "Tools for General Maximum Likelihood Estimation")
2404 "This package provides methods and functions for fitting maximum
2405 likelihood models in R. This package modifies and extends the @code{mle}
2406 classes in the @code{stats4} package.")
2407 ;; Any version of the GPL
2408 (license license:gpl2+)))
2410 (define-public r-emdbook
2417 (uri (cran-uri "emdbook" version))
2420 "0a515jdzvg87npvrh7md7zp0v5nlz7c2jr7pba5dql6slb0d8j7q"))))
2421 (build-system r-build-system)
2423 `(("r-bbmle" ,r-bbmle)
2425 ("r-lattice" ,r-lattice)
2428 ("r-rcpp" ,r-rcpp)))
2429 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
2430 (synopsis "Support functions and data for \"Ecological Models and Data\"")
2432 "This package provides auxiliary functions and data sets for \"Ecological
2433 Models and Data\", a book presenting maximum likelihood estimation and related
2434 topics for ecologists (ISBN 978-0-691-12522-0).")
2436 (license (list license:gpl2 license:gpl3))))
2438 (define-public r-lpsolve
2445 (uri (cran-uri "lpSolve" version))
2448 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
2449 (properties `((upstream-name . "lpSolve")))
2450 (build-system r-build-system)
2451 (home-page "https://cran.r-project.org/web/packages/lpSolve")
2452 (synopsis "R interface to Lp_solve to solve linear/integer programs")
2454 "Lp_solve is software for solving linear, integer and mixed integer
2455 programs. This implementation supplies a \"wrapper\" function in C and some R
2456 functions that solve general linear/integer problems, assignment problems, and
2457 transportation problems.")
2458 (license license:lgpl2.0)))
2460 (define-public r-limsolve
2467 (uri (cran-uri "limSolve" version))
2470 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
2471 (properties `((upstream-name . "limSolve")))
2472 (build-system r-build-system)
2474 `(("r-lpsolve" ,r-lpsolve)
2476 ("r-quadprog" ,r-quadprog)))
2477 (native-inputs `(("gfortran" ,gfortran)))
2478 (home-page "https://cran.r-project.org/web/packages/limSolve")
2479 (synopsis "Solving linear inverse models")
2481 "This package provides functions that:
2484 @item find the minimum/maximum of a linear or quadratic function,
2485 @item sample an underdetermined or overdetermined system,
2486 @item solve a linear system Ax=B for the unknown x.
2489 It includes banded and tridiagonal linear systems. The package calls Fortran
2490 functions from LINPACK.")
2492 (license (list license:gpl2+ license:gpl3+))))
2494 (define-public r-fitdistrplus
2496 (name "r-fitdistrplus")
2501 (uri (cran-uri "fitdistrplus" version))
2504 "10q08wsv8v3w7797jdvvv60bgrf1bi6438wf0jcqv81ays82a245"))))
2505 (build-system r-build-system)
2507 `(("r-mass" ,r-mass)
2508 ("r-npsurv" ,r-npsurv)
2509 ("r-survival" ,r-survival)))
2510 (home-page "http://riskassessment.r-forge.r-project.org")
2511 (synopsis "Fitting a parametric distribution from data")
2513 "This package extends the @code{fitdistr} function of the MASS package
2514 with several functions to help the fit of a parametric distribution to
2515 non-censored or censored data. Censored data may contain left-censored,
2516 right-censored and interval-censored values, with several lower and upper
2517 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
2518 provides moment matching (MME), quantile matching (QME) and maximum
2519 goodness-of-fit estimation (MGE) methods (available only for non-censored
2520 data). Weighted versions of MLE, MME and QME are available.")
2521 (license license:gpl2+)))
2523 (define-public r-energy
2530 (uri (cran-uri "energy" version))
2533 "13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37"))))
2534 (build-system r-build-system)
2536 `(("r-boot" ,r-boot)
2537 ("r-rcpp" ,r-rcpp)))
2538 (home-page "https://cran.r-project.org/web/packages/energy")
2539 (synopsis "Multivariate inference via the energy of data")
2541 "This package provides e-statistics (energy) tests and statistics for
2542 multivariate and univariate inference, including distance correlation,
2543 one-sample, two-sample, and multi-sample tests for comparing multivariate
2544 distributions, are implemented. Measuring and testing multivariate
2545 independence based on distance correlation, partial distance correlation,
2546 multivariate goodness-of-fit tests, clustering based on energy distance,
2547 testing for multivariate normality, distance components (disco) for
2548 non-parametric analysis of structured data, and other energy
2549 statistics/methods are implemented.")
2550 (license license:gpl2+)))
2552 (define-public r-suppdists
2554 (name "r-suppdists")
2559 (uri (cran-uri "SuppDists" version))
2562 "01j6p94m1g363nph2158fq2rmd6z3h5dvcv6aidh2d6syw131xak"))))
2563 (properties `((upstream-name . "SuppDists")))
2564 (build-system r-build-system)
2565 (home-page "https://cran.r-project.org/web/packages/SuppDists")
2566 (synopsis "Supplementary distributions")
2568 "This package provides ten distributions supplementing those built into
2569 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
2570 Spearman's rho, maximum F ratio, the Pearson product moment correlation
2571 coefficient, Johnson distributions, normal scores and generalized
2572 hypergeometric distributions. In addition two random number generators of
2573 George Marsaglia are included.")
2574 (license license:gpl2+)))
2576 (define-public r-ksamples
2583 (uri (cran-uri "kSamples" version))
2586 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
2587 (properties `((upstream-name . "kSamples")))
2588 (build-system r-build-system)
2590 `(("r-suppdists" ,r-suppdists)))
2591 (home-page "https://cran.r-project.org/web/packages/kSamples")
2592 (synopsis "K-Sample rank tests and their combinations")
2594 "This package provides tools to compares k samples using the
2595 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
2596 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
2597 test. It computes asymptotic, simulated or (limited) exact P-values, all
2598 valid under randomization, with or without ties, or conditionally under random
2599 sampling from populations, given the observed tie pattern. Except for Steel's
2600 test and the JT test it also combines these tests across several blocks of
2602 (license license:gpl2+)))
2604 (define-public r-cvst
2611 (uri (cran-uri "CVST" version))
2614 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
2615 (properties `((upstream-name . "CVST")))
2616 (build-system r-build-system)
2618 `(("r-kernlab" ,r-kernlab)
2619 ("r-matrix" ,r-matrix)))
2620 (home-page "https://cran.r-project.org/web/packages/CVST")
2621 (synopsis "Fast cross-validation via sequential testing")
2623 "This package implements the fast cross-validation via sequential
2624 testing (CVST) procedure. CVST is an improved cross-validation procedure
2625 which uses non-parametric testing coupled with sequential analysis to
2626 determine the best parameter set on linearly increasing subsets of the data.
2627 Additionally to the CVST the package contains an implementation of the
2628 ordinary k-fold cross-validation with a flexible and powerful set of helper
2629 objects and methods to handle the overall model selection process. The
2630 implementations of the Cochran's Q test with permutations and the sequential
2631 testing framework of Wald are generic and can therefore also be used in other
2633 (license license:gpl2+)))
2635 (define-public r-squarem
2642 (uri (cran-uri "SQUAREM" version))
2645 "0v4ax1v8diw2w7fdhfzz1z0bwixkmcrc39ax3y116f399rc06qbs"))))
2646 (properties `((upstream-name . "SQUAREM")))
2647 (build-system r-build-system)
2648 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
2649 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
2651 "This package provides algorithms for accelerating the convergence of
2652 slow, monotone sequences from smooth, contraction mapping such as the EM
2653 algorithm. It can be used to accelerate any smooth, linearly convergent
2654 acceleration scheme. A tutorial style introduction to this package is
2655 available in a vignette.")
2656 (license license:gpl2+)))
2658 (define-public r-lava
2665 (uri (cran-uri "lava" version))
2668 "0nfab5fgnmxh8cplg8rd8cp34fny5j0k5wn4baj51r6ck7fq9g3s"))))
2669 (build-system r-build-system)
2671 `(("r-numderiv" ,r-numderiv)
2672 ("r-squarem" ,r-squarem)
2673 ("r-survival" ,r-survival)))
2674 (home-page "https://github.com/kkholst/lava")
2675 (synopsis "Latent variable models")
2677 "This package provides tools for the estimation and simulation of latent
2679 (license license:gpl3)))
2681 (define-public r-drr
2688 (uri (cran-uri "DRR" version))
2691 "1yd1fvllfkcrwg9v322n4wkk4q4q84nvy58y4vac9pdr3yf3i4vl"))))
2692 (properties `((upstream-name . "DRR")))
2693 (build-system r-build-system)
2695 `(("r-cvst" ,r-cvst)
2696 ("r-kernlab" ,r-kernlab)
2697 ("r-matrix" ,r-matrix)))
2698 (home-page "https://cran.r-project.org/web/packages/DRR")
2699 (synopsis "Dimensionality reduction via regression")
2701 "This package provides an implementation of dimensionality reduction via
2702 regression using Kernel Ridge Regression.")
2703 (license license:gpl3)))
2705 (define-public r-prodlim
2708 (version "2019.11.13")
2712 (uri (cran-uri "prodlim" version))
2715 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
2716 (build-system r-build-system)
2718 `(("r-kernsmooth" ,r-kernsmooth)
2721 ("r-survival" ,r-survival)))
2722 (home-page "https://cran.r-project.org/web/packages/prodlim")
2723 (synopsis "Product-limit estimation for censored event history analysis")
2725 "This package provides a fast and user-friendly implementation of
2726 nonparametric estimators for censored event history (survival) analysis with
2727 the Kaplan-Meier and Aalen-Johansen methods.")
2728 (license license:gpl2+)))
2730 (define-public r-dimred
2737 (uri (cran-uri "dimRed" version))
2740 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
2741 (properties `((upstream-name . "dimRed")))
2742 (build-system r-build-system)
2745 ("r-magrittr" ,r-magrittr)))
2746 (home-page "https://github.com/gdkrmr/dimRed")
2747 (synopsis "Framework for dimensionality reduction")
2749 "This package provides a collection of dimensionality reduction
2750 techniques from R packages and provides a common interface for calling the
2752 (license license:gpl3)))
2754 (define-public r-timedate
2757 (version "3043.102")
2761 (uri (cran-uri "timeDate" version))
2764 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
2765 (properties `((upstream-name . "timeDate")))
2766 (build-system r-build-system)
2767 (home-page "https://www.rmetrics.org")
2768 (synopsis "Chronological and calendar objects")
2770 "This package provides an environment for teaching \"Financial
2771 Engineering and Computational Finance\" and for managing chronological and
2773 (license license:gpl2+)))
2775 (define-public r-magic
2782 (uri (cran-uri "magic" version))
2785 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
2786 (build-system r-build-system)
2788 `(("r-abind" ,r-abind)))
2789 (home-page "https://github.com/RobinHankin/magic.git")
2790 (synopsis "Create and investigate magic squares")
2792 "This package provides a collection of efficient, vectorized algorithms
2793 for the creation and investigation of magic squares and hypercubes, including
2794 a variety of functions for the manipulation and analysis of arbitrarily
2795 dimensioned arrays.")
2796 (license license:gpl2)))
2798 (define-public r-rmysql
2805 (uri (cran-uri "RMySQL" version))
2808 "0r4626sk78fhlgivr0c7mwg9mj29ayr0iz5x90rdl4d5nc2r6kq4"))))
2809 (properties `((upstream-name . "RMySQL")))
2810 (build-system r-build-system)
2812 `(("mariadb" ,mariadb "lib")
2813 ("mariadb-dev" ,mariadb "dev")
2816 `(("r-dbi" ,r-dbi)))
2817 (home-page "https://github.com/r-dbi/RMySQL")
2818 (synopsis "Database interface and MySQL driver for R")
2820 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
2821 package contains an old implementation based on legacy code from S-PLUS which
2822 is being phased out. A modern MySQL client based on Rcpp is available from
2823 the RMariaDB package.")
2824 (license license:gpl2)))
2826 (define-public r-rpostgresql
2828 (name "r-rpostgresql")
2833 (uri (cran-uri "RPostgreSQL" version))
2836 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
2837 (properties `((upstream-name . "RPostgreSQL")))
2838 (build-system r-build-system)
2840 `(("postgresql" ,postgresql)))
2842 `(("r-dbi" ,r-dbi)))
2843 (home-page "https://github.com/tomoakin/RPostgreSQL")
2844 (synopsis "R interface to the PostgreSQL database system")
2846 "This package provides a Database Interface (DBI) compliant driver for R
2847 to access PostgreSQL database systems.")
2848 ;; The whole package is released under GPL version 2. It includes code
2849 ;; under the PostgreSQL license.
2850 (license license:gpl2)))
2852 (define-public r-linprog
2859 (uri (cran-uri "linprog" version))
2862 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
2863 (build-system r-build-system)
2864 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
2865 (home-page "http://linprog.r-forge.r-project.org/")
2866 (synopsis "Linear programming and optimization")
2868 "This package can be used to solve Linear Programming / Linear
2869 Optimization problems by using the simplex algorithm.")
2870 (license license:gpl2+)))
2872 (define-public r-geometry
2879 (uri (cran-uri "geometry" version))
2882 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
2883 (build-system r-build-system)
2885 `(("r-magic" ,r-magic)
2886 ("r-linprog" ,r-linprog)
2887 ("r-lpsolve" ,r-lpsolve)
2889 ("r-rcppprogress" ,r-rcppprogress)))
2890 (home-page "http://geometry.r-forge.r-project.org/")
2891 (synopsis "Mesh generation and surface tesselation")
2893 "This package makes the qhull library available in R, in a similar manner
2894 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
2895 intersections about a point, Voronoi diagrams, furthest-site Delaunay
2896 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
2897 and higher dimensions. It implements the Quickhull algorithm for computing
2898 the convex hull. Qhull does not support constrained Delaunay triangulations,
2899 or mesh generation of non-convex objects, but the package does include some R
2900 functions that allow for this. Currently the package only gives access to
2901 Delaunay triangulation and convex hull computation.")
2902 ;; The Qhull sources are included and are distributed under a custom
2903 ;; non-copyleft license. The R sources are released under GPL version 2.
2904 (license (list license:gpl2
2905 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
2907 (define-public r-ddalpha
2914 (uri (cran-uri "ddalpha" version))
2917 "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3"))))
2918 (build-system r-build-system)
2921 ("r-class" ,r-class)
2922 ("r-geometry" ,r-geometry)
2925 ("r-robustbase" ,r-robustbase)
2926 ("r-sfsmisc" ,r-sfsmisc)))
2928 `(("gfortran" ,gfortran)))
2929 (home-page "https://cran.r-project.org/web/packages/ddalpha")
2930 (synopsis "Depth-Based classification and calculation of data depth")
2932 "This package contains procedures for depth-based supervised learning,
2933 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
2934 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
2935 statistical depth function to a compact low-dimensional space, where the final
2936 classification is done. It also offers an extension to functional data and
2937 routines for calculating certain notions of statistical depth functions. 50
2938 multivariate and 5 functional classification problems are included.")
2939 (license license:gpl2)))
2941 (define-public r-gower
2948 (uri (cran-uri "gower" version))
2951 "007ivwn1nagpi26qq8iih1c2l61c53glvv60n90hi341ry8vwgxg"))))
2952 (build-system r-build-system)
2953 (home-page "https://github.com/markvanderloo/gower")
2954 (synopsis "Gower's distance")
2956 "This package provides tools to compute Gower's distance (or similarity)
2957 coefficient between records, and to compute the top-n matches between records.
2958 Core algorithms are executed in parallel on systems supporting OpenMP.")
2959 (license license:gpl3)))
2961 (define-public r-rcpproll
2968 (uri (cran-uri "RcppRoll" version))
2971 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
2972 (properties `((upstream-name . "RcppRoll")))
2973 (build-system r-build-system)
2975 `(("r-rcpp" ,r-rcpp)))
2976 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
2977 (synopsis "Efficient rolling and windowed operations")
2979 "This package provides fast and efficient routines for common rolling /
2980 windowed operations. Routines for the efficient computation of windowed mean,
2981 median, sum, product, minimum, maximum, standard deviation and variance are
2983 (license license:gpl2+)))
2985 (define-public r-ipred
2992 (uri (cran-uri "ipred" version))
2995 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
2996 (build-system r-build-system)
2998 `(("r-class" ,r-class)
3001 ("r-prodlim" ,r-prodlim)
3002 ("r-rpart" ,r-rpart)
3003 ("r-survival" ,r-survival)))
3004 (home-page "https://cran.r-project.org/web/packages/ipred")
3005 (synopsis "Improved predictors")
3007 "This package provides improved predictive models by indirect
3008 classification and bagging for classification, regression and survival
3009 problems as well as resampling based estimators of prediction error.")
3010 (license license:gpl2+)))
3012 (define-public r-psych
3015 (version "1.9.12.31")
3019 (uri (cran-uri "psych" version))
3022 "02i9p6appf15hjdsi58g39bzs9as40f9qhy8m7ki30hd1fz1vrr5"))))
3023 (build-system r-build-system)
3025 `(("r-lattice" ,r-lattice)
3026 ("r-mnormt" ,r-mnormt)
3027 ("r-nlme" ,r-nlme)))
3028 (home-page "https://cran.r-project.org/web/packages/psych/")
3029 (synopsis "Procedures for psychological, psychometric, and personality research")
3031 "This package provides a general purpose toolbox for personality,
3032 psychometric theory and experimental psychology. Functions are primarily for
3033 multivariate analysis and scale construction using factor analysis, principal
3034 component analysis, cluster analysis and reliability analysis, although others
3035 provide basic descriptive statistics. Item Response Theory is done using
3036 factor analysis of tetrachoric and polychoric correlations. Functions for
3037 analyzing data at multiple levels include within and between group statistics,
3038 including correlations and factor analysis. Functions for simulating and
3039 testing particular item and test structures are included. Several functions
3040 serve as a useful front end for structural equation modeling. Graphical
3041 displays of path diagrams, factor analysis and structural equation models are
3042 created using basic graphics.")
3043 (license license:gpl2+)))
3045 (define-public r-generics
3052 (uri (cran-uri "generics" version))
3055 "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi"))))
3056 (build-system r-build-system)
3057 (home-page "https://github.com/r-lib/generics")
3058 (synopsis "Common S3 generics not provided by base R methods")
3060 "In order to reduce potential package dependencies and conflicts,
3061 generics provides a number of commonly used S3 generics that are not provided
3062 by base R methods related to model fitting.")
3063 (license license:gpl2)))
3065 (define-public r-broom
3072 (uri (cran-uri "broom" version))
3075 "1w35v1qrg8d0bm7a4gsdqkmrl9nmymsvmamy48vc046a1axzgzq1"))))
3076 (build-system r-build-system)
3078 `(("r-backports" ,r-backports)
3079 ("r-dplyr" ,r-dplyr)
3080 ("r-generics" ,r-generics)
3082 ("r-purrr" ,r-purrr)
3083 ("r-reshape2" ,r-reshape2)
3084 ("r-stringr" ,r-stringr)
3085 ("r-tibble" ,r-tibble)
3086 ("r-tidyr" ,r-tidyr)))
3087 (home-page "https://github.com/tidyverse/broom")
3088 (synopsis "Convert statistical analysis objects into tidy data frames")
3090 "This package provides tools to convert statistical analysis objects from
3091 R into tidy data frames, so that they can more easily be combined, reshaped
3092 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
3093 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
3094 summarizes a model's statistical findings such as coefficients of a
3095 regression; @code{augment}, which adds columns to the original data such as
3096 predictions, residuals and cluster assignments; and @code{glance}, which
3097 provides a one-row summary of model-level statistics.")
3098 (license license:expat)))
3100 (define-public r-recipes
3107 (uri (cran-uri "recipes" version))
3110 "1fmnka583sqm6v5bhxbllb4cd5xfqbf268aij2xgxiwckv3c0ynm"))))
3111 (build-system r-build-system)
3113 `(("r-dplyr" ,r-dplyr)
3114 ("r-generics" ,r-generics)
3116 ("r-gower" ,r-gower)
3117 ("r-ipred" ,r-ipred)
3118 ("r-lubridate" ,r-lubridate)
3119 ("r-magrittr" ,r-magrittr)
3120 ("r-matrix" ,r-matrix)
3121 ("r-purrr" ,r-purrr)
3122 ("r-rlang" ,r-rlang)
3123 ("r-tibble" ,r-tibble)
3124 ("r-tidyr" ,r-tidyr)
3125 ("r-tidyselect" ,r-tidyselect)
3126 ("r-timedate" ,r-timedate)
3127 ("r-withr" ,r-withr)))
3128 (home-page "https://github.com/topepo/recipes")
3129 (synopsis "Preprocessing tools to create design matrices")
3131 "Recipes is an extensible framework to create and preprocess design
3132 matrices. Recipes consist of one or more data manipulation and analysis
3133 \"steps\". Statistical parameters for the steps can be estimated from an
3134 initial data set and then applied to other data sets. The resulting design
3135 matrices can then be used as inputs into statistical or machine learning
3137 (license license:gpl2)))
3139 (define-public r-pdist
3146 (uri (cran-uri "pdist" version))
3149 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
3150 (build-system r-build-system)
3151 (home-page "https://github.com/jeffwong/pdist")
3152 (synopsis "Partitioned distance function")
3154 "Pdist computes the euclidean distance between rows of a matrix X and
3155 rows of another matrix Y. Previously, this could be done by binding the two
3156 matrices together and calling @code{dist}, but this creates unnecessary
3157 computation by computing the distances between a row of X and another row of
3158 X, and likewise for Y. Pdist strictly computes distances across the two
3159 matrices, not within the same matrix, making computations significantly faster
3160 for certain use cases.")
3161 (license license:gpl3+)))
3163 (define-public r-ggrepel
3170 (uri (cran-uri "ggrepel" version))
3173 "10vjrcmx8yknfbx93d9a4y3z8gafri0fhimw6hcq733dmdvkml6m"))))
3174 (build-system r-build-system)
3176 `(("r-ggplot2" ,r-ggplot2)
3178 ("r-scales" ,r-scales)))
3179 (home-page "http://github.com/slowkow/ggrepel")
3180 (synopsis "Repulsive text and label geometries for ggplot2")
3182 "This package provides text and label geometries for ggplot2 that help to
3183 avoid overlapping text labels. Labels repel away from each other and away
3184 from the data points.")
3185 (license license:gpl3)))
3187 (define-public r-corrplot
3194 (uri (cran-uri "corrplot" version))
3197 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
3198 (build-system r-build-system)
3199 (home-page "https://github.com/taiyun/corrplot")
3200 (synopsis "Visualization of a correlation matrix")
3202 "This package provides a graphical display of a correlation matrix or
3203 general matrix. It also contains some algorithms to do matrix reordering. In
3204 addition, corrplot is good at details, including choosing color, text labels,
3205 color labels, layout, etc.")
3206 ;; Any version of the GPL
3207 (license license:gpl2+)))
3209 (define-public r-stringdist
3211 (name "r-stringdist")
3216 (uri (cran-uri "stringdist" version))
3218 (base32 "1dqfakclzaf878x7mhwmqrcpcql2h9cv19fz5f3ygpajf3si5kqi"))))
3219 (build-system r-build-system)
3220 (home-page "https://github.com/markvanderloo/stringdist")
3221 (synopsis "Approximate string matching and string distance functions")
3223 "This package implements an approximate string matching version of R's
3224 native @code{match} function. It can calculate various string distances based
3225 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
3226 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
3227 Jaro-Winkler). An implementation of soundex is provided as well. Distances
3228 can be computed between character vectors while taking proper care of encoding
3229 or between integer vectors representing generic sequences.")
3230 (license license:gpl3+)))
3232 (define-public r-ucminf
3239 (uri (cran-uri "ucminf" version))
3242 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
3243 (build-system r-build-system)
3244 (native-inputs `(("gfortran" ,gfortran)))
3245 (home-page "https://cran.r-project.org/web/packages/ucminf/")
3246 (synopsis "General-purpose unconstrained non-linear optimization")
3248 "This package provides an implementation of an algorithm for
3249 general-purpose unconstrained non-linear optimization. The algorithm is of
3250 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
3251 search with a trust region type monitoring of the input to the line search
3252 algorithm. The interface of @code{ucminf} is designed for easy interchange
3253 with the package @code{optim}.")
3254 (license license:gpl2+)))
3256 (define-public r-ordinal
3259 (version "2019.12-10")
3263 (uri (cran-uri "ordinal" version))
3266 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
3267 (build-system r-build-system)
3269 `(("r-mass" ,r-mass)
3270 ("r-matrix" ,r-matrix)
3271 ("r-numderiv" ,r-numderiv)
3272 ("r-ucminf" ,r-ucminf)))
3273 (home-page "https://github.com/runehaubo/ordinal")
3274 (synopsis "Regression models for ordinal data")
3276 "This package provides an implementation of cumulative link (mixed)
3277 models also known as ordered regression models, proportional odds models,
3278 proportional hazards models for grouped survival times and ordered models.
3279 Estimation is via maximum likelihood and mixed models are fitted with the
3280 Laplace approximation and adaptive Gauss-Hermite quadrature.")
3281 (license license:gpl2+)))
3283 (define-public r-jomo
3290 (uri (cran-uri "jomo" version))
3293 "1k9l4290g350zbw1pjs871q9bxj3j2h1dilxpp06v4wy4n7d8qs0"))))
3294 (build-system r-build-system)
3296 `(("r-lme4" ,r-lme4)
3298 ("r-ordinal" ,r-ordinal)
3299 ("r-survival" ,r-survival)))
3300 (home-page "https://cran.r-project.org/web/packages/jomo/")
3301 (synopsis "Multilevel Joint Modelling Multiple Imputation")
3303 "Similarly to Schafer's package pan, jomo is a package for multilevel
3304 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
3305 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
3306 possibility of handling binary and categorical data through latent normal
3307 variables, the option to use cluster-specific covariance matrices and to
3308 impute compatibly with the substantive model.")
3309 (license license:gpl2)))
3311 (define-public r-pan
3318 (uri (cran-uri "pan" version))
3321 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
3322 (build-system r-build-system)
3323 (native-inputs `(("gfortran" ,gfortran)))
3324 (home-page "https://cran.r-project.org/web/packages/pan/")
3325 (synopsis "Multiple imputation for multivariate panel or clustered data")
3327 "This package implements multiple imputation for multivariate panel or
3329 (license license:gpl3)))
3331 (define-public r-mitml
3338 (uri (cran-uri "mitml" version))
3341 "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
3342 (build-system r-build-system)
3344 `(("r-haven" ,r-haven)
3347 (home-page "https://cran.r-project.org/web/packages/mitml/")
3348 (synopsis "Tools for multiple imputation in multilevel modeling")
3350 "This package provides tools for multiple imputation of missing data in
3351 multilevel modeling. It includes a user-friendly interface to the packages
3352 pan and jomo, and several functions for visualization, data management and the
3353 analysis of multiply imputed data sets.")
3354 (license license:gpl2+)))
3356 (define-public r-mice
3363 (uri (cran-uri "mice" version))
3366 "1wx1s1gc07iz63w4m8z0i1n5mc273f89grp5d3hfla7ypicjkasf"))))
3367 (build-system r-build-system)
3369 `(("r-broom" ,r-broom)
3370 ("r-dplyr" ,r-dplyr)
3371 ("r-lattice" ,r-lattice)
3373 ("r-mitml" ,r-mitml)
3376 ("r-rlang" ,r-rlang)
3377 ("r-rpart" ,r-rpart)
3378 ("r-survival" ,r-survival)))
3379 (home-page "https://cran.r-project.org/web/packages/mice/")
3380 (synopsis "Multivariate imputation by chained equations")
3382 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
3383 implemented by the MICE algorithm as described in @url{Van Buuren and
3384 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
3385 variable has its own imputation model. Built-in imputation models are
3386 provided for continuous data (predictive mean matching, normal), binary
3387 data (logistic regression), unordered categorical data (polytomous logistic
3388 regression) and ordered categorical data (proportional odds). MICE can also
3389 impute continuous two-level data (normal model, pan, second-level variables).
3390 Passive imputation can be used to maintain consistency between variables.
3391 Various diagnostic plots are available to inspect the quality of the
3393 ;; Any of these two versions.
3394 (license (list license:gpl2 license:gpl3))))
3396 (define-public r-truncnorm
3398 (name "r-truncnorm")
3403 (uri (cran-uri "truncnorm" version))
3406 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
3407 (build-system r-build-system)
3408 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
3409 (synopsis "Truncated normal distribution")
3410 (description "This package provides functions for the truncated normal
3411 distribution with mean equal to @code{mean} and standard deviation equal to
3412 @code{sd}. It includes density, distribution, quantile, and expected value
3413 functions, as well as a random generation function.")
3414 (license license:gpl2)))
3416 (define-public r-rsolnp
3423 (uri (cran-uri "Rsolnp" version))
3426 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
3427 (properties `((upstream-name . "Rsolnp")))
3428 (build-system r-build-system)
3430 `(("r-truncnorm" ,r-truncnorm)))
3431 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
3432 (synopsis "General non-linear optimization")
3433 (description "The Rsolnp package implements a general non-linear augmented
3434 Lagrange multiplier method solver, a @dfn{sequential quadratic
3435 programming} (SQP) based solver).")
3436 ;; Any version of the GPL.
3437 (license license:gpl2+)))
3439 (define-public r-hardyweinberg
3441 (name "r-hardyweinberg")
3446 (uri (cran-uri "HardyWeinberg" version))
3449 "1irz44q6nf95h37av868f47aakwv3jgwgw217xfsfw0afkm7s25f"))))
3450 (properties `((upstream-name . "HardyWeinberg")))
3451 (build-system r-build-system)
3453 `(("r-mice" ,r-mice)
3455 ("r-rsolnp" ,r-rsolnp)))
3456 (home-page "https://cran.r-project.org/package=HardyWeinberg")
3457 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
3459 "This package contains tools for exploring Hardy-Weinberg equilibrium for
3460 diallelic genetic marker data. All classical tests (chi-square, exact,
3461 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
3462 included in the package, as well as functions for power computation and for
3463 the simulation of marker data under equilibrium and disequilibrium. Routines
3464 for dealing with markers on the X-chromosome are included. Functions for
3465 testing equilibrium in the presence of missing data by using multiple
3466 imputation are also provided. Implements several graphics for exploring the
3467 equilibrium status of a large set of diallelic markers: ternary plots with
3468 acceptance regions, log-ratio plots and Q-Q plots.")
3469 (license license:gpl2+)))
3478 (uri (cran-uri "sm" version))
3481 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
3482 (build-system r-build-system)
3483 (native-inputs `(("gfortran" ,gfortran)))
3484 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
3485 (synopsis "Smoothing methods for nonparametric regression and density estimation")
3487 "This is software accompanying the book 'Applied Smoothing Techniques for
3488 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
3489 University Press. It provides smoothing methods for nonparametric regression
3490 and density estimation")
3491 (license license:gpl2+)))
3493 (define-public r-venndiagram
3495 (name "r-venndiagram")
3499 (uri (cran-uri "VennDiagram" version))
3502 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
3503 (properties `((upstream-name . "VennDiagram")))
3504 (build-system r-build-system)
3506 `(("r-futile-logger" ,r-futile-logger)))
3507 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
3508 (synopsis "Generate High-Resolution Venn and Euler Plots")
3510 "This package provides a set of functions to generate high-resolution
3511 Venn and Euler plots. It includes handling for several special cases,
3512 including two-case scaling, and extensive customization of plot shape and
3514 (license license:gpl2+)))
3516 (define-public r-vioplot
3523 (uri (cran-uri "vioplot" version))
3526 "1fsklymilspzz5fzlj7666x09aglaw0v4x0yfjjzy4vr5qpjc529"))))
3527 (build-system r-build-system)
3531 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
3532 (synopsis "Violin plot")
3534 "This package provides a violin plot, which is a combination of a box
3535 plot and a kernel density plot.")
3536 (license license:bsd-3)))
3538 (define-public r-rsofia
3544 ;; This package has been removed from CRAN, so we can
3545 ;; only fetch it from the archives.
3546 (uri (string-append "https://cran.r-project.org/src/"
3547 "contrib/Archive/RSofia/RSofia_"
3551 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
3552 (properties `((upstream-name . "RSofia")))
3553 (build-system r-build-system)
3555 `(("r-rcpp" ,r-rcpp)))
3556 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
3557 (synopsis "Port of sofia-ml to R")
3558 (description "This package is a port of sofia-ml to R. Sofia-ml is a
3559 suite of fast incremental algorithms for machine learning that can be used for
3560 training models for classification or ranking.")
3561 (license license:asl2.0)))
3563 (define-public r-xts
3570 (uri (cran-uri "xts" version))
3573 "0q4cc8ynp7ndmgll1jj3lxyl6wmgg89ad3wq09kjc2ngszdfc4fz"))))
3574 (build-system r-build-system)
3575 (propagated-inputs `(("r-zoo" ,r-zoo)))
3576 (home-page "https://github.com/joshuaulrich/xts")
3577 (synopsis "Extensible time series")
3579 "This package provides for uniform handling of R's different time-based
3580 data classes by extending @code{zoo}, maximizing native format information
3581 preservation and allowing for user-level customization and extension, while
3582 simplifying cross-class interoperability.")
3583 (license license:gpl2+)))
3585 (define-public r-performanceanalytics
3587 (name "r-performanceanalytics")
3592 (uri (cran-uri "PerformanceAnalytics" version))
3595 "0jhjldwyxwq7a47zmk5y1jjck7hvq92p8rlgjvdfy51hx2dmlqqd"))))
3597 `((upstream-name . "PerformanceAnalytics")))
3598 (build-system r-build-system)
3600 `(("r-quadprog" ,r-quadprog)
3603 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
3604 (synopsis "Econometric tools for performance and risk analysis")
3605 (description "This is a collection of econometric functions for
3606 performance and risk analysis. This package aims to aid practitioners and
3607 researchers in utilizing the latest research in analysis of non-normal return
3608 streams. In general, it is most tested on return (rather than price) data on
3609 a regular scale, but most functions will work with irregular return data as
3610 well, and increasing numbers of functions will work with P&L or price data
3612 ;; Either version may be picked.
3613 (license (list license:gpl2 license:gpl3))))
3615 (define-public r-laeken
3622 (uri (cran-uri "laeken" version))
3625 "1g9r3y7b0gl91hijk9awa8rjk97mqpkxinzq2cgmx0m38ng9ylpa"))))
3626 (build-system r-build-system)
3628 `(("r-boot" ,r-boot)
3629 ("r-mass" ,r-mass)))
3630 (home-page "https://cran.r-project.org/web/packages/laeken/")
3631 (synopsis "Estimation of indicators on social exclusion and poverty")
3632 (description "This package provides tools for the estimation of indicators
3633 on social exclusion and poverty, as well as an implementation of Pareto tail
3634 modeling for empirical income distributions.")
3635 (license license:gpl2+)))
3637 (define-public r-vcd
3644 (uri (cran-uri "vcd" version))
3647 "0pqf1sdp0d60aqc7721hy2zfcp57902by0i28jqbn683dd50c21a"))))
3648 (build-system r-build-system)
3650 `(("r-colorspace" ,r-colorspace)
3651 ("r-lmtest" ,r-lmtest)
3652 ("r-mass" ,r-mass)))
3653 (home-page "https://cran.r-project.org/web/packages/vcd/")
3654 (synopsis "Visualizing categorical data")
3655 (description "This package provides visualization techniques, data sets,
3656 summary and inference procedures aimed particularly at categorical data.
3657 Special emphasis is given to highly extensible grid graphics. The package was
3658 originally inspired by the book \"Visualizing Categorical Data\" by Michael
3659 Friendly and is now the main support package for a new book, \"Discrete Data
3660 Analysis with R\" by Michael Friendly and David Meyer (2015).")
3661 (license license:gpl2)))
3663 (define-public r-ica
3670 (uri (cran-uri "ica" version))
3673 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
3674 (build-system r-build-system)
3675 (home-page "https://cran.r-project.org/web/packages/ica/")
3676 (synopsis "Independent component analysis")
3677 (description "This package provides tools for @dfn{Independent Component
3678 Analysis} (ICA) using various algorithms: FastICA,
3679 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
3680 of Eigenmatrices} (JADE).")
3681 (license license:gpl2+)))
3683 (define-public r-dtw
3690 (uri (cran-uri "dtw" version))
3693 "02hyhx1sy5h3vzh9zixy18a7d47df4k5d0wyflcvlcbsbcl6p90s"))))
3694 (build-system r-build-system)
3695 (propagated-inputs `(("r-proxy" ,r-proxy)))
3696 (home-page "http://dtw.r-forge.r-project.org/")
3697 (synopsis "Dynamic Time Warping Algorithms")
3698 (description "This package provides a comprehensive implementation of
3699 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
3700 optimal (least cumulative distance) alignment between points of two time
3701 series. Common DTW variants covered include local (slope) and global (window)
3702 constraints, subsequence matches, arbitrary distance definitions,
3703 normalizations, minimum variance matching, and so on.")
3704 (license license:gpl2+)))
3706 (define-public r-sdmtools
3709 (version "1.1-221.2")
3713 (uri (cran-uri "SDMTools" version))
3716 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
3717 (properties `((upstream-name . "SDMTools")))
3718 (build-system r-build-system)
3719 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
3720 (home-page "https://www.rforge.net/SDMTools/")
3721 (synopsis "Species distribution modelling tools")
3722 (description "This package provides a set of tools for post processing
3723 the outcomes of species distribution modeling exercises. It includes novel
3724 methods for comparing models and tracking changes in distributions through
3725 time. It further includes methods for visualizing outcomes, selecting
3726 thresholds, calculating measures of accuracy and landscape fragmentation
3728 (license license:gpl3+)))
3730 (define-public r-scatterplot3d
3732 (name "r-scatterplot3d")
3737 (uri (cran-uri "scatterplot3d" version))
3740 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
3741 (build-system r-build-system)
3742 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
3743 (synopsis "3D scatter plot")
3744 (description "This package provides an implementation of scatter plots for
3745 plotting. a three dimensional point cloud.")
3746 (license license:gpl2)))
3748 (define-public r-ggridges
3755 (uri (cran-uri "ggridges" version))
3758 "03pz257aw0mkh5k75rby9givkc1ky3n5scvhjhjiz9vry9fpffmh"))))
3759 (build-system r-build-system)
3761 `(("r-ggplot2" ,r-ggplot2)
3763 ("r-scales" ,r-scales)
3764 ("r-withr" ,r-withr)))
3765 (home-page "https://github.com/clauswilke/ggridges")
3766 (synopsis "Ridgeline plots in ggplot2")
3768 "Ridgeline plots provide a convenient way of visualizing changes in
3769 distributions over time or space. This package enables the creation of such
3770 plots in @code{ggplot2}.")
3771 (license license:gpl2)))
3773 (define-public r-ggjoy
3780 (uri (cran-uri "ggjoy" version))
3783 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
3784 (build-system r-build-system)
3786 `(("r-ggplot2" ,r-ggplot2)
3787 ("r-ggridges" ,r-ggridges)))
3788 (home-page "https://github.com/clauswilke/ggjoy")
3789 (synopsis "Joyplots in ggplot2")
3790 (description "Joyplots provide a convenient way of visualizing changes in
3791 distributions over time or space. This package enables the creation of such
3792 plots in @code{ggplot2}.")
3793 (license license:gpl2)))
3795 (define-public r-cli
3802 (uri (cran-uri "cli" version))
3805 "0x28i7kj4qndk6mnn99qn9w2nfldv8csjnsn0n8phfnxq5hnmp5y"))))
3806 (build-system r-build-system)
3808 `(("r-assertthat" ,r-assertthat)
3809 ("r-crayon" ,r-crayon)
3810 ("r-fansi" ,r-fansi)
3811 ("r-glue" ,r-glue)))
3812 (home-page "https://github.com/r-lib/cli#readme")
3813 (synopsis "Helpers for developing command line interfaces")
3814 (description "This package provides a suite of tools designed to build
3815 attractive command line interfaces (CLIs). It includes tools for drawing
3816 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
3817 (license license:expat)))
3819 (define-public r-argparser
3821 (name "r-argparser")
3826 (uri (cran-uri "argparser" version))
3829 "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x"))))
3830 (build-system r-build-system)
3831 (home-page "https://bitbucket.org/djhshih/argparser")
3832 (synopsis "Command-line argument parser")
3834 "This package provides a cross-platform command-line argument parser
3835 written purely in R with no external dependencies. It is useful with the
3836 Rscript front-end and facilitates turning an R script into an executable
3838 (license license:gpl3+)))
3840 (define-public r-debugme
3847 (uri (cran-uri "debugme" version))
3850 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
3851 (build-system r-build-system)
3852 (propagated-inputs `(("r-crayon" ,r-crayon)))
3853 (home-page "https://github.com/r-lib/debugme#readme")
3854 (synopsis "Debug R packages")
3856 "This package allows the user to specify debug messages as special string
3857 constants, and control debugging of packages via environment variables.")
3858 (license license:expat)))
3860 (define-public r-processx
3867 (uri (cran-uri "processx" version))
3870 "1g6ipcaxg9y94lyrnbp7kkbqfkcdh1fyrqjjclbjp3x7iysdvazi"))))
3871 (build-system r-build-system)
3875 (home-page "https://github.com/r-lib/processx3")
3876 (synopsis "Execute and control system processes")
3878 "This package provides portable tools to run system processes in the
3879 background. It can check if a background process is running; wait on a
3880 background process to finish; get the exit status of finished processes; kill
3881 background processes and their children; restart processes. It can read the
3882 standard output and error of the processes, using non-blocking connections.
3883 @code{processx} can poll a process for standard output or error, with a
3884 timeout. It can also poll several processes at once.")
3885 (license license:expat)))
3887 (define-public r-tsp
3894 (uri (cran-uri "TSP" version))
3897 "0g44f2a4m7rfx6y51cdbr6vcmmpbwgyzpvfjksq3lb7gcpbr7xrx"))))
3898 (properties `((upstream-name . "TSP")))
3899 (build-system r-build-system)
3900 (propagated-inputs `(("r-foreach" ,r-foreach)))
3901 (home-page "https://cran.r-project.org/web/packages/TSP/")
3902 (synopsis "Traveling salesperson problem (TSP)")
3903 (description "This package provides basic infrastructure and some
3904 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
3905 traveling salesman problem).")
3906 (license license:gpl3)))
3908 (define-public r-qap
3915 (uri (cran-uri "qap" version))
3918 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
3919 (build-system r-build-system)
3920 (native-inputs `(("gfortran" ,gfortran)))
3921 (home-page "https://cran.r-project.org/web/packages/qap/")
3922 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
3923 (description "This package implements heuristics for the @dfn{quadratic
3924 assignment problem} (QAP). Currently only a simulated annealing heuristic is
3926 (license license:gpl3)))
3928 (define-public r-gclus
3935 (uri (cran-uri "gclus" version))
3938 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
3939 (build-system r-build-system)
3940 (propagated-inputs `(("r-cluster" ,r-cluster)))
3941 (home-page "https://cran.r-project.org/web/packages/gclus/")
3942 (synopsis "Clustering graphics")
3943 (description "This package orders panels in scatterplot matrices and
3944 parallel coordinate displays by some merit index. It contains various indices
3945 of merit, ordering functions, and enhanced versions of @code{pairs} and
3946 @code{parcoord} which color panels according to their merit level.")
3947 (license license:gpl2+)))
3949 (define-public r-webshot
3956 (uri (cran-uri "webshot" version))
3959 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
3960 (build-system r-build-system)
3962 `(("r-callr" ,r-callr)
3963 ("r-jsonlite" ,r-jsonlite)
3964 ("r-magrittr" ,r-magrittr)))
3965 (home-page "https://github.com/wch/webshot/")
3966 (synopsis "Take screenshots of web pages")
3968 "Webshot makes it easy to take screenshots of web pages from within R.
3969 It can also run Shiny applications locally and take screenshots of the
3970 application; and it can render and screenshot static as well as interactive R
3971 Markdown documents.")
3972 (license license:gpl2)))
3974 (define-public r-seriation
3976 (name "r-seriation")
3981 (uri (cran-uri "seriation" version))
3984 "1zbdxq0s5rc5v307b69fw9k52m0654ls7pf22lh35ggirig6lwsk"))))
3985 (build-system r-build-system)
3987 `(("r-cluster" ,r-cluster)
3988 ("r-colorspace" ,r-colorspace)
3989 ("r-dendextend" ,r-dendextend)
3990 ("r-gclus" ,r-gclus)
3991 ("r-gplots" ,r-gplots)
3994 ("r-registry" ,r-registry)
3996 (native-inputs `(("gfortran" ,gfortran)))
3997 (home-page "https://s2.smu.edu/IDA/seriation/")
3998 (synopsis "Infrastructure for ordering objects using seriation")
4000 "This package provides infrastructure for seriation with an
4001 implementation of several seriation/sequencing techniques to reorder matrices,
4002 dissimilarity matrices, and dendrograms. It also provides (optimally)
4003 reordered heatmaps, color images and clustering visualizations like
4004 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
4006 (license license:gpl3)))
4008 (define-public r-xfun
4015 (uri (cran-uri "xfun" version))
4017 (base32 "0sgh8kafi9x1glmmcp1ly827pm8q7fsfngbplr41fbb4nc9363df"))))
4018 (build-system r-build-system)
4019 (home-page "https://github.com/yihui/xfun")
4020 (synopsis "Miscellaneous functions")
4022 "This package provides miscellaneous functions commonly used in other
4023 packages maintained by Yihui Xie.")
4024 (license license:expat)))
4026 (define-public r-utf8
4033 (uri (cran-uri "utf8" version))
4036 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
4037 (build-system r-build-system)
4038 (home-page "https://github.com/patperry/r-utf8")
4039 (synopsis "Unicode text processing")
4041 "This package provides tools to process and print UTF-8 encoded
4042 international text (Unicode). Input, validate, normalize, encode, format, and
4044 (license license:asl2.0)))
4046 (define-public r-zeallot
4053 (uri (cran-uri "zeallot" version))
4056 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
4057 (build-system r-build-system)
4058 (home-page "https://github.com/nteetor/zeallot")
4059 (synopsis "Multiple, unpacking, and destructuring assignment")
4061 "This package provides a @code{%<-%} operator to perform multiple,
4062 unpacking, and destructuring assignment in R. The operator unpacks the
4063 right-hand side of an assignment into multiple values and assigns these values
4064 to variables on the left-hand side of the assignment.")
4065 (license license:expat)))
4067 (define-public r-vctrs
4074 (uri (cran-uri "vctrs" version))
4077 "008xjmlj5a5vm303wxac7bliamqwaj7mcj0jv6n9ibc8p8h93aqd"))))
4078 (build-system r-build-system)
4080 `(("r-digest" ,r-digest)
4081 ("r-ellipsis" ,r-ellipsis)
4083 ("r-rlang" ,r-rlang)))
4084 (home-page "https://github.com/r-lib/vctrs")
4085 (synopsis "Vector helpers")
4087 "There are three main goals to the @code{vctrs} package:
4090 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
4091 @code{length()} and @code{class()}. These definitions are paired with a
4092 framework for type-coercion and size-recycling.
4093 @item To define type- and size-stability as desirable function properties, use
4094 them to analyse existing base function, and to propose better alternatives.
4095 This work has been particularly motivated by thinking about the ideal
4096 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
4097 @item To provide a new @code{vctr} base class that makes it easy to create new
4098 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
4099 a few new @code{vctrs} generics, making implementation considerably simpler
4102 (license license:gpl3)))
4104 (define-public r-pillar
4111 (uri (cran-uri "pillar" version))
4114 "02sn7zw80wq33jgxk2i6m5jb83sk7y72dfhgyy0apfinv05w92ss"))))
4115 (build-system r-build-system)
4118 ("r-crayon" ,r-crayon)
4119 ("r-fansi" ,r-fansi)
4120 ("r-rlang" ,r-rlang)
4122 ("r-vctrs" ,r-vctrs)))
4123 (home-page "https://github.com/r-lib/pillar")
4124 (synopsis "Coloured formatting for columns")
4126 "This package provides a @code{pillar} generic designed for formatting
4127 columns of data using the full range of colours provided by modern
4129 (license license:gpl3)))
4131 (define-public r-uuid
4138 (uri (cran-uri "uuid" version))
4141 "1gmisd630fc8ybg845hbg13wmm3pk3npaamrh5wqbc1nqd6p0wfx"))))
4142 (build-system r-build-system)
4143 (home-page "http://www.rforge.net/uuid")
4144 (synopsis "Tools for generating and handling of UUIDs")
4146 "This package provides tools for generating and handling of
4147 @dfn{Universally Unique Identifiers} (UUIDs).")
4148 (license license:expat)))
4150 (define-public r-tinytex
4157 (uri (cran-uri "tinytex" version))
4160 "0jlcrvcqcbkimg7w40z5vhlnakb829vfgqpspm3pfl8karwzgqp6"))))
4161 (build-system r-build-system)
4163 `(("r-xfun" ,r-xfun)))
4164 (home-page "https://github.com/yihui/tinytex")
4165 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
4167 "This package provides helper functions to install and maintain the LaTeX
4168 distribution named TinyTeX, a lightweight, cross-platform, portable, and
4169 easy-to-maintain version of TeX Live. This package also contains helper
4170 functions to compile LaTeX documents, and install missing LaTeX packages
4172 (license license:expat)))
4174 (define-public r-network
4181 (uri (cran-uri "network" version))
4184 "0dnf1wl3za2lhx2lwd8smhlijl1cfhckgr8zz9piiirrfi2m2kx2"))))
4185 (build-system r-build-system)
4187 `(("r-magrittr" ,r-magrittr)
4188 ("r-tibble" ,r-tibble)))
4189 (home-page "https://statnet.org/")
4190 (synopsis "Classes for relational data")
4192 "This package provides tools to create and modify network objects. The
4193 @code{network} class can represent a range of relational data types, and
4194 supports arbitrary vertex/edge/graph attributes.")
4195 (license license:gpl2+)))
4197 (define-public r-statnet-common
4199 (name "r-statnet-common")
4204 (uri (cran-uri "statnet.common" version))
4207 "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3"))))
4209 `((upstream-name . "statnet.common")))
4210 (build-system r-build-system)
4212 `(("r-coda" ,r-coda)))
4213 (home-page "https://statnet.org")
4214 (synopsis "R scripts and utilities used by the Statnet software")
4215 (description "This package provides non-statistical utilities used by the
4216 software developed by the Statnet Project.")
4217 (license license:gpl3)))
4219 (define-public r-statcheck
4221 (name "r-statcheck")
4226 (uri (cran-uri "statcheck" version))
4229 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
4230 (build-system r-build-system)
4232 `(("r-ggplot2" ,r-ggplot2)
4234 ("r-rmarkdown" ,r-rmarkdown)))
4235 (home-page "https://cran.r-project.org/web/packages/statcheck/")
4236 (synopsis "Extract statistics from articles and recompute p-values")
4237 (description "This package can automatically extract statistical
4238 null-hypothesis significant testing (NHST) results from articles and recompute
4239 the p-values based on the reported test statistic and degrees of freedom to
4240 detect possible inconsistencies.")
4241 (license license:gpl2)))
4243 (define-public r-sna
4250 (uri (cran-uri "sna" version))
4253 "1j3i6300m686qqfmyvadim377cd3mplzgj6mandygw8brg50id8k"))))
4254 (build-system r-build-system)
4256 `(("r-network" ,r-network)
4257 ("r-statnet-common" ,r-statnet-common)))
4258 (home-page "https://statnet.org")
4259 (synopsis "Tools for social network analysis")
4261 "This package provides a range of tools for social network analysis,
4262 including node and graph-level indices, structural distance and covariance
4263 methods, structural equivalence detection, network regression, random graph
4264 generation, and 2D/3D network visualization.")
4265 (license license:gpl2+)))
4267 (define-public r-tfisher
4274 (uri (cran-uri "TFisher" version))
4277 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
4278 (properties `((upstream-name . "TFisher")))
4279 (build-system r-build-system)
4281 `(("r-matrix" ,r-matrix)
4282 ("r-mvtnorm" ,r-mvtnorm)
4284 (home-page "https://cran.r-project.org/web/packages/TFisher/")
4285 (synopsis "Optimal thresholding Fisher's p-value combination method")
4287 "This package provides the @dfn{cumulative distribution function} (CDF),
4288 quantile, and statistical power calculator for a collection of thresholding
4289 Fisher's p-value combination methods, including Fisher's p-value combination
4290 method, truncated product method and, in particular, soft-thresholding
4291 Fisher's p-value combination method which is proven to be optimal in some
4292 context of signal detection. The p-value calculator for the omnibus version
4293 of these tests are also included.")
4294 (license license:gpl2)))
4296 (define-public r-ttr
4303 (uri (cran-uri "TTR" version))
4306 "0rg22ma3x07s9djlxscfw5jcq1gbir05cwhgvwfi53x1sf4hmhdg"))))
4307 (properties `((upstream-name . "TTR")))
4308 (build-system r-build-system)
4310 `(("r-curl" ,r-curl)
4313 (home-page "https://github.com/joshuaulrich/TTR")
4314 (synopsis "Technical trading rules")
4316 "This package provides functions and data to construct technical trading
4318 (license license:gpl2)))
4320 (define-public r-leaps
4327 (uri (cran-uri "leaps" version))
4330 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
4331 (build-system r-build-system)
4332 (native-inputs `(("gfortran" ,gfortran)))
4333 (home-page "https://cran.r-project.org/web/packages/leaps/")
4334 (synopsis "Regression subset selection")
4336 "This package provides tools for regression subset selection, including
4337 exhaustive search.")
4338 (license license:gpl2+)))
4340 (define-public r-splus2r
4347 (uri (cran-uri "splus2R" version))
4350 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
4351 (properties `((upstream-name . "splus2R")))
4352 (build-system r-build-system)
4353 (native-inputs `(("gfortran" ,gfortran)))
4354 (home-page "https://cran.r-project.org/web/packages/splus2R/")
4355 (synopsis "Supplemental S-PLUS functionality in R")
4357 "Currently there are many functions in S-PLUS that are missing in R. To
4358 facilitate the conversion of S-PLUS packages to R packages, this package
4359 provides some missing S-PLUS functionality in R.")
4360 (license license:gpl2)))
4362 (define-public r-ifultools
4364 (name "r-ifultools")
4369 (uri (cran-uri "ifultools" version))
4372 "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j"))))
4373 (build-system r-build-system)
4375 `(("r-mass" ,r-mass)
4376 ("r-splus2r" ,r-splus2r)))
4377 (home-page "https://cran.r-project.org/web/packages/ifultools/")
4378 (synopsis "Insightful research tools")
4379 (description "This package provides C code used by the wmtsa, fractal, and
4381 (license license:gpl2)))
4383 (define-public r-sapa
4390 (uri (cran-uri "sapa" version))
4393 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
4394 (build-system r-build-system)
4396 `(("r-ifultools" ,r-ifultools)
4397 ("r-splus2r" ,r-splus2r)))
4398 (home-page "https://cran.r-project.org/web/packages/sapa/")
4399 (synopsis "Spectral analysis for physical applications")
4400 (description "This package provides software for the book Spectral
4401 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
4402 Cambridge University Press, 1993.")
4403 (license license:gpl2)))
4405 (define-public r-aggregation
4407 (name "r-aggregation")
4412 (uri (cran-uri "aggregation" version))
4415 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
4416 (build-system r-build-system)
4417 (home-page "https://cran.r-project.org/web/packages/aggregation/")
4418 (synopsis "Methods for p-value aggregation")
4420 "This package contains functionality for performing the following methods
4421 of p-value aggregation: Fisher's method, the Lancaster method (weighted
4422 Fisher's method), and Sidak correction.")
4423 (license license:gpl3)))
4425 (define-public r-quantmod
4432 (uri (cran-uri "quantmod" version))
4435 "0lyzaf5ypk93v6zj9gdghy05cc7cxgn9yasv1apx5r6qsjcfgwky"))))
4436 (build-system r-build-system)
4438 `(("r-curl" ,r-curl)
4442 (home-page "https://cran.r-project.org/web/packages/quantmod/")
4443 (synopsis "Quantitative financial modelling framework")
4444 (description "This package provides a quantitative financial modelling
4445 framework to allow users to specify, build, trade, and analyse quantitative
4446 financial trading strategies.")
4447 (license license:gpl3)))
4449 (define-public r-tseries
4456 (uri (cran-uri "tseries" version))
4459 "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
4460 (build-system r-build-system)
4462 `(("r-quadprog" ,r-quadprog)
4463 ("r-quantmod" ,r-quantmod)
4466 `(("gfortran" ,gfortran)))
4467 (home-page "https://cran.r-project.org/web/packages/tseries/")
4468 (synopsis "Time series analysis and computational finance")
4470 "This package provides functions relating to time series analysis and
4471 computational finance.")
4472 (license license:gpl2)))
4474 (define-public r-wmtsa
4481 (uri (cran-uri "wmtsa" version))
4484 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
4485 (build-system r-build-system)
4487 `(("r-ifultools" ,r-ifultools)
4489 ("r-splus2r" ,r-splus2r)))
4490 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
4491 (synopsis "Wavelet methods for time series analysis")
4493 "This package provides software to accompany the book \"Wavelet Methods
4494 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
4495 University Press, 2000.")
4496 (license license:gpl2)))
4498 (define-public r-tsa
4505 (uri (cran-uri "TSA" version))
4508 "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q"))))
4509 (properties `((upstream-name . "TSA")))
4510 (build-system r-build-system)
4512 `(("r-leaps" ,r-leaps)
4513 ("r-locfit" ,r-locfit)
4514 ("r-mgcv" ,r-mgcv)))
4515 (home-page "http://www.stat.uiowa.edu/~kchan/TSA.htm")
4516 (synopsis "Time series analysis")
4518 "This package contains R functions and datasets detailed in the book
4519 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
4520 Cryer and Kung-Sik Chan.")
4521 (license license:gpl2+)))
4523 (define-public r-extradistr
4525 (name "r-extradistr")
4530 (uri (cran-uri "extraDistr" version))
4533 "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3"))))
4534 (properties `((upstream-name . "extraDistr")))
4535 (build-system r-build-system)
4537 `(("r-rcpp" ,r-rcpp)))
4538 (home-page "https://github.com/twolodzko/extraDistr")
4539 (synopsis "Additional univariate and multivariate distributions")
4541 "This package implements density, distribution functions, quantile
4542 functions and random generation functions for a large number of univariate and
4543 multivariate distributions.")
4544 (license license:gpl2)))
4546 (define-public r-fractal
4553 (uri (cran-uri "fractal" version))
4556 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
4557 (build-system r-build-system)
4559 `(("r-ifultools" ,r-ifultools)
4562 ("r-scatterplot3d" ,r-scatterplot3d)
4563 ("r-splus2r" ,r-splus2r)
4564 ("r-wmtsa" ,r-wmtsa)))
4565 (home-page "https://cran.r-project.org/web/packages/fractal/")
4566 (synopsis "Fractal time series modeling and analysis")
4568 "This package provides tools for stochastic fractal and deterministic
4569 chaotic time series analysis.")
4570 (license license:gpl2)))
4572 (define-public r-urca
4579 (uri (cran-uri "urca" version))
4582 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
4583 (build-system r-build-system)
4584 (propagated-inputs `(("r-nlme" ,r-nlme)))
4585 (native-inputs `(("gfortran" ,gfortran)))
4586 (home-page "https://cran.r-project.org/web/packages/urca/")
4587 (synopsis "Unit root and cointegration tests for time series data")
4589 "This package provides unit root and cointegration tests encountered in
4590 applied econometric analysis.")
4591 (license license:gpl2+)))
4593 (define-public r-cubature
4600 (uri (cran-uri "cubature" version))
4603 "0jpyq8j7x06dpiz29w48av879ygldzgls9z810192hsymkmfaz6r"))))
4604 (build-system r-build-system)
4606 `(("r-rcpp" ,r-rcpp)))
4607 (home-page "https://github.com/bnaras/cubature")
4608 (synopsis "Adaptive multivariate integration over hypercubes")
4610 "This package is an R wrapper around the cubature C library for adaptive
4611 multivariate integration over hypercubes. This version provides both
4612 @code{hcubature} and @code{pcubature} routines in addition to a vector
4614 ;; The included cubature C library is released under GPLv2+, but the
4615 ;; wrapper declares the license to be GPLv3+.
4616 (license (list license:gpl2+ license:gpl3+))))
4618 (define-public r-trend
4625 (uri (cran-uri "trend" version))
4628 "09b6ycyfgs4xlhx6kn6qm5rl2acp58hzhv8qclzn3kb1wjjyvxy5"))))
4629 (build-system r-build-system)
4631 `(("r-extradistr" ,r-extradistr)))
4633 `(("gfortran" ,gfortran)))
4634 (home-page "https://cran.r-project.org/web/packages/trend/")
4635 (synopsis "Non-parametric trend tests and change-point detection")
4637 "The analysis of environmental data often requires the detection of
4638 trends and change-points. This package includes tests for trend
4639 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
4640 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
4641 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
4642 correlation trend test), change-point detection (Lanzante's test procedures,
4643 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
4644 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
4645 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
4646 sample Robust Rank-Order Distributional Test.")
4647 (license license:gpl3)))
4649 (define-public r-expm
4656 (uri (cran-uri "expm" version))
4659 "15k0acg2aqb2ajhwal6l7vhhp03m4lg579805d34554cl0kn9l2q"))))
4660 (build-system r-build-system)
4661 (propagated-inputs `(("r-matrix" ,r-matrix)))
4662 (native-inputs `(("gfortran" ,gfortran)))
4663 (home-page "https://r-forge.r-project.org/projects/expm/")
4664 (synopsis "Tools for matrix exponentials and related quantities")
4666 "This package provides tools for the computation of the matrix
4667 exponential, logarithm, square root, and related quantities.")
4668 (license license:gpl2+)))
4670 (define-public r-complexplus
4672 (name "r-complexplus")
4677 (uri (cran-uri "complexplus" version))
4680 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
4681 (build-system r-build-system)
4683 `(("r-expm" ,r-expm)
4684 ("r-matrix" ,r-matrix)))
4685 (home-page "https://cran.r-project.org/web/packages/complexplus/")
4686 (synopsis "Functions of complex or real variables")
4688 "This package extends several functions to the complex domain, including
4689 the matrix exponential and logarithm, and the determinant.")
4690 (license license:gpl2)))
4692 (define-public r-phontools
4694 (name "r-phontools")
4699 (uri (cran-uri "phonTools" version))
4702 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
4703 (properties `((upstream-name . "phonTools")))
4704 (build-system r-build-system)
4705 (home-page "http://www.santiagobarreda.com/rscripts.html")
4706 (synopsis "Tools for phonetic and acoustic analyses")
4708 "This package contains tools for the organization, display, and analysis
4709 of the sorts of data frequently encountered in phonetics research and
4710 experimentation, including the easy creation of IPA vowel plots, and the
4711 creation and manipulation of WAVE audio files.")
4712 (license license:bsd-2)))
4721 (uri (cran-uri "np" version))
4724 "1z4jcpx8bbgwslv42wrphfd1qfq965qjn0kmfxm5f6hbbycahcgy"))))
4725 (build-system r-build-system)
4727 `(("r-boot" ,r-boot)
4728 ("r-cubature" ,r-cubature)
4729 ("r-quadprog" ,r-quadprog)
4730 ("r-quantreg" ,r-quantreg)))
4731 (home-page "https://github.com/JeffreyRacine/R-Package-np")
4732 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
4733 (description "This package provides non-parametric (and semi-parametric)
4734 kernel methods that seamlessly handle a mix of continuous, unordered, and
4735 ordered factor data types.")
4736 ;; Any version of the GPL.
4737 (license license:gpl3+)))
4739 (define-public r-powerplus
4741 (name "r-powerplus")
4746 (uri (cran-uri "powerplus" version))
4749 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
4750 (build-system r-build-system)
4752 `(("r-complexplus" ,r-complexplus)
4755 ("r-matrix" ,r-matrix)
4756 ("r-phontools" ,r-phontools)))
4757 (home-page "https://cran.r-project.org/web/packages/powerplus/")
4758 (synopsis "Exponentiation operations")
4760 "This package provides tools for the computation of matrix and scalar
4762 (license license:gpl2)))
4764 (define-public r-egg
4771 (uri (cran-uri "egg" version))
4774 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
4775 (properties `((upstream-name . "egg")))
4776 (build-system r-build-system)
4778 `(("r-ggplot2" ,r-ggplot2)
4779 ("r-gridextra" ,r-gridextra)
4780 ("r-gtable" ,r-gtable)))
4781 (home-page "https://cran.r-project.org/web/packages/egg")
4782 (synopsis "Extensions for ggplot2")
4784 "This package provides miscellaneous functions to help customize ggplot2
4785 objects. High-level functions are provided to post-process ggplot2 layouts
4786 and allow alignment between plot panels, as well as setting panel sizes to
4787 fixed values. Other functions include a custom @code{geom}, and helper
4788 functions to enforce symmetric scales or add tags to facetted plots.")
4789 (license license:gpl3)))
4791 (define-public r-heatmaply
4793 (name "r-heatmaply")
4798 (uri (cran-uri "heatmaply" version))
4801 "0576gml3bcl7r1biigzj1rag2xzz422knbw7arc8d2gsakjj757g"))))
4802 (build-system r-build-system)
4804 `(("r-assertthat" ,r-assertthat)
4805 ("r-colorspace" ,r-colorspace)
4806 ("r-dendextend" ,r-dendextend)
4808 ("r-ggplot2" ,r-ggplot2)
4809 ("r-htmlwidgets" ,r-htmlwidgets)
4810 ("r-magrittr" ,r-magrittr)
4811 ("r-plotly" ,r-plotly)
4812 ("r-rcolorbrewer" ,r-rcolorbrewer)
4813 ("r-reshape2" ,r-reshape2)
4814 ("r-scales" ,r-scales)
4815 ("r-seriation" ,r-seriation)
4816 ("r-viridis" ,r-viridis)
4817 ("r-webshot" ,r-webshot)))
4818 (home-page "https://cran.r-project.org/package=heatmaply")
4819 (synopsis "Interactive cluster heat maps using plotly")
4821 "This package enables you to create interactive cluster heatmaps that can
4822 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
4823 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
4824 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
4825 a popular graphical method for visualizing high-dimensional data, in which a
4826 table of numbers is encoded as a grid of colored cells. The rows and columns
4827 of the matrix are ordered to highlight patterns and are often accompanied by
4829 ;; Either version of the license.
4830 (license (list license:gpl2 license:gpl3))))
4839 (uri (cran-uri "h5" version))
4842 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
4843 (build-system r-build-system)
4848 `(("which" ,which)))
4850 `(("r-rcpp" ,r-rcpp)))
4851 (home-page "https://github.com/mannau/h5")
4852 (synopsis "Interface to the HDF5 Library")
4854 "This package provides an S4 interface to the HDF5 library supporting
4855 fast storage and retrieval of R-objects like vectors, matrices and arrays to
4856 binary files in a language independent format. The HDF5 format can therefore
4857 be used as an alternative to R's save/load mechanism. Since h5 is able to
4858 access only subsets of stored data it can also handle data sets which do not
4860 (license license:bsd-2)))
4862 (define-public r-cgdsr
4869 (uri (cran-uri "cgdsr" version))
4872 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
4873 (build-system r-build-system)
4875 `(("r-httr" ,r-httr)
4876 ("r-r-methodss3" ,r-r-methodss3)
4877 ("r-r-oo" ,r-r-oo)))
4878 (home-page "https://github.com/cBioPortal/cgdsr")
4879 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
4881 "This package provides a basic set of R functions for querying the Cancer
4882 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
4883 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
4884 (license license:lgpl3)))
4886 (define-public r-import
4893 (uri (cran-uri "import" version))
4896 "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
4897 (build-system r-build-system)
4898 (home-page "https://github.com/smbache/import")
4899 (synopsis "Import mechanism for R")
4901 "This is an alternative mechanism for importing objects from packages.
4902 The syntax allows for importing multiple objects from a package with a single
4903 command in an expressive way. The import package bridges some of the gap
4904 between using @code{library} (or @code{require}) and direct (single-object)
4905 imports. Furthermore the imported objects are not placed in the current
4906 environment. It is also possible to import objects from stand-alone @code{.R}
4908 (license license:expat)))
4910 (define-public r-shinyace
4917 (uri (cran-uri "shinyAce" version))
4920 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
4921 (properties `((upstream-name . "shinyAce")))
4922 (build-system r-build-system)
4924 `(("r-shiny" ,r-shiny)
4925 ("r-jsonlite" ,r-jsonlite)))
4926 (home-page "http://cran.r-project.org/web/packages/shinyAce")
4927 (synopsis "Ace editor bindings for Shiny")
4929 "This package provides Ace editor bindings to enable a rich text editing
4930 environment within Shiny.")
4931 (license license:expat)))
4933 (define-public r-base64url
4935 (name "r-base64url")
4940 (uri (cran-uri "base64url" version))
4943 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
4944 (build-system r-build-system)
4946 `(("r-backports" ,r-backports)))
4947 (home-page "https://github.com/mllg/base64url")
4948 (synopsis "Fast and URL-safe base64 encoder and decoder")
4950 "This package provides a URL-safe base64 encoder and decoder. In
4951 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
4952 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
4953 encoder does not fill the string with trailing @code{=}. The resulting
4954 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
4955 and thus are safe to use in URLs or for file names. The package also comes
4956 with a simple base32 encoder/decoder suited for case insensitive file
4958 (license license:gpl3)))
4960 (define-public r-radiant-data
4962 (name "r-radiant-data")
4967 (uri (cran-uri "radiant.data" version))
4970 "08x7zasxf429m021482p86lx3zc6dqz2mih0id8s34isg4gafapg"))
4971 (modules '((guix build utils)))
4974 ;; Delete files that are under CC-NC-SA.
4975 (delete-file-recursively "inst/app/tools/help")
4977 (properties `((upstream-name . "radiant.data")))
4978 (build-system r-build-system)
4980 `(("r-base64enc" ,r-base64enc)
4981 ("r-broom" ,r-broom)
4984 ("r-dplyr" ,r-dplyr)
4987 ("r-ggplot2" ,r-ggplot2)
4988 ("r-gridextra" ,r-gridextra)
4989 ("r-import" ,r-import)
4990 ("r-jsonlite" ,r-jsonlite)
4991 ("r-knitr" ,r-knitr)
4992 ("r-lubridate" ,r-lubridate)
4993 ("r-magrittr" ,r-magrittr)
4994 ("r-markdown" ,r-markdown)
4995 ("r-plotly" ,r-plotly)
4996 ("r-psych" ,r-psych)
4997 ("r-readr" ,r-readr)
4998 ("r-readxl" ,r-readxl)
4999 ("r-rlang" ,r-rlang)
5000 ("r-rmarkdown" ,r-rmarkdown)
5001 ("r-rstudioapi" ,r-rstudioapi)
5002 ("r-scales" ,r-scales)
5003 ("r-shiny" ,r-shiny)
5004 ("r-shinyfiles" ,r-shinyfiles)
5005 ("r-shinyace" ,r-shinyace)
5006 ("r-stringi" ,r-stringi)
5007 ("r-tibble" ,r-tibble)
5008 ("r-tidyr" ,r-tidyr)
5009 ("r-writexl" ,r-writexl)))
5010 (home-page "https://github.com/radiant-rstats/radiant.data")
5011 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
5013 "The Radiant Data menu includes interfaces for loading, saving, viewing,
5014 visualizing, summarizing, transforming, and combining data. It also contains
5015 functionality to generate reproducible reports of the analyses conducted in
5017 (license license:agpl3)))
5019 (define-public r-algdesign
5021 (name "r-algdesign")
5026 (uri (cran-uri "AlgDesign" version))
5028 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
5029 (properties `((upstream-name . "AlgDesign")))
5030 (build-system r-build-system)
5031 (home-page "https://github.com/jvbraun/AlgDesign")
5032 (synopsis "Algorithmic experimental design")
5034 "This package provides tools to calculate exact and approximate theory
5035 experimental designs for D, A, and I criteria. Very large designs may be
5036 created. Experimental designs may be blocked or blocked designs created from
5037 a candidate list, using several criteria. The blocking can be done when whole
5038 and within plot factors interact.")
5039 (license license:gpl2+)))
5041 (define-public r-signal
5048 (uri (cran-uri "signal" version))
5051 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
5052 (build-system r-build-system)
5053 (propagated-inputs `(("r-mass" ,r-mass)))
5054 (native-inputs `(("gfortran" ,gfortran)))
5055 (home-page "https://cran.r-project.org/web/packages/signal/")
5056 (synopsis "Signal processing")
5058 "This package provides a set of signal processing functions originally
5059 written for Matlab and GNU Octave. It includes filter generation utilities,
5060 filtering functions, resampling routines, and visualization of filter models.
5061 It also includes interpolation functions.")
5062 (license license:gpl2)))
5064 (define-public r-gsubfn
5071 (uri (cran-uri "gsubfn" version))
5074 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
5075 (build-system r-build-system)
5076 (propagated-inputs `(("r-proto" ,r-proto)))
5077 (home-page "http://gsubfn.googlecode.com")
5078 (synopsis "Utilities for strings and function arguments.")
5080 "This package provides @code{gsubfn} which is like @code{gsub} but can
5081 take a replacement function or certain other objects instead of the
5082 replacement string. Matches and back references are input to the replacement
5083 function and replaced by the function output. @code{gsubfn} can be used to
5084 split strings based on content rather than delimiters and for quasi-perl-style
5085 string interpolation. The package also has facilities for translating
5086 formulas to functions and allowing such formulas in function calls instead of
5088 (license license:gpl2+)))
5090 (define-public r-sqldf
5097 (uri (cran-uri "sqldf" version))
5100 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
5101 (build-system r-build-system)
5103 `(("r-chron" ,r-chron)
5105 ("r-gsubfn" ,r-gsubfn)
5106 ("r-proto" ,r-proto)
5107 ("r-rsqlite" ,r-rsqlite)))
5108 (home-page "https://github.com/ggrothendieck/sqldf")
5109 (synopsis "Manipulate R data frames using SQL")
5111 "The @code{sqldf} function is typically passed a single argument which is
5112 an SQL select statement where the table names are ordinary R data frame names.
5113 @code{sqldf} transparently sets up a database, imports the data frames into
5114 that database, performs the SQL statement and returns the result using a
5115 heuristic to determine which class to assign to each column of the returned
5116 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
5117 used to read filtered files into R even if the original files are larger than
5118 R itself can handle.")
5119 (license license:gpl2)))
5121 (define-public r-abind
5128 (uri (cran-uri "abind" version))
5131 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
5132 (build-system r-build-system)
5133 (home-page "https://cran.r-project.org/web/packages/abind/")
5134 (synopsis "Combine multidimensional arrays")
5136 "This package provides tools to combine multidimensional arrays into a
5137 single array. This is a generalization of @code{cbind} and @code{rbind}. It
5138 works with vectors, matrices, and higher-dimensional arrays. It also provides
5139 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
5140 extracting and replacing data in arrays.")
5141 (license license:lgpl2.0+)))
5143 (define-public r-prroc
5150 (uri (cran-uri "PRROC" version))
5153 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
5154 (properties `((upstream-name . "PRROC")))
5155 (build-system r-build-system)
5156 (home-page "https://cran.r-project.org/web/packages/PRROC/")
5157 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
5159 "This package computes the areas under the @dfn{precision-recall} (PR)
5160 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
5161 contrast to other implementations, the interpolation between points of the PR
5162 curve is done by a non-linear piecewise function. In addition to the areas
5163 under the curves, the curves themselves can also be computed and plotted by a
5164 specific S3-method.")
5165 (license license:gpl3)))
5167 (define-public r-vim
5174 (uri (cran-uri "VIM" version))
5177 "08x4a4yzgp8adgrv7a3666yma4b60n64mcsnvhzmwdy023f4ysrw"))))
5178 (properties `((upstream-name . "VIM")))
5179 (build-system r-build-system)
5182 ("r-colorspace" ,r-colorspace)
5183 ("r-data-table" ,r-data-table)
5184 ("r-e1071" ,r-e1071)
5185 ("r-laeken" ,r-laeken)
5188 ("r-ranger" ,r-ranger)
5190 ("r-robustbase" ,r-robustbase)
5193 (home-page "https://github.com/alexkowa/VIM")
5194 (synopsis "Visualization and imputation of missing values")
5196 "This package provides tools for the visualization of missing and/or
5197 imputed values are introduced, which can be used for exploring the data and
5198 the structure of the missing and/or imputed values. Depending on this
5199 structure of the missing values, the corresponding methods may help to
5200 identify the mechanism generating the missing values and allows to explore the
5201 data including missing values. In addition, the quality of imputation can be
5202 visually explored using various univariate, bivariate, multiple and
5203 multivariate plot methods.")
5204 (license license:gpl2+)))
5206 (define-public r-fnn
5213 (uri (cran-uri "FNN" version))
5216 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
5217 (properties `((upstream-name . "FNN")))
5218 (build-system r-build-system)
5219 (home-page "https://cran.r-project.org/web/packages/FNN")
5220 (synopsis "Fast nearest neighbor search algorithms and applications")
5222 "This package provides cover-tree and kd-tree fast k-nearest neighbor
5223 search algorithms. Related applications including KNN classification,
5224 regression and information measures are implemented.")
5225 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
5226 ;; later can be used.
5227 (license license:gpl2+)))
5229 (define-public r-smoother
5236 (uri (cran-uri "smoother" version))
5239 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
5240 (build-system r-build-system)
5242 `(("r-ttr" ,r-ttr)))
5243 (home-page "https://cran.r-project.org/web/packages/smoother")
5244 (synopsis "Functions relating to the smoothing of numerical data")
5246 "This package provides a collection of methods for smoothing numerical
5247 data, commencing with a port of the Matlab gaussian window smoothing function.
5248 In addition, several functions typically used in smoothing of financial data
5250 (license license:gpl2)))
5252 (define-public r-riverplot
5254 (name "r-riverplot")
5259 (uri (cran-uri "riverplot" version))
5262 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
5263 (build-system r-build-system)
5264 (home-page "https://logfc.wordpress.com")
5265 (synopsis "Sankey or ribbon plots")
5267 "Sankey plots are a type of diagram that is convenient to illustrate how
5268 flow of information, resources etc. separates and joins, much like observing
5269 how rivers split and merge. For example, they can be used to compare
5270 different clusterings. This package provides an implementation of Sankey
5272 (license license:gpl2+)))
5274 (define-public r-dyn
5281 (uri (cran-uri "dyn" version))
5284 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
5285 (build-system r-build-system)
5287 `(("r-zoo" ,r-zoo)))
5288 (home-page "https://cran.r-project.org/web/packages/dyn")
5289 (synopsis "Time series regression")
5291 "This package provides the dyn class interfaces @code{ts}, @code{irts},
5292 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
5293 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
5294 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
5295 @code{randomForest::randomForest()} and other regression functions, allowing
5296 those functions to be used with time series including specifications that may
5297 contain lags, diffs and missing values.")
5299 (license license:gpl2+)))
5301 (define-public r-catdap
5308 (uri (cran-uri "catdap" version))
5311 "0i877l61f6c75pczi235rzci67w29zv1d7z5zn5p5ymndclvlpl2"))))
5312 (build-system r-build-system)
5314 `(("gfortran" ,gfortran)))
5315 (home-page "https://cran.r-project.org/web/packages/catdap/")
5316 (synopsis "Tools for categorical data analysis")
5318 "This package provides functions for analyzing multivariate data.
5319 Dependencies of the distribution of the specified variable (response
5320 variable) to other variables (explanatory variables) are derived and
5321 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
5322 (license license:gpl2+)))
5324 (define-public r-arules
5331 (uri (cran-uri "arules" version))
5334 "003c5cd3xzq39h7c19px077ygm0n1v7k83icy5zzrnkagyds2p8n"))))
5335 (build-system r-build-system)
5337 `(("r-matrix" ,r-matrix)))
5338 (home-page "https://github.com/mhahsler/arules")
5339 (synopsis "Mining association rules and frequent itemsets")
5341 "This package provides an infrastructure for representing, manipulating
5342 and analyzing transaction data and patterns (frequent itemsets and association rules).
5343 It also provides C implementations of the association mining algorithms Apriori
5345 (license license:gpl3)))
5347 (define-public r-parsedate
5349 (name "r-parsedate")
5354 (uri (cran-uri "parsedate" version))
5357 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
5358 (build-system r-build-system)
5360 `(("r-rematch2" ,r-rematch2)))
5361 (home-page "https://github.com/gaborcsardi/parsedate")
5363 "Recognize and parse dates in various formats")
5365 "This package provides three functions for dealing with dates:
5366 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
5367 time formats, @code{parse_date} parses dates in unspecified formats,
5368 and @code{format_iso_8601} formats a date in ISO 8601 format.")
5369 (license license:gpl2)))
5371 (define-public r-abc-data
5378 (uri (cran-uri "abc.data" version))
5381 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
5382 (properties `((upstream-name . "abc.data")))
5383 (build-system r-build-system)
5384 (home-page "https://cran.r-project.org/web/packages/abc.data/")
5385 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
5387 "This package contains data which are used by functions of the abc
5388 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
5389 algorithms for performing parameter estimation, model selection, and
5391 (license license:gpl3+)))
5393 (define-public r-abc
5400 (uri (cran-uri "abc" version))
5403 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
5404 (build-system r-build-system)
5406 `(("r-abc-data" ,r-abc-data)
5407 ("r-locfit" ,r-locfit)
5410 ("r-quantreg" ,r-quantreg)))
5411 (home-page "https://cran.r-project.org/web/packages/abc/")
5412 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
5414 "This package implements several @dfn{Approximate Bayesian
5415 Computation} (ABC) algorithms for performing parameter estimation, model
5416 selection, and goodness-of-fit. Cross-validation tools are also available for
5417 measuring the accuracy of ABC estimates, and to calculate the
5418 misclassification probabilities of different models.")
5419 (license license:gpl3+)))
5421 (define-public r-zip
5428 (uri (cran-uri "zip" version))
5431 "1c02amk3pl6xir5jnbfiwiv2wvpkpbkkb1w71y6lf2yk7g3d0pdb"))))
5432 (build-system r-build-system)
5433 (home-page "https://github.com/gaborcsardi/zip")
5434 (synopsis "Cross-platform Zip compression")
5436 "This package provides a cross-platform Zip compression library for R.
5437 It is a replacement for the @code{zip} function, that does not require any
5438 additional external tools on any platform.")
5439 (license license:cc0)))
5441 (define-public r-openxlsx
5448 (uri (cran-uri "openxlsx" version))
5451 "1mwxldw9i9nfksx1i6h1kfs7vmsz9fgyllbsipar4vnfyqhqp8q7"))))
5452 (build-system r-build-system)
5454 `(("r-rcpp" ,r-rcpp)
5455 ("r-stringi" ,r-stringi)
5457 (home-page "https://github.com/awalker89/openxlsx")
5458 (synopsis "Read, write and edit XLSX files")
5460 "This package simplifies the creation of Excel @code{.xlsx} files by
5461 providing a high level interface to writing, styling and editing worksheets.
5462 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
5463 and @code{XLConnect} packages with the added benefit of removing the
5464 dependency on Java.")
5465 (license license:gpl3)))
5467 (define-public r-rio
5474 (uri (cran-uri "rio" version))
5477 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
5478 (build-system r-build-system)
5480 `(("r-curl" ,r-curl)
5481 ("r-data-table" ,r-data-table)
5482 ("r-foreign" ,r-foreign)
5483 ("r-haven" ,r-haven)
5484 ("r-openxlsx" ,r-openxlsx)
5485 ("r-readxl" ,r-readxl)
5486 ("r-tibble" ,r-tibble)))
5487 (home-page "https://github.com/leeper/rio")
5488 (synopsis "Swiss-army knife for data I/O")
5490 "This package provides streamlined data import and export infrastructure
5491 by making assumptions that the user is probably willing to make: @code{import}
5492 and @code{export} determine the data structure from the file extension,
5493 reasonable defaults are used for data import and export (e.g.,
5494 @code{stringsAsFactors=FALSE}), web-based import is natively
5495 supported (including from SSL/HTTPS), compressed files can be read directly
5496 without explicit decompression, and fast import packages are used where
5497 appropriate. An additional convenience function, @code{convert}, provides a
5498 simple method for converting between file types.")
5499 (license license:gpl2)))
5501 (define-public r-maptools
5508 (uri (cran-uri "maptools" version))
5511 "0v4llkxk8qs61vq4ykvaim4k23aagdaz0p62ns7zfq02sln3pfk9"))))
5512 (build-system r-build-system)
5514 `(("r-foreign" ,r-foreign)
5515 ("r-lattice" ,r-lattice)
5517 (home-page "http://r-forge.r-project.org/projects/maptools/")
5518 (synopsis "Tools for reading and handling spatial objects")
5520 "This package provides a set of tools for manipulating and reading
5521 geographic data, in particular ESRI Shapefiles. It includes binary access to
5522 GSHHG shoreline files. The package also provides interface wrappers for
5523 exchanging spatial objects with other R packages.")
5524 ;; The C source files from shapelib are released under the Expat license.
5525 ;; The R code is released under GPL version 2 or later.
5526 (license (list license:gpl2+
5529 (define-public r-later
5536 (uri (cran-uri "later" version))
5539 "11xjavj7siz0xv2ffq1ld4bwl35jyrcfpvvs4p3ilpifxx49hyr7"))))
5540 (build-system r-build-system)
5544 ("r-rlang" ,r-rlang)))
5545 (home-page "https://github.com/r-lib/later")
5546 (synopsis "Utilities for delaying function execution")
5548 "This package provides tools to execute arbitrary R or C functions some
5549 time after the current time, after the R execution stack has emptied.")
5550 (license license:gpl2+)))
5552 (define-public r-promises
5559 (uri (cran-uri "promises" version))
5562 "01l0ydjvvy6afcg5d6pzvk1ikd3djq8n2flv8c831ksn68z0zsn8"))))
5563 (build-system r-build-system)
5565 `(("r-later" ,r-later)
5566 ("r-magrittr" ,r-magrittr)
5569 ("r-rlang" ,r-rlang)))
5570 (home-page "https://rstudio.github.io/promises")
5571 (synopsis "Abstractions for promise-based asynchronous programming")
5573 "This package provides fundamental abstractions for doing asynchronous
5574 programming in R using promises. Asynchronous programming is useful for
5575 allowing a single R process to orchestrate multiple tasks in the background
5576 while also attending to something else. Semantics are similar to JavaScript
5577 promises, but with a syntax that is idiomatic R.")
5578 (license license:expat)))
5580 (define-public r-dosnow
5587 (uri (cran-uri "doSNOW" version))
5590 "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh"))))
5591 (properties `((upstream-name . "doSNOW")))
5592 (build-system r-build-system)
5594 `(("r-foreach" ,r-foreach)
5595 ("r-iterators" ,r-iterators)
5596 ("r-snow" ,r-snow)))
5597 (home-page "https://cran.r-project.org/web/packages/doSNOW")
5598 (synopsis "Foreach parallel adaptor for the snow package")
5600 "This package provides a parallel backend for the @code{%dopar%} function
5601 using the @code{snow} package.")
5602 (license license:gpl2)))
5604 (define-public r-snowfall
5607 (version "1.84-6.1")
5610 (uri (cran-uri "snowfall" version))
5612 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
5613 (build-system r-build-system)
5615 `(("r-snow" ,r-snow)))
5616 (home-page "http://cran.r-project.org/web/packages/snowfall/")
5617 (synopsis "Easier cluster computing")
5618 (description "This package is a usability wrapper around snow for easier
5619 development of parallel R programs. This package offers e.g. extended error
5620 checks, and additional functions. All functions work in sequential mode, too,
5621 if no cluster is present or wished. The package is also designed as connector
5622 to the cluster management tool @code{sfCluster}, but can also used without
5624 (license license:gpl2+)))
5626 (define-public r-rappdirs
5633 (uri (cran-uri "rappdirs" version))
5636 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
5637 (build-system r-build-system)
5638 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
5639 (synopsis "Determine where to save data, caches, and logs")
5641 "This package provides an easy way to determine which directories on the
5642 user's computer should be used to save data, caches and logs. It is a port of
5643 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
5644 (license license:expat)))
5646 (define-public r-renv
5653 (uri (cran-uri "renv" version))
5656 "1jwnabryn77s29ybwdfzlnd7c8m05xmi69kp5qbvdxy2gjwjzcdr"))))
5657 (properties `((upstream-name . "renv")))
5658 (build-system r-build-system)
5659 (home-page "https://rstudio.github.io/renv")
5660 (synopsis "Project environments")
5662 "This package provides a dependency management toolkit for R. Using
5663 renv, you can create and manage project-local R libraries, save the state of
5664 these libraries to a lockfile, and later restore your library as required.
5665 Together, these tools can help make your projects more isolated, portable, and
5667 (license license:expat)))
5669 (define-public r-learnr
5676 (uri (cran-uri "learnr" version))
5679 "0278q9nbkc4nb0rp930kjrwyidf0v7y38d1s187m4f4bs7ha82k6"))))
5680 (build-system r-build-system)
5682 `(("r-checkmate" ,r-checkmate)
5683 ("r-ellipsis" ,r-ellipsis)
5684 ("r-evaluate" ,r-evaluate)
5685 ("r-htmltools" ,r-htmltools)
5686 ("r-htmlwidgets" ,r-htmlwidgets)
5687 ("r-jsonlite" ,r-jsonlite)
5688 ("r-knitr" ,r-knitr)
5689 ("r-markdown" ,r-markdown)
5690 ("r-rappdirs" ,r-rappdirs)
5692 ("r-rmarkdown" ,r-rmarkdown)
5693 ("r-rprojroot" ,r-rprojroot)
5694 ("r-shiny" ,r-shiny)
5695 ("r-withr" ,r-withr)))
5696 (home-page "https://rstudio.github.io/learnr/")
5697 (synopsis "Interactive tutorials for R")
5699 "This package provides tools to create interactive tutorials using R
5700 Markdown. Use a combination of narrative, figures, videos, exercises, and
5701 quizzes to create self-paced tutorials for learning about R and R packages.")
5702 (license license:asl2.0)))
5704 (define-public r-analytics
5706 (name "r-analytics")
5711 (uri (cran-uri "analytics" version))
5714 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
5715 (build-system r-build-system)
5718 ("r-cluster" ,r-cluster)
5719 ("r-fractal" ,r-fractal)
5720 ("r-lmtest" ,r-lmtest)
5723 ("r-powerplus" ,r-powerplus)
5724 ("r-robust" ,r-robust)
5725 ("r-trend" ,r-trend)
5729 (home-page "https://cran.r-project.org/web/packages/analytics/")
5730 (synopsis "Collection of data analysis tools")
5732 "This package is a collection of data analysis tools. It includes tools
5733 for regression outlier detection in a fitted linear model, stationary
5734 bootstrap using a truncated geometric distribution, a comprehensive test for
5735 weak stationarity, column means by group, weighted biplots, and a heuristic to
5736 obtain a better initial configuration in non-metric MDS.")
5737 (license license:gpl2)))
5739 (define-public r-reticulate
5741 (name "r-reticulate")
5746 (uri (cran-uri "reticulate" version))
5749 "0icb9zl9zlx75njv7y1dr450k0yw2n3q2jkr4nicnphdyfn69gkn"))))
5750 (build-system r-build-system)
5751 (inputs `(("python" ,python)))
5753 `(("r-rappdirs" ,r-rappdirs)
5754 ("r-jsonlite" ,r-jsonlite)
5755 ("r-matrix" ,r-matrix)
5756 ("r-rcpp" ,r-rcpp)))
5757 (home-page "https://github.com/rstudio/reticulate")
5758 (synopsis "R interface to Python")
5760 "This package provides an interface from R to Python modules, classes,
5761 and functions. When calling into Python, R data types are automatically
5762 converted to their equivalent Python types. When values are returned from
5763 Python to R they are converted back to R types.")
5764 (license license:asl2.0)))
5766 (define-public r-bibtex
5773 (uri (cran-uri "bibtex" version))
5776 "140hkjzdp3033cvji861rd06z1ixgpnn4n5amygqsmhnixk8ff07"))))
5777 (build-system r-build-system)
5778 (propagated-inputs `(("r-stringr" ,r-stringr)))
5779 (home-page "https://github.com/romainfrancois/bibtex")
5780 (synopsis "Bibtex parser")
5781 (description "This package provides a utility for R to parse a bibtex
5783 (license license:gpl2+)))
5785 (define-public r-ggseqlogo
5787 (name "r-ggseqlogo")
5792 (uri (cran-uri "ggseqlogo" version))
5795 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
5796 (build-system r-build-system)
5797 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
5798 (home-page "https://github.com/omarwagih/ggseqlogo")
5799 (synopsis "ggplot2 extension for drawing genetic sequence logos")
5801 "The range of functions provided by this package makes it possible to
5802 draw highly versatile genomic sequence logos. Features include, but are not
5803 limited to, modifying colour schemes and fonts used to draw the logo,
5804 generating multiple logo plots, and aiding the visualisation with annotations.
5805 Sequence logos can easily be combined with other ggplot2 plots.")
5806 ;; Unspecified version of the LGPL.
5807 (license license:lgpl3+)))
5809 (define-public r-ggsci
5816 (uri (cran-uri "ggsci" version))
5819 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
5820 (build-system r-build-system)
5822 `(("r-ggplot2" ,r-ggplot2)
5823 ("r-scales" ,r-scales)))
5824 (home-page "https://nanx.me/ggsci/")
5825 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
5827 "This package provides a collection of ggplot2 color palettes inspired by
5828 plots in scientific journals, data visualization libraries, science fiction
5829 movies, and TV shows.")
5830 (license license:gpl3)))
5832 (define-public r-ggsignif
5839 (uri (cran-uri "ggsignif" version))
5842 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
5843 (build-system r-build-system)
5845 `(("r-ggplot2" ,r-ggplot2)))
5846 (home-page "https://github.com/const-ae/ggsignif")
5847 (synopsis "Significance brackets for ggplot2")
5849 "Enrich your ggplots with group-wise comparisons. This package provides
5850 an easy way to indicate if two groups are significantly different. Commonly
5851 this is shown by a bracket on top connecting the groups of interest which
5852 itself is annotated with the level of significance. The package provides a
5853 single layer that takes the groups for comparison and the test as arguments
5854 and adds the annotation to the plot.")
5855 (license license:gpl3)))
5857 (define-public r-ggpubr
5864 (uri (cran-uri "ggpubr" version))
5867 "0ln1gh3zlfx5s7zqcpvfdiksq74v1pma5kwkhc6r0riqnjjd19pf"))))
5868 (build-system r-build-system)
5870 `(("r-cowplot" ,r-cowplot)
5871 ("r-dplyr" ,r-dplyr)
5872 ("r-ggplot2" ,r-ggplot2)
5873 ("r-ggrepel" ,r-ggrepel)
5874 ("r-ggsci" ,r-ggsci)
5875 ("r-ggsignif" ,r-ggsignif)
5877 ("r-gridextra" ,r-gridextra)
5878 ("r-magrittr" ,r-magrittr)
5879 ("r-polynom" ,r-polynom)
5880 ("r-purrr" ,r-purrr)
5881 ("r-rlang" ,r-rlang)
5882 ("r-scales" ,r-scales)
5883 ("r-tidyr" ,r-tidyr)))
5884 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
5885 (synopsis "ggplot2-based publication-ready plots")
5887 "The ggplot2 package is an excellent and flexible package for elegant
5888 data visualization in R. However the default generated plots require some
5889 formatting before we can send them for publication. The ggpubr package
5890 provides some easy-to-use functions for creating and customizing ggplot2-based
5891 publication-ready plots.")
5892 (license license:gpl2)))
5894 (define-public r-ellipse
5901 (uri (cran-uri "ellipse" version))
5904 "0g82vc51m3c1k0hnpp2zla6amxxgk2mmkl8ssnsc49jv3599r6hs"))))
5905 (build-system r-build-system)
5906 (home-page "https://cran.r-project.org/web/packages/ellipse/")
5907 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
5909 "This package contains various routines for drawing ellipses and
5910 ellipse-like confidence regions, implementing the plots described in Murdoch
5911 and Chow (1996), A graphical display of large correlation matrices, The
5912 American Statistician 50, 178-180. There are also routines implementing the
5913 profile plots described in Bates and Watts (1988), Nonlinear Regression
5914 Analysis and its Applications.")
5915 (license license:gpl2+)))
5917 (define-public r-flashclust
5919 (name "r-flashclust")
5924 (uri (cran-uri "flashClust" version))
5927 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
5928 (properties `((upstream-name . "flashClust")))
5929 (build-system r-build-system)
5930 (native-inputs `(("gfortran" ,gfortran)))
5931 (home-page "https://cran.r-project.org/web/packages/flashClust/")
5932 (synopsis "Implementation of optimal hierarchical clustering")
5934 "This package provides a fast implementation of hierarchical
5936 (license license:gpl2+)))
5938 (define-public r-factominer
5940 (name "r-factominer")
5945 (uri (cran-uri "FactoMineR" version))
5948 "1b2jsv8vlaynknd7nlra6fdmr56n7678q5s28rqmagbadiqwvj4h"))))
5949 (properties `((upstream-name . "FactoMineR")))
5950 (build-system r-build-system)
5953 ("r-cluster" ,r-cluster)
5954 ("r-ellipse" ,r-ellipse)
5955 ("r-flashclust" ,r-flashclust)
5956 ("r-ggplot2" ,r-ggplot2)
5957 ("r-ggrepel" ,r-ggrepel)
5958 ("r-lattice" ,r-lattice)
5959 ("r-leaps" ,r-leaps)
5961 ("r-scatterplot3d" ,r-scatterplot3d)))
5962 (home-page "http://factominer.free.fr")
5963 (synopsis "Multivariate exploratory data analysis and data mining")
5965 "This package provides exploratory data analysis methods to summarize,
5966 visualize and describe datasets. The main principal component methods are
5967 available, those with the largest potential in terms of applications:
5968 principal component analysis (PCA) when variables are quantitative,
5969 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
5970 variables are categorical, Multiple Factor Analysis when variables are
5971 structured in groups, etc. and hierarchical cluster analysis.")
5972 (license license:gpl2+)))
5974 (define-public r-factoextra
5976 (name "r-factoextra")
5981 (uri (cran-uri "factoextra" version))
5984 "0bpsbcmp6jpa9qk53dhfzghrz98dh0h0n68brl7rjz724yjbvhn8"))))
5985 (build-system r-build-system)
5987 `(("r-abind" ,r-abind)
5988 ("r-cluster" ,r-cluster)
5989 ("r-dendextend" ,r-dendextend)
5990 ("r-factominer" ,r-factominer)
5991 ("r-ggplot2" ,r-ggplot2)
5992 ("r-ggpubr" ,r-ggpubr)
5993 ("r-ggrepel" ,r-ggrepel)
5994 ("r-reshape2" ,r-reshape2)
5995 ("r-tidyr" ,r-tidyr)))
5996 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
5997 (synopsis "Extract and visualize the results of multivariate data analyses")
5999 "This package provides some easy-to-use functions to extract and
6000 visualize the output of multivariate data analyses, including
6001 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
6002 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
6003 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
6004 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
6005 packages. It contains also functions for simplifying some clustering analysis
6006 steps and provides ggplot2-based elegant data visualization.")
6007 (license license:gpl2)))
6009 (define-public r-fansi
6016 (uri (cran-uri "fansi" version))
6019 "028ywjy538psnmdnddvy5jr3idzffr4hikzr4x97x0m30g4fws9w"))))
6020 (build-system r-build-system)
6022 `(("r-knitr" ,r-knitr))) ; for vignettes
6023 (home-page "https://github.com/brodieG/fansi")
6024 (synopsis "ANSI control sequence aware string functions")
6026 "This package provides counterparts to R string manipulation functions
6027 that account for the effects of ANSI text formatting control sequences.")
6028 (license license:gpl2+)))
6030 (define-public r-nbclust
6037 (uri (cran-uri "NbClust" version))
6040 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
6041 (properties `((upstream-name . "NbClust")))
6042 (build-system r-build-system)
6043 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
6044 (synopsis "Determine the best number of clusters in a data set")
6046 "NbClust provides 30 indexes for determining the optimal number of
6047 clusters in a data set and offers the best clustering scheme from different
6048 results to the user.")
6049 (license license:gpl2)))
6051 (define-public r-hdf5r
6058 (uri (cran-uri "hdf5r" version))
6061 "0hvi2cvyv6zlxgpawnmsihxclp2ln88slbrnmaxagmjswskxsrpx"))))
6062 (build-system r-build-system)
6067 `(("r-bit64" ,r-bit64)
6069 (home-page "https://hhoeflin.github.io/hdf5r")
6070 (synopsis "Interface to the HDF5 binary data format")
6072 "HDF5 is a data model, library and file format for storing and managing
6073 large amounts of data. This package provides a nearly feature complete,
6074 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
6075 functionality is added so that HDF5 objects behave very similar to their
6076 corresponding R counterparts.")
6077 (license license:asl2.0)))
6079 (define-public r-itertools
6081 (name "r-itertools")
6086 (uri (cran-uri "itertools" version))
6089 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
6090 (build-system r-build-system)
6092 `(("r-iterators" ,r-iterators)))
6093 (home-page "https://cran.r-project.org/web/packages/itertools/")
6094 (synopsis "Iterator tools")
6096 "This package provides various tools for creating iterators, many
6097 patterned after functions in the Python @code{itertools} module, and others
6098 patterned after functions in the snow package.")
6099 (license license:gpl2)))
6101 (define-public r-polynom
6108 (uri (cran-uri "polynom" version))
6111 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
6112 (build-system r-build-system)
6113 (home-page "https://cran.r-project.org/web/packages/polynom/")
6114 (synopsis "Functions for univariate polynomial manipulations")
6116 "This package provides a collection of functions to implement a class for
6117 univariate polynomial manipulations.")
6118 (license license:gpl2)))
6120 (define-public r-gbrd
6127 (uri (cran-uri "gbRd" version))
6130 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
6131 (properties `((upstream-name . "gbRd")))
6132 (build-system r-build-system)
6133 (home-page "https://cran.r-project.org/web/packages/gbRd/")
6134 (synopsis "Utilities for processing Rd objects and files")
6136 "This package provides utilities for processing Rd objects and files.
6137 Extract argument descriptions and other parts of the help pages of
6139 (license license:gpl2+)))
6141 (define-public r-rjags
6148 (uri (cran-uri "rjags" version))
6151 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
6152 (build-system r-build-system)
6154 `(("r-coda" ,r-coda)))
6158 `(("pkg-config" ,pkg-config)))
6159 (home-page "http://mcmc-jags.sourceforge.net")
6160 (synopsis "Bayesian graphical models using MCMC")
6162 "This package provides an R interface to the JAGS MCMC library. JAGS is
6163 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
6164 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
6165 (license license:gpl2)))
6167 (define-public r-rdpack
6174 (uri (cran-uri "Rdpack" version))
6177 "080y15p2hl4jsq91ak2f1y2kx1iqq5c5wzyx3zyhjwp01cahy0jq"))))
6178 (properties `((upstream-name . "Rdpack")))
6179 (build-system r-build-system)
6181 `(("r-bibtex" ,r-bibtex)
6182 ("r-gbrd" ,r-gbrd)))
6183 (home-page "https://github.com/GeoBosh/Rdpack")
6184 (synopsis "Update and manipulate Rd documentation objects")
6186 "This package provides functions for manipulation of R documentation
6187 objects, including functions @code{reprompt()} and @code{ereprompt()} for
6188 updating Rd documentation for functions, methods and classes; it also includes
6189 Rd macros for citations and import of references from bibtex files for use in
6190 Rd files and roxygen2 comments, as well as many functions for manipulation of
6191 references and Rd files.")
6192 (license license:gpl2+)))
6194 (define-public r-officer
6201 (uri (cran-uri "officer" version))
6204 "1i6jmnbkx7gd0qyf6akhizmxp7y1dh3h7a886mcbmrzka9d60zh4"))))
6205 (build-system r-build-system)
6207 `(("r-base64enc" ,r-base64enc)
6208 ("r-digest" ,r-digest)
6209 ("r-htmltools" ,r-htmltools)
6210 ("r-magrittr" ,r-magrittr)
6213 ("r-rlang" ,r-rlang)
6217 (home-page "https://davidgohel.github.io/officer")
6218 (synopsis "Manipulation of Word and PowerPoint documents")
6220 "This package provides tools to access and manipulate Word and PowerPoint
6221 documents from R. The package focuses on tabular and graphical reporting from
6222 R; it also provides two functions that let users get document content into
6223 data objects. A set of functions lets add and remove images, tables and
6224 paragraphs of text in new or existing documents. When working with PowerPoint
6225 presentations, slides can be added or removed; shapes inside slides can also
6226 be added or removed. When working with Word documents, a cursor can be used
6227 to help insert or delete content at a specific location in the document.")
6228 (license license:gpl3)))
6230 (define-public r-abn
6237 (uri (cran-uri "abn" version))
6240 "19w6bdjyp4zwqs6p0flry4qxqynf9rh8ykdrfrp61wrdf7kysw0d"))))
6241 (build-system r-build-system)
6245 `(("r-lme4" ,r-lme4)
6249 ("r-rcpparmadillo" ,r-rcpparmadillo)
6250 ("r-rjags" ,r-rjags)))
6251 (home-page "https://r-bayesian-networks.org/")
6252 (synopsis "Modelling multivariate data with additive bayesian networks")
6254 "Bayesian network analysis is a form of probabilistic graphical models
6255 which derives from empirical data a directed acyclic graph, DAG, describing
6256 the dependency structure between random variables. An additive Bayesian
6257 network model consists of a form of a DAG where each node comprises a
6258 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
6259 equivalent to Bayesian multivariate regression using graphical modelling, they
6260 generalises the usual multivariable regression, GLM, to multiple dependent
6261 variables. This package provides routines to help determine optimal Bayesian
6262 network models for a given data set, where these models are used to identify
6263 statistical dependencies in messy, complex data.")
6264 (license license:gpl2+)))
6266 (define-public r-acd
6273 (uri (cran-uri "ACD" version))
6276 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
6277 (properties `((upstream-name . "ACD")))
6278 (build-system r-build-system)
6279 (home-page "https://cran.r-project.org/web/packages/ACD/")
6280 (synopsis "Categorical data analysis with complete or missing responses")
6282 "This package provides tools for categorical data analysis with complete
6283 or missing responses.")
6284 (license license:gpl2+)))
6286 (define-public r-acdm
6293 (uri (cran-uri "ACDm" version))
6296 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
6297 (properties `((upstream-name . "ACDm")))
6298 (build-system r-build-system)
6300 `(("r-dplyr" ,r-dplyr)
6301 ("r-ggplot2" ,r-ggplot2)
6303 ("r-rsolnp" ,r-rsolnp)
6305 (home-page "https://cran.r-project.org/web/packages/ACDm/")
6306 (synopsis "Tools for Autoregressive Conditional Duration Models")
6308 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
6309 and Russell, 1998) models. It creates trade, price or volume durations from
6310 transactions (tic) data, performs diurnal adjustments, fits various ACD models
6312 (license license:gpl2+)))
6314 (define-public r-overlap
6321 (uri (cran-uri "overlap" version))
6324 "1j3m6ir1chdz0si2fhcw6gs7c9h09bv0chz18rpzxsywww6d4rzy"))))
6325 (build-system r-build-system)
6326 (home-page "https://cran.r-project.org/web/packages/overlap/")
6327 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
6329 "This package provides functions to fit kernel density functions to data
6330 on temporal activity patterns of animals; estimate coefficients of overlapping
6331 of densities for two species; and calculate bootstrap estimates of confidence
6333 (license license:gpl3+)))
6335 (define-public r-snakecase
6337 (name "r-snakecase")
6342 (uri (cran-uri "snakecase" version))
6345 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
6346 (build-system r-build-system)
6348 `(("r-stringi" ,r-stringi)
6349 ("r-stringr" ,r-stringr)))
6350 (home-page "https://github.com/Tazinho/snakecase")
6351 (synopsis "Convert strings into any case")
6353 "This package provides a consistent, flexible and easy to use tool to
6354 parse and convert strings into cases like snake or camel among others.")
6355 (license license:gpl3)))
6357 (define-public r-prediction
6359 (name "r-prediction")
6364 (uri (cran-uri "prediction" version))
6367 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
6368 (build-system r-build-system)
6370 `(("r-data-table" ,r-data-table)))
6371 (home-page "https://github.com/leeper/prediction")
6372 (synopsis "Tidy, type-safe prediction methods")
6374 "This package provides the @code{prediction()} function, a type-safe
6375 alternative to @code{predict()} that always returns a data frame. The package
6376 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
6377 from the @code{stats} package, as well as numerous other model classes from
6378 other add-on packages.")
6379 (license license:expat)))
6381 (define-public r-insight
6388 (uri (cran-uri "insight" version))
6391 "1bkcwvjpfy4q4k478x8x42yiqz6v0fk6z6hfp6fli3h63smlmck0"))))
6392 (build-system r-build-system)
6393 (home-page "https://easystats.github.io/insight/")
6394 (synopsis "Easy access to model information for various model objects")
6396 "This package provides a tool to provide an easy, intuitive and
6397 consistent access to information contained in various R models, like model
6398 formulas, model terms, information about random effects, data that was used to
6399 fit the model or data from response variables. The package mainly revolves
6400 around two types of functions: Functions that find (the names of) information,
6401 starting with @code{find_}, and functions that get the underlying data,
6402 starting with @code{get_}. The package has a consistent syntax and works with
6403 many different model objects, where otherwise functions to access these
6404 information are missing.")
6405 (license license:gpl3)))
6407 (define-public r-sjlabelled
6409 (name "r-sjlabelled")
6414 (uri (cran-uri "sjlabelled" version))
6417 "1vnx067mxnvz4jzhmpiarda8ln6habzj02qikvkix5piiy85sqcw"))))
6418 (build-system r-build-system)
6420 `(("r-haven" ,r-haven)
6421 ("r-insight" ,r-insight)))
6422 (home-page "https://github.com/strengejacke/sjlabelled")
6423 (synopsis "Labelled data utility functions")
6425 "This package provides a collection of functions dealing with labelled
6426 data, like reading and writing data between R and other statistical software
6427 packages. This includes easy ways to get, set or change value and variable
6428 label attributes, to convert labelled vectors into factors or numeric (and
6429 vice versa), or to deal with multiple declared missing values.")
6430 (license license:gpl3)))
6432 (define-public r-sjmisc
6439 (uri (cran-uri "sjmisc" version))
6442 "0w8l9grmp4q775jrf4q6rxx36ld5daz9b0gdxyyh42xfihk6m62h"))))
6443 (build-system r-build-system)
6445 `(("r-dplyr" ,r-dplyr)
6446 ("r-insight" ,r-insight)
6447 ("r-magrittr" ,r-magrittr)
6448 ("r-purrr" ,r-purrr)
6449 ("r-rlang" ,r-rlang)
6450 ("r-sjlabelled" ,r-sjlabelled)
6451 ("r-tidyselect" ,r-tidyselect)))
6452 (home-page "https://github.com/strengejacke/sjmisc")
6453 (synopsis "Data and variable transformation functions")
6455 "This package is a collection of miscellaneous utility functions,
6456 supporting data transformation tasks like recoding, dichotomizing or grouping
6457 variables, setting and replacing missing values. The data transformation
6458 functions also support labelled data, and all integrate seamlessly into a
6459 tidyverse workflow.")
6460 (license license:gpl3)))
6462 (define-public r-nortest
6469 (uri (cran-uri "nortest" version))
6472 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
6473 (build-system r-build-system)
6474 (home-page "https://cran.r-project.org/web/packages/nortest/")
6475 (synopsis "Tests for normality")
6477 "This package provides five omnibus tests for testing the composite
6478 hypothesis of normality.")
6479 (license license:gpl2+)))
6481 (define-public r-moonbook
6488 (uri (cran-uri "moonBook" version))
6491 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
6492 (properties `((upstream-name . "moonBook")))
6493 (build-system r-build-system)
6495 `(("r-magrittr" ,r-magrittr)
6496 ("r-nortest" ,r-nortest)
6497 ("r-purrr" ,r-purrr)
6498 ("r-sjmisc" ,r-sjmisc)
6499 ("r-stringr" ,r-stringr)
6500 ("r-survival" ,r-survival)))
6501 (home-page "https://github.com/cardiomoon/moonBook")
6502 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
6504 "This package provides several analysis-related functions for the book
6505 entitled \"R statistics and graph for medical articles\" (written in Korean),
6506 version 1, by Keon-Woong Moon with Korean demographic data with several plot
6508 (license license:gpl2)))
6510 (define-public r-flextable
6512 (name "r-flextable")
6517 (uri (cran-uri "flextable" version))
6520 "1f869f2dfqkzhf6yix7xcbs8rn1nwq3sg623h74zg6h1pl6px66w"))))
6521 (build-system r-build-system)
6523 `(("r-base64enc" ,r-base64enc)
6524 ("r-data-table" ,r-data-table)
6525 ("r-gdtools" ,r-gdtools)
6526 ("r-htmltools" ,r-htmltools)
6527 ("r-knitr" ,r-knitr)
6528 ("r-officer" ,r-officer)
6529 ("r-rlang" ,r-rlang)
6530 ("r-rmarkdown" ,r-rmarkdown)
6531 ("r-xml2" ,r-xml2)))
6532 (home-page "https://davidgohel.github.io/flextable")
6533 (synopsis "Functions for tabular reporting")
6535 "This package provides tools to create pretty tables for HTML documents
6536 and other formats. Functions are provided to let users create tables, modify
6537 and format their content. It extends the @code{officer} package and can be
6538 used within R markdown documents when rendering to HTML and to Word
6540 (license license:gpl3)))
6542 (define-public r-writexl
6549 (uri (cran-uri "writexl" version))
6552 "09fhdip6igcg97fjx4c7727cx2lb49l4d74l4i8rg2bag2s5lrj3"))))
6553 (build-system r-build-system)
6554 (inputs `(("zlib" ,zlib)))
6555 (home-page "https://github.com/ropensci/writexl")
6556 (synopsis "Export data frames to xlsx format")
6558 "This package provides a data frame to xlsx exporter based on
6560 (license license:bsd-2)))
6562 (define-public r-biasedurn
6564 (name "r-biasedurn")
6569 (uri (cran-uri "BiasedUrn" version))
6572 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
6573 (properties `((upstream-name . "BiasedUrn")))
6574 (build-system r-build-system)
6575 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
6576 (synopsis "Biased Urn model distributions")
6578 "This package provides statistical models of biased sampling in the form
6579 of univariate and multivariate noncentral hypergeometric distributions,
6580 including Wallenius' noncentral hypergeometric distribution and Fisher's
6581 noncentral hypergeometric distribution (also called extended hypergeometric
6583 (license license:gpl3)))
6585 (define-public r-goplot
6592 (uri (cran-uri "GOplot" version))
6595 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
6596 (properties `((upstream-name . "GOplot")))
6597 (build-system r-build-system)
6599 `(("r-ggdendro" ,r-ggdendro)
6600 ("r-ggplot2" ,r-ggplot2)
6601 ("r-gridextra" ,r-gridextra)
6602 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6603 (home-page "https://github.com/wencke/wencke.github.io")
6604 (synopsis "Visualization of functional analysis data")
6606 "This package provides an implementation of multilayered visualizations
6607 for enhanced graphical representation of functional analysis data. It
6608 combines and integrates omics data derived from expression and functional
6609 annotation enrichment analyses. Its plotting functions have been developed
6610 with an hierarchical structure in mind: starting from a general overview to
6611 identify the most enriched categories (modified bar plot, bubble plot) to a
6612 more detailed one displaying different types of relevant information for the
6613 molecules in a given set of categories (circle plot, chord plot, cluster plot,
6614 Venn diagram, heatmap).")
6615 (license license:gpl2)))
6617 (define-public r-getopt
6624 (uri (cran-uri "getopt" version))
6627 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
6628 (build-system r-build-system)
6629 (home-page "https://github.com/trevorld/getopt")
6630 (synopsis "Command-line option processor for R")
6632 "This package is designed to be used with Rscript to write shebang
6633 scripts that accept short and long options. Many users will prefer to
6634 use the packages @code{optparse} or @code{argparse} which add extra
6635 features like automatically generated help options and usage texts,
6636 support for default values, positional argument support, etc.")
6637 (license license:gpl2+)))
6639 (define-public r-findpython
6641 (name "r-findpython")
6646 (uri (cran-uri "findpython" version))
6649 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
6650 (build-system r-build-system)
6651 (home-page "https://github.com/trevorld/findpython")
6652 (synopsis "Functions to find an acceptable Python binary")
6654 "This package was designed to find an acceptable Python binary that
6655 matches version and feature constraints.")
6656 (license license:expat)))
6658 ;; This in not the same as "r-argparser"
6659 (define-public r-argparse
6666 (uri (cran-uri "argparse" version))
6669 "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l"))))
6670 (build-system r-build-system)
6671 (inputs `(("python" ,python)))
6673 `(("r-findpython" ,r-findpython)
6674 ("r-jsonlite" ,r-jsonlite)
6676 (home-page "https://github.com/trevorld/argparse")
6677 (synopsis "Command line optional and positional argument parser")
6679 "This package provides a command line parser to be used with Rscript to
6680 write shebang scripts that gracefully accept positional and optional arguments
6681 and automatically generate usage notices.")
6682 (license license:gpl2+)))
6684 (define-public r-hash
6691 (uri (cran-uri "hash" version))
6694 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
6695 (build-system r-build-system)
6696 (home-page "https://cran.r-project.org/web/packages/hash/")
6697 (synopsis "Implementation of hash/associated arrays/dictionaries")
6699 "This package implements a data structure similar to hashes in Perl and
6700 dictionaries in Python but with a purposefully R flavor. For objects of
6701 appreciable size, access using hashes outperforms native named lists and
6703 (license license:gpl2+)))
6705 (define-public r-orddom
6712 (uri (cran-uri "orddom" version))
6715 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
6716 (build-system r-build-system)
6717 (propagated-inputs `(("r-psych" ,r-psych)))
6718 (home-page "https://cran.r-project.org/web/packages/orddom/")
6719 (synopsis "Ordinal dominance statistics")
6721 "This package provides tools to compute ordinal, statistics and effect
6722 sizes as an alternative to mean comparison: Cliff's delta or success rate
6723 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
6724 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
6725 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
6726 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
6727 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
6728 Group (Non-)Overlap considerations.")
6729 (license license:gpl2)))
6731 (define-public r-deriv
6738 (uri (cran-uri "Deriv" version))
6741 "03mlfy8jzzzbh2l18gnmw0a71n9savx4cw72yhkxq93v2xj8fy3n"))))
6742 (properties `((upstream-name . "Deriv")))
6743 (build-system r-build-system)
6744 (home-page "https://cran.r-project.org/web/packages/Deriv")
6745 (synopsis "Symbolic differentiation")
6747 "This package provides an R-based solution for symbolic differentiation.
6748 It admits user-defined functions as well as function substitution in arguments
6749 of functions to be differentiated. Some symbolic simplification is part of
6751 (license license:gpl3+)))
6753 (define-public r-doby
6760 (uri (cran-uri "doBy" version))
6763 "1d0d6pwai1g4i5jls0jm9va29ci5hy92n5957608f3fzi1jwy635"))))
6764 (properties `((upstream-name . "doBy")))
6765 (build-system r-build-system)
6767 `(("r-broom" ,r-broom)
6768 ("r-deriv" ,r-deriv)
6769 ("r-dplyr" ,r-dplyr)
6770 ("r-magrittr" ,r-magrittr)
6772 ("r-matrix" ,r-matrix)
6774 ("r-pbkrtest" ,r-pbkrtest)
6775 ("r-tibble" ,r-tibble)))
6776 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
6777 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
6779 "This package contains:
6782 @item facilities for working with grouped data: @code{do}
6783 something to data stratified @code{by} some variables.
6784 @item implementations of least-squares means, general linear contrasts, and
6785 @item miscellaneous other utilities.
6787 (license license:gpl2+)))
6789 (define-public r-refgenome
6791 (name "r-refgenome")
6796 (uri (cran-uri "refGenome" version))
6799 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
6800 (properties `((upstream-name . "refGenome")))
6801 (build-system r-build-system)
6805 ("r-rsqlite" ,r-rsqlite)))
6806 (home-page "https://cran.r-project.org/web/packages/refGenome/")
6808 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
6810 "This package contains functionality for importing and managing of
6811 downloaded genome annotation data from the Ensembl genome browser (European
6812 Bioinformatics Institute) and from the UCSC genome browser (University of
6813 California, Santa Cruz) and annotation routines for genomic positions and
6814 splice site positions.")
6815 (license license:gpl2)))
6817 (define-public r-basix
6824 (uri (cran-uri "BASIX" version))
6827 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
6828 (properties `((upstream-name . "BASIX")))
6829 (build-system r-build-system)
6830 (home-page "https://cran.r-project.org/web/packages/BASIX/")
6831 (synopsis "Efficient C/C++ toolset for R")
6833 "BASIX provides some efficient C/C++ implementations of native R
6834 procedures to speed up calculations in R.")
6835 (license license:gpl2)))
6837 (define-public r-blockfest
6839 (name "r-blockfest")
6844 (uri (cran-uri "BlockFeST" version))
6847 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
6848 (properties `((upstream-name . "BlockFeST")))
6849 (build-system r-build-system)
6850 (propagated-inputs `(("r-basix" ,r-basix)))
6851 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
6852 (synopsis "Bayesian calculation of region-specific fixation index")
6854 "This package provides an R implementation of an extension of the
6855 BayeScan software for codominant markers, adding the option to group
6856 individual SNPs into pre-defined blocks. A typical application of this new
6857 approach is the identification of genomic regions, genes, or gene sets
6858 containing one or more SNPs that evolved under directional selection.")
6859 (license license:gpl2)))
6861 (define-public r-proc
6868 (uri (cran-uri "pROC" version))
6871 "0qkp1byl2xspxaaf0by6mvvrhg7wlz6fxmynz2hkh0ds24w7ig9m"))))
6872 (properties `((upstream-name . "pROC")))
6873 (build-system r-build-system)
6875 `(("r-plyr" ,r-plyr)
6876 ("r-rcpp" ,r-rcpp)))
6877 (home-page "http://expasy.org/tools/pROC/")
6878 (synopsis "Display and analyze ROC curves")
6880 "This package provides tools for visualizing, smoothing and comparing
6881 receiver operating characteristic (ROC curves). The area under the
6882 curve (AUC) can be compared with statistical tests based on U-statistics or
6883 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
6884 (license license:gpl3+)))
6886 (define-public r-rootsolve
6888 (name "r-rootsolve")
6893 (uri (cran-uri "rootSolve" version))
6896 "0rj7c4zcrzgz7sb0vgvh7swpfafnw4040cxp7ypas3s8fnihn54l"))))
6897 (properties `((upstream-name . "rootSolve")))
6898 (build-system r-build-system)
6899 (native-inputs `(("gfortran" ,gfortran)))
6900 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
6901 (synopsis "Tools for the analysis of ordinary differential equations")
6903 "This package provides routines to find the root of nonlinear functions,
6904 and to perform steady-state and equilibrium analysis of @dfn{ordinary
6905 differential equations} (ODE). It includes routines that:
6908 @item generate gradient and jacobian matrices (full and banded),
6909 @item find roots of non-linear equations by the Newton-Raphson method,
6910 @item estimate steady-state conditions of a system of (differential) equations
6911 in full, banded or sparse form, using the Newton-Raphson method, or by
6912 dynamically running,
6913 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
6914 and 3-D partial differential equations, that have been converted to ordinary
6915 differential equations by numerical differencing (using the method-of-lines
6918 (license license:gpl2+)))
6920 (define-public r-abcanalysis
6922 (name "r-abcanalysis")
6927 (uri (cran-uri "ABCanalysis" version))
6929 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
6930 (properties `((upstream-name . "ABCanalysis")))
6931 (build-system r-build-system)
6932 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
6933 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
6934 (synopsis "Computed ABC Analysis")
6936 "Multivariate data sets often differ in several factors or derived statistical
6937 parameters, which have to be selected for a valid interpretation. Basing this
6938 selection on traditional statistical limits leads occasionally to the perception
6939 of losing information from a data set. This package provides tools to calculate
6940 these limits on the basis of the mathematical properties of the distribution of
6941 the analyzed items.")
6942 (license license:gpl3)))
6944 (define-public r-slam
6951 (uri (cran-uri "slam" version))
6953 (base32 "12fggw2c7hz3bpvsaqm24g3r6lbpq6jgli24g7x5j859iak5cqv9"))))
6954 (build-system r-build-system)
6955 (home-page "https://cran.r-project.org/web/packages/slam/")
6956 (synopsis "Sparse lightweight arrays and matrices")
6958 "This package contains data structures and algorithms for sparse arrays and matrices,
6959 based on index arrays and simple triplet representations, respectively.")
6960 (license license:gpl2)))
6962 (define-public r-manipulatewidget
6964 (name "r-manipulatewidget")
6969 (uri (cran-uri "manipulateWidget" version))
6971 (base32 "1zagrbwkn2d50zzw8i2vyb1hsq4cydmfsqiy1a2qlp6zrv8a6q9x"))))
6973 `((upstream-name . "manipulateWidget")))
6974 (build-system r-build-system)
6976 `(("r-base64enc" ,r-base64enc)
6977 ("r-codetools" ,r-codetools)
6978 ("r-htmltools" ,r-htmltools)
6979 ("r-htmlwidgets" ,r-htmlwidgets)
6980 ("r-knitr" ,r-knitr)
6981 ("r-miniui" ,r-miniui)
6982 ("r-shiny" ,r-shiny)
6983 ("r-webshot" ,r-webshot)))
6984 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
6985 (synopsis "Add even more interactivity to interactive charts")
6987 "This package lets you create in just a few lines of R code a nice user interface to
6988 modify the data or the graphical parameters of one or multiple interactive
6989 charts. It is useful to quickly explore visually some data or for package
6990 developers to generate user interfaces easy to maintain.")
6991 (license license:gpl2+)))
7000 (uri (cran-uri "A3" version))
7002 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
7003 (properties `((upstream-name . "A3")))
7004 (build-system r-build-system)
7006 `(("r-pbapply" ,r-pbapply)
7007 ("r-xtable" ,r-xtable)))
7008 (home-page "https://cran.r-project.org/web/packages/A3/")
7009 (synopsis "Error metrics for predictive models")
7011 "This package supplies tools for tabulating and analyzing the results of predictive
7012 models. The methods employed are applicable to virtually any predictive model
7013 and make comparisons between different methodologies straightforward.")
7014 (license license:gpl2+)))
7016 (define-public r-infotheo
7023 (uri (cran-uri "infotheo" version))
7026 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
7027 (build-system r-build-system)
7028 (home-page "http://homepage.meyerp.com/software")
7029 (synopsis "Information-theoretic measures")
7031 "This package implements various measures of information theory based on
7032 several entropy estimators.")
7033 (license license:gpl3+)))
7035 (define-public r-abcoptim
7042 (uri (cran-uri "ABCoptim" version))
7044 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
7045 (properties `((upstream-name . "ABCoptim")))
7046 (build-system r-build-system)
7047 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
7048 (home-page "https://github.com/gvegayon/ABCoptim/")
7049 (synopsis "Optimization of Artificial Bee Colony algorithm")
7051 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
7052 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
7053 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
7054 algorithms, and uses only common control parameters such as colony size and
7055 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
7056 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
7057 This version is a work-in-progress and is written in R code.")
7058 (license license:expat)))
7060 (define-public r-abcp2
7067 (uri (cran-uri "ABCp2" version))
7069 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
7070 (properties `((upstream-name . "ABCp2")))
7071 (build-system r-build-system)
7072 (propagated-inputs `(("r-mass" ,r-mass)))
7073 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
7074 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
7076 "This package tests the goodness of fit of a distribution of offspring to the Normal,
7077 Poisson, and Gamma distribution and estimates the proportional paternity of the
7078 second male (P2) based on the best fit distribution.")
7079 (license license:gpl2)))
7081 (define-public r-abcrf
7088 (uri (cran-uri "abcrf" version))
7090 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
7091 (build-system r-build-system)
7093 `(("r-doparallel" ,r-doparallel)
7094 ("r-foreach" ,r-foreach)
7096 ("r-matrixstats" ,r-matrixstats)
7097 ("r-ranger" ,r-ranger)
7099 ("r-rcpparmadillo" ,r-rcpparmadillo)
7100 ("r-readr" ,r-readr)
7101 ("r-stringr" ,r-stringr)))
7102 (home-page "https://cran.r-project.org/web/packages/abcrf/")
7103 (synopsis "Approximate bayesian computation via random forests")
7105 "This package performs approximate bayesian computation (ABC) model choice and
7106 parameter inference via random forests. This machine learning tool named random
7107 forests (RF) can conduct selection among the highly complex models covered by
7109 (license license:gpl2+)))
7111 (define-public r-abctools
7118 (uri (cran-uri "abctools" version))
7120 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
7121 (build-system r-build-system)
7124 ("r-abind" ,r-abind)
7125 ("r-hmisc" ,r-hmisc)
7126 ("r-plyr" ,r-plyr)))
7127 (home-page "https://github.com/dennisprangle/abctools/")
7128 (synopsis "Tools for ABC analyses")
7130 "This @code{r-abctools} package provides tools for approximate Bayesian computation
7131 including summary statistic selection and assessing coverage. This includes
7132 recent dimension reduction algorithms to tune the choice of summary statistics,
7133 and coverage methods to tune the choice of threshold.")
7134 (license license:gpl2+)))
7136 (define-public r-ggstance
7143 (uri (cran-uri "ggstance" version))
7145 (base32 "0kdksay61hyb6612b07r84chh7a9aibjyclk3qcypvr9aang8hkh"))))
7146 (build-system r-build-system)
7148 `(("r-ggplot2" ,r-ggplot2)
7150 ("r-rlang" ,r-rlang)
7151 ("r-withr" ,r-withr)))
7152 (home-page "https://cran.r-project.org/web/packages/ggstance/")
7153 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
7155 "This package is a @code{r-ggplot2} extension that provides flipped components:
7157 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
7158 @item vertical versions of @code{r-ggplot2} positions.
7160 (license license:gpl3)))
7162 (define-public r-mosaiccore
7164 (name "r-mosaiccore")
7169 (uri (cran-uri "mosaicCore" version))
7171 (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
7172 (properties `((upstream-name . "mosaicCore")))
7173 (build-system r-build-system)
7175 `(("r-dplyr" ,r-dplyr)
7176 ("r-lazyeval" ,r-lazyeval)
7178 ("r-rlang" ,r-rlang)
7179 ("r-tidyr" ,r-tidyr)))
7180 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
7181 (synopsis "Common utilities for mosaic family packages")
7183 "Common utilities used in other Mosaic family packages are collected here.")
7184 (license license:gpl2+)))
7186 (define-public r-ggformula
7188 (name "r-ggformula")
7193 (uri (cran-uri "ggformula" version))
7195 (base32 "16ycabhnp78fsiv1dc63ccgh9gmpsy2683vbmq0fdzl6w3pd87sr"))))
7196 (build-system r-build-system)
7198 `(("r-ggplot2" ,r-ggplot2)
7199 ("r-ggstance" ,r-ggstance)
7200 ("r-magrittr" ,r-magrittr)
7201 ("r-mosaiccore" ,r-mosaiccore)
7202 ("r-rlang" ,r-rlang)
7203 ("r-stringr" ,r-stringr)
7204 ("r-tibble" ,r-tibble)
7205 ("r-tidyr" ,r-tidyr)))
7206 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
7207 (synopsis "Formula interface for the @code{r-ggplot2}")
7209 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
7210 gf_density(), and so on, bring the formula interface to ggplot(). This captures
7211 and extends the excellent simplicity of the lattice-graphics formula interface,
7212 while providing the intuitive capabilities of @code{r-ggplot2}.")
7213 (license license:expat)))
7215 (define-public r-mosaicdata
7217 (name "r-mosaicdata")
7222 (uri (cran-uri "mosaicData" version))
7224 (base32 "04z0mdm52mykqsxsinhmsihn181zf6cw321gayk2rjp7lj7mwdq9"))))
7225 (properties `((upstream-name . "mosaicData")))
7226 (build-system r-build-system)
7227 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
7228 (synopsis "Data sets for project Mosaic")
7230 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
7231 used to teach mathematics, statistics, computation and modeling.")
7232 (license license:gpl2+)))
7234 (define-public r-raster
7241 (uri (cran-uri "raster" version))
7244 "0faxv71hlxkblvbi3ps1vfzm3wwi0brwzmpsr5114bddcqyiqkvn"))))
7245 (build-system r-build-system)
7247 `(("r-rcpp" ,r-rcpp)
7249 (home-page "https://www.rspatial.org/")
7250 (synopsis "Geographic data analysis and modeling")
7252 "The package implements basic and high-level functions for reading,
7253 writing, manipulating, analyzing and modeling of gridded spatial data.
7254 Processing of very large files is supported.")
7255 (license license:gpl3+)))
7257 (define-public r-mosaic
7264 (uri (cran-uri "mosaic" version))
7266 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
7267 (build-system r-build-system)
7269 `(("r-broom" ,r-broom)
7270 ("r-dplyr" ,r-dplyr)
7271 ("r-ggdendro" ,r-ggdendro)
7272 ("r-ggformula" ,r-ggformula)
7273 ("r-ggplot2" ,r-ggplot2)
7274 ("r-ggrepel" ,r-ggrepel)
7276 ("r-gridextra" ,r-gridextra)
7277 ("r-lattice" ,r-lattice)
7278 ("r-latticeextra" ,r-latticeextra)
7279 ("r-lazyeval" ,r-lazyeval)
7281 ("r-matrix" ,r-matrix)
7282 ("r-mosaiccore" ,r-mosaiccore)
7283 ("r-mosaicdata" ,r-mosaicdata)
7284 ("r-readr" ,r-readr)
7285 ("r-tidyr" ,r-tidyr)))
7286 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
7287 (synopsis "Mathematics, statistics, and computation teaching utilities")
7289 "This package contain data sets and utilities from
7290 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
7291 statistics, computation and modeling. Project MOSAIC is a community of
7292 educators working to tie together aspects of quantitative work that students
7293 in science, technology, engineering and mathematics will need in their
7294 professional lives, but which are usually taught in isolation, if at all.")
7295 (license license:gpl2+)))
7297 (define-public r-abd
7304 (uri (cran-uri "abd" version))
7306 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
7307 (build-system r-build-system)
7309 `(("r-lattice" ,r-lattice)
7310 ("r-mosaic" ,r-mosaic)
7311 ("r-nlme" ,r-nlme)))
7312 (home-page "https://cran.r-project.org/web/packages/abd/")
7313 (synopsis "Analysis of biological data")
7315 "The @code{r-abd} package contains data sets and sample code for the Analysis of
7316 biological data by Michael Whitlock and Dolph Schluter.")
7317 (license license:gpl2)))
7319 (define-public r-svgui
7326 (uri (cran-uri "svGUI" version))
7328 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
7329 (properties `((upstream-name . "svGUI")))
7330 (build-system r-build-system)
7331 (home-page "https://github.com/SciViews/svGUI/")
7332 (synopsis "Functions for managing GUI clients in R")
7334 "The SciViews @code{svGUI} package eases the management of Graphical User
7335 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
7336 centralizes info about GUI elements currently used, and it dispatches GUI
7337 calls to the particular toolkits in use in function of the context.")
7338 (license license:gpl2)))
7340 (define-public r-svdialogs
7342 (name "r-svdialogs")
7347 (uri (cran-uri "svDialogs" version))
7349 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
7350 (properties `((upstream-name . "svDialogs")))
7351 (build-system r-build-system)
7354 ("zenity" ,zenity)))
7356 `(("r-rstudioapi" ,r-rstudioapi)
7357 ("r-svgui" ,r-svgui)))
7358 (home-page "https://github.com/SciViews/svDialogs/")
7359 (synopsis "Portable dialog boxes")
7361 "This package helps to construct standard dialog boxes for your GUI, including
7362 message boxes, input boxes, list, file or directory selection, and others. In
7363 case R cannot display GUI dialog boxes, a simpler command line version of these
7364 interactive elements is also provided as a fallback solution.")
7365 (license license:gpl2)))
7367 (define-public r-abe
7374 (uri (cran-uri "abe" version))
7377 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
7378 (build-system r-build-system)
7379 (home-page "https://cran.r-project.org/web/packages/abe/")
7380 (synopsis "Augmented backward elimination")
7382 "This package performs augmented backward elimination and checks the
7383 stability of the obtained model. Augmented backward elimination combines
7384 significance or information based criteria with the change in estimate to
7385 either select the optimal model for prediction purposes or to serve as a tool
7386 to obtain a practically sound, highly interpretable model.")
7387 (license license:gpl2+)))
7389 (define-public r-abf2
7396 (uri (cran-uri "abf2" version))
7398 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
7399 (build-system r-build-system)
7400 (home-page "https://cran.r-project.org/web/packages/abf2/")
7401 (synopsis "Load gap-free axon @code{r-abf2} files")
7403 "This package loads electrophysiology data from ABF2 files, as created by
7404 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
7405 mode are currently supported.")
7406 (license license:artistic2.0)))
7408 (define-public r-abhgenotyper
7410 (name "r-abhgenotyper")
7415 (uri (cran-uri "ABHgenotypeR" version))
7417 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
7418 (properties `((upstream-name . "ABHgenotypeR")))
7419 (build-system r-build-system)
7421 `(("r-ggplot2" ,r-ggplot2)
7422 ("r-reshape2" ,r-reshape2)))
7423 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
7424 (synopsis "Visualize and manipulate ABH genotypes")
7426 "The @code{r-abhgenotyper} package provides simple imputation,
7427 error-correction and plotting capacities for genotype data. The package is
7428 supposed to serve as an intermediate but independent analysis tool between the
7429 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
7430 not found in either TASSEL or @code{r-qtl} in addition to visualization of
7431 genotypes as \"graphical genotypes\".")
7432 (license license:gpl3)))
7434 (define-public r-furrr
7441 (uri (cran-uri "furrr" version))
7444 "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx"))))
7445 (build-system r-build-system)
7447 `(("r-future" ,r-future)
7448 ("r-globals" ,r-globals)
7449 ("r-purrr" ,r-purrr)
7450 ("r-rlang" ,r-rlang)))
7451 (home-page "https://github.com/DavisVaughan/furrr")
7452 (synopsis "Apply mapping functions in parallel using futures")
7454 "This package provides implementations of the family of @code{map()}
7455 functions from the @code{purrr} package that can be resolved using any
7456 @code{future}-supported backend, e.g. parallel on the local machine or
7457 distributed on a compute cluster.")
7458 (license license:lgpl2.1+)))
7460 (define-public r-abjutils
7467 (uri (cran-uri "abjutils" version))
7469 (base32 "0n4zps65y3zg0gfzlv97w91si52a9izkncirskbkj5x9hk0nhxcv"))))
7470 (build-system r-build-system)
7472 `(("r-devtools" ,r-devtools)
7473 ("r-dplyr" ,r-dplyr)
7474 ("r-furrr" ,r-furrr)
7475 ("r-future" ,r-future)
7478 ("r-magrittr" ,r-magrittr)
7479 ("r-progress" ,r-progress)
7480 ("r-purrr" ,r-purrr)
7481 ("r-readr" ,r-readr)
7482 ("r-rlang" ,r-rlang)
7483 ("r-rstudioapi" ,r-rstudioapi)
7484 ("r-scales" ,r-scales)
7485 ("r-stringi" ,r-stringi)
7486 ("r-stringr" ,r-stringr)
7487 ("r-tibble" ,r-tibble)
7488 ("r-tidyr" ,r-tidyr)))
7489 (home-page "https://github.com/abjur/abjutils/")
7490 (synopsis "Collection of tools for jurimetrical analysis")
7492 "This package implements general purpose tools, such as functions for
7493 sampling and basic manipulation of Brazilian lawsuits identification number.
7494 It also implements functions for text cleaning, such as accentuation
7496 (license license:expat)))
7498 (define-public r-abnormality
7500 (name "r-abnormality")
7505 (uri (cran-uri "abnormality" version))
7507 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
7508 (build-system r-build-system)
7510 `(("r-mass" ,r-mass)
7511 ("r-matrix" ,r-matrix)))
7512 (home-page "https://cran.r-project.org/web/packages/abnormality/")
7513 (synopsis "Measure a subject's abnormality with respect to a reference population")
7515 "This package contains functions to implement the methodology and
7516 considerations laid out by Marks et al. in the article \"Measuring abnormality
7517 in high dimensional spaces: applications in biomechanical gait analysis\".
7518 Using high-dimensional datasets to measure a subject's overall level of
7519 abnormality as compared to a reference population is often needed in outcomes
7521 (license license:expat)))
7523 (define-public r-abodoutlier
7525 (name "r-abodoutlier")
7530 (uri (cran-uri "abodOutlier" version))
7532 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
7533 (properties `((upstream-name . "abodOutlier")))
7534 (build-system r-build-system)
7536 `(("r-cluster" ,r-cluster)))
7537 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
7538 (synopsis "Angle-based outlier detection")
7540 "This package performs angle-based outlier detection on a given data
7541 frame. It offers three methods to process data:
7543 @item full but slow implementation using all the data that has cubic
7545 @item a fully randomized method;
7546 @item a method using k-nearest neighbours.
7548 These algorithms are well suited for high dimensional data outlier
7550 (license license:expat)))
7552 (define-public r-abps
7559 (uri (cran-uri "ABPS" version))
7561 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
7562 (properties `((upstream-name . "ABPS")))
7563 (build-system r-build-system)
7564 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
7565 (home-page "https://cran.r-project.org/web/packages/ABPS/")
7566 (synopsis "Abnormal blood profile score to detect blood doping")
7568 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
7569 The ABPS is a part of the Athlete biological passport program of the World
7570 anti-doping agency, which combines several blood parameters into a single
7571 score in order to detect blood doping. The package also contains functions to
7572 calculate other scores used in anti-doping programs, such as the ratio of
7573 hemoglobin to reticulocytes (OFF-score), as well as example data.")
7574 (license license:gpl2+)))
7576 (define-public r-parmigene
7578 (name "r-parmigene")
7583 (uri (cran-uri "parmigene" version))
7586 "1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d"))))
7587 (build-system r-build-system)
7588 (home-page "https://cran.r-project.org/web/packages/parmigene/")
7589 (synopsis "Mutual information estimation for gene network reconstruction")
7591 "This package provides a parallel estimation of the mutual information
7592 based on entropy estimates from k-nearest neighbors distances and algorithms
7593 for the reconstruction of gene regulatory networks.")
7594 (license license:agpl3+)))
7596 (define-public r-pscl
7603 (uri (cran-uri "pscl" version))
7605 (base32 "1phf3awsfr4ncqfqzin5m1pz0g7y1zhbcm2sz7358ssw914fd7rc"))))
7606 (build-system r-build-system)
7608 `(("r-mass" ,r-mass)))
7609 (home-page "https://github.com/atahk/pscl/")
7610 (synopsis "Political science computational laboratory")
7612 "The @code{pscl} is an R package providing classes and methods for:
7614 @item Bayesian analysis of roll call data (item-response models);
7615 @item elementary Bayesian statistics;
7616 @item maximum likelihood estimation of zero-inflated and hurdle models for count
7618 @item utility functions.
7620 (license license:gpl2)))
7622 (define-public r-accelmissing
7624 (name "r-accelmissing")
7629 (uri (cran-uri "accelmissing" version))
7631 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
7632 (build-system r-build-system)
7634 `(("r-mice" ,r-mice)
7635 ("r-pscl" ,r-pscl)))
7636 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
7637 (synopsis "Missing value imputation for accelerometer data")
7639 "This package provides a statistical method to impute the missing values in
7640 accelerometer data. The methodology includes both parametric and
7641 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
7642 model. It also provides multiple functions to preprocess the accelerometer data
7643 previous to the missing data imputation. These include detecting the wearing
7644 and the non-wearing time, selecting valid days and subjects, and creating plots.")
7645 (license license:gpl2+)))
7647 (define-public r-mhsmm
7654 (uri (cran-uri "mhsmm" version))
7656 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
7657 (build-system r-build-system)
7658 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
7659 (home-page "https://github.com/jaredo/mhsmm/")
7660 (synopsis "Inference for hidden Markov and semi-Markov models")
7662 "The @code{r-mhsmm} package implements estimation and prediction methods for
7663 hidden Markov and semi-Markov models for multiple observation sequences. Such
7664 techniques are of interest when observed data is thought to be dependent on some
7665 unobserved (or hidden) state. Also, this package is suitable for equidistant
7666 time series data, with multivariate and/or missing data. Allows user defined
7667 emission distributions.")
7668 (license license:gpl2+)))
7670 (define-public r-nleqslv
7677 (uri (cran-uri "nleqslv" version))
7679 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
7680 (build-system r-build-system)
7681 (native-inputs `(("gfortran" ,gfortran)))
7682 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
7683 (synopsis "Solve systems of nonlinear equations")
7685 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
7686 Broyden or a Newton method with a choice of global strategies such as line
7687 search and trust region. There are options for using a numerical or user
7688 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
7689 singular or ill-conditioned Jacobian.")
7690 (license license:gpl2+)))
7692 (define-public r-physicalactivity
7694 (name "r-physicalactivity")
7699 (uri (cran-uri "PhysicalActivity" version))
7701 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
7703 `((upstream-name . "PhysicalActivity")))
7704 (build-system r-build-system)
7705 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
7706 (synopsis "Procesing accelerometer data for physical activity measurement")
7708 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
7709 for classification of monitor wear and nonwear time intervals in accelerometer
7710 data collected to assess physical activity. The package also contains functions
7711 for making plots of accelerometer data and obtaining the summary of various
7712 information including daily monitor wear time and the mean monitor wear time
7713 during valid days. The revised package version 0.2-1 improved the functions
7714 regarding speed, robustness and add better support for time zones and daylight
7715 saving. In addition, several functions were added:
7717 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
7718 @item the @code{markPAI} can categorize physical activity intensity level based
7719 on user-defined cut-points of accelerometer counts.
7721 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
7722 @code{queryActigraph} functions.")
7723 (license license:gpl3+)))
7725 (define-public r-acc
7732 (uri (cran-uri "acc" version))
7734 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
7735 (build-system r-build-system)
7737 `(("r-circlize" ,r-circlize)
7739 ("r-ggplot2" ,r-ggplot2)
7740 ("r-iterators" ,r-iterators)
7741 ("r-mhsmm" ,r-mhsmm)
7742 ("r-nleqslv" ,r-nleqslv)
7743 ("r-physicalactivity" ,r-physicalactivity)
7745 ("r-r-utils" ,r-r-utils)
7747 ("r-rcpparmadillo" ,r-rcpparmadillo)
7748 ("r-rsqlite" ,r-rsqlite)
7750 (home-page "https://cran.r-project.org/web/packages/acc/")
7751 (synopsis "Exploring accelerometer data")
7753 "This package processes accelerometer data from uni-axial and tri-axial devices
7754 and generates data summaries. Also, includes functions to plot, analyze, and
7755 simulate accelerometer data.")
7756 (license license:gpl2+)))
7758 (define-public r-rbenchmark
7760 (name "r-rbenchmark")
7765 (uri (cran-uri "rbenchmark" version))
7767 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
7768 (build-system r-build-system)
7769 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
7770 (synopsis "Benchmarking routine for R")
7772 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
7773 and is intended to facilitate benchmarking of arbitrary R code. The library
7774 consists of just one function, benchmark, which is a simple wrapper around
7775 system.time. Given a specification of the benchmarking process (counts of
7776 replications, evaluation environment) and an arbitrary number of expressions,
7777 benchmark evaluates each of the expressions in the specified environment,
7778 replicating the evaluation as many times as specified, and returning the results
7779 conveniently wrapped into a data frame.")
7780 (license license:gpl2+)))
7782 (define-public r-mitools
7789 (uri (cran-uri "mitools" version))
7792 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
7793 (build-system r-build-system)
7794 (propagated-inputs `(("r-dbi" ,r-dbi)))
7795 (home-page "https://cran.r-project.org/web/packages/mitools/")
7796 (synopsis "Tools for multiple imputation of missing data")
7798 "This package provides tools to perform analyses and combine results from
7799 multiple-imputation datasets.")
7800 (license license:gpl2)))
7802 (define-public r-magick
7809 (uri (cran-uri "magick" version))
7812 "182b4wahkq9q0scn99mql4vm9fp92nja0r5yizc4x9rjl492ahd8"))))
7813 (build-system r-build-system)
7815 `(("imagemagick" ,imagemagick)
7818 `(("r-curl" ,r-curl)
7819 ("r-magrittr" ,r-magrittr)
7820 ("r-rcpp" ,r-rcpp)))
7822 `(("pkg-config" ,pkg-config)))
7823 (home-page "https://github.com/ropensci/magick")
7824 (synopsis "Advanced graphics and image-processing in R")
7826 "This package provides bindings to ImageMagick, a comprehensive image
7827 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
7828 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
7829 operations are vectorized via the Magick++ STL meaning they operate either on
7830 a single frame or a series of frames for working with layers, collages, or
7831 animation. In RStudio, images are automatically previewed when printed to the
7832 console, resulting in an interactive editing environment.")
7833 (license license:expat)))
7835 (define-public r-survey
7842 (uri (cran-uri "survey" version))
7845 "1f31dvh48gzzan13pdrwh84ls35x9116095i7mdrcbrhz809r8dy"))))
7846 (build-system r-build-system)
7848 `(("r-lattice" ,r-lattice)
7849 ("r-matrix" ,r-matrix)
7850 ("r-minqa" ,r-minqa)
7851 ("r-mitools" ,r-mitools)
7852 ("r-numderiv" ,r-numderiv)
7853 ("r-survival" ,r-survival)))
7854 (home-page "http://r-survey.r-forge.r-project.org/survey/")
7855 (synopsis "Analysis of complex survey samples")
7857 "This package provides tools for the analysis of complex survey samples.
7858 The provided features include: summary statistics, two-sample tests, rank
7859 tests, generalised linear models, cumulative link models, Cox models,
7860 loglinear models, and general maximum pseudolikelihood estimation for
7861 multistage stratified, cluster-sampled, unequally weighted survey samples;
7862 variances by Taylor series linearisation or replicate weights;
7863 post-stratification, calibration, and raking; two-phase subsampling designs;
7864 graphics; PPS sampling without replacement; principal components, and factor
7866 ;; Either version of the GPL.
7867 (license (list license:gpl2 license:gpl3))))
7869 (define-public r-gee
7876 (uri (cran-uri "gee" version))
7879 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
7880 (properties `((upstream-name . "gee")))
7881 (build-system r-build-system)
7883 `(("gfortran" ,gfortran)))
7884 (home-page "https://cran.r-project.org/web/packages/gee/")
7885 (synopsis "Generalized estimation equation solver")
7887 "This package provides a solver for generalized estimation equations.")
7888 (license license:gpl2)))
7890 (define-public r-tab
7897 (uri (cran-uri "tab" version))
7900 "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
7901 (properties `((upstream-name . "tab")))
7902 (build-system r-build-system)
7904 `(("r-dplyr" ,r-dplyr)
7906 ("r-knitr" ,r-knitr)
7908 ("r-survey" ,r-survey)
7909 ("r-survival" ,r-survival)
7910 ("r-xtable" ,r-xtable)))
7911 (home-page "https://cran.r-project.org/web/packages/tab/")
7912 (synopsis "Create summary tables for statistical reports")
7914 "This package contains functions for creating various types of summary
7915 tables, e.g. comparing characteristics across levels of a categorical variable
7916 and summarizing fitted generalized linear models, generalized estimating
7917 equations, and Cox proportional hazards models. Functions are available to
7918 handle data from simple random samples as well as complex surveys.")
7919 (license license:gpl3+)))
7921 (define-public r-dvmisc
7928 (uri (cran-uri "dvmisc" version))
7930 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
7931 (build-system r-build-system)
7933 `(("r-cubature" ,r-cubature)
7934 ("r-data-table" ,r-data-table)
7935 ("r-dplyr" ,r-dplyr)
7936 ("r-ggplot2" ,r-ggplot2)
7938 ("r-mvtnorm" ,r-mvtnorm)
7939 ("r-pracma" ,r-pracma)
7940 ("r-rbenchmark" ,r-rbenchmark)
7942 ("r-survey" ,r-survey)
7944 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
7945 (synopsis "Faster computation of common statistics and miscellaneous functions")
7947 "This package implements faster versions of base R functions (e.g. mean, standard
7948 deviation, covariance, weighted mean), mostly written in C++, along with
7949 miscellaneous functions for various purposes (e.g. create the histogram with
7950 fitted probability density function or probability mass function curve, create
7951 the body mass index groups, assess the linearity assumption in logistic
7953 (license license:gpl2)))
7955 (define-public r-accelerometry
7957 (name "r-accelerometry")
7962 (uri (cran-uri "accelerometry" version))
7964 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
7965 (build-system r-build-system)
7967 `(("r-dvmisc" ,r-dvmisc)
7968 ("r-rcpp" ,r-rcpp)))
7969 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
7970 (synopsis "Functions for processing accelerometer data")
7972 "This package provides a collection of functions that perform operations on
7973 time-series accelerometer data, such as identify the non-wear time, flag minutes
7974 that are part of an activity bout, and find the maximum 10-minute average count
7975 value. The functions are generally very flexible, allowing for a variety of
7976 algorithms to be implemented.")
7977 (license license:gpl3)))
7979 (define-public r-absim
7986 (uri (cran-uri "AbSim" version))
7988 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
7989 (properties `((upstream-name . "AbSim")))
7990 (build-system r-build-system)
7993 ("r-powerlaw" ,r-powerlaw)))
7994 (home-page "https://cran.r-project.org/web/packages/AbSim/")
7995 (synopsis "Time resolved simulations of antibody repertoires")
7997 "This package provides simulation methods for the evolution of antibody repertoires.
7998 The heavy and light chain variable region of both human and C57BL/6 mice can
7999 be simulated in a time-dependent fashion. Both single lineages using one set of
8000 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
8001 with an initial V-D-J recombination event, starting the first phylogenetic tree.
8002 Upon completion, the main loop of the algorithm begins, with each iteration
8003 representing one simulated time step. Various mutation events are possible at
8004 each time step, contributing to a diverse final repertoire.")
8005 (license license:gpl2)))
8007 (define-public r-quic
8014 (uri (cran-uri "QUIC" version))
8016 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
8017 (properties `((upstream-name . "QUIC")))
8018 (build-system r-build-system)
8019 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
8020 (synopsis "Regularized sparse inverse covariance matrix estimation")
8022 "This package implements the regularized Gaussian maximum likelihood
8023 estimation of the inverse of a covariance matrix. It uses Newton's method and
8024 coordinate descent to solve the regularized inverse covariance matrix
8025 estimation problem.")
8026 ;; The project home page states that the release is under GPLv3 or later.
8027 ;; The CRAN page only says GPL-3.
8028 (license license:gpl3+)))
8030 (define-public r-abundant
8037 (uri (cran-uri "abundant" version))
8039 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
8040 (build-system r-build-system)
8042 `(("r-quic" ,r-quic)))
8043 (home-page "https://cran.r-project.org/web/packages/abundant/")
8044 (synopsis "Abundant regression and high-dimensional principal fitted components")
8046 "This package provides tools to fit and predict with the high-dimensional
8047 principal fitted components model. This model is described by Cook, Forzani,
8048 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
8049 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
8050 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
8051 (license license:gpl2+)))
8053 (define-public r-ac3net
8060 (uri (cran-uri "Ac3net" version))
8062 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
8063 (properties `((upstream-name . "Ac3net")))
8064 (build-system r-build-system)
8066 `(("r-data-table" ,r-data-table)))
8067 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
8068 (synopsis "Inferring directional conservative causal core gene networks")
8069 (description "This package infers directional Conservative causal core
8070 (gene) networks (C3NET). This is a version of the algorithm C3NET with
8071 directional network.")
8072 (license license:gpl3+)))
8074 (define-public r-aca
8081 (uri (cran-uri "ACA" version))
8083 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
8084 (properties `((upstream-name . "ACA")))
8085 (build-system r-build-system)
8086 (home-page "https://cran.r-project.org/web/packages/ACA/")
8087 (synopsis "Abrupt change-point or aberration detection in point series")
8089 "This package offers an interactive function for the detection of breakpoints in
8091 ;; Any version of the GPL
8092 (license (list license:gpl2+ license:gpl3+))))
8094 (define-public r-acceptancesampling
8096 (name "r-acceptancesampling")
8101 (uri (cran-uri "AcceptanceSampling" version))
8103 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
8105 `((upstream-name . "AcceptanceSampling")))
8106 (build-system r-build-system)
8107 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
8108 (synopsis "Creation and evaluation of acceptance sampling plans")
8110 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
8111 acceptance sampling plans. Acceptance sampling is a methodology commonly used
8112 in quality control and improvement. International standards of acceptance
8113 sampling provide sampling plans for specific circumstances. The aim of this
8114 package is to provide an easy-to-use interface to visualize single, double or
8115 multiple sampling plans. In addition, methods have been provided to enable the
8116 user to assess sampling plans against pre-specified levels of performance, as
8117 measured by the probability of acceptance for a given level of quality in the
8119 (license license:gpl3+)))
8121 (define-public r-acclma
8128 (uri (cran-uri "ACCLMA" version))
8130 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
8131 (properties `((upstream-name . "ACCLMA")))
8132 (build-system r-build-system)
8133 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
8134 (synopsis "ACC & LMA graph plotting")
8136 "This package contains a function that imports data from a @acronym{CSV,
8137 Comma-Separated Values} file, or uses manually entered data from the format (x,
8138 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
8139 Curve} vs @acronym{LOI, Line of Independence} graph and
8140 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
8141 function is @code{plotLMA} (source file, header) that takes a data set and plots the
8142 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
8143 string) was passed, a manual data entry window is opened. The header parameter
8144 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
8145 a header row or not. The dataset should contain only one independent variable
8146 (x) and one dependent variable (y) and can contain a weight for each
8148 (license license:gpl2)))
8150 (define-public r-aspi
8157 (uri (cran-uri "aspi" version))
8159 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
8160 (build-system r-build-system)
8162 "https://cran.r-project.org/web/packages/aspi/")
8164 "Analysis of symmetry of parasitic infections")
8166 "This package provides tools for the analysis and visualization of bilateral
8167 asymmetry in parasitic infections.")
8168 (license license:gpl3+)))
8170 (define-public r-sandwich
8177 (uri (cran-uri "sandwich" version))
8180 "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv"))))
8181 (build-system r-build-system)
8183 `(("r-zoo" ,r-zoo)))
8184 (home-page "https://cran.r-project.org/web/packages/sandwich/")
8185 (synopsis "Robust Covariance Matrix Estimators")
8187 "This package provides model-robust standard error estimators for
8188 cross-sectional, time series, clustered, panel, and longitudinal data.")
8189 ;; Either version of the license.
8190 (license (list license:gpl2 license:gpl3))))
8192 (define-public r-th-data
8199 (uri (cran-uri "TH.data" version))
8202 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
8203 (properties `((upstream-name . "TH.data")))
8204 (build-system r-build-system)
8206 `(("r-mass" ,r-mass)
8207 ("r-survival" ,r-survival)))
8208 (home-page "https://cran.r-project.org/web/packages/TH.data/")
8209 (synopsis "Shared data sets")
8211 "This package contains supporting data sets that are used in other
8212 packages maintained by Torsten Hothorn.")
8213 (license license:gpl3)))
8215 (define-public r-multcomp
8222 (uri (cran-uri "multcomp" version))
8225 "14c2f10rz546w7ly5f4r6wnd07yj5gic38an17gxny1vf2nsff0b"))))
8226 (build-system r-build-system)
8228 `(("r-codetools" ,r-codetools)
8229 ("r-mvtnorm" ,r-mvtnorm)
8230 ("r-sandwich" ,r-sandwich)
8231 ("r-survival" ,r-survival)
8232 ("r-th-data" ,r-th-data)))
8233 (home-page "https://cran.r-project.org/web/packages/multcomp/")
8234 (synopsis "Simultaneous inference in general parametric models")
8236 "Simultaneous tests and confidence intervals for general linear
8237 hypotheses in parametric models, including linear, generalized linear, linear
8238 mixed effects, and survival models. The package includes demos reproducing
8239 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
8240 Hothorn, Westfall, 2010, CRC Press).")
8241 (license license:gpl2)))
8243 (define-public r-emmeans
8246 (version "1.4.3.01")
8250 (uri (cran-uri "emmeans" version))
8253 "16v5j31516nbqnj2zhgqvyp5yxd4zcs5zi0aspa5plr2qikvrkmg"))))
8254 (build-system r-build-system)
8256 `(("r-estimability" ,r-estimability)
8257 ("r-mvtnorm" ,r-mvtnorm)
8258 ("r-numderiv" ,r-numderiv)
8260 ("r-xtable" ,r-xtable)))
8261 (home-page "https://github.com/rvlenth/emmeans")
8262 (synopsis "Estimated marginal means, aka least-squares means")
8264 "This package provides tools to obtain @dfn{estimated marginal
8265 means} (EMMs) for many linear, generalized linear, and mixed models. It can
8266 be used to compute contrasts or linear functions of EMMs, trends, and
8267 comparisons of slopes.")
8268 ;; Either version of the license.
8269 (license (list license:gpl2 license:gpl3))))
8271 (define-public r-pwr
8278 (uri (cran-uri "pwr" version))
8281 "0r5g781lr677vp3zyhgmi7r68c87l8gd05l1s3ffnxgn5wf043sm"))))
8282 (build-system r-build-system)
8284 `(("r-knitr" ,r-knitr)))
8285 (home-page "https://github.com/heliosdrm/pwr")
8286 (synopsis "Basic functions for power analysis")
8288 "This package provides power analysis functions along the lines of
8290 (license license:gpl3+)))
8292 (define-public r-libcoin
8299 (uri (cran-uri "libcoin" version))
8302 "1cm9x1dlg9f7fh7n5nw3x4a7rl88c7ylrlc8x3rx4mq5w1j42x0a"))))
8303 (build-system r-build-system)
8304 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8305 (home-page "https://cran.r-project.org/web/packages/libcoin")
8306 (synopsis "Linear test statistics for permutation inference")
8308 "This package provides basic infrastructure for linear test statistics
8309 and permutation inference in the framework of Strasser and Weber (1999).")
8310 (license license:gpl2)))
8312 (define-public r-coin
8319 (uri (cran-uri "coin" version))
8322 "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx"))))
8323 (build-system r-build-system)
8325 `(("r-libcoin" ,r-libcoin)
8326 ("r-matrixstats" ,r-matrixstats)
8327 ("r-modeltools" ,r-modeltools)
8328 ("r-multcomp" ,r-multcomp)
8329 ("r-mvtnorm" ,r-mvtnorm)
8330 ("r-survival" ,r-survival)))
8331 (home-page "http://coin.r-forge.r-project.org")
8332 (synopsis "Conditional inference procedures in a permutation test framework")
8334 "This package provides conditional inference procedures for the general
8335 independence problem including two-sample, K-sample (non-parametric ANOVA),
8336 correlation, censored, ordered and multivariate problems.")
8337 (license license:gpl2)))
8339 (define-public r-bayesplot
8341 (name "r-bayesplot")
8346 (uri (cran-uri "bayesplot" version))
8349 "0sq0ajnm96hmlqf1cv5n2gshh3qdij4n1zbm7qrniz2q6b5aj342"))))
8350 (build-system r-build-system)
8352 `(("pandoc" ,ghc-pandoc)
8353 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
8355 `(("r-dplyr" ,r-dplyr)
8356 ("r-ggplot2" ,r-ggplot2)
8357 ("r-ggridges" ,r-ggridges)
8359 ("r-reshape2" ,r-reshape2)
8360 ("r-rlang" ,r-rlang)
8361 ("r-tibble" ,r-tibble)
8362 ("r-tidyselect" ,r-tidyselect)))
8363 (home-page "https://mc-stan.org/bayesplot")
8364 (synopsis "Plotting for Bayesian models")
8366 "This package provides plotting functions for posterior analysis, model
8367 checking, and MCMC diagnostics. The package is designed not only to provide
8368 convenient functionality for users, but also a common set of functions that
8369 can be easily used by developers working on a variety of R packages for
8370 Bayesian modeling.")
8371 (license license:gpl3+)))
8373 (define-public r-tmb
8380 (uri (cran-uri "TMB" version))
8383 "0lly12hdi99iklwr0vg9xkyhi038w4gncbf895qcwbndmqp0lx44"))))
8384 (properties `((upstream-name . "TMB")))
8385 (build-system r-build-system)
8387 `(("r-matrix" ,r-matrix)
8388 ("r-rcppeigen" ,r-rcppeigen)))
8389 (home-page "http://tmb-project.org")
8390 (synopsis "Template model builder: a general random effect tool")
8392 "With this tool, a user should be able to quickly implement complex
8393 random effect models through simple C++ templates. The package combines
8394 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
8395 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
8396 from R) to obtain an efficient implementation of the applied Laplace
8397 approximation with exact derivatives. Key features are: Automatic sparseness
8398 detection, parallelism through BLAS and parallel user templates.")
8399 (license license:gpl2)))
8401 (define-public r-sjstats
8408 (uri (cran-uri "sjstats" version))
8410 (base32 "0gagqbcmimlvxhpjkmd3s17mbrz5n937qksca1hvm6kj4rk37hzb"))))
8411 (build-system r-build-system)
8413 `(("r-bayestestr" ,r-bayestestr)
8414 ("r-broom" ,r-broom)
8415 ("r-dplyr" ,r-dplyr)
8416 ("r-effectsize" ,r-effectsize)
8417 ("r-emmeans" ,r-emmeans)
8418 ("r-insight" ,r-insight)
8420 ("r-magrittr" ,r-magrittr)
8422 ("r-modelr" ,r-modelr)
8423 ("r-parameters" ,r-parameters)
8424 ("r-performance" ,r-performance)
8425 ("r-purrr" ,r-purrr)
8426 ("r-rlang" ,r-rlang)
8427 ("r-sjlabelled" ,r-sjlabelled)
8428 ("r-sjmisc" ,r-sjmisc)
8429 ("r-tidyr" ,r-tidyr)))
8430 (home-page "https://github.com/strengejacke/sjstats")
8431 (synopsis "Functions for common statistical computations")
8433 "This package provides a collection of convenient functions for common
8434 statistical computations, which are not directly provided by R's @code{base}
8435 or @code{stats} packages. This package aims at providing, first, shortcuts
8436 for statistical measures, which otherwise could only be calculated with
8437 additional effort. Second, these shortcut functions are generic, and can be
8438 applied not only to vectors, but also to other objects as well. The focus of
8439 most functions lies on summary statistics or fit measures for regression
8440 models, including generalized linear models, mixed effects models and Bayesian
8442 (license license:gpl3)))
8444 (define-public r-glmmtmb
8451 (uri (cran-uri "glmmTMB" version))
8454 "035hkywa37bz555fv6znxd4hfcs5w884365wfnwk4jx5vann4vvb"))))
8455 (properties `((upstream-name . "glmmTMB")))
8456 (build-system r-build-system)
8458 `(("r-lme4" ,r-lme4)
8459 ("r-matrix" ,r-matrix)
8461 ("r-rcppeigen" ,r-rcppeigen)
8464 `(("r-knitr" ,r-knitr))) ; for vignettes
8465 (home-page "https://github.com/glmmTMB")
8466 (synopsis "Generalized linear mixed models")
8468 "Fit linear and generalized linear mixed models with various extensions,
8469 including zero-inflation. The models are fitted using maximum likelihood
8470 estimation via the Template Model Builder. Random effects are assumed to be
8471 Gaussian on the scale of the linear predictor and are integrated out using the
8472 Laplace approximation. Gradients are calculated using automatic
8474 (license license:agpl3+)))
8476 (define-public r-bayestestr
8478 (name "r-bayestestr")
8483 (uri (cran-uri "bayestestR" version))
8486 "01kqvky1ndd1q64rzmqh5yfzz36ci8yhy4w16gjnw4c257ikhvd8"))))
8487 (properties `((upstream-name . "bayestestR")))
8488 (build-system r-build-system)
8490 `(("r-insight" ,r-insight)))
8491 (home-page "https://github.com/easystats/bayestestR")
8492 (synopsis "Describe Bayesian models and posterior distributions")
8494 "This package provides utilities to understand and describe posterior
8495 distributions and Bayesian models. It includes point-estimates such as
8496 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
8497 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
8498 ROPE percentage and pd).")
8499 (license license:gpl3)))
8501 (define-public r-performance
8503 (name "r-performance")
8508 (uri (cran-uri "performance" version))
8511 "1164585ywbnrcy7an57kifh2gdb6g08z9pxw75ywqdcfyd51i3dz"))))
8512 (build-system r-build-system)
8514 `(("r-bayestestr" ,r-bayestestr)
8515 ("r-insight" ,r-insight)))
8516 (home-page "https://easystats.github.io/performance/")
8517 (synopsis "Assessment of regression models performance")
8519 "This package provides utilities for computing measures to assess model
8520 quality, which are not directly provided by R's @code{base} or @code{stats}
8521 packages. These include e.g. measures like r-squared, intraclass correlation
8522 coefficient, root mean squared error or functions to check models for
8523 overdispersion, singularity or zero-inflation and more. Functions apply to a
8524 large variety of regression models, including generalized linear models, mixed
8525 effects models and Bayesian models.")
8526 (license license:gpl3)))
8528 (define-public r-ggeffects
8530 (name "r-ggeffects")
8535 (uri (cran-uri "ggeffects" version))
8538 "1djz82xww86h8f33m2vm40lliicppgyhm6hyn3h6rzrqjrlrsmdw"))))
8539 (build-system r-build-system)
8541 `(("r-insight" ,r-insight)
8542 ("r-magrittr" ,r-magrittr)
8544 ("r-purrr" ,r-purrr)
8545 ("r-sjlabelled" ,r-sjlabelled)
8546 ("r-sjmisc" ,r-sjmisc)))
8547 (home-page "https://github.com/strengejacke/ggeffects")
8548 (synopsis "Create tidy data frames of marginal effects for ggplot")
8550 "This package provides tools to compute marginal effects from statistical
8551 models and return the result as tidy data frames. These data frames are ready
8552 to use with the @code{ggplot2} package. Marginal effects can be calculated
8553 for many different models. Interaction terms, splines and polynomial terms
8554 are also supported. The two main functions are @code{ggpredict()} and
8555 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
8556 results using @code{ggplot2}.")
8557 (license license:gpl3)))
8559 (define-public r-effectsize
8561 (name "r-effectsize")
8566 (uri (cran-uri "effectsize" version))
8569 "0dd7nbkg8kmash9zh2gg08m7hbpsqwpkvkdhinfqkbg5d0jinhq8"))))
8570 (properties `((upstream-name . "effectsize")))
8571 (build-system r-build-system)
8573 `(("r-bayestestr" ,r-bayestestr)
8574 ("r-insight" ,r-insight)
8575 ("r-parameters" ,r-parameters)))
8576 (home-page "https://github.com/easystats/effectsize")
8577 (synopsis "Indices of effect size and standardized parameters")
8579 "This package provides utilities to work with indices of effect size and
8580 standardized parameters for a wide variety of models, allowing computation and
8581 conversion of indices such as Cohen's d, r, odds, etc.")
8582 (license license:gpl3)))
8584 (define-public r-sjplot
8591 (uri (cran-uri "sjPlot" version))
8593 (base32 "16721a5006q0gv45zjcwnkykxhjkzpq5n35vhik0g0ixgm3a2vci"))))
8594 (properties `((upstream-name . "sjPlot")))
8595 (build-system r-build-system)
8597 `(("r-bayestestr" ,r-bayestestr)
8598 ("r-dplyr" ,r-dplyr)
8599 ("r-effectsize" ,r-effectsize)
8600 ("r-forcats" ,r-forcats)
8601 ("r-ggeffects" ,r-ggeffects)
8602 ("r-ggplot2" ,r-ggplot2)
8603 ("r-insight" ,r-insight)
8604 ("r-knitr" ,r-knitr)
8606 ("r-parameters" ,r-parameters)
8607 ("r-performance" ,r-performance)
8608 ("r-purrr" ,r-purrr)
8609 ("r-rlang" ,r-rlang)
8610 ("r-scales" ,r-scales)
8611 ("r-sjlabelled" ,r-sjlabelled)
8612 ("r-sjmisc" ,r-sjmisc)
8613 ("r-sjstats" ,r-sjstats)
8614 ("r-tidyr" ,r-tidyr)))
8615 (home-page "https://strengejacke.github.io/sjPlot/")
8616 (synopsis "Data visualization for statistics in social science")
8618 "This package represents a collection of plotting and table output
8619 functions for data visualization. Results of various statistical
8620 analyses (that are commonly used in social sciences) can be visualized using
8621 this package, including simple and cross tabulated frequencies, histograms,
8622 box plots, (generalized) linear models, mixed effects models, principal
8623 component analysis and correlation matrices, cluster analyses, scatter plots,
8624 stacked scales, effects plots of regression models (including interaction
8625 terms) and much more. This package supports labelled data.")
8626 (license license:gpl3)))
8628 (define-public r-ini
8635 (uri (cran-uri "ini" version))
8638 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
8639 (build-system r-build-system)
8640 (home-page "https://github.com/dvdscripter/ini")
8641 (synopsis "Read and write configuration files")
8643 "This package provides tools to parse simple @code{.ini} configuration
8644 files to an structured list. Users can manipulate this resulting list with
8645 @code{lapply()} functions. This same structured list can be used to write
8646 back to file after modifications.")
8647 (license license:gpl3)))
8656 (uri (cran-uri "gh" version))
8659 "1bc9bn1078s664hc806dh0y1ncxif77q479rfmxfir9z7hwaz7yy"))))
8660 (build-system r-build-system)
8665 ("r-jsonlite" ,r-jsonlite)))
8666 (home-page "https://github.com/r-lib/gh#readme")
8667 (synopsis "Access the GitHub API via R")
8669 "This package provides a minimal R client to access the GitHub API.")
8670 (license license:expat)))
8679 (uri (cran-uri "fs" version))
8682 "1g26rgx13dzigp2vrlld6h28q33lwbax97zvwdrq2pc3iz54v4yn"))))
8683 (build-system r-build-system)
8685 `(("r-rcpp" ,r-rcpp)))
8687 `(("pkg-config" ,pkg-config)))
8688 (home-page "https://fs.r-lib.org")
8689 (synopsis "Cross-platform file system operations based on libuv")
8691 "This package provides a cross-platform interface to file system
8692 operations, built on top of the libuv C library.")
8693 (license license:gpl3)))
8695 (define-public r-clisymbols
8697 (name "r-clisymbols")
8702 (uri (cran-uri "clisymbols" version))
8705 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
8706 (build-system r-build-system)
8707 (home-page "https://github.com/gaborcsardi/clisymbols")
8708 (synopsis "Unicode symbols at the R prompt")
8710 "This package provides a small subset of Unicode symbols, that are useful
8711 when building command line applications. They fall back to alternatives on
8712 terminals that do not support Unicode.")
8713 (license license:expat)))
8715 (define-public r-usethis
8722 (uri (cran-uri "usethis" version))
8725 "07an5wbikilg7cb3q6x5aykw8dfqnjrc3wpfb7gjmy0d9fh20fcy"))))
8726 (build-system r-build-system)
8728 `(("r-clipr" ,r-clipr)
8729 ("r-clisymbols" ,r-clisymbols)
8730 ("r-crayon" ,r-crayon)
8735 ("r-git2r" ,r-git2r)
8737 ("r-purrr" ,r-purrr)
8738 ("r-rlang" ,r-rlang)
8739 ("r-rprojroot" ,r-rprojroot)
8740 ("r-rstudioapi" ,r-rstudioapi)
8741 ("r-whisker" ,r-whisker)
8742 ("r-withr" ,r-withr)
8743 ("r-yaml" ,r-yaml)))
8744 (home-page "https://github.com/r-lib/usethis")
8745 (synopsis "Automate R package and project setup")
8747 "This package helps you to automate R package and project setup tasks
8748 that are otherwise performed manually. This includes setting up unit testing,
8749 test coverage, continuous integration, Git, GitHub integration, licenses,
8750 Rcpp, RStudio projects, and more.")
8751 (license license:gpl3)))
8753 (define-public r-sessioninfo
8755 (name "r-sessioninfo")
8760 (uri (cran-uri "sessioninfo" version))
8763 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
8764 (build-system r-build-system)
8767 ("r-withr" ,r-withr)))
8768 (home-page "https://github.com/r-lib/sessioninfo#readme")
8769 (synopsis "R session information")
8771 "This package provides tools to query and print information about the
8772 current R session. It is similar to @code{utils::sessionInfo()}, but includes
8773 more information about packages, and where they were installed from.")
8774 (license license:gpl2)))
8776 (define-public r-remotes
8783 (uri (cran-uri "remotes" version))
8786 "19v8dmnk9l4i9m64p7zgmj7y1vhnnwhi5kyn0k5d034zzkvchi49"))))
8787 (build-system r-build-system)
8788 (home-page "https://github.com/r-lib/remotes#readme")
8789 (synopsis "R package installation from remote repositories")
8791 "Download and install R packages stored in GitHub, BitBucket, or plain
8792 subversion or git repositories. This package is a lightweight replacement of
8793 the @code{install_*} functions in the @code{devtools} package. Indeed most of
8794 the code was copied over from @code{devtools}.")
8795 (license license:gpl2+)))
8797 (define-public r-xopen
8804 (uri (cran-uri "xopen" version))
8807 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
8808 (build-system r-build-system)
8810 `(("r-processx" ,r-processx)))
8811 (home-page "https://github.com/r-lib/xopen#readme")
8812 (synopsis "Open system files, URLs, anything")
8814 "This package provides a cross-platform solution to open files,
8815 directories or URLs with their associated programs.")
8816 (license license:expat)))
8818 (define-public r-rcmdcheck
8820 (name "r-rcmdcheck")
8825 (uri (cran-uri "rcmdcheck" version))
8828 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
8829 (build-system r-build-system)
8831 `(("r-callr" ,r-callr)
8833 ("r-crayon" ,r-crayon)
8835 ("r-digest" ,r-digest)
8836 ("r-pkgbuild" ,r-pkgbuild)
8837 ("r-prettyunits" ,r-prettyunits)
8839 ("r-rprojroot" ,r-rprojroot)
8840 ("r-sessioninfo" ,r-sessioninfo)
8841 ("r-withr" ,r-withr)
8842 ("r-xopen" ,r-xopen)))
8843 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
8844 (synopsis "Run R CMD check from R and capture results")
8846 "Run @code{R CMD check} from R programmatically, and capture the results
8847 of the individual checks.")
8848 (license license:expat)))
8850 (define-public r-rapportools
8852 (name "r-rapportools")
8857 (uri (cran-uri "rapportools" version))
8860 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
8861 (build-system r-build-system)
8863 `(("r-pander" ,r-pander)
8865 ("r-reshape" ,r-reshape)))
8866 (home-page "https://cran.r-project.org/web/packages/rapportools/")
8867 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
8869 "This package provides helper functions that act as wrappers to more
8870 advanced statistical methods with the advantage of having sane defaults for
8872 (license license:agpl3+)))
8874 (define-public r-pander
8881 (uri (cran-uri "pander" version))
8884 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
8885 (build-system r-build-system)
8887 `(("r-digest" ,r-digest)
8888 ("r-rcpp" ,r-rcpp)))
8889 (home-page "https://rapporter.github.io/pander")
8890 (synopsis "Render R objects into Pandoc's markdown")
8892 "The main aim of the pander R package is to provide a minimal and easy
8893 tool for rendering R objects into Pandoc's markdown. The package is also
8894 capable of exporting/converting complex Pandoc documents (reports) in various
8896 ;; This package is licensed under either the AGPLv3+ or the very rarely
8898 (license license:agpl3+)))
8900 (define-public r-summarytools
8902 (name "r-summarytools")
8907 (uri (cran-uri "summarytools" version))
8910 "1n695baz56mg4f13xjjadfq0xalw5xsn6xicil0yap5hgi8fsr3a"))))
8911 (build-system r-build-system)
8913 `(("r-checkmate" ,r-checkmate)
8914 ("r-dplyr" ,r-dplyr)
8915 ("r-htmltools" ,r-htmltools)
8916 ("r-lubridate" ,r-lubridate)
8917 ("r-magick" ,r-magick)
8918 ("r-matrixstats" ,r-matrixstats)
8919 ("r-pander" ,r-pander)
8921 ("r-rapportools" ,r-rapportools)
8922 ("r-rcurl" ,r-rcurl)
8923 ("r-tibble" ,r-tibble)
8924 ("r-tidyr" ,r-tidyr)))
8925 (home-page "https://github.com/dcomtois/summarytools")
8926 (synopsis "Tools to quickly and neatly summarize data")
8928 "This package provides tools for data frame summaries, cross-tabulations,
8929 weight-enabled frequency tables and common univariate statistics in concise
8930 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
8931 good point-of-entry for exploring data, both for experienced and new R
8933 (license license:gpl2)))
8935 (define-public r-lsei
8942 (uri (cran-uri "lsei" version))
8945 "1xl06fb3is744pxlh42wx5hn1h0ab1k31wnmsmh0524kxzcyp0a7"))))
8946 (build-system r-build-system)
8948 `(("gfortran" ,gfortran)))
8949 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
8950 (synopsis "Solve regression problems under equality/inequality constraints")
8952 "It contains functions that solve least squares linear regression
8953 problems under linear equality/inequality constraints. Functions for solving
8954 quadratic programming problems are also available, which transform such
8955 problems into least squares ones first.")
8956 (license license:gpl2+)))
8958 (define-public r-npsurv
8965 (uri (cran-uri "npsurv" version))
8968 "1wq4c9yfha5azjhrn40iiqkshmvh611sa90jp3lh82n4bl9zfk20"))))
8969 (build-system r-build-system)
8971 `(("r-lsei" ,r-lsei)))
8972 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
8973 (synopsis "Nonparametric survival analysis")
8975 "This package contains functions for non-parametric survival analysis of
8976 exact and interval-censored observations.")
8977 (license license:gpl2+)))
8979 (define-public r-clusteval
8981 (name "r-clusteval")
8986 (uri (cran-uri "clusteval" version))
8989 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
8990 (build-system r-build-system)
8992 `(("r-mvtnorm" ,r-mvtnorm)
8993 ("r-rcpp" ,r-rcpp)))
8994 (home-page "https://cran.r-project.org/web/packages/clusteval/")
8995 (synopsis "Evaluation of clustering algorithms")
8997 "This R package provides a suite of tools to evaluate clustering
8998 algorithms, clusterings, and individual clusters.")
8999 (license license:expat)))
9001 (define-public r-tweedie
9008 (uri (cran-uri "tweedie" version))
9011 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
9012 (build-system r-build-system)
9013 (native-inputs `(("gfortran" ,gfortran)))
9014 (home-page "https://cran.r-project.org/web/packages/tweedie/")
9015 (synopsis "Evaluation of Tweedie exponential family models")
9017 "Maximum likelihood computations for Tweedie families, including the
9018 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
9019 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
9020 and related methods.")
9021 (license license:gpl2+)))
9023 (define-public r-rcppgsl
9030 (uri (cran-uri "RcppGSL" version))
9032 (base32 "0cnw2k7cfqrm79r6j283aybflxig80x4n4rjkfp2317wf10mrsa5"))))
9033 (properties `((upstream-name . "RcppGSL")))
9034 (build-system r-build-system)
9036 `(("r-rcpp" ,r-rcpp)
9039 `(("r-knitr" ,r-knitr))) ; for vignettes
9040 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
9041 (synopsis "Rcpp integration for GSL vectors and matrices")
9043 "The GNU Scientific Library (or GSL) is a collection of numerical
9044 routines for scientific computing. It is particularly useful for C and C++
9045 programs as it provides a standard C interface to a wide range of mathematical
9046 routines. There are over 1000 functions in total with an extensive test
9047 suite. The RcppGSL package provides an easy-to-use interface between GSL data
9048 structures and R using concepts from Rcpp which is itself a package that eases
9049 the interfaces between R and C++.")
9050 (license license:gpl2+)))
9052 (define-public r-mvabund
9059 (uri (cran-uri "mvabund" version))
9062 "0la935gsiryfc0zixxr1dqj0av271x96pqxbi3bp6dksbw5gm68k"))))
9063 (build-system r-build-system)
9065 `(("r-mass" ,r-mass)
9067 ("r-rcppgsl" ,r-rcppgsl)
9068 ("r-statmod" ,r-statmod)
9069 ("r-tweedie" ,r-tweedie)))
9070 (home-page "https://cran.r-project.org/web/packages/mvabund/")
9071 (synopsis "Statistical methods for analysing multivariate abundance data")
9073 "This package provides a set of tools for displaying, modeling and
9074 analysing multivariate abundance data in community ecology.")
9075 (license license:lgpl2.1+)))
9077 (define-public r-afex
9084 (uri (cran-uri "afex" version))
9087 "0h3p1svgk1ap3lj08fi8nzdb3710h99bv150krf1x8wci1a0r1if"))))
9088 (build-system r-build-system)
9092 ("r-lmertest" ,r-lmertest)
9093 ("r-pbkrtest" ,r-pbkrtest)
9094 ("r-reshape2" ,r-reshape2)))
9095 (home-page "https://afex.singmann.science/")
9096 (synopsis "Analysis of factorial experiments")
9098 "This package provides convenience functions for analyzing factorial
9099 experiments using ANOVA or mixed models.")
9100 (license license:gpl2+)))
9102 (define-public r-lmertest
9109 (uri (cran-uri "lmerTest" version))
9112 "0r2vvs3nl6p8xla3gd943khb4ixp0alvspqpnz2y6n3wk8zgh3jj"))))
9113 (properties `((upstream-name . "lmerTest")))
9114 (build-system r-build-system)
9116 `(("r-ggplot2" ,r-ggplot2)
9119 ("r-numderiv" ,r-numderiv)))
9120 (home-page "https://github.com/runehaubo/lmerTestR")
9121 (synopsis "Tests in linear mixed effects models")
9123 "This package provides p-values in type I, II or III anova and summary
9124 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
9125 method. A Kenward-Roger method is also available via the @code{pbkrtest}
9126 package. Model selection methods include step, drop1 and anova-like tables
9127 for random effects (ranova). Methods for Least-Square means (LS-means) and
9128 tests of linear contrasts of fixed effects are also available.")
9129 (license license:gpl2+)))
9131 (define-public r-r2glmm
9138 (uri (cran-uri "r2glmm" version))
9141 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
9142 (build-system r-build-system)
9144 `(("r-afex" ,r-afex)
9145 ("r-data-table" ,r-data-table)
9146 ("r-dplyr" ,r-dplyr)
9147 ("r-ggplot2" ,r-ggplot2)
9148 ("r-gridextra" ,r-gridextra)
9149 ("r-lmertest" ,r-lmertest)
9151 ("r-matrix" ,r-matrix)
9153 ("r-pbkrtest" ,r-pbkrtest)))
9154 (home-page "https://github.com/bcjaeger/r2glmm")
9155 (synopsis "Compute R squared for mixed (multilevel) models")
9157 "This package computes model and semi partial R squared with confidence
9158 limits for the linear and generalized linear mixed model (LMM and GLMM). The
9159 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
9160 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
9162 (license license:gpl2)))
9164 (define-public r-weights
9171 (uri (cran-uri "weights" version))
9174 "0186bfpkhxngrshac6bpg37alp6slwhwd43inrm8hqg0vhpfgc4c"))))
9175 (build-system r-build-system)
9177 `(("r-gdata" ,r-gdata)
9178 ("r-hmisc" ,r-hmisc)
9179 ("r-mice" ,r-mice)))
9181 "https://cran.r-project.org/web/packages/weights/")
9182 (synopsis "Weighting and weighted statistics")
9183 (description "This package Provides a variety of functions for producing
9184 simple weighted statistics, such as weighted Pearson's correlations, partial
9185 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
9186 includes some software for quickly recoding survey data and plotting point
9187 estimates from interaction terms in regressions (and multiply imputed
9188 regressions). NOTE: Weighted partial correlation calculations pulled to
9190 (license license:gpl2+)))
9192 (define-public r-rcppannoy
9194 (name "r-rcppannoy")
9199 (uri (cran-uri "RcppAnnoy" version))
9202 "1wiigx5g5788j6lyc3f6bs1rsvc4alyc3052g35hxl1giinxmhn4"))))
9203 (properties `((upstream-name . "RcppAnnoy")))
9204 (build-system r-build-system)
9206 `(("r-rcpp" ,r-rcpp)))
9208 `(("r-knitr" ,r-knitr))) ; for vignettes
9209 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
9210 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
9212 "Annoy is a small C++ library for Approximate Nearest Neighbors written
9213 for efficient memory usage as well an ability to load from and save to disk.
9214 This package provides an R interface.")
9215 ;; Annoy is released under ASL 2.0, but this wrapper is released under
9217 (license (list license:gpl2+ license:asl2.0))))
9219 (define-public r-rcpphnsw
9226 (uri (cran-uri "RcppHNSW" version))
9229 "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv"))))
9230 (properties `((upstream-name . "RcppHNSW")))
9231 (build-system r-build-system)
9232 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9233 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
9234 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
9236 "Hnswlib is a C++ library for approximate nearest neighbors. This
9237 package provides a minimal R interface by relying on the Rcpp package.")
9238 ;; hnswlib is released under Version 2.0 of the Apache License.
9239 (license (list license:gpl3 license:asl2.0))))
9241 (define-public r-rcppparallel
9243 (name "r-rcppparallel")
9248 (uri (cran-uri "RcppParallel" version))
9251 "0p13f2mywjr7gmskf8ri4y8p5yr1bvr4xrpw2w11vdvafwz1vcia"))))
9252 (properties `((upstream-name . "RcppParallel")))
9253 (build-system r-build-system)
9254 (home-page "http://rcppcore.github.io/RcppParallel")
9255 (synopsis "Parallel programming tools for Rcpp")
9257 "This package provides high level functions for parallel programming with
9258 Rcpp. For example, the @code{parallelFor()} function can be used to convert
9259 the work of a standard serial @code{for} loop into a parallel one and the
9260 @code{parallelReduce()} function can be used for accumulating aggregates or
9262 (license license:gpl2)))
9264 (define-public r-ncdf4
9271 (uri (cran-uri "ncdf4" version))
9274 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
9275 (build-system r-build-system)
9277 `(("netcdf" ,netcdf)
9279 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
9280 (synopsis "R interface to Unidata netCDF format data files")
9282 "This package provides a high-level R interface to data files written
9283 using Unidata's netCDF library (version 4 or earlier), which are binary data
9284 files that are portable across platforms and include metadata information in
9285 addition to the data sets. Using this package, netCDF files can be opened and
9286 data sets read in easily. It is also easy to create new netCDF dimensions,
9287 variables, and files, in either version 3 or 4 format, and manipulate existing
9289 (license license:gpl3+)))
9291 (define-public r-biocmanager
9293 (name "r-biocmanager")
9298 (uri (cran-uri "BiocManager" version))
9300 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
9301 (properties `((upstream-name . "BiocManager")))
9302 (build-system r-build-system)
9303 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
9304 (synopsis "Access the Bioconductor project package repository")
9306 "This package provides a convenient tool to install and update
9307 Bioconductor packages.")
9308 (license license:artistic2.0)))
9310 (define-public r-rgl
9313 (version "0.100.30")
9317 (uri (cran-uri "rgl" version))
9320 "0rzqzskcwf2ah4yr62x5rjwf7yh90d43h39gk7jmfc5lc08zaxc5"))))
9321 (build-system r-build-system)
9323 `(("pkg-config" ,pkg-config)))
9325 `(("freetype" ,freetype)
9329 ("ghc-pandoc" ,ghc-pandoc)
9332 `(("r-crosstalk" ,r-crosstalk)
9333 ("r-htmltools" ,r-htmltools)
9334 ("r-htmlwidgets" ,r-htmlwidgets)
9335 ("r-jsonlite" ,r-jsonlite)
9336 ("r-knitr" ,r-knitr)
9337 ("r-magrittr" ,r-magrittr)
9338 ("r-manipulatewidget" ,r-manipulatewidget)
9339 ("r-shiny" ,r-shiny)))
9340 (home-page "https://r-forge.r-project.org/projects/rgl/")
9341 (synopsis "3D visualization using OpenGL")
9343 "This package provides medium to high level functions for 3D interactive graphics,
9344 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
9345 as functions for constructing representations of geometric
9346 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
9347 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
9348 image formats, including PNG, Postscript, SVG, PGF.")
9349 ;; Any version of the GPL.
9350 (license (list license:gpl2+ license:gpl3+))))
9352 (define-public r-multicool
9354 (name "r-multicool")
9359 (uri (cran-uri "multicool" version))
9362 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
9363 (build-system r-build-system)
9364 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9365 (home-page "https://cran.r-project.org/web/packages/multicool/")
9366 (synopsis "Permutations of multisets in cool-lex order")
9368 "This package provides a set of tools to permute multisets without loops
9369 or hash tables and to generate integer partitions. Cool-lex order is similar
9370 to colexicographical order.")
9371 (license license:gpl2)))
9373 (define-public r-misc3d
9380 (uri (cran-uri "misc3d" version))
9383 "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
9384 (build-system r-build-system)
9385 (home-page "https://cran.r-project.org/web/packages/misc3d/")
9386 (synopsis "Miscellaneous 3D Plots")
9388 "This package provides a collection of miscellaneous 3d plots, including
9390 ;; Any version of the GPL.
9391 (license (list license:gpl2+ license:gpl3+))))
9400 (uri (cran-uri "ks" version))
9402 (base32 "0hcccjfqnzdxkmnfzq8c5a7yhc138azwyl7rp29d1vl1jawwrwfq"))))
9403 (build-system r-build-system)
9406 ("r-kernlab" ,r-kernlab)
9407 ("r-kernsmooth" ,r-kernsmooth)
9408 ("r-matrix" ,r-matrix)
9409 ("r-mclust" ,r-mclust)
9411 ("r-multicool" ,r-multicool)
9412 ("r-mvtnorm" ,r-mvtnorm)))
9413 (home-page "http://www.mvstat.net/tduong/")
9414 (synopsis "Kernel smoothing")
9416 "This package provides kernel smoothers for univariate and multivariate
9417 data, including density functions, density derivatives, cumulative
9418 distributions, modal clustering, discriminant analysis, and two-sample
9419 hypothesis testing.")
9420 ;; Either version of the GPL.
9421 (license (list license:gpl2 license:gpl3))))
9423 (define-public r-feature
9430 (uri (cran-uri "feature" version))
9433 "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
9434 (build-system r-build-system)
9437 ("r-misc3d" ,r-misc3d)
9439 (home-page "http://www.mvstat.net/tduong/")
9440 (synopsis "Inferential feature significance for kernel density estimation")
9442 "The feature package contains functions to display and compute kernel
9443 density estimates, significant gradient and significant curvature regions.
9444 Significant gradient and/or curvature regions often correspond to significant
9445 features (e.g. local modes).")
9446 ;; Either version of the GPL.
9447 (license (list license:gpl2 license:gpl3))))
9449 (define-public r-arm
9456 (uri (cran-uri "arm" version))
9459 "0vvp90jygajd6ydky57z66wqjq9msfbl88irj5jbsray574mh4bg"))))
9460 (build-system r-build-system)
9462 `(("r-abind" ,r-abind)
9466 ("r-matrix" ,r-matrix)
9467 ("r-nlme" ,r-nlme)))
9468 (home-page "https://cran.r-project.org/web/packages/arm/")
9469 (synopsis "Data analysis using regression and multilevel/hierarchical models")
9471 "This package provides functions to accompany A. Gelman and J. Hill,
9472 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
9473 University Press, 2007.")
9474 (license license:gpl3+)))
9476 (define-public r-circular
9483 (uri (cran-uri "circular" version))
9486 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
9487 (build-system r-build-system)
9489 `(("r-boot" ,r-boot)
9490 ("r-mvtnorm" ,r-mvtnorm)))
9492 `(("gfortran" ,gfortran)))
9493 (home-page "https://cran.r-project.org/web/packages/circular/")
9494 (synopsis "Circular statistics")
9496 "This package provides tools for circular statistics, from \"Topics in
9497 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
9499 (license license:gpl2+)))
9501 (define-public r-activity
9508 (uri (cran-uri "activity" version))
9511 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
9512 (build-system r-build-system)
9514 `(("r-circular" ,r-circular)
9515 ("r-insol" ,r-insol)
9516 ("r-pbapply" ,r-pbapply)))
9517 (home-page "https://cran.r-project.org/web/packages/activity/")
9518 (synopsis "Animal activity statistics")
9520 "This package provides functions to fit kernel density functions to
9521 animal activity time data; plot activity distributions; quantify overall
9522 levels of activity; statistically compare activity metrics through
9523 bootstrapping; and evaluate variation in linear variables with time (or other
9524 circular variables).")
9525 (license license:gpl3)))
9527 (define-public r-ouch
9534 (uri (cran-uri "ouch" version))
9537 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
9538 (build-system r-build-system)
9539 (propagated-inputs `(("r-subplex" ,r-subplex)))
9540 (home-page "http://kingaa.github.io/ouch/")
9541 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
9543 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
9544 for evolution along a phylogenetic tree.")
9545 (license license:gpl2+)))
9547 (define-public r-fmsb
9554 (uri (cran-uri "fmsb" version))
9557 "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
9558 (build-system r-build-system)
9559 (home-page "http://minato.sip21c.org/msb/")
9560 (synopsis "Functions for medical statistics book with demographic data")
9562 "This package provides several utility functions for the book entitled
9563 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
9564 Japan, 2007) with Japanese demographic data and some demographic analysis
9565 related functions.")
9566 (license license:gpl2+)))
9568 (define-public r-stabledist
9570 (name "r-stabledist")
9575 (uri (cran-uri "stabledist" version))
9578 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
9579 (build-system r-build-system)
9580 (home-page "http://www.rmetrics.org")
9581 (synopsis "Stable distribution functions")
9583 "This package provides density, probability and quantile functions, and
9584 random number generation for (skew) stable distributions, using the
9585 parametrizations of Nolan.")
9586 (license license:gpl2+)))
9588 (define-public r-gsl
9595 (uri (cran-uri "gsl" version))
9598 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
9599 (build-system r-build-system)
9602 (home-page "https://cran.r-project.org/web/packages/gsl")
9603 (synopsis "Wrapper for the GNU Scientific Library")
9605 "This package provides an R wrapper for the special functions and quasi
9606 random number generators of the GNU Scientific Library.")
9607 (license license:gpl2+)))
9609 (define-public r-adgoftest
9611 (name "r-adgoftest")
9616 (uri (cran-uri "ADGofTest" version))
9619 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
9620 (properties `((upstream-name . "ADGofTest")))
9621 (build-system r-build-system)
9622 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
9623 (synopsis "Anderson-Darling GoF test")
9625 "This package provides an implementation of the Anderson-Darling GoF test
9626 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
9627 Anderson-Darling Distribution\".")
9628 ;; Any version of the GPL.
9629 (license license:gpl3+)))
9631 (define-public r-softimpute
9633 (name "r-softimpute")
9638 (uri (cran-uri "softImpute" version))
9641 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
9642 (properties `((upstream-name . "softImpute")))
9643 (build-system r-build-system)
9645 `(("r-matrix" ,r-matrix)))
9647 `(("gfortran" ,gfortran)))
9648 (home-page "https://cran.r-project.org/web/packages/softImpute")
9649 (synopsis "Matrix completion via iterative soft-thresholded SVD")
9651 "This package provides iterative methods for matrix completion that use
9652 nuclear-norm regularization. The package includes procedures for centering
9653 and scaling rows, columns or both, and for computing low-rank @dfn{single
9654 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
9656 (license license:gpl2)))
9658 (define-public r-fftwtools
9660 (name "r-fftwtools")
9665 (uri (cran-uri "fftwtools" version))
9668 "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6"))))
9669 (build-system r-build-system)
9670 (inputs `(("fftw" ,fftw)))
9671 (home-page "https://github.com/krahim/fftwtools")
9672 (synopsis "Wrapper for FFTW3")
9674 "This package provides a wrapper for several FFTW functions. It provides
9675 access to the two-dimensional FFT, the multivariate FFT, and the
9676 one-dimensional real to complex FFT using the FFTW3 library. The package
9677 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
9678 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
9679 The FFT functions have a parameter that allows them to not return the
9680 redundant complex conjugate when the input is real data.")
9681 (license license:gpl2+)))
9683 (define-public r-tiff
9690 (uri (cran-uri "tiff" version))
9693 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
9694 (build-system r-build-system)
9696 `(("libtiff" ,libtiff)
9697 ("libjpeg" ,libjpeg)
9699 (home-page "http://www.rforge.net/tiff/")
9700 (synopsis "Read and write TIFF images")
9702 "This package provides an easy and simple way to read, write and display
9703 bitmap images stored in the TIFF format. It can read and write both files and
9704 in-memory raw vectors.")
9705 ;; Either of these two license versions.
9706 (license (list license:gpl2 license:gpl3))))
9708 (define-public r-nlp
9715 (uri (cran-uri "NLP" version))
9718 "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w"))))
9719 (properties `((upstream-name . "NLP")))
9720 (build-system r-build-system)
9721 (home-page "https://cran.r-project.org/web/packages/NLP/")
9722 (synopsis "Natural language processing infrastructure")
9724 "This package provides basic classes and methods for Natural Language
9726 (license license:gpl3)))
9735 (uri (cran-uri "tm" version))
9738 "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh"))))
9739 (properties `((upstream-name . "tm")))
9740 (build-system r-build-system)
9746 ("r-xml2" ,r-xml2)))
9747 (home-page "http://tm.r-forge.r-project.org/")
9748 (synopsis "Text mining package")
9750 "This package provides a framework for text mining applications within R.")
9751 (license license:gpl3)))
9753 (define-public r-waveslim
9760 (uri (cran-uri "waveslim" version))
9763 "0mky0nb4xxp8rybp87mxw2f1q6k400wpxv01zr4injv7ja6028xk"))))
9764 (build-system r-build-system)
9766 `(("gfortran" ,gfortran)))
9767 (home-page "http://waveslim.blogspot.com")
9768 (synopsis "Basic wavelet routines for signal processing")
9770 "This package provides basic wavelet routines for time series (1D),
9771 image (2D) and array (3D) analysis. The code provided here is based on
9772 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
9773 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
9774 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
9775 pairs (Selesnick 2001, 2002).")
9776 (license license:bsd-3)))
9778 (define-public r-wordcloud
9780 (name "r-wordcloud")
9785 (uri (cran-uri "wordcloud" version))
9788 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
9789 (build-system r-build-system)
9791 `(("r-rcolorbrewer" ,r-rcolorbrewer)
9793 ;; The "tm" package is only "suggested" according to CRAN, but the
9794 ;; wordcloud package cannot be loaded without it.
9796 (home-page "https://cran.r-project.org/web/packages/wordcloud")
9797 (synopsis "Word clouds")
9799 "This package provides functionality to create pretty word clouds,
9800 visualize differences and similarity between documents, and avoid
9801 over-plotting in scatter plots with text.")
9802 (license license:lgpl2.1)))
9804 (define-public r-colorramps
9806 (name "r-colorramps")
9811 (uri (cran-uri "colorRamps" version))
9814 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
9815 (properties `((upstream-name . "colorRamps")))
9816 (build-system r-build-system)
9817 (home-page "https://cran.r-project.org/web/packages/colorRamps")
9818 (synopsis "Build color tables")
9819 (description "This package provides features to build gradient color
9821 ;; Any version of the GPL
9822 (license license:gpl3+)))
9824 (define-public r-tidytree
9831 (uri (cran-uri "tidytree" version))
9833 (base32 "1bnzs62z2l8ck2h9gabmxvayizv4nfn8dmyzry83fv0cspjbyiv7"))))
9834 (build-system r-build-system)
9837 ("r-dplyr" ,r-dplyr)
9838 ("r-lazyeval" ,r-lazyeval)
9839 ("r-magrittr" ,r-magrittr)
9840 ("r-rlang" ,r-rlang)
9841 ("r-tibble" ,r-tibble)))
9842 (home-page "https://github.com/GuangchuangYu/tidytree")
9843 (synopsis "Tidy tool for phylogenetic tree data manipulation")
9845 "Phylogenetic trees generally contain multiple components including nodes,
9846 edges, branches and associated data. This package provides an approach to
9847 convert tree objects to tidy data frames. It also provides tidy interfaces to
9848 manipulate tree data.")
9849 (license license:artistic2.0)))
9851 (define-public r-rvcheck
9858 (uri (cran-uri "rvcheck" version))
9860 (base32 "1a3xlzi4n1rqiapfa180aif7n7nws8pbg8k3nk7ccaczvmni38aw"))))
9861 (build-system r-build-system)
9863 `(("r-biocmanager" ,r-biocmanager)
9864 ("r-rlang" ,r-rlang)))
9865 (home-page "https://cran.r-project.org/web/packages/rvcheck")
9866 (synopsis "R package version check")
9868 "This package provides tools to check the latest release version of R and
9869 R packages (on CRAN, Bioconductor or Github).")
9870 (license license:artistic2.0)))
9872 (define-public r-docopt
9879 (uri (cran-uri "docopt" version))
9882 "06zknnd0c5s2y0hbddzdlr3m63ib783izpck6pgz7sjbab5pd068"))))
9883 (build-system r-build-system)
9884 (home-page "https://github.com/docopt/docopt.R")
9885 (synopsis "Command-line interface specification language")
9887 "This package enables you to define a command-line interface by just
9888 giving it a description in the specific format.")
9889 (license license:expat)))
9891 (define-public r-sparsesvd
9893 (name "r-sparsesvd")
9898 (uri (cran-uri "sparsesvd" version))
9901 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
9902 (build-system r-build-system)
9903 (propagated-inputs `(("r-matrix" ,r-matrix)))
9904 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
9905 (synopsis "Sparse truncated singular value decomposition")
9907 "This package provides a Wrapper around the SVDLIBC library
9908 for (truncated) singular value decomposition of a sparse matrix. Currently,
9909 only sparse real matrices in Matrix package format are supported.")
9910 ;; SVDLIBC is released under BSD-2. The R interface is released under
9912 (license (list license:bsd-3 license:bsd-2))))
9914 (define-public r-speedglm
9921 (uri (cran-uri "speedglm" version))
9924 "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz"))))
9925 (build-system r-build-system)
9927 `(("r-mass" ,r-mass)
9928 ("r-matrix" ,r-matrix)))
9929 (home-page "https://cran.r-project.org/web/packages/speedglm")
9930 (synopsis "Fit linear and generalized linear models to large data sets")
9932 "This package provides tools for fitting linear models and generalized
9933 linear models to large data sets by updating algorithms.")
9934 ;; Any version of the GPL
9935 (license license:gpl2+)))
9937 (define-public r-densityclust
9939 (name "r-densityclust")
9944 (uri (cran-uri "densityClust" version))
9947 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
9948 (properties `((upstream-name . "densityClust")))
9949 (build-system r-build-system)
9952 ("r-ggplot2" ,r-ggplot2)
9953 ("r-ggrepel" ,r-ggrepel)
9954 ("r-gridextra" ,r-gridextra)
9955 ("r-rcolorbrewer" ,r-rcolorbrewer)
9957 ("r-rtsne" ,r-rtsne)))
9958 (home-page "https://cran.r-project.org/web/packages/densityClust")
9959 (synopsis "Clustering by fast search and find of density peaks")
9961 "This package provides an improved implementation (based on k-nearest
9962 neighbors) of the density peak clustering algorithm, originally described by
9963 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
9964 large datasets (> 100,000 samples) very efficiently.")
9965 (license license:gpl2+)))
9967 (define-public r-combinat
9974 (uri (cran-uri "combinat" version))
9977 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
9978 (build-system r-build-system)
9979 (home-page "https://cran.r-project.org/web/packages/combinat")
9980 (synopsis "Combinatorics utilities")
9981 (description "This package provides assorted routines for combinatorics.")
9982 (license license:gpl2)))
9984 (define-public r-qlcmatrix
9986 (name "r-qlcmatrix")
9991 (uri (cran-uri "qlcMatrix" version))
9994 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
9995 (properties `((upstream-name . "qlcMatrix")))
9996 (build-system r-build-system)
9998 `(("r-docopt" ,r-docopt)
9999 ("r-matrix" ,r-matrix)
10001 ("r-sparsesvd" ,r-sparsesvd)))
10002 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
10003 (synopsis "Sparse matrix functions for quantitative language comparison")
10005 "This package provides an extension of the functionality of the Matrix
10006 package for using sparse matrices. Some of the functions are very general,
10007 while other are highly specific for the special data format used for
10008 @dfn{quantitative language comparison} (QLC).")
10009 (license license:gpl3)))
10011 (define-public r-ddrtree
10018 (uri (cran-uri "DDRTree" version))
10021 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
10022 (properties `((upstream-name . "DDRTree")))
10023 (build-system r-build-system)
10026 ("r-irlba" ,r-irlba)
10028 ("r-rcppeigen" ,r-rcppeigen)))
10029 (home-page "https://cran.r-project.org/web/packages/DDRTree")
10030 (synopsis "Learning principal graphs with DDRTree")
10032 "This package provides an implementation of the framework of
10033 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
10034 dimensional space while constructs a principal tree which passes through the
10035 middle of the data simultaneously. DDRTree shows superiority to
10036 alternatives (Wishbone, DPT) for inferring the ordering as well as the
10037 intrinsic structure of single cell genomics data. In general, it could be
10038 used to reconstruct the temporal progression as well as the bifurcation
10039 structure of any data type.")
10040 (license license:asl2.0)))
10042 (define-public r-corpcor
10049 (uri (cran-uri "corpcor" version))
10052 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
10053 (build-system r-build-system)
10054 (home-page "http://strimmerlab.org/software/corpcor/")
10055 (synopsis "Efficient estimation of covariance and (partial) correlation")
10057 "This package implements a James-Stein-type shrinkage estimator for the
10058 covariance matrix, with separate shrinkage for variances and correlations.
10059 Furthermore, functions are available for fast singular value decomposition,
10060 for computing the pseudoinverse, and for checking the rank and positive
10061 definiteness of a matrix.")
10062 (license license:gpl3+)))
10064 (define-public r-rspectra
10066 (name "r-rspectra")
10071 (uri (cran-uri "RSpectra" version))
10074 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
10075 (properties `((upstream-name . "RSpectra")))
10076 (build-system r-build-system)
10078 `(("r-matrix" ,r-matrix)
10080 ("r-rcppeigen" ,r-rcppeigen)))
10081 (home-page "https://github.com/yixuan/RSpectra")
10082 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
10084 "This package provides an R interface to the Spectra library for
10085 large-scale eigenvalue and SVD problems. It is typically used to compute a
10086 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
10087 which is usually more efficient than @code{eigen()} if k << n.")
10089 (license license:mpl2.0)))
10091 (define-public r-vbsr
10098 (uri (cran-uri "vbsr" version))
10101 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
10102 (build-system r-build-system)
10103 (home-page "https://cran.r-project.org/web/packages/vbsr")
10104 (synopsis "Variational Bayes spike regression regularized linear models")
10106 "This package provides an efficient algorithm for solving ultra-sparse
10107 regularized regression models using a variational Bayes algorithm with a spike
10108 prior. The algorithm is solved on a path, with coordinate updates, and is
10109 capable of generating very sparse models. Very general model
10110 diagnostics for controlling type-1 errors are also provided.")
10111 (license license:gpl2)))
10113 (define-public r-flare
10116 (version "1.6.0.2")
10120 (uri (cran-uri "flare" version))
10123 "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
10124 (build-system r-build-system)
10126 `(("r-igraph" ,r-igraph)
10127 ("r-lattice" ,r-lattice)
10129 ("r-matrix" ,r-matrix)))
10130 (home-page "https://cran.r-project.org/web/packages/flare")
10131 (synopsis "Family of Lasso regression implementations")
10133 "This package provides implementations of a family of Lasso variants
10134 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
10135 high dimensional sparse linear models.")
10136 (license license:gpl2)))
10138 (define-public r-lassopv
10145 (uri (cran-uri "lassopv" version))
10148 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
10149 (build-system r-build-system)
10150 (propagated-inputs `(("r-lars" ,r-lars)))
10151 (home-page "https://github.com/lingfeiwang/lassopv")
10152 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
10154 "This package enables you to estimate the p-values for predictors x
10155 against target variable y in Lasso regression, using the regularization
10156 strength when each predictor enters the active set of regularization path for
10157 the first time as the statistic.")
10158 (license license:gpl3)))
10160 (define-public r-splitstackshape
10162 (name "r-splitstackshape")
10167 (uri (cran-uri "splitstackshape" version))
10170 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
10171 (build-system r-build-system)
10173 `(("r-data-table" ,r-data-table)))
10174 (home-page "https://github.com/mrdwab/splitstackshape")
10175 (synopsis "Stack and reshape datasets after splitting concatenated values")
10177 "Online data collection tools like Google Forms often export
10178 multiple-response questions with data concatenated in cells. The
10179 @code{concat.split} (cSplit) family of functions provided by this package
10180 splits such data into separate cells. This package also includes functions to
10181 stack groups of columns and to reshape wide data, even when the data are
10182 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
10183 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
10185 (license license:gpl3)))
10187 (define-public r-tfmpvalue
10189 (name "r-tfmpvalue")
10194 (uri (cran-uri "TFMPvalue" version))
10197 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
10198 (properties `((upstream-name . "TFMPvalue")))
10199 (build-system r-build-system)
10200 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10201 (home-page "https://github.com/ge11232002/TFMPvalue")
10202 (synopsis "P-value computation for position weight matrices")
10204 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
10205 identification from sequence/alignments, we are interested in the significance
10206 of certain match scores. TFMPvalue provides the accurate calculation of a
10207 p-value with a score threshold for position weight matrices, or the score with
10208 a given p-value. It is an interface to code originally made available by
10209 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
10210 Touzet and Varre (2007).")
10211 (license license:gpl2)))
10213 (define-public r-rnifti
10220 (uri (cran-uri "RNifti" version))
10223 "0hfid40pgfi1ykqka8y3v0m7h0iyd6fbvycvqlad3ibmbg621f0w"))))
10224 (properties `((upstream-name . "RNifti")))
10225 (build-system r-build-system)
10226 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10227 (home-page "https://github.com/jonclayden/RNifti")
10228 (synopsis "Fast R and C++ access to NIfTI images")
10230 "This package provides very fast read and write access to images stored
10231 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
10232 compiled C and interpreted R code. It also provides a C/C++ API that can be
10233 used by other packages.")
10234 (license license:gpl2)))
10236 (define-public r-shades
10243 (uri (cran-uri "shades" version))
10246 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
10247 (build-system r-build-system)
10248 (home-page "https://github.com/jonclayden/shades")
10249 (synopsis "Simple color manipulation")
10251 "This package provides functions for easily manipulating colors,
10252 creating color scales and calculating color distances.")
10253 (license license:bsd-3)))
10255 (define-public r-ore
10262 (uri (cran-uri "ore" version))
10264 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
10265 (build-system r-build-system)
10266 (home-page "https://github.com/jonclayden/ore")
10267 (synopsis "R interface to the Onigmo regular expression library")
10269 "This package provides an alternative to R's built-in functionality for
10270 handling regular expressions, based on the Onigmo library. It offers
10271 first-class compiled regex objects, partial matching and function-based
10272 substitutions, amongst other features.")
10273 (license license:bsd-3)))
10275 (define-public r-reportr
10282 (uri (cran-uri "reportr" version))
10285 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
10286 (build-system r-build-system)
10287 (propagated-inputs `(("r-ore" ,r-ore)))
10288 (home-page "https://github.com/jonclayden/reportr")
10289 (synopsis "General message and error reporting system")
10291 "This package provides a system for reporting messages, which offers
10292 certain useful features over the standard R system, such as the incorporation
10293 of output consolidation, message filtering, assertions, expression
10294 substitution, automatic generation of stack traces for debugging, and
10295 conditional reporting based on the current \"output level\".")
10296 (license license:gpl2)))
10298 (define-public r-tractor-base
10300 (name "r-tractor-base")
10305 (uri (cran-uri "tractor.base" version))
10308 "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i"))))
10309 (properties `((upstream-name . "tractor.base")))
10310 (build-system r-build-system)
10313 ("r-reportr" ,r-reportr)
10314 ("r-rnifti" ,r-rnifti)
10315 ("r-shades" ,r-shades)))
10316 (home-page "http://www.tractor-mri.org.uk")
10317 (synopsis "Read, manipulate and visualize magnetic resonance images")
10319 "This package provides functions for working with magnetic resonance
10320 images. It supports reading and writing of popular file formats (DICOM,
10321 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
10322 visualization; flexible image manipulation; metadata and sparse image
10324 (license license:gpl2)))
10326 (define-public r-grimport
10328 (name "r-grimport")
10333 (uri (cran-uri "grImport" version))
10336 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
10337 (properties `((upstream-name . "grImport")))
10338 (build-system r-build-system)
10340 `(("ghostscript" ,ghostscript)))
10342 `(("r-xml" ,r-xml)))
10343 (home-page "https://cran.r-project.org/web/packages/grImport")
10344 (synopsis "Convert, import, and draw PostScript pictures")
10346 "This package provides functions for converting, importing, and drawing
10347 PostScript pictures in R plots.")
10348 (license license:gpl2+)))
10350 (define-public r-grimport2
10352 (name "r-grimport2")
10357 (uri (cran-uri "grImport2" version))
10360 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
10361 (properties `((upstream-name . "grImport2")))
10362 (build-system r-build-system)
10364 `(("r-base64enc" ,r-base64enc)
10368 (home-page "https://cran.r-project.org/web/packages/grImport2/")
10369 (synopsis "Import SVG graphics")
10371 "This package provides functions for importing external vector images and
10372 drawing them as part of R plots. This package is different from the
10373 @code{grImport} package because, where that package imports PostScript format
10374 images, this package imports SVG format images. Furthermore, this package
10375 imports a specific subset of SVG, so external images must be preprocessed
10376 using a package like @code{rsvg} to produce SVG that this package can import.
10377 SVG features that are not supported by R graphics, such as gradient fills, can
10378 be imported and then exported via the @code{gridSVG} package.")
10379 (license license:gpl2+)))
10381 (define-public r-kohonen
10388 (uri (cran-uri "kohonen" version))
10391 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
10392 (build-system r-build-system)
10394 `(("r-rcpp" ,r-rcpp)))
10395 (home-page "https://cran.r-project.org/web/packages/kohonen")
10396 (synopsis "Supervised and unsupervised self-organising maps")
10398 "This package provides functions to train @dfn{self-organising
10399 maps} (SOMs). Also interrogation of the maps and prediction using trained
10400 maps are supported. The name of the package refers to Teuvo Kohonen, the
10401 inventor of the SOM.")
10402 (license license:gpl2+)))
10404 (define-public r-nnls
10411 (uri (cran-uri "nnls" version))
10414 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
10415 (build-system r-build-system)
10416 (native-inputs `(("gfortran" ,gfortran)))
10417 (home-page "https://cran.r-project.org/web/packages/nnls")
10418 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
10420 "This package provides an R interface to the Lawson-Hanson implementation
10421 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
10422 the combination of non-negative and non-positive constraints.")
10423 (license license:gpl2+)))
10425 (define-public r-iso
10432 (uri (cran-uri "Iso" version))
10435 "014mm5b1f7i6nwlz3kyg1biph0y542kcx5bd13p68cv5a928qzid"))))
10436 (properties `((upstream-name . "Iso")))
10437 (build-system r-build-system)
10438 (native-inputs `(("gfortran" ,gfortran)))
10439 (home-page "http://www.stat.auckland.ac.nz/~rolf/")
10440 (synopsis "Functions to perform isotonic regression")
10442 "This package provides support for linear order and unimodal
10443 order (univariate) isotonic regression and bivariate isotonic regression with
10444 linear order on both variables.")
10445 (license license:gpl2+)))
10447 (define-public r-chemometricswithr
10449 (name "r-chemometricswithr")
10454 (uri (cran-uri "ChemometricsWithR" version))
10457 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
10459 `((upstream-name . "ChemometricsWithR")))
10460 (build-system r-build-system)
10462 `(("r-devtools" ,r-devtools)
10463 ("r-kohonen" ,r-kohonen)
10466 (home-page "https://github.com/rwehrens/CWR")
10467 (synopsis "Chemometrics with R")
10469 "This package provides functions and scripts used in the book
10470 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
10471 Life Sciences\" by Ron Wehrens, Springer (2011).")
10472 (license license:gpl2+)))
10474 (define-public r-als
10481 (uri (cran-uri "ALS" version))
10484 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
10485 (properties `((upstream-name . "ALS")))
10486 (build-system r-build-system)
10489 ("r-nnls" ,r-nnls)))
10490 (home-page "https://cran.r-project.org/web/packages/ALS")
10491 (synopsis "Multivariate curve resolution alternating least squares")
10493 "Alternating least squares is often used to resolve components
10494 contributing to data with a bilinear structure; the basic technique may be
10495 extended to alternating constrained least squares. This package provides an
10496 implementation of @dfn{multivariate curve resolution alternating least
10497 squares} (MCR-ALS).
10499 Commonly applied constraints include unimodality, non-negativity, and
10500 normalization of components. Several data matrices may be decomposed
10501 simultaneously by assuming that one of the two matrices in the bilinear
10502 decomposition is shared between datasets.")
10503 (license license:gpl2+)))
10505 (define-public r-strucchange
10507 (name "r-strucchange")
10512 (uri (cran-uri "strucchange" version))
10515 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
10516 (build-system r-build-system)
10518 `(("r-sandwich" ,r-sandwich)
10520 (home-page "https://cran.r-project.org/web/packages/strucchange")
10521 (synopsis "Testing, monitoring, and dating structural changes")
10523 "This package provides tools for testing, monitoring and dating
10524 structural changes in (linear) regression models. It features tests/methods
10525 from the generalized fluctuation test framework as well as from the F
10526 test (Chow test) framework. This includes methods to fit, plot and test
10527 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
10528 statistics, respectively. It is possible to monitor incoming data online
10529 using fluctuation processes. Finally, the breakpoints in regression models
10530 with structural changes can be estimated together with confidence intervals.
10531 Emphasis is always given to methods for visualizing the data.")
10532 ;; Either of these two GPL versions
10533 (license (list license:gpl2 license:gpl3))))
10535 (define-public r-pixmap
10542 (uri (cran-uri "pixmap" version))
10545 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
10546 (build-system r-build-system)
10547 (home-page "https://cran.r-project.org/web/packages/pixmap")
10548 (synopsis "Tools for bitmap images")
10550 "This package provides functions for importing, exporting, plotting and
10551 other manipulations of bitmapped images.")
10552 (license license:gpl2)))
10554 (define-public r-rapidjsonr
10556 (name "r-rapidjsonr")
10561 (uri (cran-uri "rapidjsonr" version))
10564 "0h4phjjhykbb45rg5b1xn48vqxdcvcngbm0416ds8in7j469wbwd"))))
10565 (build-system r-build-system)
10566 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
10567 (synopsis "JSON parser")
10569 "This package provides JSON parsing capability through the Rapidjson
10571 (license license:expat)))
10573 (define-public r-ontologyindex
10575 (name "r-ontologyindex")
10580 (uri (cran-uri "ontologyIndex" version))
10583 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
10584 (properties `((upstream-name . "ontologyIndex")))
10585 (build-system r-build-system)
10586 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
10587 (synopsis "Functions for processing ontologies in R")
10589 "This package provides functions for reading ontologies into R as lists
10590 and manipulating sets of ontological terms.")
10591 (license license:gpl2+)))
10593 (define-public r-gargle
10600 (uri (cran-uri "gargle" version))
10603 "08zhfk2sl342w35i5n2c93ayypg3z0kbl0020l3y9adqka1vazgx"))))
10604 (build-system r-build-system)
10609 ("r-jsonlite" ,r-jsonlite)
10610 ("r-rlang" ,r-rlang)
10611 ("r-withr" ,r-withr)))
10612 (home-page "https://gargle.r-lib.org")
10613 (synopsis "Utilities for working with Google APIs")
10615 "This package provides utilities for working with Google APIs. This
10616 includes functions and classes for handling common credential types and for
10617 preparing, executing, and processing HTTP requests.")
10618 (license license:expat)))
10620 (define-public r-bigrquery
10622 (name "r-bigrquery")
10627 (uri (cran-uri "bigrquery" version))
10630 "1ggh2gngr5x0g6y7d55y6kvn94anf7qi1bkc28cjmw61hxjq38fb"))))
10631 (build-system r-build-system)
10633 `(("r-assertthat" ,r-assertthat)
10634 ("r-bit64" ,r-bit64)
10637 ("r-gargle" ,r-gargle)
10640 ("r-jsonlite" ,r-jsonlite)
10641 ("r-prettyunits" ,r-prettyunits)
10642 ("r-progress" ,r-progress)
10643 ("r-rapidjsonr" ,r-rapidjsonr)
10645 ("r-rlang" ,r-rlang)
10646 ("r-tibble" ,r-tibble)))
10647 (home-page "https://github.com/rstats-db/bigrquery")
10648 (synopsis "R interface to Google's BigQuery API")
10650 "This package provides an R interface to Google's BigQuery database.")
10651 (license license:gpl3)))
10653 (define-public r-gmp
10656 (version "0.5-13.6")
10660 (uri (cran-uri "gmp" version))
10663 "0j2sz2nw41y9306rl1b8hbn0spz7453z5iawcq0bvslyrhc1d9ir"))))
10664 (build-system r-build-system)
10667 (modify-phases %standard-phases
10668 (add-after 'unpack 'set-CC
10669 (lambda _ (setenv "CC" "gcc") #t)))))
10670 (inputs `(("gmp" ,gmp)))
10671 (home-page "https://cran.r-project.org/web/packages/gmp")
10672 (synopsis "Multiple precision arithmetic")
10674 "This package supports multiple precision arithmetic (big integers and
10675 rationals, prime number tests, matrix computation), \"arithmetic without
10676 limitations\" using the GNU Multiple Precision library.")
10677 ;; Any version of the GPL.
10678 (license license:gpl3+)))
10680 (define-public r-rmpfr
10687 (uri (cran-uri "Rmpfr" version))
10690 "09kw7hyca8xc09r2d88qj81cclar8acaq5q9q5rw9f49iffda0rr"))))
10691 (properties `((upstream-name . "Rmpfr")))
10692 (build-system r-build-system)
10697 `(("r-gmp" ,r-gmp)))
10699 `(("pkg-config" ,pkg-config)))
10700 (home-page "http://rmpfr.r-forge.r-project.org/")
10701 (synopsis "R bindings to the MPFR library")
10703 "This package supports arithmetic (via S4 classes and methods) for
10704 arbitrary precision floating point numbers, including transcendental
10705 functions. To this end, the package interfaces with the @dfn{Multiple
10706 Precision Floating-Point Reliable} (MPFR) library.")
10707 (license license:gpl2+)))
10709 (define-public r-assertive-base
10711 (name "r-assertive-base")
10716 (uri (cran-uri "assertive.base" version))
10719 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
10721 `((upstream-name . "assertive.base")))
10722 (build-system r-build-system)
10723 (home-page "https://bitbucket.org/richierocks/assertive.base")
10724 (synopsis "Core of the assertive package")
10726 "This package provides a minimal set of predicates and assertions used by
10727 the assertive package. This is mainly for use by other package developers who
10728 want to include run-time testing features in their own packages.")
10729 (license license:gpl3+)))
10731 (define-public r-assertive-properties
10733 (name "r-assertive-properties")
10738 (uri (cran-uri "assertive.properties" version))
10741 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
10743 `((upstream-name . "assertive.properties")))
10744 (build-system r-build-system)
10746 `(("r-assertive-base" ,r-assertive-base)))
10747 (home-page "https://bitbucket.org/richierocks/assertive.properties")
10748 (synopsis "Assertions to check properties of variables")
10750 "This package provides a set of predicates and assertions for checking
10751 the properties of variables, such as length, names and attributes. This is
10752 mainly for use by other package developers who want to include run-time
10753 testing features in their own packages.")
10754 (license license:gpl3+)))
10756 (define-public r-assertive-numbers
10758 (name "r-assertive-numbers")
10763 (uri (cran-uri "assertive.numbers" version))
10766 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
10768 `((upstream-name . "assertive.numbers")))
10769 (build-system r-build-system)
10771 `(("r-assertive-base" ,r-assertive-base)))
10772 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
10773 (synopsis "Assertions to check properties of numbers")
10775 "This package provides a set of predicates and assertions for checking
10776 the properties of numbers. This is mainly for use by other package developers
10777 who want to include run-time testing features in their own packages.")
10778 (license license:gpl3+)))
10780 (define-public r-assertive-sets
10782 (name "r-assertive-sets")
10787 (uri (cran-uri "assertive.sets" version))
10790 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
10792 `((upstream-name . "assertive.sets")))
10793 (build-system r-build-system)
10795 `(("r-assertive-base" ,r-assertive-base)))
10796 (home-page "https://bitbucket.org/richierocks/assertive.sets")
10797 (synopsis "Assertions to check properties of sets")
10799 "This package provides a set of predicates and assertions for checking
10800 the properties of sets. This is mainly for use by other package developers
10801 who want to include run-time testing features in their own packages.")
10802 (license license:gpl3+)))
10804 (define-public r-assertive-matrices
10806 (name "r-assertive-matrices")
10811 (uri (cran-uri "assertive.matrices" version))
10814 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
10816 `((upstream-name . "assertive.matrices")))
10817 (build-system r-build-system)
10819 `(("r-assertive-base" ,r-assertive-base)))
10820 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
10821 (synopsis "Assertions to check properties of matrices")
10823 "This package provides a set of predicates and assertions for checking
10824 the properties of matrices. This is mainly for use by other package
10825 developers who want to include run-time testing features in their own
10827 (license license:gpl3+)))
10829 (define-public r-assertive-models
10831 (name "r-assertive-models")
10836 (uri (cran-uri "assertive.models" version))
10839 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
10841 `((upstream-name . "assertive.models")))
10842 (build-system r-build-system)
10844 `(("r-assertive-base" ,r-assertive-base)))
10845 (home-page "https://bitbucket.org/richierocks/assertive.models")
10846 (synopsis "Assertions to check properties of models")
10848 "This package provides a set of predicates and assertions for checking
10849 the properties of models. This is mainly for use by other package developers
10850 who want to include run-time testing features in their own packages.")
10851 (license license:gpl3+)))
10853 (define-public r-assertive-reflection
10855 (name "r-assertive-reflection")
10860 (uri (cran-uri "assertive.reflection" version))
10863 "19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj"))))
10865 `((upstream-name . "assertive.reflection")))
10866 (build-system r-build-system)
10868 `(("r-assertive-base" ,r-assertive-base)))
10869 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
10870 (synopsis "Assertions for checking the state of R")
10872 "This package provides a set of predicates and assertions for checking
10873 the state and capabilities of R, the operating system it is running on, and
10874 the IDE being used. This is mainly for use by other package developers who
10875 want to include run-time testing features in their own packages.")
10876 (license license:gpl3+)))
10878 (define-public r-assertive-types
10880 (name "r-assertive-types")
10885 (uri (cran-uri "assertive.types" version))
10888 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
10890 `((upstream-name . "assertive.types")))
10891 (build-system r-build-system)
10893 `(("r-assertive-base" ,r-assertive-base)
10894 ("r-assertive-properties" ,r-assertive-properties)
10895 ("r-codetools" ,r-codetools)))
10896 (home-page "https://bitbucket.org/richierocks/assertive.types")
10897 (synopsis "Assertions to check types of variables")
10899 "This package provides a set of predicates and assertions for checking
10900 the types of variables. This is mainly for use by other package developers
10901 who want to include run-time testing features in their own packages.")
10902 (license license:gpl3+)))
10904 (define-public r-assertive-files
10906 (name "r-assertive-files")
10911 (uri (cran-uri "assertive.files" version))
10914 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
10916 `((upstream-name . "assertive.files")))
10917 (build-system r-build-system)
10919 `(("r-assertive-base" ,r-assertive-base)
10920 ("r-assertive-numbers" ,r-assertive-numbers)))
10921 (home-page "https://bitbucket.org/richierocks/assertive.files")
10922 (synopsis "Assertions to check properties of files")
10924 "This package provides a set of predicates and assertions for checking
10925 the properties of files and connections. This is mainly for use by other
10926 package developers who want to include run-time testing features in their own
10928 (license license:gpl3+)))
10930 (define-public r-assertive-code
10932 (name "r-assertive-code")
10937 (uri (cran-uri "assertive.code" version))
10940 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
10942 `((upstream-name . "assertive.code")))
10943 (build-system r-build-system)
10945 `(("r-assertive-base" ,r-assertive-base)
10946 ("r-assertive-properties" ,r-assertive-properties)
10947 ("r-assertive-types" ,r-assertive-types)))
10948 (home-page "https://bitbucket.org/richierocks/assertive.code")
10949 (synopsis "Assertions to check properties of code")
10951 "This package provides a set of predicates and assertions for checking
10952 the properties of code. This is mainly for use by other package developers
10953 who want to include run-time testing features in their own packages.")
10954 (license license:gpl3+)))
10956 (define-public r-assertive-datetimes
10958 (name "r-assertive-datetimes")
10963 (uri (cran-uri "assertive.datetimes" version))
10966 "00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78"))))
10968 `((upstream-name . "assertive.datetimes")))
10969 (build-system r-build-system)
10971 `(("r-assertive-base" ,r-assertive-base)
10972 ("r-assertive-types" ,r-assertive-types)))
10973 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
10974 (synopsis "Assertions to check properties of dates and times")
10976 "This package provides a set of predicates and assertions for checking
10977 the properties of dates and times. This is mainly for use by other package
10978 developers who want to include run-time testing features in their own
10980 (license license:gpl3+)))
10982 (define-public r-assertive-strings
10984 (name "r-assertive-strings")
10989 (uri (cran-uri "assertive.strings" version))
10992 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
10994 `((upstream-name . "assertive.strings")))
10995 (build-system r-build-system)
10997 `(("r-assertive-base" ,r-assertive-base)
10998 ("r-assertive-types" ,r-assertive-types)
10999 ("r-stringi" ,r-stringi)))
11000 (home-page "https://bitbucket.org/richierocks/assertive.strings")
11001 (synopsis "Assertions to check properties of strings")
11003 "This package provides a set of predicates and assertions for checking
11004 the properties of strings. This is mainly for use by other package developers
11005 who want to include run-time testing features in their own packages.")
11006 (license license:gpl3+)))
11008 (define-public r-assertive-data-us
11010 (name "r-assertive-data-us")
11015 (uri (cran-uri "assertive.data.us" version))
11018 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
11020 `((upstream-name . "assertive.data.us")))
11021 (build-system r-build-system)
11023 `(("r-assertive-base" ,r-assertive-base)
11024 ("r-assertive-strings" ,r-assertive-strings)))
11025 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
11026 (synopsis "Assertions to check properties of strings")
11028 "This package provides a set of predicates and assertions for checking
11029 the properties of US-specific complex data types. This is mainly for use by
11030 other package developers who want to include run-time testing features in
11031 their own packages.")
11032 (license license:gpl3+)))
11034 (define-public r-assertive-data-uk
11036 (name "r-assertive-data-uk")
11041 (uri (cran-uri "assertive.data.uk" version))
11044 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
11046 `((upstream-name . "assertive.data.uk")))
11047 (build-system r-build-system)
11049 `(("r-assertive-base" ,r-assertive-base)
11050 ("r-assertive-strings" ,r-assertive-strings)))
11051 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
11052 (synopsis "Assertions to check properties of strings")
11054 "This package provides a set of predicates and assertions for checking
11055 the properties of UK-specific complex data types. This is mainly for use by
11056 other package developers who want to include run-time testing features in
11057 their own packages.")
11058 (license license:gpl3+)))
11060 (define-public r-assertive-data
11062 (name "r-assertive-data")
11067 (uri (cran-uri "assertive.data" version))
11070 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
11072 `((upstream-name . "assertive.data")))
11073 (build-system r-build-system)
11075 `(("r-assertive-base" ,r-assertive-base)
11076 ("r-assertive-strings" ,r-assertive-strings)))
11077 (home-page "https://bitbucket.org/richierocks/assertive.data")
11078 (synopsis "Assertions to check properties of data")
11080 "This package provides a set of predicates and assertions for checking
11081 the properties of (country independent) complex data types. This is mainly
11082 for use by other package developers who want to include run-time testing
11083 features in their own packages.")
11084 (license license:gpl3+)))
11086 (define-public r-assertive
11088 (name "r-assertive")
11093 (uri (cran-uri "assertive" version))
11096 "0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3"))))
11097 (build-system r-build-system)
11099 `(("r-assertive-base" ,r-assertive-base)
11100 ("r-assertive-code" ,r-assertive-code)
11101 ("r-assertive-data" ,r-assertive-data)
11102 ("r-assertive-data-uk" ,r-assertive-data-uk)
11103 ("r-assertive-data-us" ,r-assertive-data-us)
11104 ("r-assertive-datetimes" ,r-assertive-datetimes)
11105 ("r-assertive-files" ,r-assertive-files)
11106 ("r-assertive-matrices" ,r-assertive-matrices)
11107 ("r-assertive-models" ,r-assertive-models)
11108 ("r-assertive-numbers" ,r-assertive-numbers)
11109 ("r-assertive-properties" ,r-assertive-properties)
11110 ("r-assertive-reflection" ,r-assertive-reflection)
11111 ("r-assertive-sets" ,r-assertive-sets)
11112 ("r-assertive-strings" ,r-assertive-strings)
11113 ("r-assertive-types" ,r-assertive-types)
11114 ("r-knitr" ,r-knitr)))
11115 (home-page "https://bitbucket.org/richierocks/assertive")
11116 (synopsis "Readable check functions to ensure code integrity")
11118 "This package provides lots of predicates (@code{is_*} functions) to
11119 check the state of your variables, and assertions (@code{assert_*} functions)
11120 to throw errors if they aren't in the right form.")
11121 (license license:gpl3+)))
11123 (define-public r-dotcall64
11125 (name "r-dotcall64")
11130 (uri (cran-uri "dotCall64" version))
11133 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
11134 (properties `((upstream-name . "dotCall64")))
11135 (build-system r-build-system)
11136 (native-inputs `(("gfortran" ,gfortran)))
11137 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
11138 (synopsis "Enhanced foreign function interface supporting long vectors")
11140 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
11141 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
11142 supports long vectors, arguments of type 64-bit integer, and provides a
11143 mechanism to avoid unnecessary copies of read-only and write-only arguments.
11144 This makes it a convenient and fast interface to C/C++ and Fortran code.")
11145 (license license:gpl2+)))
11147 (define-public r-spam
11154 (uri (cran-uri "spam" version))
11156 (base32 "0ry0a76cljlmilrzcriiizcidxyhq1i7i9bqhvl1qda81ld8hifi"))))
11157 (build-system r-build-system)
11159 `(("r-dotcall64" ,r-dotcall64)))
11160 (native-inputs `(("gfortran" ,gfortran)))
11161 (home-page "https://www.math.uzh.ch/pages/spam/")
11162 (synopsis "Sparse matrix algebra")
11164 "This package provides a set of functions for sparse matrix algebra.
11165 Differences with other sparse matrix packages are:
11168 @item it only supports (essentially) one sparse matrix format;
11169 @item it is based on transparent and simple structure(s);
11170 @item it is tailored for MCMC calculations within G(M)RF;
11171 @item and it is fast and scalable (with the extension package @code{spam64}).
11173 ;; Either of these licenses
11174 (license (list license:bsd-3 license:lgpl2.0))))
11176 (define-public r-fields
11183 (uri (cran-uri "fields" version))
11185 (base32 "173zm5vr236ydiq0v27qy0l3x7h9fc7jly38iakg77j26i0a01il"))))
11186 (build-system r-build-system)
11188 `(("r-maps" ,r-maps)
11189 ("r-spam" ,r-spam)))
11191 `(("gfortran" ,gfortran)))
11192 (home-page "https://www.image.ucar.edu/fields")
11193 (synopsis "Tools for spatial data")
11195 "This is a package for curve, surface and function fitting with an
11196 emphasis on splines, spatial data and spatial statistics. The major methods
11197 include cubic, and thin plate splines, Kriging, and compactly supported
11198 covariance functions for large data sets.")
11199 (license license:gpl2+)))
11201 (define-public r-spatialextremes
11203 (name "r-spatialextremes")
11204 (version "2.0-7.2")
11208 (uri (cran-uri "SpatialExtremes" version))
11211 "0aqq9ryxi4xsdqjhc1lhb7ai8szs7m2vys6nn0ygps1w3pm4xwj8"))))
11213 `((upstream-name . "SpatialExtremes")))
11214 (build-system r-build-system)
11216 `(("r-fields" ,r-fields)
11217 ("r-maps" ,r-maps)))
11218 (home-page "http://spatialextremes.r-forge.r-project.org/")
11219 (synopsis "Modelling spatial extremes")
11221 "This package provides tools for the statistical modelling of spatial
11222 extremes using max-stable processes, copula or Bayesian hierarchical models.
11223 More precisely, this package allows (conditional) simulations from various
11224 parametric max-stable models, analysis of the extremal spatial dependence, the
11225 fitting of such processes using composite likelihoods or least square (simple
11226 max-stable processes only), model checking and selection and prediction.")
11227 (license license:gpl2+)))
11229 (define-public r-drc
11236 (uri (cran-uri "drc" version))
11239 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
11240 (build-system r-build-system)
11243 ("r-gtools" ,r-gtools)
11245 ("r-multcomp" ,r-multcomp)
11246 ("r-plotrix" ,r-plotrix)
11247 ("r-scales" ,r-scales)))
11248 (home-page "https://cran.r-project.org/web/packages/drc")
11249 (synopsis "Analysis of dose-response curves")
11251 "This package provides a suite of flexible and versatile model fitting
11252 and after-fitting functions for the analysis of dose-response data.")
11253 (license license:gpl2+)))
11255 (define-public r-rmeta
11262 (uri (cran-uri "rmeta" version))
11265 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
11266 (build-system r-build-system)
11267 (home-page "https://cran.r-project.org/web/packages/rmeta")
11268 (synopsis "Tools for meta-analysis")
11270 "This package provides functions for simple fixed and random effects
11271 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
11272 draws standard summary plots, funnel plots, and computes summaries and tests
11273 for association and heterogeneity.")
11274 (license license:gpl2)))
11276 (define-public r-bootstrap
11278 (name "r-bootstrap")
11283 (uri (cran-uri "bootstrap" version))
11286 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
11287 (build-system r-build-system)
11288 (native-inputs `(("gfortran" ,gfortran)))
11289 (home-page "https://cran.r-project.org/web/packages/bootstrap")
11290 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
11292 "This package provides software and data for the book \"An Introduction
11293 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
11294 This package is primarily provided for projects already based on it, and for
11295 support of the book. New projects should preferentially use the recommended
11296 package \"boot\".")
11297 (license license:bsd-3)))
11299 (define-public r-survivalroc
11301 (name "r-survivalroc")
11306 (uri (cran-uri "survivalROC" version))
11309 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
11310 (properties `((upstream-name . "survivalROC")))
11311 (build-system r-build-system)
11312 (home-page "https://cran.r-project.org/web/packages/survivalROC")
11313 (synopsis "Time-dependent ROC curve estimation from censored survival data")
11315 "Compute time-dependent ROC curve from censored survival data using
11316 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
11317 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
11318 (license license:gpl2+)))
11320 (define-public r-longitudinal
11322 (name "r-longitudinal")
11327 (uri (cran-uri "longitudinal" version))
11330 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
11331 (build-system r-build-system)
11332 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
11333 (home-page "http://strimmerlab.org/software/longitudinal/")
11334 (synopsis "Analysis of multiple time course data")
11336 "This package contains general data structures and functions for
11337 longitudinal data with multiple variables, repeated measurements, and
11338 irregularly spaced time points. It also implements a shrinkage estimator of
11339 dynamical correlation and dynamical covariance.")
11340 (license license:gpl3+)))
11342 (define-public r-genenet
11349 (uri (cran-uri "GeneNet" version))
11352 "0w52apk0nnr8nsskf26ff7ana8xiksr8wqmkjxzwhzgg7fncm61p"))))
11353 (properties `((upstream-name . "GeneNet")))
11354 (build-system r-build-system)
11356 `(("r-corpcor" ,r-corpcor)
11357 ("r-fdrtool" ,r-fdrtool)
11358 ("r-longitudinal" ,r-longitudinal)))
11359 (home-page "http://strimmerlab.org/software/genenet/")
11360 (synopsis "Modeling and inferring gene networks")
11362 "This package analyzes gene expression (time series) data with focus on
11363 the inference of gene networks. In particular, GeneNet implements the methods
11364 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
11365 for learning large-scale gene association networks (including assignment of
11366 putative directions).")
11367 (license license:gpl3+)))
11369 (define-public r-rbamtools
11371 (name "r-rbamtools")
11372 (version "2.16.17")
11376 (uri (cran-uri "rbamtools" version))
11379 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
11380 (build-system r-build-system)
11381 (inputs `(("zlib" ,zlib)))
11383 `(("r-refgenome" ,r-refgenome)))
11384 (home-page "https://cran.r-project.org/web/packages/rbamtools")
11385 (synopsis "Read and write BAM (binary alignment) files")
11387 "This package provides an R interface to functions of the SAMtools
11389 (license license:artistic2.0)))
11391 (define-public r-protviz
11398 (uri (cran-uri "protViz" version))
11401 "0cznzm1ijlq33yd5wsa61prav77y2vi698w0n2fx1xcv504c4bjv"))))
11402 (properties `((upstream-name . "protViz")))
11403 (build-system r-build-system)
11404 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11405 (home-page "https://github.com/protViz/protViz/")
11406 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
11408 "This package helps with quality checks, visualizations and analysis of
11409 mass spectrometry data, coming from proteomics experiments. The package is
11410 developed, tested and used at the Functional Genomics Center Zurich, where it
11411 is used mainly for prototyping, teaching, and having fun with proteomics data.
11412 But it can also be used to do data analysis for small scale data sets.")
11413 (license license:gpl3)))
11415 (define-public r-cmprsk
11422 (uri (cran-uri "cmprsk" version))
11424 (base32 "0xhgfg5b4i9skkaxp7gzkafgg5bqs5q1rp4hpw2jjmykg2nifn99"))))
11425 (build-system r-build-system)
11427 `(("r-survival" ,r-survival)))
11429 `(("gfortran" ,gfortran)))
11430 (home-page "https://cran.r-project.org/web/packages/cmprsk")
11431 (synopsis "Subdistribution analysis of competing risks")
11433 "This package provides tool for estimation, testing and regression
11434 modeling of subdistribution functions in competing risks, as described in
11435 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
11436 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
11437 A proportional hazards model for the subdistribution of a competing risk,
11438 JASA, 94:496-509.")
11439 (license license:gpl2+)))
11441 (define-public r-etm
11448 (uri (cran-uri "etm" version))
11451 "1yivbq8y0ijcl1m4nir4q9hp4pi6iphwxgjprygsdf7vp98wq677"))))
11452 (build-system r-build-system)
11454 `(("r-data-table" ,r-data-table)
11455 ("r-lattice" ,r-lattice)
11457 ("r-rcpparmadillo" ,r-rcpparmadillo)
11458 ("r-survival" ,r-survival)))
11459 (home-page "https://cran.r-project.org/web/packages/etm")
11460 (synopsis "Empirical transition matrix")
11462 "The @dfn{empirical transition matrix} (etm) package permits to estimate
11463 the matrix of transition probabilities for any time-inhomogeneous multistate
11464 model with finite state space using the Aalen-Johansen estimator.")
11465 (license license:expat)))
11467 (define-public r-epi
11474 (uri (cran-uri "Epi" version))
11477 "046y10vwks5y84pzccmrn6d4pd6qz70imvp1hw5ywp8fnwzfh4g5"))))
11478 (properties `((upstream-name . "Epi")))
11479 (build-system r-build-system)
11481 `(("r-cmprsk" ,r-cmprsk)
11482 ("r-data-table" ,r-data-table)
11485 ("r-matrix" ,r-matrix)
11487 ("r-numderiv" ,r-numderiv)
11489 ("r-survival" ,r-survival)
11491 (home-page "http://BendixCarstensen.com/Epi/")
11492 (synopsis "Statistical analysis in epidemiology")
11494 "This package provides functions for demographic and epidemiological
11495 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
11496 particular representation, manipulation and simulation of multistate data -
11497 the Lexis suite of functions, which includes interfaces to the @code{mstate},
11498 @code{etm} and @code{cmprsk} packages. It also contains functions for
11499 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
11500 data and some useful functions for tabulation and plotting, as well as a
11501 number of epidemiological data sets.")
11502 (license license:gpl2)))
11504 (define-public r-ppls
11507 (version "1.6-1.1")
11511 (uri (cran-uri "ppls" version))
11514 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
11515 (build-system r-build-system)
11516 (propagated-inputs `(("r-mass" ,r-mass)))
11517 (home-page "https://cran.r-project.org/web/packages/ppls")
11518 (synopsis "Penalized partial least squares")
11520 "This package contains linear and nonlinear regression methods based on
11521 partial least squares and penalization techniques. Model parameters are
11522 selected via cross-validation, and confidence intervals ans tests for the
11523 regression coefficients can be conducted via jackknifing.")
11524 (license license:gpl2+)))
11526 (define-public r-huge
11533 (uri (cran-uri "huge" version))
11535 (base32 "07n3j1va2z4v30rj22cww72khgzbz2xsp0yc0qswlrwyxi4my5i3"))))
11536 (build-system r-build-system)
11538 `(("r-igraph" ,r-igraph)
11540 ("r-matrix" ,r-matrix)
11542 ("r-rcppeigen" ,r-rcppeigen)))
11543 (home-page "https://cran.r-project.org/web/packages/huge")
11544 (synopsis "High-dimensional undirected graph estimation")
11546 "This package provides a general framework for high-dimensional
11547 undirected graph estimation. It integrates data preprocessing, neighborhood
11548 screening, graph estimation, and model selection techniques into a pipeline.")
11549 (license license:gpl2)))
11551 (define-public r-parcor
11558 (uri (cran-uri "parcor" version))
11561 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
11562 (build-system r-build-system)
11565 ("r-genenet" ,r-genenet)
11566 ("r-glmnet" ,r-glmnet)
11568 ("r-ppls" ,r-ppls)))
11569 (home-page "https://cran.r-project.org/web/packages/parcor")
11570 (synopsis "Regularized estimation of partial correlation matrices")
11572 "This package estimates the matrix of partial correlations based on
11573 different regularized regression methods: lasso, adaptive lasso, PLS, and
11574 Ridge Regression. In addition, the package provides model selection for
11575 lasso, adaptive lasso and Ridge regression based on cross-validation.")
11576 (license license:gpl2+)))
11578 (define-public r-mcmc
11585 (uri (cran-uri "mcmc" version))
11588 "1fc6a6asn53lx7x7pnlb5mb716nv4pcmbp99f1i30y4hzygihfj4"))))
11589 (build-system r-build-system)
11590 (home-page "http://www.stat.umn.edu/geyer/mcmc/")
11591 (synopsis "Markov chain Monte Carlo")
11593 "This package simulates continuous distributions of random vectors using
11594 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
11595 function that evaluates the log unnormalized density. Algorithms are random
11596 walk Metropolis algorithm (function @code{metrop}), simulated
11597 tempering (function @code{temper}), and morphometric random walk
11598 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
11599 by change of variable.")
11600 (license license:expat)))
11602 (define-public r-listenv
11609 (uri (cran-uri "listenv" version))
11612 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
11613 (build-system r-build-system)
11615 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11616 (home-page "https://github.com/HenrikBengtsson/listenv")
11617 (synopsis "Environments behaving (almost) as lists")
11619 "This package implements list environments. List environments are
11620 environments that have list-like properties. For instance, the elements of a
11621 list environment are ordered and can be accessed and iterated over using index
11623 (license license:lgpl2.1+)))
11625 (define-public r-globals
11632 (uri (cran-uri "globals" version))
11635 "1ha8iasgijp4q3v2b0b17y1wh7cd3nvzd9b03w49qm2bidkaf68m"))))
11636 (build-system r-build-system)
11638 `(("r-codetools" ,r-codetools)))
11639 (home-page "https://github.com/HenrikBengtsson/globals")
11640 (synopsis "Identify global objects in R expressions")
11642 "This package provides tools to identify global (\"unknown\" or \"free\")
11643 objects in R expressions by code inspection using various strategies, e.g.
11644 conservative or liberal. The objective of this package is to make it as
11645 simple as possible to identify global objects for the purpose of exporting
11646 them in distributed compute environments.")
11647 (license license:lgpl2.1+)))
11649 (define-public r-future
11656 (uri (cran-uri "future" version))
11659 "1xaqh0b2knf5bp23mc0kriq0iqhqna31q3b7d960piqjhzrb03dm"))))
11660 (build-system r-build-system)
11662 `(("r-digest" ,r-digest)
11663 ("r-globals" ,r-globals)
11664 ("r-listenv" ,r-listenv)))
11666 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11667 (home-page "https://github.com/HenrikBengtsson/future")
11668 (synopsis "Unified parallel and distributed processing in R")
11670 "The purpose of this package is to provide a lightweight and unified
11671 Future API for sequential and parallel processing of R expression via futures.
11672 This package implements sequential, multicore, multisession, and cluster
11673 futures. With these, R expressions can be evaluated on the local machine, in
11674 parallel a set of local machines, or distributed on a mix of local and remote
11675 machines. Extensions to this package implement additional backends for
11676 processing futures via compute cluster schedulers etc. Because of its unified
11677 API, there is no need to modify any code in order to switch from sequential on
11678 the local machine to, say, distributed processing on a remote compute cluster.")
11679 (license license:lgpl2.1+)))
11681 (define-public r-future-apply
11683 (name "r-future-apply")
11688 (uri (cran-uri "future.apply" version))
11691 "1kgq6dv96hdy35kysqkn606nj7s9dp4ibgpm6n46gqhc5n75lzkk"))))
11692 (properties `((upstream-name . "future.apply")))
11693 (build-system r-build-system)
11695 `(("r-future" ,r-future)
11696 ("r-globals" ,r-globals)))
11698 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11699 (home-page "https://github.com/HenrikBengtsson/future.apply")
11700 (synopsis "Apply function to elements in parallel using futures")
11702 "This package provides implementations of @code{apply()},
11703 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
11704 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
11705 can be resolved using any future-supported backend, e.g. parallel on the local
11706 machine or distributed on a compute cluster.")
11707 (license license:gpl2+)))
11709 (define-public r-rsvd
11716 (uri (cran-uri "rsvd" version))
11719 "0fia77y5fxnhwkcxlgp98ygb8fdfraky75x80hkf7kvvpwc5rzn8"))))
11720 (build-system r-build-system)
11722 `(("r-matrix" ,r-matrix)))
11723 (home-page "https://github.com/erichson/rSVD")
11724 (synopsis "Randomized singular value decomposition")
11726 "Low-rank matrix decompositions are fundamental tools and widely used for
11727 data analysis, dimension reduction, and data compression. Classically, highly
11728 accurate deterministic matrix algorithms are used for this task. However, the
11729 emergence of large-scale data has severely challenged our computational
11730 ability to analyze big data. The concept of randomness has been demonstrated
11731 as an effective strategy to quickly produce approximate answers to familiar
11732 problems such as the @dfn{singular value decomposition} (SVD). This package
11733 provides several randomized matrix algorithms such as the randomized singular
11734 value decomposition (@code{rsvd}), randomized principal component
11735 analysis (@code{rpca}), randomized robust principal component
11736 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
11737 and the randomized CUR decomposition (@code{rcur}). In addition several plot
11738 functions are provided.")
11739 (license license:gpl3+)))
11741 (define-public r-sloop
11748 (uri (cran-uri "sloop" version))
11751 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
11752 (build-system r-build-system)
11754 `(("r-codetools" ,r-codetools)
11755 ("r-crayon" ,r-crayon)
11756 ("r-purrr" ,r-purrr)
11757 ("r-rlang" ,r-rlang)
11758 ("r-tibble" ,r-tibble)))
11759 (home-page "https://github.com/r-lib/sloop")
11760 (synopsis "Helpers for object-oriented programming in R")
11762 "This package provides a collection of helper functions designed to
11763 help you to better understand object oriented programming in R, particularly
11765 (license license:gpl3)))
11767 (define-public r-capushe
11774 (uri (cran-uri "capushe" version))
11777 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
11778 (build-system r-build-system)
11779 (propagated-inputs `(("r-mass" ,r-mass)))
11780 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
11781 (synopsis "Calibrating penalties using slope heuristics")
11783 "This package provides tools for the calibration of penalized criteria
11784 for model selection. The calibration methods available are based on the slope
11786 (license license:gpl2+)))
11788 (define-public r-dorng
11795 (uri (cran-uri "doRNG" version))
11798 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
11799 (properties `((upstream-name . "doRNG")))
11800 (build-system r-build-system)
11802 `(("r-foreach" ,r-foreach)
11803 ("r-iterators" ,r-iterators)
11804 ("r-rngtools" ,r-rngtools)))
11805 (home-page "https://renozao.github.io/doRNG/")
11806 (synopsis "Generic reproducible parallel backend for foreach loops")
11808 "This package provides functions to perform reproducible parallel
11809 @code{foreach} loops, using independent random streams as generated by
11810 L'Ecuyer's combined multiple-recursive generator. It enables to easily
11811 convert standard @code{%dopar%} loops into fully reproducible loops,
11812 independently of the number of workers, the task scheduling strategy, or the
11813 chosen parallel environment and associated foreach backend.")
11814 (license license:gpl2+)))
11816 (define-public r-blockmodeling
11818 (name "r-blockmodeling")
11823 (uri (cran-uri "blockmodeling" version))
11826 "11v9903y9dwlzaqp8sx0fsibcg82phvappddy37r8lnxd4vchsd2"))))
11827 (build-system r-build-system)
11829 `(("r-doparallel" ,r-doparallel)
11830 ("r-dorng" ,r-dorng)
11831 ("r-foreach" ,r-foreach)
11832 ("r-matrix" ,r-matrix)))
11833 (native-inputs `(("gfortran" ,gfortran)))
11834 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
11835 (synopsis "Generalized and classical blockmodeling of valued networks")
11837 "This package is primarily meant as an implementation of generalized
11838 blockmodeling for valued networks. In addition, measures of similarity or
11839 dissimilarity based on structural equivalence and regular equivalence (REGE
11840 algorithms) can be computed and partitioned matrices can be plotted.")
11841 (license license:gpl2+)))
11843 (define-public r-upsetr
11850 (uri (cran-uri "UpSetR" version))
11853 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
11854 (properties `((upstream-name . "UpSetR")))
11855 (build-system r-build-system)
11857 `(("r-ggplot2" ,r-ggplot2)
11858 ("r-gridextra" ,r-gridextra)
11860 ("r-scales" ,r-scales)))
11861 (home-page "https://github.com/hms-dbmi/UpSetR")
11862 (synopsis "Visualize intersecting sets")
11864 "This package provides a more scalable alternative to Venn and Euler
11865 diagrams for visualizing intersecting sets. Create visualizations of
11866 intersecting sets using a novel matrix design, along with visualizations of
11867 several common set, element and attribute related tasks.")
11868 (license license:expat)))
11870 ;; This package includes a JavaScript file, which is not minified. When
11871 ;; upgrading please check that there are no new minified JavaScript files.
11872 (define-public r-shinybs
11879 (uri (cran-uri "shinyBS" version))
11882 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
11883 (properties `((upstream-name . "shinyBS")))
11884 (build-system r-build-system)
11885 ;; The tests spawn Shiny browser apps. They cannot be run
11886 ;; non-interactively.
11887 (arguments '(#:tests? #f))
11889 `(("r-htmltools" ,r-htmltools)
11890 ("r-shiny" ,r-shiny)))
11891 (home-page "https://ebailey78.github.io/shinyBS/")
11892 (synopsis "Twitter Bootstrap components for Shiny")
11894 "This package adds additional Twitter Bootstrap components to Shiny.")
11895 (license license:gpl3)))
11897 (define-public r-outliers
11899 (name "r-outliers")
11904 (uri (cran-uri "outliers" version))
11907 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
11908 (build-system r-build-system)
11909 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
11910 (synopsis "Tests for outliers")
11912 "This package provides a collection of some tests commonly used for
11913 identifying outliers.")
11914 (license license:gpl2+)))
11916 (define-public r-bayesm
11923 (uri (cran-uri "bayesm" version))
11925 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
11926 (build-system r-build-system)
11928 `(("r-rcpp" ,r-rcpp)
11929 ("r-rcpparmadillo" ,r-rcpparmadillo)))
11930 (home-page "http://www.perossi.org/home/bsm-1")
11931 (synopsis "Bayesian inference for marketing/micro-econometrics")
11933 "This package covers many important models used in marketing and
11934 micro-econometrics applications, including Bayes Regression (univariate or
11935 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
11936 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
11937 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
11938 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
11939 Estimation with normal base, Hierarchical Linear Models with normal prior and
11940 covariates, Hierarchical Linear Models with a mixture of normals prior and
11941 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
11942 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
11943 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
11944 analysis of choice-based conjoint data, Bayesian treatment of linear
11945 instrumental variables models, Analysis of Multivariate Ordinal survey data
11946 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
11947 Coefficient Logit Models.")
11948 (license license:gpl2+)))
11950 (define-public r-tensora
11957 (uri (cran-uri "tensorA" version))
11960 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
11961 (properties `((upstream-name . "tensorA")))
11962 (build-system r-build-system)
11963 (home-page "http://www.stat.boogaart.de/tensorA")
11964 (synopsis "Advanced tensor arithmetic with named indices")
11966 "This package provides convenience functions for advanced linear algebra
11967 with tensors and computation with datasets of tensors on a higher level
11968 abstraction. It includes Einstein and Riemann summing conventions, dragging,
11969 co- and contravariate indices, and parallel computations on sequences of
11971 (license license:gpl2+)))
11973 (define-public r-rarpack
11980 (uri (cran-uri "rARPACK" version))
11983 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
11984 (properties `((upstream-name . "rARPACK")))
11985 (build-system r-build-system)
11986 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
11987 (home-page "https://github.com/yixuan/rARPACK")
11988 (synopsis "Solvers for large scale eigenvalue and SVD problems")
11990 "This package was previously an R wrapper of the ARPACK library, and now
11991 a shell of the R package RSpectra, an R interface to the Spectra library for
11992 solving large scale eigenvalue/vector problems. The current version of
11993 rARPACK simply imports and exports the functions provided by RSpectra. New
11994 users of rARPACK are advised to switch to the RSpectra package.")
11995 (license license:bsd-3)))
11997 (define-public r-compositions
11999 (name "r-compositions")
12004 (uri (cran-uri "compositions" version))
12007 "103hbmibrf1n333pn4xpll1gqqsv4szms0n5gdq7zak31aar0bg4"))))
12008 (build-system r-build-system)
12010 `(("r-bayesm" ,r-bayesm)
12011 ("r-robustbase" ,r-robustbase)
12012 ("r-tensora" ,r-tensora)))
12013 (home-page "http://www.stat.boogaart.de/compositions")
12014 (synopsis "Compositional data analysis")
12016 "This package provides functions for the consistent analysis of
12017 compositional data (e.g. portions of substances) and positive
12018 numbers (e.g. concentrations).")
12019 (license license:gpl2+)))
12021 (define-public r-cobs
12028 (uri (cran-uri "cobs" version))
12031 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
12032 (build-system r-build-system)
12034 `(("r-quantreg" ,r-quantreg)
12035 ("r-sparsem" ,r-sparsem)))
12036 (home-page "https://cran.r-project.org/web/packages/cobs")
12037 (synopsis "Constrained B-Splines (sparse matrix based)")
12039 "This package provides qualitatively constrained (regression) smoothing
12040 splines via linear programming and sparse matrices.")
12041 (license license:gpl2+)))
12043 (define-public r-drimpute
12045 (name "r-drimpute")
12050 (uri (cran-uri "DrImpute" version))
12053 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
12054 (properties `((upstream-name . "DrImpute")))
12055 (build-system r-build-system)
12057 `(("r-rcpp" ,r-rcpp)
12058 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12059 (home-page "https://github.com/ikwak2/DrImpute")
12060 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
12062 "This is an R package for imputing dropout events. Many statistical
12063 methods in cell type identification, visualization and lineage reconstruction
12064 do not account for dropout events. DrImpute can improve the performance of
12065 such software by imputing dropout events.")
12066 (license license:gpl3)))
12068 (define-public r-gamlss-dist
12070 (name "r-gamlss-dist")
12075 (uri (cran-uri "gamlss.dist" version))
12077 (base32 "1rl7hzdg5xpvaq3yyzwxhsaqzzs0qidi3ibv454fisijgv8l4vqw"))))
12078 (properties `((upstream-name . "gamlss.dist")))
12079 (build-system r-build-system)
12080 (propagated-inputs `(("r-mass" ,r-mass)))
12081 (home-page "http://www.gamlss.org/")
12082 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
12084 "This package provides a set of distributions which can be used for
12085 modelling the response variables in Generalized Additive Models for Location
12086 Scale and Shape. The distributions can be continuous, discrete or mixed
12087 distributions. Extra distributions can be created, by transforming, any
12088 continuous distribution defined on the real line, to a distribution defined on
12089 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
12090 transformation, respectively.")
12091 ;; Either version of the GPL.
12092 (license (list license:gpl2 license:gpl3))))
12094 ;; This package includes JavaScript files, which are not minified. When
12095 ;; upgrading please check that there are no new minified JavaScript files.
12096 (define-public r-shinyjs
12103 (uri (cran-uri "shinyjs" version))
12106 "14k8y313ppj23m9rhlk8jc94x6sbn3qrsnx6xrijiyv8m8dii1l9"))))
12107 (build-system r-build-system)
12109 `(("r-digest" ,r-digest)
12110 ("r-htmltools" ,r-htmltools)
12111 ("r-jsonlite" ,r-jsonlite)
12112 ("r-shiny" ,r-shiny)))
12113 (home-page "https://deanattali.com/shinyjs")
12114 (synopsis "Improve the user experience of your Shiny apps")
12116 "Perform common useful JavaScript operations in Shiny apps that will
12117 greatly improve your apps without having to know any JavaScript. Examples
12118 include: hiding an element, disabling an input, resetting an input back to its
12119 original value, delaying code execution by a few seconds, and many more useful
12120 functions for both the end user and the developer. Shinyjs can also be used
12121 to easily call your own custom JavaScript functions from R.")
12122 (license license:agpl3+)))
12124 ;; This package includes minified JavaScript files. When upgrading please
12125 ;; check that there are no new minified JavaScript files.
12126 (define-public r-colourpicker
12128 (name "r-colourpicker")
12133 (uri (cran-uri "colourpicker" version))
12136 "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
12137 (build-system r-build-system)
12139 `(#:modules ((guix build utils)
12140 (guix build r-build-system)
12144 (modify-phases %standard-phases
12145 (add-after 'unpack 'process-javascript
12146 (lambda* (#:key inputs #:allow-other-keys)
12147 (with-directory-excursion "inst"
12151 `((,(assoc-ref inputs "js-salvattore")
12152 "examples/colourInput/www/salvattore.min.js")
12153 (,(assoc-ref inputs "js-jquery")
12154 "htmlwidgets/lib/jquery/jquery.min.js")
12155 ("www/shared/colourpicker/js/colourpicker.js"
12156 "www/shared/colourpicker/js/colourpicker.min.js"))))
12157 (lambda (sources targets)
12158 (for-each (lambda (source target)
12159 (format #t "Processing ~a --> ~a~%"
12161 (delete-file target)
12162 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
12163 (call-with-output-file target
12165 (dump-port minified port)))))
12166 sources targets))))
12169 `(("r-ggplot2" ,r-ggplot2)
12170 ("r-htmltools" ,r-htmltools)
12171 ("r-htmlwidgets" ,r-htmlwidgets)
12172 ("r-jsonlite" ,r-jsonlite)
12173 ("r-miniui" ,r-miniui)
12174 ("r-shiny" ,r-shiny)
12175 ("r-shinyjs" ,r-shinyjs)))
12177 `(("uglify-js" ,uglify-js)
12181 (uri "https://code.jquery.com/jquery-3.3.1.js")
12184 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
12188 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
12191 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
12192 (home-page "https://github.com/daattali/colourpicker")
12193 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
12195 "This package provides a color picker that can be used as an input in
12196 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
12197 custom color palettes, and many more options. A plot color helper tool is
12198 available as an RStudio Addin, which helps you pick colors to use in your
12199 plots. A more generic color picker RStudio Addin is also provided to let you
12200 select colors to use in your R code.")
12201 (license license:expat)))
12203 (define-public r-ggextra
12210 (uri (cran-uri "ggExtra" version))
12213 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
12214 (properties `((upstream-name . "ggExtra")))
12215 (build-system r-build-system)
12217 `(("r-colourpicker" ,r-colourpicker)
12218 ("r-ggplot2" ,r-ggplot2)
12219 ("r-gtable" ,r-gtable)
12220 ("r-miniui" ,r-miniui)
12222 ("r-scales" ,r-scales)
12223 ("r-shiny" ,r-shiny)
12224 ("r-shinyjs" ,r-shinyjs)))
12225 (home-page "https://github.com/daattali/ggExtra")
12226 (synopsis "Marginal histograms for ggplot2 and other enhancements")
12228 "This package is a collection of functions and layers to enhance ggplot2.
12229 The flagship function is @code{ggMarginal()}, which can be used to add
12230 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
12231 (license license:expat)))
12233 (define-public r-minpack-lm
12235 (name "r-minpack-lm")
12240 (uri (cran-uri "minpack.lm" version))
12243 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
12244 (properties `((upstream-name . "minpack.lm")))
12245 (build-system r-build-system)
12246 (native-inputs `(("gfortran" ,gfortran)))
12247 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
12248 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
12250 "The @code{nls.lm} function provides an R interface to @code{lmder} and
12251 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
12252 problems by a modification of the Levenberg-Marquardt algorithm, with support
12253 for lower and upper parameter bounds. The implementation can be used via
12254 @code{nls}-like calls using the @code{nlsLM} function.")
12255 (license license:gpl3)))
12257 (define-public r-moments
12264 (uri (cran-uri "moments" version))
12267 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
12268 (build-system r-build-system)
12269 (home-page "https://cran.r-project.org/web/packages/moments")
12270 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
12272 "This package provides functions to calculate: moments, Pearson's
12273 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
12274 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
12275 (license license:gpl2+)))
12277 (define-public r-msir
12284 (uri (cran-uri "msir" version))
12287 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
12288 (build-system r-build-system)
12290 `(("r-mclust" ,r-mclust)))
12291 (home-page "https://cran.r-project.org/web/packages/msir")
12292 (synopsis "Model-based sliced inverse regression")
12294 "This is an R package for dimension reduction based on finite Gaussian
12295 mixture modeling of inverse regression.")
12296 (license license:gpl2+)))
12298 (define-public r-pbivnorm
12300 (name "r-pbivnorm")
12305 (uri (cran-uri "pbivnorm" version))
12308 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
12309 (build-system r-build-system)
12310 (native-inputs `(("gfortran" ,gfortran)))
12311 (home-page "https://github.com/brentonk/pbivnorm")
12312 (synopsis "Vectorized bivariate normal CDF")
12314 "This package provides a vectorized R function for calculating
12315 probabilities from a standard bivariate normal CDF.")
12316 (license license:gpl2+)))
12318 (define-public r-lavaan
12325 (uri (cran-uri "lavaan" version))
12328 "04kvsh2m6mnzlhv83phr3hjzy4sx1ck6f7dgsm7xb8cs84dnxszy"))))
12329 (build-system r-build-system)
12331 `(("r-mass" ,r-mass)
12332 ("r-mnormt" ,r-mnormt)
12333 ("r-numderiv" ,r-numderiv)
12334 ("r-pbivnorm" ,r-pbivnorm)))
12335 (home-page "http://lavaan.ugent.be")
12336 (synopsis "Latent variable analysis")
12338 "This package provides tools to fit a variety of latent variable models,
12339 including confirmatory factor analysis, structural equation modeling and
12340 latent growth curve models.")
12341 (license license:gpl2+)))
12343 (define-public r-nonnest2
12345 (name "r-nonnest2")
12350 (uri (cran-uri "nonnest2" version))
12353 "1bq44qqmm59j91m0sny4xnqmxqlga4cm48qdsw8xfs3x19xwmxk6"))))
12354 (build-system r-build-system)
12356 `(("r-compquadform" ,r-compquadform)
12357 ("r-lavaan" ,r-lavaan)
12358 ("r-mvtnorm" ,r-mvtnorm)
12359 ("r-sandwich" ,r-sandwich)))
12360 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
12361 (synopsis "Tests of non-nested models")
12363 "This package allows for testing of non-nested models. It includes tests
12364 of model distinguishability and of model fit that can be applied to both
12365 nested and non-nested models. The package also includes functionality to
12366 obtain confidence intervals associated with AIC and BIC.")
12367 ;; Either version of the GPL.
12368 (license (list license:gpl2 license:gpl3))))
12370 (define-public r-penalized
12372 (name "r-penalized")
12377 (uri (cran-uri "penalized" version))
12380 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
12381 (build-system r-build-system)
12383 `(("r-rcpp" ,r-rcpp)
12384 ("r-rcpparmadillo" ,r-rcpparmadillo)
12385 ("r-survival" ,r-survival)))
12386 (home-page "https://cran.r-project.org/web/packages/penalized/")
12387 (synopsis "Penalized estimation in GLMs and in the Cox model")
12389 "This package provides tools for fitting possibly high dimensional
12390 penalized regression models. The penalty structure can be any combination of
12391 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
12392 constraint on the regression coefficients. The supported regression models
12393 are linear, logistic and Poisson regression and the Cox Proportional Hazards
12394 model. Cross-validation routines allow optimization of the tuning
12396 (license license:gpl2+)))
12398 (define-public r-zim
12405 (uri (cran-uri "ZIM" version))
12408 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
12409 (properties `((upstream-name . "ZIM")))
12410 (build-system r-build-system)
12411 (propagated-inputs `(("r-mass" ,r-mass)))
12412 (home-page "https://github.com/biostatstudio/ZIM")
12413 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
12415 "Analyze count time series with excess zeros. Two types of statistical
12416 models are supported: Markov regression and state-space models. They are also
12417 known as observation-driven and parameter-driven models respectively in the
12418 time series literature. The functions used for Markov regression or
12419 observation-driven models can also be used to fit ordinary regression models
12420 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
12421 negative binomial (ZINB) assumption. The package also contains miscellaneous
12422 functions to compute density, distribution, quantile, and generate random
12423 numbers from ZIP and ZINB distributions.")
12424 (license license:gpl3)))
12426 (define-public r-nor1mix
12433 (uri (cran-uri "nor1mix" version))
12436 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
12437 (build-system r-build-system)
12438 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
12439 (synopsis "Normal (1-d) mixture models")
12441 "This package provides S3 classes and methods for one-dimensional normal
12442 mixture models, for, e.g., density estimation or clustering algorithms
12443 research and teaching; it provides the widely used Marron-Wand densities. It
12444 also provides tools for efficient random number generation and graphics.")
12445 (license license:gpl2+)))
12447 (define-public r-beanplot
12449 (name "r-beanplot")
12454 (uri (cran-uri "beanplot" version))
12457 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
12458 (build-system r-build-system)
12459 (home-page "https://cran.r-project.org/web/packages/beanplot/")
12460 (synopsis "Visualization via beanplots")
12462 "This package provides beanplots, an alternative to
12463 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
12465 (license license:gpl2)))
12467 (define-public r-pbdzmq
12474 (uri (cran-uri "pbdZMQ" version))
12477 "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
12478 (properties `((upstream-name . "pbdZMQ")))
12479 (build-system r-build-system)
12481 `(("zeromq" ,zeromq)
12484 `(("pkg-config" ,pkg-config)))
12485 (home-page "https://pbdr.org/")
12486 (synopsis "R interface to ZeroMQ")
12488 "ZeroMQ is a well-known library for high-performance asynchronous
12489 messaging in scalable, distributed applications. This package provides high
12490 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
12491 interactive client/server programming frameworks. A few wrapper functions
12492 compatible with @code{rzmq} are also provided.")
12493 (license license:gpl3)))
12495 (define-public r-repr
12502 (uri (cran-uri "repr" version))
12505 "0wn9fdddqjgn0bdfl75x89rcxahbgqs324bhg0pfq6va5q2mlbbw"))))
12506 (build-system r-build-system)
12508 `(("r-base64enc" ,r-base64enc)
12509 ("r-htmltools" ,r-htmltools)
12510 ("r-jsonlite" ,r-jsonlite)
12511 ("r-pillar" ,r-pillar)))
12512 (home-page "https://cran.r-project.org/web/packages/repr/")
12513 (synopsis "Serializable representations")
12515 "This package provides string and binary representations of objects for
12516 several formats and MIME types.")
12517 (license license:gpl3)))
12519 (define-public r-irdisplay
12521 (name "r-irdisplay")
12526 (uri (cran-uri "IRdisplay" version))
12529 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
12530 (properties `((upstream-name . "IRdisplay")))
12531 (build-system r-build-system)
12533 `(("r-repr" ,r-repr)))
12534 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
12535 (synopsis "Jupyter display machinery")
12537 "This package provides an interface to the rich display capabilities of
12538 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
12539 running IRkernel session.")
12540 (license license:expat)))
12542 (define-public r-irkernel
12544 (name "r-irkernel")
12549 (uri (cran-uri "IRkernel" version))
12552 "1viqxs91dys1z4cf7gb59rmqvzb8lc7jdp4azrpmhgwa8qf46s94"))))
12553 (properties `((upstream-name . "IRkernel")))
12554 (build-system r-build-system)
12557 (modify-phases %standard-phases
12558 (add-after 'install 'install-kernelspec
12559 (lambda* (#:key outputs #:allow-other-keys)
12560 (let ((out (assoc-ref outputs "out")))
12561 (setenv "HOME" "/tmp")
12562 (invoke "jupyter" "kernelspec" "install"
12565 (string-append out "/site-library/IRkernel/kernelspec"))
12566 ;; Record the absolute file name of the 'R' executable in
12568 (substitute* (string-append out "/share/jupyter"
12569 "/kernels/ir/kernel.json")
12571 (string-append "[\"" (which "R") "\",")))
12574 `(("jupyter" ,jupyter)))
12576 `(("r-crayon" ,r-crayon)
12577 ("r-digest" ,r-digest)
12578 ("r-evaluate" ,r-evaluate)
12579 ("r-irdisplay" ,r-irdisplay)
12580 ("r-jsonlite" ,r-jsonlite)
12581 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
12582 ("r-minimal" ,r-minimal)
12583 ("r-pbdzmq" ,r-pbdzmq)
12585 ("r-uuid" ,r-uuid)))
12586 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
12587 (synopsis "Native R kernel for Jupyter")
12589 "The R kernel for the Jupyter environment executes R code which the
12590 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
12592 (license license:expat)))
12594 (define-public r-gmodels
12601 (uri (cran-uri "gmodels" version))
12604 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
12605 (build-system r-build-system)
12607 `(("r-gdata" ,r-gdata)
12608 ("r-mass" ,r-mass)))
12609 (home-page "https://cran.r-project.org/web/packages/gmodels/")
12610 (synopsis "Various R programming tools for model fitting")
12612 "This package provides various R programming tools for model fitting.")
12613 (license license:gpl2)))
12615 (define-public r-apcluster
12617 (name "r-apcluster")
12622 (uri (cran-uri "apcluster" version))
12625 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
12626 (build-system r-build-system)
12628 `(("r-matrix" ,r-matrix)
12629 ("r-rcpp" ,r-rcpp)))
12630 (home-page "https://cran.r-project.org/web/packages/apcluster/")
12631 (synopsis "Affinity propagation clustering")
12633 "This package implements affinity propagation clustering introduced by
12634 Frey and Dueck (2007). The package further provides leveraged affinity
12635 propagation and an algorithm for exemplar-based agglomerative clustering that
12636 can also be used to join clusters obtained from affinity propagation. Various
12637 plotting functions are available for analyzing clustering results.")
12638 (license license:gpl2+)))
12640 (define-public r-valr
12647 (uri (cran-uri "valr" version))
12650 "14jhrwkiwmha3vlmm7b50n2xxyizj6ddmy89gb20mpzq7qhz1ika"))))
12651 (build-system r-build-system)
12653 `(("r-broom" ,r-broom)
12654 ("r-dplyr" ,r-dplyr)
12655 ("r-ggplot2" ,r-ggplot2)
12657 ("r-readr" ,r-readr)
12658 ("r-rlang" ,r-rlang)
12659 ("r-stringr" ,r-stringr)
12660 ("r-tibble" ,r-tibble)))
12661 (home-page "http://github.com/rnabioco/valr")
12662 (synopsis "Genome interval arithmetic in R")
12664 "This package enables you to read and manipulate genome intervals and
12665 signals. It provides functionality similar to command-line tool suites within
12666 R, enabling interactive analysis and visualization of genome-scale data.")
12667 (license license:expat)))
12669 (define-public r-rematch2
12671 (name "r-rematch2")
12676 (uri (cran-uri "rematch2" version))
12679 "00cznm6rk33b53w7zybkz7549bnydc66znpi5mb0xd24pmqp0rvq"))))
12680 (build-system r-build-system)
12682 `(("r-tibble" ,r-tibble)))
12683 (home-page "https://github.com/r-lib/rematch2")
12684 (synopsis "Tidy output from regular expression matching")
12686 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
12687 return the match results in tidy data frames.")
12688 (license license:expat)))
12690 (define-public r-picante
12697 (uri (cran-uri "picante" version))
12700 "1bcq2j7fs89c2jib68qq6la67rxyg9raryf162mwvjakpf6k19l1"))))
12701 (build-system r-build-system)
12705 ("r-vegan" ,r-vegan)))
12706 (home-page "https://cran.r-project.org/web/packages/picante/")
12707 (synopsis "Integrating phylogenies and ecology")
12709 "This package provides functions for phylocom integration, community
12710 analyses, null-models, traits and evolution. It implements numerous
12711 ecophylogenetic approaches including measures of community phylogenetic and
12712 trait diversity, phylogenetic signal, estimation of trait values for
12713 unobserved taxa, null models for community and phylogeny randomizations, and
12714 utility functions for data input/output and phylogeny plotting. A full
12715 description of package functionality and methods are provided by Kembel et
12717 (license license:gpl2)))
12719 (define-public r-reinforcelearn
12721 (name "r-reinforcelearn")
12726 (uri (cran-uri "reinforcelearn" version))
12729 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
12730 (build-system r-build-system)
12732 `(("r-checkmate" ,r-checkmate)
12734 ("r-purrr" ,r-purrr)
12736 (home-page "https://markusdumke.github.io/reinforcelearn")
12737 (synopsis "Reinforcement learning")
12739 "This package implements reinforcement learning environments and
12740 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
12741 can be used with function approximation, eligibility traces (Singh & Sutton,
12742 1996) and experience replay (Mnih et al., 2013).")
12743 (license license:expat)))
12745 (define-public r-lemon
12752 (uri (cran-uri "lemon" version))
12755 "0wsn5bfg10wq4dnrgpyraz2bzx9p19c7hf1pwj3h4zmpqfgsdbpw"))))
12756 (build-system r-build-system)
12758 `(("r-ggplot2" ,r-ggplot2)
12759 ("r-gridextra" ,r-gridextra)
12760 ("r-gtable" ,r-gtable)
12761 ("r-knitr" ,r-knitr)
12762 ("r-lattice" ,r-lattice)
12764 ("r-scales" ,r-scales)))
12765 (home-page "https://github.com/stefanedwards/lemon")
12766 (synopsis "Freshen up your ggplot2 plots")
12768 "This package provides functions for working with legends and axis lines
12769 of ggplot2, facets that repeat axis lines on all panels, and some knitr
12771 (license license:gpl3)))
12773 (define-public r-wgaim
12780 (uri (cran-uri "wgaim" version))
12782 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
12783 (build-system r-build-system)
12785 `(("r-ggplot2" ,r-ggplot2)
12787 (home-page "https://cran.r-project.org/web/packages/wgaim")
12788 (synopsis "Whole genome average interval mapping for QTL detection")
12790 "This package integrates sophisticated mixed modelling methods with a
12791 whole genome approach to detecting significant QTL in linkage maps.")
12792 (license license:gpl2+)))
12794 (define-public r-bedr
12801 (uri (cran-uri "bedr" version))
12804 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
12805 (build-system r-build-system)
12807 `(("r-data-table" ,r-data-table)
12808 ("r-r-utils" ,r-r-utils)
12809 ("r-testthat" ,r-testthat)
12810 ("r-venndiagram" ,r-venndiagram)
12813 ("bedtools" ,bedtools)
12814 ("htslib" ,htslib))) ; for tabix
12816 `(("r-knitr" ,r-knitr))) ; for vignettes
12817 (home-page "https://cran.r-project.org/web/packages/bedr")
12818 (synopsis "Genomic region processing")
12820 "This package is for genomic regions processing using command line tools
12821 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
12822 utilities to perform genome arithmetic e.g indexing, formatting and merging.
12823 The bedr package's API enhances access to these tools as well as offers
12824 additional utilities for genomic regions processing.")
12825 (license license:gpl2)))
12827 (define-public r-sets
12834 (uri (cran-uri "sets" version))
12837 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
12838 (properties `((upstream-name . "sets")))
12839 (build-system r-build-system)
12840 (home-page "https://cran.r-project.org/web/packages/sets")
12841 (synopsis "Sets, generalized sets, customizable sets and intervals")
12843 "This package provides data structures and basic operations for ordinary
12844 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
12845 customizable sets, and intervals.")
12846 (license license:gpl2)))
12848 (define-public r-partitions
12850 (name "r-partitions")
12855 (uri (cran-uri "partitions" version))
12858 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
12859 (build-system r-build-system)
12862 ("r-polynom" ,r-polynom)
12863 ("r-sets" ,r-sets)))
12864 (home-page "https://cran.r-project.org/web/packages/partitions")
12865 (synopsis "Additive partitions of integers")
12867 "This package provides tools to enumerates the partitions, unequal
12868 partitions, and restricted partitions of an integer; the three corresponding
12869 partition functions are also given.")
12870 ;; Any version of the GPL
12871 (license license:gpl2+)))
12873 (define-public r-brobdingnag
12875 (name "r-brobdingnag")
12880 (uri (cran-uri "Brobdingnag" version))
12883 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
12884 (properties `((upstream-name . "Brobdingnag")))
12885 (build-system r-build-system)
12886 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
12887 (synopsis "Very large numbers in R")
12889 "This package handles very large numbers in R. Real numbers are held
12890 using their natural logarithms, plus a logical flag indicating sign. The
12891 package includes a vignette that gives a step-by-step introduction to using S4
12893 ;; Any version of the GPL
12894 (license license:gpl2+)))
12896 (define-public r-untb
12903 (uri (cran-uri "untb" version))
12906 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
12907 (build-system r-build-system)
12909 `(("r-brobdingnag" ,r-brobdingnag)
12910 ("r-partitions" ,r-partitions)
12911 ("r-polynom" ,r-polynom)))
12912 (home-page "https://github.com/RobinHankin/untb.git")
12913 (synopsis "Ecological drift under the UNTB")
12915 "This package provides numerical simulations, and visualizations, of
12916 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
12917 (license license:gpl2+)))
12919 (define-public r-stepwise
12921 (name "r-stepwise")
12926 (uri (cran-uri "stepwise" version))
12929 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
12930 (build-system r-build-system)
12931 (home-page "http://stat.sfu.ca/statgen/research/stepwise.html")
12932 (synopsis "Stepwise detection of recombination breakpoints")
12934 "This package provides a stepwise approach to identifying recombination
12935 breakpoints in a genomic sequence alignment.")
12936 (license license:gpl2+)))
12938 (define-public r-snpmaxsel
12940 (name "r-snpmaxsel")
12945 (uri (cran-uri "SNPmaxsel" version))
12948 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
12949 (properties `((upstream-name . "SNPmaxsel")))
12950 (build-system r-build-system)
12952 `(("r-combinat" ,r-combinat)
12953 ("r-mvtnorm" ,r-mvtnorm)))
12954 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
12955 (synopsis "Maximally selected statistics for SNP data")
12957 "This package implements asymptotic methods related to maximally selected
12958 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
12960 (license license:gpl2+)))
12962 (define-public r-acsnminer
12964 (name "r-acsnminer")
12965 (version "0.16.8.25")
12968 (uri (cran-uri "ACSNMineR" version))
12971 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
12972 (properties `((upstream-name . "ACSNMineR")))
12973 (build-system r-build-system)
12975 `(("r-ggplot2" ,r-ggplot2)
12976 ("r-gridextra" ,r-gridextra)))
12977 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
12978 (synopsis "Gene enrichment analysis")
12980 "This package provides tools to compute and represent gene set enrichment
12981 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
12982 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
12983 enrichment can be run with hypergeometric test or Fisher exact test, and can
12984 use multiple corrections. Visualization of data can be done either by
12985 barplots or heatmaps.")
12986 (license license:gpl2+)))
12988 (define-public r-seqinr
12995 (uri (cran-uri "seqinr" version))
12998 "0j30za6kji6y3v09cvcydiacnp65pv6ig8aw7cydl47l5s9chky4"))))
12999 (build-system r-build-system)
13001 `(("r-ade4" ,r-ade4)
13002 ("r-segmented" ,r-segmented)))
13005 (home-page "http://seqinr.r-forge.r-project.org/")
13006 (synopsis "Biological sequences retrieval and analysis")
13008 "This package provides tools for exploratory data analysis and data
13009 visualization of biological sequence (DNA and protein) data. It also includes
13010 utilities for sequence data management under the ACNUC system.")
13011 (license license:gpl2+)))
13013 (define-public r-units
13020 (uri (cran-uri "units" version))
13023 "02nls8m0r1r7kljs4x35naz3szq62hyqyd5vracf1xwi1kz5kdsh"))))
13024 (build-system r-build-system)
13026 `(("udunits" ,udunits)))
13028 `(("r-rcpp" ,r-rcpp)))
13029 (home-page "https://github.com/r-quantities/units/")
13030 (synopsis "Measurement Units for R Vectors")
13032 "This package provides support for measurement units in R vectors,
13033 matrices and arrays: automatic propagation, conversion, derivation and
13034 simplification of units; raising errors in case of unit incompatibility. It
13035 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
13037 (license license:gpl2)))
13039 (define-public r-classint
13041 (name "r-classint")
13046 (uri (cran-uri "classInt" version))
13049 "0w980hrw8sgfdfyd5dsimalq7gwhvqm7507abk7k363pvgks23dv"))))
13050 (properties `((upstream-name . "classInt")))
13051 (build-system r-build-system)
13053 `(("r-class" ,r-class)
13054 ("r-e1071" ,r-e1071)
13055 ("r-kernsmooth" ,r-kernsmooth)))
13056 (native-inputs `(("gfortran" ,gfortran)))
13057 (home-page "https://github.com/r-spatial/classInt/")
13058 (synopsis "Choose univariate class intervals")
13060 "This package provides selected commonly used methods for choosing
13061 univariate class intervals for mapping or other graphics purposes.")
13062 (license license:gpl2+)))
13064 (define-public r-spdata
13071 (uri (cran-uri "spData" version))
13074 "190msrrpn226x27pcnck4ac34f9k4xcn26cyz2apdri2nzkr6zbw"))))
13075 (properties `((upstream-name . "spData")))
13076 (build-system r-build-system)
13077 (home-page "https://github.com/Nowosad/spData")
13078 (synopsis "Datasets for spatial analysis")
13080 "This a package containing diverse spatial datasets for demonstrating,
13081 benchmarking and teaching spatial data analysis. It includes R data of class
13082 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
13083 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
13084 of the datasets are designed to illustrate specific analysis techniques.
13085 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
13086 illustrate point pattern analysis techniques.")
13087 (license license:cc0)))
13089 (define-public r-learnbayes
13091 (name "r-learnbayes")
13096 (uri (cran-uri "LearnBayes" version))
13099 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
13100 (properties `((upstream-name . "LearnBayes")))
13101 (build-system r-build-system)
13102 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
13103 (synopsis "Functions for learning Bayesian inference")
13105 "This package provides a collection of functions helpful in learning the
13106 basic tenets of Bayesian statistical inference. It contains functions for
13107 summarizing basic one and two parameter posterior distributions and predictive
13108 distributions. It contains MCMC algorithms for summarizing posterior
13109 distributions defined by the user. It also contains functions for regression
13110 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
13112 (license license:gpl2+)))
13114 (define-public r-deldir
13121 (uri (cran-uri "deldir" version))
13124 "0790dwxb2mz1ffz8gd5vwdr0if2q76dzy3vab5rsykf9kz72n4g0"))))
13125 (build-system r-build-system)
13126 (native-inputs `(("gfortran" ,gfortran)))
13127 (home-page "https://cran.r-project.org/web/packages/deldir")
13128 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
13130 "This package provides tools for calculating the Delaunay triangulation
13131 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
13132 of a planar point set. It plots triangulations and tessellations in various
13133 ways, clips tessellations to sub-windows, calculates perimeters of
13134 tessellations, and summarizes information about the tiles of the
13136 (license license:gpl2+)))
13138 (define-public r-sf
13145 (uri (cran-uri "sf" version))
13148 "05dyq0vcz2f1fl03hk3v1a4nz4s84yyqw4rc9w9cwfq71gvm9qwf"))))
13149 (build-system r-build-system)
13156 `(("r-classint" ,r-classint)
13158 ("r-magrittr" ,r-magrittr)
13160 ("r-units" ,r-units)))
13161 (native-inputs `(("pkg-config" ,pkg-config)))
13162 (home-page "https://github.com/r-spatial/sf/")
13163 (synopsis "Simple features for R")
13165 "This package provides support for simple features, a standardized way to
13166 encode spatial vector data. It binds to GDAL for reading and writing data, to
13167 GEOS for geometrical operations, and to PROJ for projection conversions and
13168 datum transformations.")
13169 ;; Either of these licenses
13170 (license (list license:gpl2 license:expat))))
13172 (define-public r-spdep
13179 (uri (cran-uri "spdep" version))
13182 "1f8cjffqqc6rnb3n4qym70ca6nz2kvrsd3g587wrqdr79nnbwnrk"))))
13183 (build-system r-build-system)
13185 `(("r-boot" ,r-boot)
13187 ("r-deldir" ,r-deldir)
13189 ("r-gmodels" ,r-gmodels)
13190 ("r-learnbayes" ,r-learnbayes)
13192 ("r-matrix" ,r-matrix)
13196 ("r-spdata" ,r-spdata)))
13197 (home-page "https://github.com/r-spatial/spdep/")
13198 (synopsis "Spatial dependence: weighting schemes, statistics and models")
13200 "This package provides a collection of functions to create spatial
13201 weights matrix objects from polygon contiguities, from point patterns by
13202 distance and tessellations, for summarizing these objects, and for permitting
13203 their use in spatial data analysis, including regional aggregation by minimum
13205 (license license:gpl2+)))
13207 (define-public r-adegenet
13209 (name "r-adegenet")
13214 (uri (cran-uri "adegenet" version))
13217 "01fgrgbiddz2q4l3mx637hhwbs7r0c43yw7vpwl8p8pwbm3nykz0"))))
13218 (build-system r-build-system)
13220 `(("r-ade4" ,r-ade4)
13223 ("r-dplyr" ,r-dplyr)
13224 ("r-ggplot2" ,r-ggplot2)
13225 ("r-igraph" ,r-igraph)
13227 ("r-reshape2" ,r-reshape2)
13228 ("r-seqinr" ,r-seqinr)
13229 ("r-shiny" ,r-shiny)
13230 ("r-spdep" ,r-spdep)
13231 ("r-vegan" ,r-vegan)))
13232 (home-page "https://github.com/thibautjombart/adegenet")
13233 (synopsis "Exploratory analysis of genetic and genomic data")
13235 "This package provides a toolset for the exploration of genetic and
13236 genomic data. Adegenet provides formal (S4) classes for storing and handling
13237 various genetic data, including genetic markers with varying ploidy and
13238 hierarchical population structure (@code{genind} class), alleles counts by
13239 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
13240 also implements original multivariate methods (DAPC, sPCA), graphics,
13241 statistical tests, simulation tools, distance and similarity measures, and
13242 several spatial methods. A range of both empirical and simulated datasets is
13243 also provided to illustrate various methods.")
13244 (license license:gpl2+)))
13246 (define-public r-pegas
13253 (uri (cran-uri "pegas" version))
13255 (base32 "0sb8cmz4d238mcb56hv9fa0cagm00k82r7aj4cj4lxa1flxlpy8p"))))
13256 (build-system r-build-system)
13258 `(("r-adegenet" ,r-adegenet)
13260 (home-page "http://ape-package.ird.fr/pegas.html")
13261 (synopsis "Population and evolutionary genetics analysis system")
13263 "This package provides functions for reading, writing, plotting,
13264 analysing, and manipulating allelic and haplotypic data, including from VCF
13265 files, and for the analysis of population nucleotide sequences and
13266 micro-satellites including coalescent analyses, linkage disequilibrium,
13267 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
13268 minimum spanning tree and network, and median-joining networks.")
13269 (license license:gpl2+)))
13271 (define-public r-rmetasim
13273 (name "r-rmetasim")
13278 (uri (cran-uri "rmetasim" version))
13281 "0sz4mdprdi6sgkfwfdvh2hr9nxiwq17sw0vggq3cvs7lzb0i6m9r"))))
13282 (build-system r-build-system)
13284 `(("r-ade4" ,r-ade4)
13285 ("r-adegenet" ,r-adegenet)
13286 ("r-gtools" ,r-gtools)
13287 ("r-pegas" ,r-pegas)))
13288 (home-page "https://cran.r-project.org/web/packages/rmetasim")
13289 (synopsis "Individual-based population genetic simulation environment")
13291 "This package provides an interface between R and the metasim simulation
13292 engine. The simulation environment is documented in: Strand, A.(2002),
13293 Metasim 1.0: an individual-based environment for simulating population
13294 genetics of complex population dynamics.")
13296 (license license:gpl2+)))
13298 (define-public r-genetics
13300 (name "r-genetics")
13301 (version "1.3.8.1.2")
13305 (uri (cran-uri "genetics" version))
13308 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
13309 (build-system r-build-system)
13311 `(("r-combinat" ,r-combinat)
13312 ("r-gdata" ,r-gdata)
13313 ("r-gtools" ,r-gtools)
13315 ("r-mvtnorm" ,r-mvtnorm)))
13316 (home-page "https://cran.r-project.org/web/packages/genetics/")
13317 (synopsis "Population genetics")
13319 "This package provides classes and methods for handling genetic data.
13320 It includes classes to represent genotypes and haplotypes at single markers up
13321 to multiple markers on multiple chromosomes. Function include allele
13322 frequencies, flagging homo/heterozygotes, flagging carriers of certain
13323 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
13324 and testing for linkage disequilibrium, ...")
13325 ;; Any GPL version.
13326 (license license:gpl2+)))
13328 (define-public r-snp-plotter
13330 (name "r-snp-plotter")
13335 (uri (cran-uri "snp.plotter" version))
13338 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
13339 (properties `((upstream-name . "snp.plotter")))
13340 (build-system r-build-system)
13341 (propagated-inputs `(("r-genetics" ,r-genetics)))
13342 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
13343 (synopsis "Plot p-values using single SNP and/or haplotype data")
13345 "This package helps you create plots of p-values using single SNP and/or
13346 haplotype data. Main features of the package include options to display a
13347 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
13348 datasets simultaneously. Plots can be created using global and/or individual
13349 haplotype p-values along with single SNP p-values. Images are created as
13350 either PDF/EPS files.")
13351 (license license:gpl2+)))
13353 (define-public r-polspline
13355 (name "r-polspline")
13360 (uri (cran-uri "polspline" version))
13362 (base32 "0c7fnxpqpy3hibiim4yib6l6bq363s97wwvllxp4lp8h06fjcyyn"))))
13363 (build-system r-build-system)
13364 (native-inputs `(("gfortran" ,gfortran)))
13365 (home-page "https://cran.r-project.org/web/packages/polspline/")
13366 (synopsis "Polynomial spline routines")
13368 "This package provides routines for the polynomial spline fitting
13369 routines hazard regression, hazard estimation with flexible tails, logspline,
13370 lspec, polyclass, and polymars.")
13371 (license license:gpl2+)))
13373 (define-public r-rms
13380 (uri (cran-uri "rms" version))
13382 (base32 "19knh1sw0icw6jh9wfb2hq5jf49i2qfvp9myvqm5paa495689x9q"))))
13383 (build-system r-build-system)
13385 `(("r-ggplot2" ,r-ggplot2)
13386 ("r-hmisc" ,r-hmisc)
13387 ("r-htmltable" ,r-htmltable)
13388 ("r-htmltools" ,r-htmltools)
13389 ("r-lattice" ,r-lattice)
13390 ("r-multcomp" ,r-multcomp)
13392 ("r-polspline" ,r-polspline)
13393 ("r-quantreg" ,r-quantreg)
13394 ("r-rpart" ,r-rpart)
13395 ("r-sparsem" ,r-sparsem)
13396 ("r-survival" ,r-survival)))
13397 (native-inputs `(("gfortran" ,gfortran)))
13398 (home-page "http://biostat.mc.vanderbilt.edu/rms")
13399 (synopsis "Regression modeling strategies")
13401 "This is a package for regression modeling, testing, estimation,
13402 validation, graphics, prediction, and typesetting by storing enhanced model
13403 design attributes in the fit. The rms package is a collection of functions
13404 that assist with and streamline modeling. It also contains functions for
13405 binary and ordinal logistic regression models, ordinal models for continuous Y
13406 with a variety of distribution families, and the Buckley-James multiple
13407 regression model for right-censored responses, and implements penalized
13408 maximum likelihood estimation for logistic and ordinary linear models. The
13409 package works with almost any regression model, but it was especially written
13410 to work with binary or ordinal regression models, Cox regression, accelerated
13411 failure time models, ordinary linear models, the Buckley-James model,
13412 generalized least squares for serially or spatially correlated observations,
13413 generalized linear models, and quantile regression.")
13414 (license license:gpl2+)))
13416 (define-public r-haplo-stats
13418 (name "r-haplo-stats")
13423 (uri (cran-uri "haplo.stats" version))
13426 "19kxascqq5qz0zdxx0w837ji207y1z2ggxkl4vmlbay03k2dw2mx"))))
13427 (properties `((upstream-name . "haplo.stats")))
13428 (build-system r-build-system)
13430 `(("r-rms" ,r-rms)))
13432 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
13433 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
13434 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
13436 "This package provides routines for the analysis of indirectly measured
13437 haplotypes. The statistical methods assume that all subjects are unrelated
13438 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
13439 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
13440 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
13441 examples in the vignette.")
13442 (license license:gpl2+)))
13444 (define-public r-bqtl
13451 (uri (cran-uri "bqtl" version))
13454 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
13455 (build-system r-build-system)
13456 (native-inputs `(("gfortran" ,gfortran)))
13457 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
13458 (synopsis "Bayesian QTL mapping toolkit")
13460 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
13461 lines. It includes maximum likelihood and Bayesian tools.")
13462 (license license:gpl2+)))
13464 (define-public r-ibdreg
13471 (uri (cran-uri "ibdreg" version))
13474 "1kaa5q1byi30wzr0mw4w2cv1ssxprzcwf91wrpqwkgcsdy7dkh2g"))))
13475 (build-system r-build-system)
13476 (home-page "https://www.mayo.edu/research/labs/\
13477 statistical-genetics-genetic-epidemiology/software")
13478 (synopsis "Regression methods for IBD linkage with covariates")
13480 "This package provides a method to test genetic linkage with covariates
13481 by regression methods with response IBD sharing for relative pairs. Account
13482 for correlations of IBD statistics and covariates for relative pairs within
13483 the same pedigree.")
13484 (license license:gpl2+)))
13486 (define-public r-dlmap
13493 (uri (cran-uri "dlmap" version))
13496 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
13497 (build-system r-build-system)
13499 `(("r-ibdreg" ,r-ibdreg)
13503 ("r-wgaim" ,r-wgaim)))
13504 (home-page "https://cran.r-project.org/web/packages/dlmap/")
13505 (synopsis "Detection localization mapping for QTL")
13507 "This is package for QTL mapping in a mixed model framework with separate
13508 detection and localization stages. The first stage detects the number of QTL
13509 on each chromosome based on the genetic variation due to grouped markers on
13510 the chromosome; the second stage uses this information to determine the most
13511 likely QTL positions. The mixed model can accommodate general fixed and
13512 random effects, including spatial effects in field trials and pedigree
13513 effects. It is applicable to backcrosses, doubled haploids, recombinant
13514 inbred lines, F2 intercrosses, and association mapping populations.")
13515 (license license:gpl2)))
13517 (define-public r-ldheatmap
13519 (name "r-ldheatmap")
13524 (uri (cran-uri "LDheatmap" version))
13527 "1r0j8bihi5z1x0sgaf7dwzpsw9i0nc1vylvipvc0cia2ka1lr9dc"))))
13528 (properties `((upstream-name . "LDheatmap")))
13529 (build-system r-build-system)
13531 `(("r-genetics" ,r-genetics)
13533 ("r-snpstats" ,r-snpstats)))
13534 (home-page "http://stat.sfu.ca/statgen/research/ldheatmap.html")
13535 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
13537 "This package provides tools to produce a graphical display, as a heat
13538 map, of measures of pairwise linkage disequilibria between SNPs. Users may
13539 optionally include the physical locations or genetic map distances of each SNP
13541 (license license:gpl3)))
13543 (define-public r-hwde
13550 (uri (cran-uri "hwde" version))
13553 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
13554 (build-system r-build-system)
13555 (home-page "https://cran.r-project.org/web/packages/hwde/")
13556 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
13558 "This package fits models for genotypic disequilibria, as described in
13559 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
13560 terms are available that account for first order interactions between loci.
13561 It also implements, for a single locus in a single population, a conditional
13562 exact test for Hardy-Weinberg equilibrium.")
13563 (license license:gpl2+)))
13565 (define-public r-tdthap
13572 (uri (cran-uri "tdthap" version))
13575 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
13576 (build-system r-build-system)
13577 (home-page "https://cran.r-project.org/web/packages/tdthap/")
13578 (synopsis "TDT tests for extended haplotypes")
13580 "Functions and examples are provided for transmission/disequilibrium
13581 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
13582 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
13583 (license license:artistic2.0)))
13585 (define-public r-sparql
13591 (uri (cran-uri "SPARQL" version))
13594 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
13595 (properties `((upstream-name . "SPARQL")))
13596 (build-system r-build-system)
13598 `(("r-rcurl" ,r-rcurl)
13600 (home-page "https://cran.r-project.org/web/packages/SPARQL")
13601 (synopsis "SPARQL client for R")
13602 (description "This package provides an interface to use SPARQL to pose
13603 SELECT or UPDATE queries to an end-point.")
13604 ;; The only license indication is found in the DESCRIPTION file,
13605 ;; which states GPL-3. So we cannot assume GPLv3+.
13606 (license license:gpl3)))
13608 (define-public r-bookdown
13610 (name "r-bookdown")
13614 (uri (cran-uri "bookdown" version))
13617 "10b4gnd6z3w13pysqqan43blxcbk7bgbzc7wr83b23ag1lh2n40j"))))
13618 (build-system r-build-system)
13620 `(("r-htmltools" ,r-htmltools)
13621 ("r-knitr" ,r-knitr)
13622 ("r-rmarkdown" ,r-rmarkdown)
13623 ("r-tinytex" ,r-tinytex)
13625 ("pandoc" ,ghc-pandoc)))
13626 (home-page "https://github.com/rstudio/bookdown")
13627 (synopsis "Authoring books and technical documents with R markdown")
13628 (description "This package provides output formats and utilities for
13629 authoring books and technical documents with R Markdown.")
13630 (license license:gpl3)))
13632 (define-public r-optparse
13634 (name "r-optparse")
13639 (uri (cran-uri "optparse" version))
13642 "0wyrc42ja3ab5szx46zmz8lm7vzfqxkjca0m0sms8g9hqbmmay6d"))))
13643 (build-system r-build-system)
13645 `(("r-getopt" ,r-getopt)))
13646 (home-page "https://github.com/trevorld/optparse")
13647 (synopsis "Command line option parser")
13649 "This package provides a command line parser inspired by Python's
13650 @code{optparse} library to be used with Rscript to write shebang scripts
13651 that accept short and long options.")
13652 (license license:gpl2+)))
13654 (define-public r-wgcna
13661 (uri (cran-uri "WGCNA" version))
13664 "1s7gy5vd7x67hpgli8r7ba2z99w3psiyv5hqmrh94zw141dg210a"))))
13665 (properties `((upstream-name . "WGCNA")))
13666 (build-system r-build-system)
13668 `(("r-annotationdbi" ,r-annotationdbi)
13669 ("r-doparallel" ,r-doparallel)
13670 ("r-dynamictreecut" ,r-dynamictreecut)
13671 ("r-fastcluster" ,r-fastcluster)
13672 ("r-foreach" ,r-foreach)
13673 ("r-go-db" ,r-go-db)
13674 ("r-hmisc" ,r-hmisc)
13675 ("r-impute" ,r-impute)
13677 ("r-robust" ,r-robust)
13678 ("r-survival" ,r-survival)
13679 ("r-matrixstats" ,r-matrixstats)
13680 ("r-preprocesscore" ,r-preprocesscore)))
13682 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
13683 (synopsis "Weighted correlation network analysis")
13685 "This package provides functions necessary to perform Weighted
13686 Correlation Network Analysis on high-dimensional data. It includes functions
13687 for rudimentary data cleaning, construction and summarization of correlation
13688 networks, module identification and functions for relating both variables and
13689 modules to sample traits. It also includes a number of utility functions for
13690 data manipulation and visualization.")
13691 (license license:gpl2+)))
13693 (define-public r-kernlab
13700 (uri (cran-uri "kernlab" version))
13702 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
13703 (build-system r-build-system)
13704 (home-page "https://cran.r-project.org/web/packages/kernlab")
13705 (synopsis "Kernel-based machine learning tools")
13707 "This package provides kernel-based machine learning methods for
13708 classification, regression, clustering, novelty detection, quantile regression
13709 and dimensionality reduction. Among other methods @code{kernlab} includes
13710 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
13712 (license license:gpl2)))
13714 (define-public r-hierfstat
13716 (name "r-hierfstat")
13717 (version "0.04-22")
13721 (uri (cran-uri "hierfstat" version))
13724 "1fav2v2996v5kb1ffa6v5wxfm921syxg6as034vd3j4jfhdibyfx"))))
13725 (build-system r-build-system)
13727 `(("r-ade4" ,r-ade4)
13728 ("r-adegenet" ,r-adegenet)
13729 ("r-gtools" ,r-gtools)))
13730 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
13731 (synopsis "Estimation and tests of hierarchical F-statistics")
13733 "This package allows the estimation of hierarchical F-statistics from
13734 haploid or diploid genetic data with any numbers of levels in the hierarchy,
13735 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
13736 are also given to test via randomisations the significance of each F and
13737 variance components, using the likelihood-ratio statistics G.")
13738 (license license:gpl2+)))
13740 (define-public r-hapassoc
13742 (name "r-hapassoc")
13747 (uri (cran-uri "hapassoc" version))
13750 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
13751 (build-system r-build-system)
13752 (home-page "http://stat.sfu.ca/statgen/research/hapassoc.html")
13753 (synopsis "Inference of trait associations with SNP haplotypes")
13755 "Hapassoc performs likelihood inference of trait associations with
13756 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
13757 functions are developed primarily for data collected in cohort or
13758 cross-sectional studies. They can accommodate uncertain haplotype phase and
13759 handle missing genotypes at some SNPs.")
13760 (license license:gpl2)))
13762 (define-public r-sampling
13764 (name "r-sampling")
13769 (uri (cran-uri "sampling" version))
13772 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
13773 (build-system r-build-system)
13775 `(("r-lpsolve" ,r-lpsolve)
13776 ("r-mass" ,r-mass)))
13777 (home-page "https://cran.r-project.org/web/packages/sampling/")
13778 (synopsis "Survey sampling")
13780 "This package provides functions for drawing and calibrating samples.")
13781 (license license:gpl2+)))
13783 (define-public r-r2html
13790 (uri (cran-uri "R2HTML" version))
13793 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
13794 (properties `((upstream-name . "R2HTML")))
13795 (build-system r-build-system)
13796 (home-page "https://github.com/nalimilan/R2HTML")
13797 (synopsis "HTML export for R objects")
13799 "This package includes HTML functions and methods to write in an HTML
13800 file. Thus, making HTML reports is easy. It includes a function that allows
13801 redirection on the fly, which appears to be very useful for teaching purposes,
13802 as the student can keep a copy of the produced output to keep all that they
13803 did during the course. The package comes with a vignette describing how to
13804 write HTML reports for statistical analysis. Finally, a driver for Sweave
13805 allows to parse HTML flat files containing R code and to automatically write
13806 the corresponding outputs (tables and graphs).")
13807 (license license:gpl2+)))
13809 (define-public r-rjava
13816 (uri (cran-uri "rJava" version))
13819 "0s9cjy1wh7snmbqwznh8f1r4ipylr7mgda4a979z963a8lqy32n2"))))
13820 (properties `((upstream-name . "rJava")))
13821 (build-system r-build-system)
13823 `(#:modules ((guix build utils)
13824 (guix build r-build-system)
13827 (modify-phases %standard-phases
13828 (add-after 'unpack 'set-JAVA_HOME
13829 (lambda* (#:key inputs #:allow-other-keys)
13830 (let ((jdk (assoc-ref inputs "jdk")))
13831 (setenv "JAVA_HOME" jdk)
13832 (setenv "JAVA" (which "java"))
13833 (setenv "JAR" (which "jar"))
13834 (setenv "JAVAC" (which "javac"))
13835 (setenv "JAVAH" (which "javah"))
13836 (setenv "JAVA_CPPFLAGS"
13837 (string-append "-I" jdk "/include "
13838 "-I" jdk "/include/linux"))
13839 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
13840 ((lib) (setenv "JAVA_LIBS" lib))
13841 (_ (error "Could not find libjvm.so"))))
13845 ("jdk" ,icedtea-8 "jdk")
13848 (home-page "http://www.rforge.net/rJava/")
13849 (synopsis "Low-Level R to Java interface")
13851 "This package provides a low-level interface to the Java VM very much
13852 like .C/.Call and friends. It allows the creation of objects, calling methods
13853 and accessing fields.")
13854 (license license:gpl2)))
13856 (define-public r-svmisc
13863 (uri (cran-uri "svMisc" version))
13866 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
13867 (properties `((upstream-name . "svMisc")))
13868 (build-system r-build-system)
13869 (home-page "https://github.com/SciViews/svMisc")
13870 (synopsis "Miscellaneous functions for SciViews")
13872 "This package provides miscellaneous functions for SciViews or general
13873 use, including tools to manage a temporary environment attached to the search
13874 path for temporary variables you do not want to @code{save()} or
13875 @code{load()}; test the current platform; showing progress bars, etc.")
13876 (license license:gpl2)))
13878 (define-public r-xyz
13885 (uri (cran-uri "xyz" version))
13888 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
13889 (build-system r-build-system)
13891 `(("r-rcpp" ,r-rcpp)))
13892 (home-page "https://cran.r-project.org/web/packages/xyz/")
13893 (synopsis "Algorithm for fast interaction search in high-dimensional data")
13895 "High dimensional interaction search by brute force requires a quadratic
13896 computational cost in the number of variables. The xyz algorithm provably
13897 finds strong interactions in almost linear time. For details of the algorithm
13898 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
13899 interaction search in high-dimensional data.")
13900 ;; Any version of the GPL.
13901 (license license:gpl2+)))
13903 (define-public r-rttf2pt1
13905 (name "r-rttf2pt1")
13910 (uri (cran-uri "Rttf2pt1" version))
13913 "0b3f2zkmbyshn19cnaaf042d0zwf43l9jnkqizfhxxwb93a4c1jn"))))
13914 (properties `((upstream-name . "Rttf2pt1")))
13915 (build-system r-build-system)
13916 (home-page "https://github.com/wch/Rttf2pt1")
13917 (synopsis "Font conversion utility")
13919 "This package contains the program @code{ttf2pt1}, for use with the
13920 @code{extrafont} package.")
13921 ;; Most of the files are covered under the Expat license. Some files are
13922 ;; covered under BSD-3. Deviations for individual files are recorded in
13923 ;; the LICENSE file.
13924 (license (list license:bsd-3 license:expat
13925 (license:non-copyleft "file://LICENSE")))))
13927 (define-public r-extrafontdb
13929 (name "r-extrafontdb")
13934 (uri (cran-uri "extrafontdb" version))
13937 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
13938 (build-system r-build-system)
13939 (home-page "https://github.com/wch/extrafontdb")
13940 (synopsis "Database for the extrafont package")
13942 "This package holds the database for the @code{extrafont} package.")
13943 (license license:gpl2)))
13945 (define-public r-extrafont
13947 (name "r-extrafont")
13952 (uri (cran-uri "extrafont" version))
13955 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
13956 (build-system r-build-system)
13958 `(("r-extrafontdb" ,r-extrafontdb)
13959 ("r-rttf2pt1" ,r-rttf2pt1)))
13960 (home-page "https://github.com/wch/extrafont")
13961 (synopsis "Tools for using fonts in R")
13963 "The extrafont package makes it easier to use fonts other than the basic
13964 PostScript fonts that R uses. Fonts that are imported into extrafont can be
13965 used with PDF or PostScript output files. There are two hurdles for using
13966 fonts in PDF (or Postscript) output files:
13969 @item Making R aware of the font and the dimensions of the characters.
13970 @item Embedding the fonts in the PDF file so that the PDF can be displayed
13971 properly on a device that doesn't have the font. This is usually needed if
13972 you want to print the PDF file or share it with others.
13975 The extrafont package makes both of these things easier.")
13976 (license license:gpl2)))
13978 (define-public r-xkcd
13985 (uri (cran-uri "xkcd" version))
13988 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
13989 (build-system r-build-system)
13991 `(("r-extrafont" ,r-extrafont)
13992 ("r-ggplot2" ,r-ggplot2)
13993 ("r-hmisc" ,r-hmisc)))
13994 (home-page "https://cran.r-project.org/web/packages/xkcd/")
13995 (synopsis "Plot ggplot2 graphics in the XKCD style")
13997 "This package provides the means to plot ggplot2 graphs in the style of
13998 the XKCD web comic.")
13999 (license license:gpl3)))
14001 (define-public r-msigdbr
14008 (uri (cran-uri "msigdbr" version))
14011 "19p8z617m3my8la7n1qgb1s2msf940r372im3q30qkbcx3qxg3sd"))))
14012 (build-system r-build-system)
14014 `(("r-dplyr" ,r-dplyr)
14015 ("r-magrittr" ,r-magrittr)
14016 ("r-rlang" ,r-rlang)
14017 ("r-tibble" ,r-tibble)))
14018 (home-page "https://github.com/igordot/msigdbr")
14019 (synopsis "MSigDB gene sets for multiple organisms")
14021 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
14022 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
14023 software in a standard R data frame with key-value pairs. Included are the
14024 original human gene symbols and Entrez IDs as well as the equivalents for
14025 various frequently studied model organisms such as mouse, rat, pig, fly, and
14027 ;; The package is covered under the Expat license, but the upstream MSigDB
14028 ;; files are made available under the Creative Commons Attribution 4.0
14029 ;; International license.
14030 (license (list license:expat license:cc-by4.0))))
14032 (define-public r-gridgraphics
14034 (name "r-gridgraphics")
14039 (uri (cran-uri "gridGraphics" version))
14042 "1kr3p54bkv2q7agxrva30y9bkwkiq1k2cfl5z1kvyjv6f5xi4w5p"))))
14043 (properties `((upstream-name . "gridGraphics")))
14044 (build-system r-build-system)
14045 (home-page "https://github.com/pmur002/gridgraphics")
14046 (synopsis "Redraw base graphics using @code{grid} graphics")
14048 "This package provides functions to convert a page of plots drawn with
14049 the @code{graphics} package into identical output drawn with the @code{grid}
14050 package. The result looks like the original @code{graphics}-based plot, but
14051 consists of @code{grid} grobs and viewports that can then be manipulated with
14052 @code{grid} functions (e.g., edit grobs and revisit viewports).")
14053 (license license:gpl2+)))
14055 (define-public r-farver
14062 (uri (cran-uri "farver" version))
14065 "1k75v07dsfkjra2gsgxg9s55cw3b46b1nh960kqphq7cg7gr058f"))))
14066 (build-system r-build-system)
14067 (home-page "https://github.com/thomasp85/farver")
14068 (synopsis "Vectorized color conversion and comparison")
14070 "The encoding of color can be handled in many different ways, using
14071 different color spaces. As different color spaces have different uses,
14072 efficient conversion between these representations are important. This
14073 package provides a set of functions that gives access to very fast color space
14074 conversion and comparisons implemented in C++, and offers 100-fold speed
14075 improvements over the @code{convertColor} function in the @code{grDevices}
14077 (license license:expat)))
14079 (define-public r-ggplotify
14081 (name "r-ggplotify")
14086 (uri (cran-uri "ggplotify" version))
14089 "0nv3wdmxnc5ww9m3xlgnb0jp30j45dg33nqc6gg3y36svg8anjcg"))))
14090 (build-system r-build-system)
14092 `(("r-ggplot2" ,r-ggplot2)
14093 ("r-gridgraphics" ,r-gridgraphics)
14094 ("r-rvcheck" ,r-rvcheck)))
14095 (home-page "https://github.com/GuangchuangYu/ggplotify")
14096 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
14098 "This package provides tools to convert plot function calls (using
14099 expression or formula) to @code{grob} or @code{ggplot} objects that are
14100 compatible with the @code{grid} and @code{ggplot2} environment. With this
14101 package, we are able to e.g. use @code{cowplot} to align plots produced by
14102 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
14103 converting them to @code{ggplot} objects.")
14104 (license license:artistic2.0)))
14106 (define-public r-triebeard
14108 (name "r-triebeard")
14113 (uri (cran-uri "triebeard" version))
14116 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
14117 (build-system r-build-system)
14118 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
14119 (home-page "https://github.com/Ironholds/triebeard/")
14120 (synopsis "Radix trees in Rcpp")
14122 "Radix trees, or tries, are key-value data structures optimized for
14123 efficient lookups, similar in purpose to hash tables. This package provides
14124 an implementation of radix trees for use in R programming and in developing
14125 packages with Rcpp.")
14126 (license license:expat)))
14128 (define-public r-tweenr
14135 (uri (cran-uri "tweenr" version))
14138 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
14139 (build-system r-build-system)
14141 `(("r-farver" ,r-farver)
14142 ("r-magrittr" ,r-magrittr)
14144 ("r-rlang" ,r-rlang)))
14145 (home-page "https://github.com/thomasp85/tweenr")
14146 (synopsis "Interpolate data for smooth animations")
14148 "In order to create smooth animation between states of data, tweening is
14149 necessary. This package provides a range of functions for creating tweened
14150 data that can be used as basis for animation. Furthermore it adds a number of
14151 vectorized interpolaters for common R data types such as numeric, date and
14153 (license license:expat)))
14155 (define-public r-polyclip
14157 (name "r-polyclip")
14162 (uri (cran-uri "polyclip" version))
14165 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
14166 (build-system r-build-system)
14167 (native-inputs `(("pkg-config" ,pkg-config)))
14168 (home-page "http://www.angusj.com/delphi/clipper.php")
14169 (synopsis "Polygon clipping")
14171 "This package provides an R port of the library Clipper. It performs
14172 polygon clipping operations (intersection, union, set minus, set difference)
14173 for polygonal regions of arbitrary complexity, including holes. It computes
14174 offset polygons (spatial buffer zones, morphological dilations, Minkowski
14175 dilations) for polygonal regions and polygonal lines. It computes the
14176 Minkowski Sum of general polygons. There is a function for removing
14177 self-intersections from polygon data.")
14178 (license license:boost1.0)))
14180 (define-public r-urltools
14182 (name "r-urltools")
14187 (uri (cran-uri "urltools" version))
14190 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
14191 (build-system r-build-system)
14193 `(("r-rcpp" ,r-rcpp)
14194 ("r-triebeard" ,r-triebeard)))
14195 (home-page "https://github.com/Ironholds/urltools/")
14196 (synopsis "Vectorized tools for URL handling and parsing")
14198 "This package provides a toolkit for all URL-handling needs, including
14199 encoding and decoding, parsing, parameter extraction and modification. All
14200 functions are designed to be both fast and entirely vectorized. It is
14201 intended to be useful for people dealing with web-related datasets, such as
14202 server-side logs, although may be useful for other situations involving large
14204 (license license:expat)))
14206 (define-public r-ggforce
14213 (uri (cran-uri "ggforce" version))
14216 "04926cqrda6psvy2nzkkw4czwyxdp7fnxg76byp14v12kgd72lm0"))))
14217 (build-system r-build-system)
14219 `(("r-ggplot2" ,r-ggplot2)
14220 ("r-gtable" ,r-gtable)
14222 ("r-polyclip" ,r-polyclip)
14224 ("r-rcppeigen" ,r-rcppeigen)
14225 ("r-rlang" ,r-rlang)
14226 ("r-scales" ,r-scales)
14227 ("r-tidyselect" ,r-tidyselect)
14228 ("r-tweenr" ,r-tweenr)
14229 ("r-withr" ,r-withr)))
14230 (home-page "https://ggforce.data-imaginist.com")
14231 (synopsis "Accelerating ggplot2")
14233 "The aim of the ggplot2 package is to aid in visual data investigations.
14234 This focus has led to a lack of facilities for composing specialized plots.
14235 Thi package aims to be a collection of mainly new statistics and geometries
14236 that fills this gap.")
14237 (license license:expat)))
14239 (define-public r-europepmc
14241 (name "r-europepmc")
14246 (uri (cran-uri "europepmc" version))
14249 "1ngqs1sqzkbwv98dd5z4cxj8bnz41wyd0g060a2vpqi3s99s4i2h"))))
14250 (build-system r-build-system)
14252 `(("r-dplyr" ,r-dplyr)
14254 ("r-jsonlite" ,r-jsonlite)
14256 ("r-progress" ,r-progress)
14257 ("r-purrr" ,r-purrr)
14258 ("r-urltools" ,r-urltools)
14259 ("r-xml2" ,r-xml2)))
14260 (home-page "https://github.com/ropensci/europepmc/")
14261 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
14263 "This package provides an R Client for the
14264 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
14265 Service}. It gives access to both metadata on life science literature and
14266 open access full texts. Europe PMC indexes all PubMed content and other
14267 literature sources including Agricola, a bibliographic database of citations
14268 to the agricultural literature, or Biological Patents. In addition to
14269 bibliographic metadata, the client allows users to fetch citations and
14270 reference lists. Links between life-science literature and other EBI
14271 databases, including ENA, PDB or ChEMBL are also accessible.")
14272 (license license:gpl3)))
14274 (define-public r-ggraph
14281 (uri (cran-uri "ggraph" version))
14284 "0qj7w3af0pgmd9mil6y571jikfkln7b8csvzg6b08spwbglfy1s3"))))
14285 (build-system r-build-system)
14287 `(("r-digest" ,r-digest)
14288 ("r-dplyr" ,r-dplyr)
14289 ("r-ggforce" ,r-ggforce)
14290 ("r-ggplot2" ,r-ggplot2)
14291 ("r-ggrepel" ,r-ggrepel)
14292 ("r-graphlayouts" ,r-graphlayouts)
14293 ("r-gtable" ,r-gtable)
14294 ("r-igraph" ,r-igraph)
14297 ("r-rlang" ,r-rlang)
14298 ("r-scales" ,r-scales)
14299 ("r-tidygraph" ,r-tidygraph)
14300 ("r-viridis" ,r-viridis)))
14301 (home-page "https://cran.r-project.org/web/packages/ggraph/")
14302 (synopsis "Implementation of grammar of graphics for graphs and networks")
14304 "The grammar of graphics as implemented in ggplot2 is a poor fit for
14305 graph and network visualizations due to its reliance on tabular data input.
14306 The ggraph package is an extension of the ggplot2 API tailored to graph
14307 visualizations and provides the same flexible approach to building up plots
14309 (license license:gpl3)))
14311 (define-public r-varselrf
14313 (name "r-varselrf")
14318 (uri (cran-uri "varSelRF" version))
14321 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
14322 (properties `((upstream-name . "varSelRF")))
14323 (build-system r-build-system)
14325 `(("r-randomforest" ,r-randomforest)))
14326 (home-page "http://ligarto.org/rdiaz/Software/Software.html")
14327 (synopsis "Variable selection using random forests")
14329 "This package provides tools for the variable selection from random
14330 forests using both backwards variable elimination (for the selection of small
14331 sets of non-redundant variables) and selection based on the importance
14332 spectrum (somewhat similar to scree plots; for the selection of large,
14333 potentially highly-correlated variables). The main applications are in
14334 high-dimensional data (e.g., microarray data, and other genomics and
14335 proteomics applications).")
14336 (license license:gpl2+)))
14338 (define-public r-pamr
14345 (uri (cran-uri "pamr" version))
14348 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
14349 (build-system r-build-system)
14351 `(("r-cluster" ,r-cluster)
14352 ("r-survival" ,r-survival)))
14353 (native-inputs `(("gfortran" ,gfortran)))
14354 (home-page "https://cran.r-project.org/web/packages/pamr/")
14355 (synopsis "Prediction Analysis for Microarrays")
14357 "This package provides some functions for sample classification in
14359 (license license:gpl2)))
14361 (define-public r-rda
14364 (version "1.0.2-2.1")
14368 (uri (cran-uri "rda" version))
14371 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
14372 (build-system r-build-system)
14373 (home-page "https://cran.r-project.org/web/packages/rda/")
14374 (synopsis "Shrunken centroids regularized discriminant analysis")
14376 "This package provides tools for shrunken centroids regularized
14377 discriminant analysis for the purpose of classifying high dimensional data.")
14378 (license license:gpl2+)))
14380 (define-public r-ggvis
14387 (uri (cran-uri "ggvis" version))
14390 "091i9f17912j8qcyxppjgwzjnyqj7769ixs9d2gjg6f2clskqdw2"))))
14391 (build-system r-build-system)
14393 `(("r-assertthat" ,r-assertthat)
14394 ("r-dplyr" ,r-dplyr)
14395 ("r-htmltools" ,r-htmltools)
14396 ("r-jsonlite" ,r-jsonlite)
14397 ("r-lazyeval" ,r-lazyeval)
14398 ("r-magrittr" ,r-magrittr)
14399 ("r-shiny" ,r-shiny)))
14400 (home-page "https://ggvis.rstudio.com/")
14401 (synopsis "Interactive grammar of graphics")
14403 "This package is a data visualization package for R providing an
14404 implementation of an interactive grammar of graphics, taking the best parts of
14405 ggplot2, combining them with the reactive framework of Shiny and drawing web
14406 graphics using Vega.")
14407 (license license:gpl2)))
14409 (define-public r-gbm
14416 (uri (cran-uri "gbm" version))
14419 "0vs6ljaqhwwpgr8wlbhmm4v147rd82kl16rpaijqiylxcc8dxyq6"))))
14420 (build-system r-build-system)
14422 `(("r-gridextra" ,r-gridextra)
14423 ("r-lattice" ,r-lattice)
14424 ("r-survival" ,r-survival)))
14425 (home-page "https://github.com/gbm-developers/gbm")
14426 (synopsis "Generalized boosted regression models")
14428 "This package is an implementation of extensions to Freund and Schapire's
14429 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
14430 regression methods for least squares, absolute loss, t-distribution loss,
14431 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
14432 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
14433 and Learning to Rank measures (LambdaMart).")
14434 (license license:gpl2+)))
14436 (define-public r-threejs
14443 (uri (cran-uri "threejs" version))
14446 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
14447 (build-system r-build-system)
14449 `(#:modules ((guix build utils)
14450 (guix build r-build-system)
14454 (modify-phases %standard-phases
14455 (add-after 'unpack 'process-javascript
14456 (lambda* (#:key inputs #:allow-other-keys)
14457 (with-directory-excursion "inst"
14461 `((,(assoc-ref inputs "js-jquery")
14462 "htmlwidgets/lib/jquery/jquery.min.js")
14463 (,(assoc-ref inputs "js-threejs-111")
14464 "htmlwidgets/lib/threejs-111/three.min.js"))))
14465 (lambda (sources targets)
14466 (for-each (lambda (source target)
14467 (format #t "Processing ~a --> ~a~%"
14469 (delete-file target)
14470 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14471 (call-with-output-file target
14473 (dump-port minified port)))))
14474 sources targets))))
14477 `(("r-base64enc" ,r-base64enc)
14478 ("r-crosstalk" ,r-crosstalk)
14479 ("r-htmlwidgets" ,r-htmlwidgets)
14480 ("r-igraph" ,r-igraph)))
14482 `(("uglify-js" ,uglify-js)
14486 (uri "https://code.jquery.com/jquery-1.12.4.js")
14489 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
14493 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
14496 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
14497 (home-page "https://bwlewis.github.io/rthreejs")
14498 (synopsis "Interactive 3D scatter plots, networks and globes")
14500 "Create interactive 3D scatter plots, network plots, and globes in R
14501 using the three.js visualization library.")
14502 (license license:expat)))
14504 (define-public r-mlbench
14511 (uri (cran-uri "mlbench" version))
14514 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
14515 (build-system r-build-system)
14516 (home-page "https://cran.r-project.org/web/packages/mlbench/")
14517 (synopsis "Machine learning benchmark problems")
14519 "This package provides a collection of artificial and real-world machine
14520 learning benchmark problems, including, e.g., several data sets from the UCI
14522 (license license:gpl2)))
14524 (define-public r-mpm
14531 (uri (cran-uri "mpm" version))
14534 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
14535 (build-system r-build-system)
14537 `(("r-kernsmooth" ,r-kernsmooth)
14538 ("r-mass" ,r-mass)))
14539 (home-page "http://mpm.r-forge.r-project.org")
14540 (synopsis "Multivariate projection methods")
14542 "This is a package for exploratory graphical analysis of multivariate
14543 data, specifically gene expression data with different projection methods:
14544 principal component analysis, correspondence analysis, spectral map
14546 (license license:gpl2+)))
14548 (define-public r-png
14554 (uri (cran-uri "png" version))
14557 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
14558 (build-system r-build-system)
14560 `(("libpng" ,libpng)
14562 (home-page "https://www.rforge.net/png/")
14563 (synopsis "Read and write PNG images")
14565 "This package provides an easy and simple way to read, write and display
14566 bitmap images stored in the PNG format. It can read and write both files and
14567 in-memory raw vectors.")
14568 ;; Any of these GPL versions.
14569 (license (list license:gpl2 license:gpl3))))
14571 (define-public r-ggcorrplot
14573 (name "r-ggcorrplot")
14578 (uri (cran-uri "ggcorrplot" version))
14581 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
14582 (build-system r-build-system)
14584 `(("r-ggplot2" ,r-ggplot2)
14585 ("r-reshape2" ,r-reshape2)))
14586 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
14587 (synopsis "Visualization of a correlation matrix using ggplot2")
14589 "The ggcorrplot package can be used to visualize easily a correlation
14590 matrix using ggplot2. It provides a solution for reordering the correlation
14591 matrix and displays the significance level on the plot. It also includes a
14592 function for computing a matrix of correlation p-values.")
14593 (license license:gpl2)))
14595 (define-public r-flexdashboard
14597 (name "r-flexdashboard")
14598 (version "0.5.1.1")
14602 (uri (cran-uri "flexdashboard" version))
14605 "0fy3nbrr67zqgd44r2mc850s5sp0hzfcw3zqs15m8kxzj1aw067x"))))
14606 (build-system r-build-system)
14608 `(#:modules ((guix build utils)
14609 (guix build r-build-system)
14613 (ice-9 textual-ports))
14615 (modify-phases %standard-phases
14616 (add-after 'unpack 'process-javascript
14617 (lambda* (#:key inputs #:allow-other-keys)
14618 (with-directory-excursion "inst"
14619 ;; Concatenate all components of prism.js
14620 (let ((contents (string-join
14621 (map (lambda (name)
14622 (call-with-input-file
14623 (assoc-ref inputs name)
14627 "js-prism-line-numbers"))
14629 (call-with-output-file "prism-src.js"
14630 (cut display contents <>)))
14634 `(("www/stickytableheaders/jquery.stickytableheaders.js"
14635 "www/stickytableheaders/jquery.stickytableheaders.min.js")
14637 "www/sly/sly.min.js")
14639 "www/prism/prism.js")
14640 (,(assoc-ref inputs "js-raphael")
14641 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
14642 (,(assoc-ref inputs "js-featherlight")
14643 "www/featherlight/featherlight.min.js"))))
14644 (lambda (sources targets)
14645 (for-each (lambda (source target)
14646 (format #t "Processing ~a --> ~a~%"
14648 (delete-file target)
14649 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14650 (call-with-output-file target
14652 (dump-port minified port)))))
14653 sources targets))))
14656 `(("r-htmltools" ,r-htmltools)
14657 ("r-htmlwidgets" ,r-htmlwidgets)
14658 ("r-jsonlite" ,r-jsonlite)
14659 ("r-knitr" ,r-knitr)
14660 ("r-rmarkdown" ,r-rmarkdown)
14661 ("r-shiny" ,r-shiny)))
14663 `(("uglify-js" ,uglify-js)
14667 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
14670 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
14674 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
14677 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
14681 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
14684 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
14685 ("js-prism-line-numbers"
14688 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
14691 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
14695 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
14698 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
14699 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
14700 (synopsis "R Markdown format for flexible dashboards")
14702 "This package provides an R Markdown format for converting an R Markdown
14703 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
14704 of its components to the containing web page.")
14705 (license license:expat)))
14707 (define-public r-preseqr
14714 (uri (cran-uri "preseqR" version))
14717 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
14718 (properties `((upstream-name . "preseqR")))
14719 (build-system r-build-system)
14721 `(("r-polynom" ,r-polynom)))
14722 (home-page "https://cran.r-project.org/web/packages/preseqR/")
14723 (synopsis "Predicting species accumulation curves")
14725 "This package can be used to predict the r-species accumulation
14726 curve (r-SAC), which is the number of species represented at least r times as
14727 a function of the sampling effort. When r = 1, the curve is known as the
14728 species accumulation curve, or the library complexity curve in high-throughput
14729 genomic sequencing. The package includes both parametric and nonparametric
14730 methods, as described by Deng C, et al. (2018).")
14731 (license license:gpl3)))
14733 (define-public r-mapplots
14735 (name "r-mapplots")
14740 (uri (cran-uri "mapplots" version))
14743 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
14744 (build-system r-build-system)
14745 (home-page "https://cran.r-project.org/web/packages/mapplots/")
14746 (synopsis "Data visualization on maps")
14748 "This package helps you create simple maps; add sub-plots like pie plots
14749 to a map or any other plot; format, plot and export gridded data. The package
14750 was developed for displaying fisheries data but most functions can be used for
14751 more generic data visualisation.")
14752 (license license:gpl2+)))
14754 (define-public r-pmcmr
14761 (uri (cran-uri "PMCMR" version))
14764 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
14765 (properties `((upstream-name . "PMCMR")))
14766 (build-system r-build-system)
14767 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
14768 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
14770 "This is a deprecated package for calculating pairwise multiple
14771 comparisons of mean rank sums. This package is superseded by the novel
14772 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
14773 compatibility of dependent packages for some time.")
14774 (license license:gpl3+)))
14776 (define-public r-downloader
14778 (name "r-downloader")
14783 (uri (cran-uri "downloader" version))
14786 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
14787 (build-system r-build-system)
14789 `(("r-digest" ,r-digest)))
14790 (home-page "https://github.com/wch/downloader")
14791 (synopsis "Download files over HTTP and HTTPS")
14793 "This package provides a wrapper for the @code{download.file} function,
14794 making it possible to download files over HTTPS across platforms. The
14795 @code{RCurl} package provides this functionality (and much more) but has
14796 external dependencies. This package has is implemented purely in R.")
14797 (license license:gpl2)))
14799 (define-public r-rex
14806 (uri (cran-uri "rex" version))
14809 "0alsadgjgass3wr8y5d247j12qqzg454sc84vpskclrkmz778g5x"))))
14810 (build-system r-build-system)
14812 `(("r-lazyeval" ,r-lazyeval)
14813 ("r-magrittr" ,r-magrittr)))
14814 (home-page "https://github.com/kevinushey/rex")
14815 (synopsis "Friendly regular expressions")
14817 "This package provides a friendly interface for the construction of
14818 regular expressions. Regular expressions are a very powerful feature, however
14819 they are often difficult to interpret. Rex allows you to build complex
14820 regular expressions from human readable expressions")
14821 (license license:expat)))
14823 (define-public r-xmlparsedata
14825 (name "r-xmlparsedata")
14830 (uri (cran-uri "xmlparsedata" version))
14833 "0gjr3l5z5dp276lchr2649as1rkj56d2mlvbr66yg393zzw50lsh"))))
14834 (properties `((upstream-name . "xmlparsedata")))
14835 (build-system r-build-system)
14836 (home-page "https://github.com/r-lib/xmlparsedata#readme")
14837 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
14839 "This package provides tools to convert the output of
14840 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
14841 @code{XPath}, and is easier to manipulate in general.")
14842 (license license:expat)))
14844 (define-public r-cyclocomp
14846 (name "r-cyclocomp")
14851 (uri (cran-uri "cyclocomp" version))
14854 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
14855 (properties `((upstream-name . "cyclocomp")))
14856 (build-system r-build-system)
14858 `(("r-callr" ,r-callr)
14859 ("r-crayon" ,r-crayon)
14861 ("r-remotes" ,r-remotes)
14862 ("r-withr" ,r-withr)))
14863 (home-page "https://github.com/MangoTheCat/cyclocomp")
14864 (synopsis "Cyclomatic complexity of R code")
14866 "Cyclomatic complexity is a software metric, used to indicate the
14867 complexity of a program. It is a quantitative measure of the number of
14868 linearly independent paths through a program's source code. This package
14869 provides tools to compute this metric.")
14870 (license license:expat)))
14872 (define-public r-lintr
14879 (uri (cran-uri "lintr" version))
14882 "09gbci4v5n4gsfzminly8332fw7faxdi1kkyvpa10dydx02sjcwb"))))
14883 (properties `((upstream-name . "lintr")))
14884 (build-system r-build-system)
14886 `(("r-codetools" ,r-codetools)
14887 ("r-crayon" ,r-crayon)
14888 ("r-cyclocomp" ,r-cyclocomp)
14889 ("r-digest" ,r-digest)
14891 ("r-jsonlite" ,r-jsonlite)
14892 ("r-knitr" ,r-knitr)
14894 ("r-rstudioapi" ,r-rstudioapi)
14895 ("r-stringdist" ,r-stringdist)
14896 ("r-testthat" ,r-testthat)
14898 ("r-xmlparsedata" ,r-xmlparsedata)))
14899 (home-page "https://github.com/jimhester/lintr")
14900 (synopsis "Linter for R code")
14901 (description "This package checks adherence to a given style, syntax
14902 errors and possible semantic issues. It supports on the fly checking of R
14903 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
14904 (license license:expat)))
14906 (define-public r-sctransform
14908 (name "r-sctransform")
14913 (uri (cran-uri "sctransform" version))
14916 "07v3lzccsrkh1glfxd1q20r8f8gl9ls5az0s1dvxm4vcls0hlhyn"))))
14917 (build-system r-build-system)
14919 `(("r-future-apply" ,r-future-apply)
14920 ("r-ggplot2" ,r-ggplot2)
14921 ("r-gridextra" ,r-gridextra)
14923 ("r-matrix" ,r-matrix)
14925 ("r-rcppeigen" ,r-rcppeigen)
14926 ("r-reshape2" ,r-reshape2)))
14927 (home-page "https://github.com/ChristophH/sctransform")
14928 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
14930 "This package provides a normalization method for single-cell UMI count
14931 data using a variance stabilizing transformation. The transformation is based
14932 on a negative binomial regression model with regularized parameters. As part
14933 of the same regression framework, this package also provides functions for
14934 batch correction, and data correction.")
14935 (license license:gpl3)))
14937 (define-public r-styler
14944 (uri (cran-uri "styler" version))
14947 "0rdbz60x8bymis6r6188ia1y0ip3nhf5y363i4cmakr618irjab9"))))
14948 (build-system r-build-system)
14950 `(("r-backports" ,r-backports)
14952 ("r-magrittr" ,r-magrittr)
14953 ("r-purrr" ,r-purrr)
14954 ("r-rematch2" ,r-rematch2)
14955 ("r-rlang" ,r-rlang)
14956 ("r-rprojroot" ,r-rprojroot)
14957 ("r-tibble" ,r-tibble)
14958 ("r-withr" ,r-withr)
14959 ("r-xfun" ,r-xfun)))
14960 (home-page "https://github.com/r-lib/styler")
14961 (synopsis "Non-invasive pretty printing of R code")
14963 "This is a package for pretty-printing R code without changing the user's
14964 formatting intent.")
14965 (license license:gpl3)))
14967 (define-public r-scrime
14974 (uri (cran-uri "scrime" version))
14977 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
14978 (build-system r-build-system)
14979 (home-page "https://cran.r-project.org/web/packages/scrime/")
14980 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
14982 "This package provides tools for the analysis of high-dimensional data
14983 developed/implemented at the group \"Statistical Complexity Reduction In
14984 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
14985 the functions can also be applied to other types of categorical data.")
14986 (license license:gpl2)))
14988 (define-public r-pbmcapply
14990 (name "r-pbmcapply")
14995 (uri (cran-uri "pbmcapply" version))
14998 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
14999 (build-system r-build-system)
15000 (home-page "https://github.com/kvnkuang/pbmcapply")
15001 (synopsis "Track the progress of apply procedures with a progress bar")
15003 "This light-weight package helps you track and visualize the progress of
15004 parallel versions of vectorized R functions of the @code{mc*apply} family.")
15005 (license license:expat)))
15007 (define-public r-blme
15014 (uri (cran-uri "blme" version))
15017 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
15018 (build-system r-build-system)
15019 (propagated-inputs `(("r-lme4" ,r-lme4)))
15020 (home-page "https://github.com/vdorie/blme")
15021 (synopsis "Bayesian linear mixed-effects models")
15023 "This package provides tools for maximum a posteriori estimation for
15024 linear and generalized linear mixed-effects models in a Bayesian setting. It
15025 extends the lme4 package.")
15026 (license license:gpl2+)))
15028 (define-public r-batchtools
15030 (name "r-batchtools")
15035 (uri (cran-uri "batchtools" version))
15038 "16x524hvy9d8p7r4fi1c8mixcvzgsjbf3y0vxaa56ssbbab4p7f9"))))
15039 (build-system r-build-system)
15041 `(("r-backports" ,r-backports)
15042 ("r-base64url" ,r-base64url)
15044 ("r-checkmate" ,r-checkmate)
15045 ("r-data-table" ,r-data-table)
15046 ("r-digest" ,r-digest)
15048 ("r-progress" ,r-progress)
15050 ("r-rappdirs" ,r-rappdirs)
15051 ("r-stringi" ,r-stringi)
15052 ("r-withr" ,r-withr)))
15053 (home-page "https://github.com/mllg/batchtools")
15054 (synopsis "Tools for computation on batch systems")
15056 "As a successor of the packages BatchJobs and BatchExperiments, this
15057 package provides a parallel implementation of the Map function for high
15058 performance computing systems managed by various schedulers. A multicore and
15059 socket mode allow the parallelization on a local machines, and multiple
15060 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
15061 the package provides an abstraction mechanism to define large-scale computer
15062 experiments in a well-organized and reproducible way.")
15063 (license license:lgpl3)))
15065 (define-public r-clue
15072 (uri (cran-uri "clue" version))
15075 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
15076 (build-system r-build-system)
15077 (propagated-inputs `(("r-cluster" ,r-cluster)))
15078 (home-page "https://cran.r-project.org/web/packages/clue/")
15079 (synopsis "Tools for analyzing cluster ensembles")
15080 (description "Cluster ensembles are collections of individual solutions to
15081 a given clustering problem which are useful or necessary to consider in a wide
15082 range of applications. This R package provides an extensible computational
15083 environment for creating and analyzing cluster ensembles, with basic data
15084 structures for representing partitions and hierarchies, and facilities for
15085 computing on them, including methods for measuring proximity and obtaining
15086 consensus and secondary clusterings.")
15087 (license license:gpl2)))
15089 (define-public r-sitmo
15096 (uri (cran-uri "sitmo" version))
15099 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
15100 (build-system r-build-system)
15101 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
15102 (home-page "https://github.com/coatless/sitmo/")
15103 (synopsis "Parallel pseudo random number generator header files")
15105 "This package provides two high quality and fast PPRNGs that may be used
15106 in an OpenMP parallel environment. In addition, there is a generator for one
15107 dimensional low-discrepancy sequence.")
15108 (license license:expat)))
15110 (define-public r-dqrng
15117 (uri (cran-uri "dqrng" version))
15120 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
15121 (build-system r-build-system)
15125 ("r-sitmo" ,r-sitmo)))
15126 (home-page "https://www.daqana.org/dqrng")
15127 (synopsis "Fast pseudo random number generators")
15129 "Several fast random number generators are provided as C++ header-only
15130 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
15131 Additionally, fast functions for generating random numbers according to a
15132 uniform, normal and exponential distribution are included. The latter two use
15133 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
15134 functions are exported to R and as a C++ interface and are enabled for use
15135 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
15136 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
15137 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
15138 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
15139 ;; whole is distributed under the terms of the AGPL 3.
15140 (license license:agpl3)))
15142 (define-public r-dalex
15149 (uri (cran-uri "DALEX" version))
15152 "1zviaf7530v8w996lbma0vplabrapgwldi7h70pr0439sxaqd421"))))
15153 (properties `((upstream-name . "DALEX")))
15154 (build-system r-build-system)
15155 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
15156 (home-page "https://pbiecek.github.io/DALEX/")
15157 (synopsis "Descriptive machine learning explanations")
15159 "Machine Learning models are widely used and have various applications in
15160 classification or regression. Models created with boosting, bagging, stacking
15161 or similar techniques are often used due to their high performance, but such
15162 black-box models usually lack interpretability. The DALEX package contains
15163 various explainers that help to understand the link between input variables
15164 and model output.")
15165 ;; Any version of the GPL
15166 (license license:gpl3+)))
15168 (define-public r-enrichr
15175 (uri (cran-uri "enrichR" version))
15178 "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
15179 (properties `((upstream-name . "enrichR")))
15180 (build-system r-build-system)
15182 `(("r-httr" ,r-httr)
15183 ("r-rjson" ,r-rjson)))
15184 (home-page "https://cran.r-project.org/web/packages/enrichR/")
15185 (synopsis "R Interface to Enrichr database for analyzing gene sets")
15187 "This package provides an R interface to all Enrichr databases, a
15188 web-based tool for analyzing gene sets and returns any enrichment of common
15189 annotated biological functions.")
15190 (license license:gpl2+)))
15192 (define-public r-plot3d
15199 (uri (cran-uri "plot3D" version))
15202 "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
15203 (properties `((upstream-name . "plot3D")))
15204 (build-system r-build-system)
15205 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
15206 (home-page "https://cran.r-project.org/web/packages/plot3D")
15207 (synopsis "Plot multi-dimensional data")
15209 "This package provides functions for viewing 2D and 3D data, including
15210 perspective plots, slice plots, surface plots, scatter plots, etc. It
15211 includes data sets from oceanography.")
15212 (license license:gpl3+)))
15214 (define-public r-ggfortify
15216 (name "r-ggfortify")
15221 (uri (cran-uri "ggfortify" version))
15224 "191q2z7w0l4v7swjlxs2hjgbjngw2838688s7ygnj0kigsm310f3"))))
15225 (build-system r-build-system)
15227 `(("r-dplyr" ,r-dplyr)
15228 ("r-ggplot2" ,r-ggplot2)
15229 ("r-gridextra" ,r-gridextra)
15230 ("r-scales" ,r-scales)
15231 ("r-stringr" ,r-stringr)
15232 ("r-tibble" ,r-tibble)
15233 ("r-tidyr" ,r-tidyr)))
15234 (home-page "https://github.com/sinhrks/ggfortify")
15235 (synopsis "Data visualization tools for statistical analysis results")
15237 "This package provides unified plotting tools for statistics commonly
15238 used, such as GLM, time series, PCA families, clustering and survival
15239 analysis. The package offers a single plotting interface for these analysis
15240 results and plots in a unified style using the @code{ggplot2} package.")
15241 (license license:gpl2)))
15243 (define-public r-refmanager
15245 (name "r-refmanager")
15250 (uri (cran-uri "RefManageR" version))
15253 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
15254 (properties `((upstream-name . "RefManageR")))
15255 (build-system r-build-system)
15257 `(("r-bibtex" ,r-bibtex)
15259 ("r-jsonlite" ,r-jsonlite)
15260 ("r-lubridate" ,r-lubridate)
15262 ("r-stringr" ,r-stringr)
15263 ("r-xml2" ,r-xml2)))
15264 (home-page "https://github.com/ropensci/RefManageR/")
15265 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
15267 "This package provides tools for importing and working with bibliographic
15268 references. It greatly enhances the @code{bibentry} class by providing a
15269 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
15270 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
15271 by various formats for name lists (author by last names, translator by full
15272 names, etc.). Entries can be updated, combined, sorted, printed in a number
15273 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
15274 into R and converted to @code{BibEntry} objects.")
15275 ;; Any of these licenses may be picked.
15276 (license (list license:gpl2 license:gpl3 license:bsd-3))))
15278 (define-public r-citr
15285 (uri (cran-uri "citr" version))
15288 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
15289 (build-system r-build-system)
15291 `(("r-assertthat" ,r-assertthat)
15294 ("r-miniui" ,r-miniui)
15295 ("r-refmanager" ,r-refmanager)
15296 ("r-rstudioapi" ,r-rstudioapi)
15297 ("r-shiny" ,r-shiny)
15298 ("r-shinyjs" ,r-shinyjs)
15299 ("r-yaml" ,r-yaml)))
15300 (home-page "https://github.com/crsh/citr")
15301 (synopsis "RStudio add-in to insert Markdown citations")
15303 "This package provides functions and an RStudio add-in that search a
15304 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
15305 the current document.")
15306 (license license:expat)))
15308 (define-public r-xgboost
15311 (version "0.90.0.2")
15315 (uri (cran-uri "xgboost" version))
15318 "1gy9rzg43mjpfis893vf15drmbigfn0481zrzss9ajnmnk0q8194"))))
15319 (build-system r-build-system)
15321 `(("r-data-table" ,r-data-table)
15322 ("r-magrittr" ,r-magrittr)
15323 ("r-matrix" ,r-matrix)
15324 ("r-stringi" ,r-stringi)))
15325 (home-page "https://github.com/dmlc/xgboost")
15326 (synopsis "Extreme gradient boosting")
15328 "This package provides an R interface to Extreme Gradient Boosting, which
15329 is an efficient implementation of the gradient boosting framework from Chen
15330 and Guestrin (2016). The package includes efficient linear model solver and
15331 tree learning algorithms. The package can automatically do parallel
15332 computation on a single machine. It supports various objective functions,
15333 including regression, classification and ranking. The package is made to be
15334 extensible, so that users are also allowed to define their own objectives
15336 (license license:asl2.0)))
15338 (define-public r-umap
15341 (version "0.2.4.1")
15345 (uri (cran-uri "umap" version))
15348 "1pnh3hv8ihiz2nszqp797lkrdhhna2a6mzpizbsk0s9m8cj4wxva"))))
15349 (build-system r-build-system)
15351 `(("r-openssl" ,r-openssl)
15353 ("r-reticulate" ,r-reticulate)
15354 ("r-rspectra" ,r-rspectra)))
15355 (home-page "https://github.com/tkonopka/umap")
15356 (synopsis "Uniform manifold approximation and projection")
15358 "Uniform manifold approximation and projection is a technique for
15359 dimension reduction. This package provides an interface to the UMAP algorithm
15360 in R, including a translation of the original algorithm into R.")
15361 (license license:expat)))
15363 (define-public r-uwot
15370 (uri (cran-uri "uwot" version))
15373 "0pz9wa89xq4d119q86lskrznf979m0r1db8iaprcz7kxbi6b8lrj"))))
15374 (build-system r-build-system)
15376 `(("r-dqrng" ,r-dqrng)
15378 ("r-irlba" ,r-irlba)
15379 ("r-matrix" ,r-matrix)
15381 ("r-rcppannoy" ,r-rcppannoy)
15382 ("r-rcppparallel" ,r-rcppparallel)
15383 ("r-rcppprogress" ,r-rcppprogress)
15384 ("r-rspectra" ,r-rspectra)))
15385 (home-page "https://github.com/jlmelville/uwot")
15386 (synopsis "Uniform manifold approximation and projection")
15388 "This package provides an implementation of the Uniform Manifold
15389 Approximation and Projection dimensionality reduction by McInnes et
15390 al. (2018). It also provides means to transform new data and to carry out
15391 supervised dimensionality reduction. An implementation of the related
15392 LargeVis method of Tang et al. (2016) is also provided.")
15393 (license license:gpl3)))
15395 (define-public r-kableextra
15397 (name "r-kableextra")
15402 (uri (cran-uri "kableExtra" version))
15405 "1nicvw06xsf3a1f5c10mih07b76m2v5s5h165vmz0qx6n1a3492i"))))
15406 (properties `((upstream-name . "kableExtra")))
15407 (build-system r-build-system)
15409 `(("r-digest" ,r-digest)
15411 ("r-htmltools" ,r-htmltools)
15412 ("r-knitr" ,r-knitr)
15413 ("r-magrittr" ,r-magrittr)
15414 ("r-readr" ,r-readr)
15415 ("r-rmarkdown" ,r-rmarkdown)
15416 ("r-rstudioapi" ,r-rstudioapi)
15417 ("r-rvest" ,r-rvest)
15418 ("r-scales" ,r-scales)
15419 ("r-stringr" ,r-stringr)
15420 ("r-viridislite" ,r-viridislite)
15421 ("r-webshot" ,r-webshot)
15422 ("r-xml2" ,r-xml2)))
15423 (home-page "https://haozhu233.github.io/kableExtra/")
15424 (synopsis "Construct complex tables with pipe syntax")
15426 "Build complex HTML or LaTeX tables using @code{kable()} from
15427 @code{knitr} and the piping syntax from @code{magrittr}. The function
15428 @code{kable()} is a light weight table generator coming from @code{knitr}.
15429 This package simplifies the way to manipulate the HTML or LaTeX codes
15430 generated by @code{kable()} and allows users to construct complex tables and
15431 customize styles using a readable syntax.")
15432 (license license:expat)))
15434 (define-public r-glasso
15441 (uri (cran-uri "glasso" version))
15443 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
15444 (build-system r-build-system)
15445 (native-inputs `(("gfortran" ,gfortran)))
15446 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
15447 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
15449 "This is a package for estimation of a sparse inverse covariance matrix
15450 using a lasso (L1) penalty. Facilities are provided for estimates along a
15451 path of values for the regularization parameter.")
15452 (license license:gpl2)))
15454 (define-public r-rhpcblasctl
15456 (name "r-rhpcblasctl")
15457 (version "0.20-17")
15461 (uri (cran-uri "RhpcBLASctl" version))
15464 "0iwc06blr5sx7rylwczi2jrha8sk8qs0jklflwpidl0zj1jxdggp"))))
15465 (properties `((upstream-name . "RhpcBLASctl")))
15466 (build-system r-build-system)
15467 (home-page "http://prs.ism.ac.jp/~nakama/Rhpc/")
15468 (synopsis "Control the number of threads on BLAS")
15470 "This package allows you to control the number of threads the BLAS
15471 library uses. It is also possible to control the number of threads in
15473 (license license:agpl3+)))
15475 (define-public r-lda
15482 (uri (cran-uri "lda" version))
15485 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
15486 (build-system r-build-system)
15487 (home-page "https://cran.r-project.org/web/packages/lda/")
15488 (synopsis "Collapsed Gibbs sampling methods for topic models")
15490 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
15491 related models. This includes (but is not limited to) sLDA, corrLDA, and the
15492 mixed-membership stochastic blockmodel. Inference for all of these models is
15493 implemented via a fast collapsed Gibbs sampler written in C. Utility
15494 functions for reading/writing data typically used in topic models, as well as
15495 tools for examining posterior distributions are also included.")
15496 ;; Any version of the LGPL
15497 (license license:lgpl3+)))
15499 (define-public r-rann-l1
15506 (uri (cran-uri "RANN.L1" version))
15509 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
15510 (properties `((upstream-name . "RANN.L1")))
15511 (build-system r-build-system)
15512 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
15513 (synopsis "Fast nearest neighbour search using L1 metric")
15515 "This package provides tools to find the k nearest neighbours for every
15516 point in a given dataset in O(N log N) time using Arya and Mount's ANN
15517 library. There is support for approximate as well as exact searches, fixed
15518 radius searches and @code{bd} as well as @code{kd} trees. The distance is
15519 computed using the L1 (Manhattan, taxicab) metric.")
15520 (license license:gpl3+)))
15522 (define-public r-leiden
15529 (uri (cran-uri "leiden" version))
15532 "0kf6fxqf5l5vilm9g7vspc18daw84cwhpafs5szb1skwd6vrfdzw"))))
15533 (properties `((upstream-name . "leiden")))
15534 (build-system r-build-system)
15536 `(("r-igraph" ,r-igraph)
15537 ("r-matrix" ,r-matrix)
15538 ("r-reticulate" ,r-reticulate)))
15539 (home-page "https://github.com/TomKellyGenetics/leiden")
15540 (synopsis "R implementation of Leiden clustering algorithm")
15542 "This package implements the Python @code{leidenalg} module to be called
15543 in R. It enables clustering using the Leiden algorithm for partitioning a
15544 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
15545 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
15546 (license license:gpl3)))
15548 (define-public r-patchwork
15549 ;; There has been no public release yet.
15550 (let ((commit "fd7958bae3e7a1e30237c751952e412a0a1d1242")
15553 (name "r-patchwork")
15554 (version (git-version "0.0.1" revision commit))
15558 (uri (git-reference
15559 (url "https://github.com/thomasp85/patchwork.git")
15561 (file-name (git-file-name name version))
15564 "00fq520xwy1ysg4k8x48x9b0yy9wyi8y8zj6dvxjg4bwx0yyp6s4"))))
15565 (build-system r-build-system)
15567 `(("r-ggplot2" ,r-ggplot2)
15568 ("r-gtable" ,r-gtable)))
15569 (home-page "https://github.com/thomasp85/patchwork")
15570 (synopsis "Compose ggplot2 plots")
15572 "The @code{ggplot2} package provides a strong API for sequentially
15573 building up a plot, but does not concern itself with composition of multiple
15574 plots. Patchwork is a package that expands the API to allow for arbitrarily
15575 complex composition of plots by providing mathmatical operators for combining
15577 (license license:expat))))
15579 (define-public r-liger
15586 (uri (git-reference
15587 (url "https://github.com/MacoskoLab/liger.git")
15588 (commit (string-append "v" version))))
15589 (file-name (git-file-name name version))
15592 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
15593 (modules '((guix build utils)))
15596 (delete-file "inst/java/ModularityOptimizer.jar")
15598 (build-system r-build-system)
15601 (modify-phases %standard-phases
15602 (add-after 'unpack 'build-java-part
15603 (lambda* (#:key inputs #:allow-other-keys)
15604 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
15605 (for-each (lambda (file) (invoke "javac" file))
15606 (find-files "." "\\.java$"))
15607 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
15608 (find-files "." "\\.class$"))
15611 `(("r-cowplot" ,r-cowplot)
15612 ("r-dosnow" ,r-dosnow)
15613 ("r-dplyr" ,r-dplyr)
15615 ("r-foreach" ,r-foreach)
15616 ("r-ggplot2" ,r-ggplot2)
15617 ("r-ggrepel" ,r-ggrepel)
15618 ("r-hmisc" ,r-hmisc)
15620 ("r-irlba" ,r-irlba)
15621 ("r-matrix" ,r-matrix)
15622 ("r-mclust" ,r-mclust)
15623 ("r-patchwork" ,r-patchwork)
15625 ("r-rann-l1" ,r-rann-l1)
15627 ("r-rcpparmadillo" ,r-rcpparmadillo)
15628 ("r-riverplot" ,r-riverplot)
15629 ("r-rtsne" ,r-rtsne)
15630 ("r-snow" ,r-snow)))
15632 `(("jdk" ,icedtea "jdk")
15633 ;; See https://github.com/MacoskoLab/liger/issues/96
15634 ;; The optimizer is released under the Expat license.
15638 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
15641 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
15643 ("r-knitr" ,r-knitr))) ; for vignettes
15644 (home-page "https://github.com/MacoskoLab/liger")
15645 (synopsis "Integrate and analyze multiple single-cell datasets")
15647 "LIGER is a package for integrating and analyzing multiple single-cell
15648 datasets, developed and maintained by the Macosko lab. It relies on
15649 integrative non-negative matrix factorization to identify shared and
15650 dataset-specific factors.")
15651 (license license:gpl3)))
15653 (define-public r-harmony
15654 ;; There are no tagged commits
15655 (let ((commit "4d1653870d4dd70fff1807c182882db1fbf9af5a")
15659 (version (git-version "1.0" revision commit))
15663 (uri (git-reference
15664 (url "https://github.com/immunogenomics/harmony")
15666 (file-name (git-file-name name version))
15669 "1gasdldr4aalr9h2q9kmm3y4i7azkgnhdn4bmvsszs7lg9xacw85"))))
15670 (build-system r-build-system)
15672 `(("r-cowplot" ,r-cowplot)
15673 ("r-dplyr" ,r-dplyr)
15674 ("r-ggplot2" ,r-ggplot2)
15675 ("r-irlba" ,r-irlba)
15676 ("r-matrix" ,r-matrix)
15678 ("r-rcpparmadillo" ,r-rcpparmadillo)
15679 ("r-rcppprogress" ,r-rcppprogress)
15680 ("r-rlang" ,r-rlang)
15681 ("r-tibble" ,r-tibble)
15682 ("r-tidyr" ,r-tidyr)))
15683 (home-page "https://github.com/immunogenomics/harmony")
15684 (synopsis "Integration of single cell sequencing data")
15686 "This package provides an implementation of the Harmony algorithm for
15687 single cell integration, described in Korsunsky et al
15688 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
15689 function and interfaces to external frameworks.")
15690 (license license:gpl3))))
15692 (define-public r-covr
15699 (uri (cran-uri "covr" version))
15701 (base32 "0p44kr6yz5sqza5zvq6divqglzkpv0if9pjpjmzhmdaaddjrqzg5"))))
15702 (properties `((upstream-name . "covr")))
15703 (build-system r-build-system)
15705 `(("r-crayon" ,r-crayon)
15706 ("r-digest" ,r-digest)
15708 ("r-jsonlite" ,r-jsonlite)
15710 ("r-withr" ,r-withr)
15711 ("r-yaml" ,r-yaml)))
15712 (home-page "https://github.com/r-lib/covr")
15713 (synopsis "Test coverage for R packages")
15715 "Thisp package enables you to track and report code coverage for your
15716 package and (optionally) upload the results to a coverage service. Code
15717 coverage is a measure of the amount of code being exercised by a set of tests.
15718 It is an indirect measure of test quality and completeness. This package is
15719 compatible with any testing methodology or framework and tracks coverage of
15720 both R code and compiled C/C++/FORTRAN code.")
15721 (license license:gpl3)))
15723 (define-public r-systemfonts
15725 (name "r-systemfonts")
15730 (uri (cran-uri "systemfonts" version))
15733 "0m0ljid683xcam2f14x7k2zv1yx4npac38a3gfv11vhxfbnpgp0z"))))
15734 (properties `((upstream-name . "systemfonts")))
15735 (build-system r-build-system)
15737 `(("fontconfig" ,fontconfig)
15738 ("freetype" ,freetype)
15741 `(("pkg-config" ,pkg-config)))
15742 (home-page "https://github.com/r-lib/systemfonts")
15743 (synopsis "System native font finding")
15745 "This package provides system native access to the font catalogue. As
15746 font handling varies between systems it is difficult to correctly locate
15747 installed fonts across different operating systems. The 'systemfonts' package
15748 provides bindings to the native libraries for finding font files that can then
15749 be used further by e.g. graphic devices.")
15750 (license license:expat)))
15752 (define-public r-graphlayouts
15754 (name "r-graphlayouts")
15759 (uri (cran-uri "graphlayouts" version))
15762 "03dizbhhdhnzbj2i5zvqgs617kwcv4h2pha4f16adic0fph1rxl3"))))
15763 (properties `((upstream-name . "graphlayouts")))
15764 (build-system r-build-system)
15766 `(("r-igraph" ,r-igraph)
15768 ("r-rcpparmadillo" ,r-rcpparmadillo)))
15769 (home-page "https://github.com/schochastics/graphlayouts")
15770 (synopsis "Additional layout algorithms for network visualizations")
15772 "This package provides several layout algorithms to visualize networks
15773 which are not part of the igraph library. Most are based on the concept of
15774 stress majorization by Gansner et al. (2004)
15775 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms allow to
15776 emphasize hidden group structures in networks or focus on specific nodes.")
15777 (license license:expat)))
15779 (define-public r-tidygraph
15781 (name "r-tidygraph")
15786 (uri (cran-uri "tidygraph" version))
15789 "1zpsarm74afbc7p5dlyb0whc09670qdcddw1ckb25cfc9hfh0hjn"))))
15790 (properties `((upstream-name . "tidygraph")))
15791 (build-system r-build-system)
15793 `(("r-dplyr" ,r-dplyr)
15794 ("r-igraph" ,r-igraph)
15795 ("r-magrittr" ,r-magrittr)
15796 ("r-pillar" ,r-pillar)
15799 ("r-rlang" ,r-rlang)
15800 ("r-tibble" ,r-tibble)
15801 ("r-tidyr" ,r-tidyr)))
15802 (home-page "https://github.com/thomasp85/tidygraph")
15803 (synopsis "Tidy API for graph manipulation")
15805 "This package provides a graph implementation that can be thought of as
15806 two tidy data frames describing node and edge data respectively. It provides
15807 an approach to manipulate these two virtual data frames using the API defined
15808 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
15809 common graph algorithms.")
15810 (license license:expat)))
15812 (define-public r-soupx
15813 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
15817 (version (git-version "0.3.1" revision commit))
15821 (uri (git-reference
15822 (url "https://github.com/constantAmateur/SoupX")
15824 (file-name (git-file-name name version))
15827 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
15828 (properties `((upstream-name . "SoupX")))
15829 (build-system r-build-system)
15831 `(("r-ggplot2" ,r-ggplot2)
15832 ("r-matrix" ,r-matrix)
15833 ("r-seurat" ,r-seurat)))
15834 (home-page "https://github.com/constantAmateur/SoupX")
15835 (synopsis "Single cell mRNA Soup eXterminator")
15837 "This package provides a package for quantifying, profiling and
15838 removing cell free mRNA contamination (the \"soup\") from droplet based single
15839 cell RNA-seq experiments.")
15840 (license license:gpl2))))
15842 (define-public r-assertr
15849 (uri (cran-uri "assertr" version))
15852 "0g4ii6vhp0155a29ljhs64a09x0nzy5ybvwwchhk4mkcgsvnvfkj"))))
15853 (build-system r-build-system)
15855 `(("r-dplyr" ,r-dplyr)
15857 ("r-rlang" ,r-rlang)))
15859 `(("r-knitr" ,r-knitr))) ; needed for vignette
15860 (home-page "https://github.com/ropensci/assertr")
15861 (synopsis "Assertive programming for R analysis pipelines")
15863 "This package provides functionality to assert conditions that have to be
15864 met so that errors in data used in analysis pipelines can fail quickly. It is
15865 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
15867 (license license:expat)))
15869 (define-public r-parameters
15871 (name "r-parameters")
15876 (uri (cran-uri "parameters" version))
15879 "0xkdn1079sr6kgyhc1zmn9imca4bghnxs3f91h0z7vkzjj73qdbi"))))
15880 (properties `((upstream-name . "parameters")))
15881 (build-system r-build-system)
15883 `(("r-bayestestr" ,r-bayestestr)
15884 ("r-insight" ,r-insight)))
15885 (home-page "https://cran.r-project.org/web/packages/parameters")
15886 (synopsis "Processing of model parameters")
15888 "This package provides utilities for processing the parameters of various
15889 statistical models. Beyond computing p values, CIs, and other indices for a
15890 wide variety of models, this package implements features like standardization
15891 or bootstrapping of parameters and models, feature reduction (feature
15892 extraction and variable selection) as well as conversion between indices of
15894 (license license:gpl3)))
15896 (define-public r-rgdal
15903 (uri (cran-uri "rgdal" version))
15905 (base32 "1jd691amf3ghznq5im15gvhl6v6k25klpl75m4ngrqf9xlxaa3as"))))
15906 (properties `((upstream-name . "rgdal")))
15907 (build-system r-build-system)
15915 `(("pkg-config" ,pkg-config)))
15916 (home-page "http://rgdal.r-forge.r-project.org")
15917 (synopsis "Bindings for the Geospatial Data Abstraction Library")
15919 "This package provides bindings to the Geospatial Data Abstraction
15920 Library (GDAL) and access to projection/transformation operations from the
15922 (license license:gpl2+)))
15924 (define-public r-insol
15931 (uri (cran-uri "insol" version))
15934 "1d2vqmbp94ff80mfkmq4a8y12r6ryym8hh1568ip9qbn7snc64v1"))))
15935 (properties `((upstream-name . "insol")))
15936 (build-system r-build-system)
15938 `(("r-raster" ,r-raster)))
15940 `(("gfortran" ,gfortran)))
15941 (home-page "https://meteoexploration.com/R/insol/index.html")
15942 (synopsis "Tools for calculating solar radiation")
15944 "This package provides functions to compute insolation on tilted
15945 surfaces, computes atmospheric transmittance and related parameters such as:
15946 Earth radius vector, declination, sunset and sunrise, daylength, equation of
15947 time, vector in the direction of the sun, vector normal to surface, and some
15948 atmospheric physics.")
15949 (license license:gpl2+)))
15951 (define-public r-lifecycle
15953 (name "r-lifecycle")
15958 (uri (cran-uri "lifecycle" version))
15961 "11rk7hkw63rfrf4aqmb4xrb88kg95xh8hajpjvjfwjym2v02h74n"))))
15962 (properties `((upstream-name . "lifecycle")))
15963 (build-system r-build-system)
15965 `(("r-glue" ,r-glue)
15966 ("r-rlang" ,r-rlang)))
15967 (home-page "https://github.com/r-lib/lifecycle")
15968 (synopsis "Manage the life cycle of your package functions")
15970 "Manage the life cycle of your exported functions with shared
15971 conventions, documentation badges, and non-invasive deprecation warnings. The
15972 lifecycle package defines four development stages (experimental, maturing,
15973 stable, and questioning) and three deprecation stages (soft-deprecated,
15974 deprecated, and defunct). It makes it easy to insert badges corresponding to
15975 these stages in your documentation. Usage of deprecated functions are
15976 signalled with increasing levels of non-invasive verbosity.")
15977 (license license:gpl3)))
15979 (define-public r-assertable
15981 (name "r-assertable")
15986 (uri (cran-uri "assertable" version))
15989 "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
15990 (build-system r-build-system)
15992 `(("r-data-table" ,r-data-table)))
15993 (home-page "https://cran.r-project.org/web/packages/assertable/")
15994 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
15995 (description "This package provides simple, flexible assertions on
15996 data.frame or data.table objects with verbose output for vetting. While other
15997 assertion packages apply towards more general use-cases, @code{assertable} is
15998 tailored towards tabular data. It includes functions to check variable names
15999 and values, whether the dataset contains all combinations of a given set of
16000 unique identifiers, and whether it is a certain length. In addition,
16001 @code{assertable} includes utility functions to check the existence of target
16002 files and to efficiently import multiple tabular data files into one
16004 (license license:gpl3)))
16006 (define-public r-quadprog
16008 (name "r-quadprog")
16013 (uri (cran-uri "quadprog" version))
16015 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
16016 (build-system r-build-system)
16018 `(("gfortran" ,gfortran)))
16019 (home-page "https://cran.r-project.org/web/packages/quadprog")
16020 (synopsis "Functions to solve quadratic programming problems")
16022 "This package contains routines and documentation for solving quadratic
16023 programming problems.")
16024 (license license:gpl3+)))
16026 (define-public r-desolve
16033 (uri (cran-uri "deSolve" version))
16035 (base32 "05sax045qrk550gsn2i7krb9rbg51rx88x4v190acsigqknxffrv"))))
16036 (properties `((upstream-name . "deSolve")))
16037 (build-system r-build-system)
16039 `(("gfortran" ,gfortran)))
16040 (home-page "https://desolve.r-forge.r-project.org/")
16041 (synopsis "Solvers for initial value problems of differential equations")
16042 (description "This package provides functions that solve initial value
16043 problems of a system of first-order @dfn{ordinary differential
16044 equations} (ODE), of @dfn{partial differential equations} (PDE), of
16045 @dfn{differential algebraic equations} (DAE), and of delay differential
16046 equations. The functions provide an interface to the FORTRAN functions
16047 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
16048 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
16049 C-implementation of solvers of the Runge-Kutta family with fixed or variable
16050 time steps. The package contains routines designed for solving ODEs resulting
16051 from 1-D, 2-D and 3-D partial differential equations that have been converted
16052 to ODEs by numerical differencing.")
16053 (license license:gpl2+)))
16055 (define-public r-pracma
16061 (uri (cran-uri "pracma" version))
16063 (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc"))))
16064 (build-system r-build-system)
16065 (home-page "https://cran.r-project.org/web/packages/pracma/")
16066 (synopsis "Practical numerical math functions")
16067 (description "This package provides functions for numerical analysis and
16068 linear algebra, numerical optimization, differential equations, plus some
16069 special functions. It uses Matlab function names where appropriate to simplify
16071 (license license:gpl3+)))
16073 (define-public r-subplex
16080 (uri (cran-uri "subplex" version))
16083 "10cbgbx1bgsax5z7gz6716g360xpq4mvq19cf4qqrxv02mmwz57z"))))
16084 (build-system r-build-system)
16086 `(("gfortran" ,gfortran)))
16087 (home-page "https://cran.r-project.org/web/packages/subplex")
16088 (synopsis "Unconstrained optimization using the subplex algorithm")
16090 "This package implements the Subplex optimization algorithm.
16091 It solves unconstrained optimization problems using a simplex method on
16092 subspaces. The method is well suited for optimizing objective functions that
16093 are noisy or are discontinuous at the solution.")
16094 (license license:gpl3+)))
16096 (define-public r-txtplot
16103 (uri (cran-uri "txtplot" version))
16106 "1949ab1bzvysdb79g8x1gaknj0ih3d6g63pv9512h5m5l3a6c31h"))))
16107 (build-system r-build-system)
16108 (home-page "https://cran.r-project.org/web/packages/txtplot/")
16109 (synopsis "Text-based plotting")
16110 (description "This package provides functions to produce rudimentary ASCII
16111 graphics directly in the terminal window. This package provides a basic
16112 plotting function (and equivalents of curve, density, acf and barplot) as well
16113 as a boxplot function.")
16114 (license license:lgpl3+)))
16116 (define-public r-bio3d
16123 (uri (cran-uri "bio3d" version))
16126 "07rw6c2d95gb5myxh31727j0jrchd0xisa3x89jjmf4zzs3vv7v7"))))
16127 (properties `((upstream-name . "bio3d")))
16128 (build-system r-build-system)
16129 (inputs `(("zlib" ,zlib)))
16130 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
16131 (home-page "http://thegrantlab.org/bio3d/")
16132 (synopsis "Biological structure analysis")
16134 "This package provides utilities to process, organize and explore protein
16135 structure, sequence and dynamics data. Features include the ability to read
16136 and write structure, sequence and dynamic trajectory data, perform sequence
16137 and structure database searches, data summaries, atom selection, alignment,
16138 superposition, rigid core identification, clustering, torsion analysis,
16139 distance matrix analysis, structure and sequence conservation analysis, normal
16140 mode analysis, principal component analysis of heterogeneous structure data,
16141 and correlation network analysis from normal mode and molecular dynamics data.
16142 In addition, various utility functions are provided to enable the statistical
16143 and graphical power of the R environment to work with biological sequence and
16145 (license license:gpl2+)))
16147 (define-public r-bios2cor
16149 (name "r-bios2cor")
16154 (uri (cran-uri "Bios2cor" version))
16157 "1rrz0vs6wbkwys3l5jv1rdnlhyb4r1q9pv7jlnmsx6c1b4f4vz5n"))))
16158 (properties `((upstream-name . "Bios2cor")))
16159 (build-system r-build-system)
16161 `(("r-bigmemory" ,r-bigmemory)
16162 ("r-bio3d" ,r-bio3d)
16163 ("r-circular" ,r-circular)
16164 ("r-igraph" ,r-igraph)))
16165 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
16166 (synopsis "From biological sequences and simulations to correlation analysis")
16168 "This package provides utilities for computation and analysis of
16169 correlation/covariation in multiple sequence alignments and in side chain
16170 motions during molecular dynamics simulations. Features include the
16171 computation of correlation/covariation scores using a variety of scoring
16172 functions between either sequence positions in alignments or side chain
16173 dihedral angles in molecular dynamics simulations and utilities to analyze the
16174 correlation/covariation matrix through a variety of tools including network
16175 representation and principal components analysis. In addition, several
16176 utility functions are based on the R graphical environment to provide friendly
16177 tools for help in data interpretation.")
16178 (license license:gpl2+)))
16180 ;; This package includes minified JavaScript files. When upgrading please
16181 ;; check that there are no new minified JavaScript files.
16182 (define-public r-networkd3
16184 (name "r-networkd3")
16189 (uri (cran-uri "networkD3" version))
16192 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
16195 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
16197 (properties `((upstream-name . "networkD3")))
16198 (build-system r-build-system)
16200 `(#:modules ((guix build utils)
16201 (guix build r-build-system)
16205 (modify-phases %standard-phases
16206 (add-after 'unpack 'process-javascript
16207 (lambda* (#:key inputs #:allow-other-keys)
16208 (with-directory-excursion "inst/htmlwidgets/lib/"
16212 `((,(assoc-ref inputs "d3.v4.js")
16213 "d3-4.5.0/d3.min.js"))))
16214 (lambda (sources targets)
16215 (for-each (lambda (source target)
16216 (format #t "Processing ~a --> ~a~%"
16218 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16219 (call-with-output-file target
16221 (dump-port minified port)))))
16222 sources targets))))
16225 `(("uglify-js" ,uglify-js)
16226 ;; NOTE: Make sure that this version of d3 is still valid when
16227 ;; upgrading the package.
16231 (uri "https://d3js.org/d3.v4.js")
16234 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
16236 `(("r-htmlwidgets" ,r-htmlwidgets)
16237 ("r-igraph" ,r-igraph)
16238 ("r-magrittr" ,r-magrittr)))
16239 (home-page "https://cran.r-project.org/package=networkD3")
16240 (synopsis "D3 JavaScript network graphs from R")
16242 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
16244 (license license:gpl3+)))
16246 (define-public r-aasea
16253 (uri (cran-uri "aaSEA" version))
16256 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
16257 (properties `((upstream-name . "aaSEA")))
16258 (build-system r-build-system)
16260 `(("r-bios2cor" ,r-bios2cor)
16262 ("r-hmisc" ,r-hmisc)
16263 ("r-magrittr" ,r-magrittr)
16264 ("r-networkd3" ,r-networkd3)
16265 ("r-plotly" ,r-plotly)
16266 ("r-seqinr" ,r-seqinr)
16267 ("r-shiny" ,r-shiny)
16268 ("r-shinydashboard" ,r-shinydashboard)))
16269 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
16270 (synopsis "Amino acid substitution effect analyzer")
16272 "Given a protein multiple sequence alignment, it is a daunting task to
16273 assess the effects of substitutions along sequence length. The aaSEA package
16274 is intended to help researchers to rapidly analyze property changes caused by
16275 single, multiple and correlated amino acid substitutions in proteins.")
16276 (license license:gpl3)))
16278 (define-public r-abacus
16285 (uri (cran-uri "ABACUS" version))
16288 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
16289 (properties `((upstream-name . "ABACUS")))
16290 (build-system r-build-system)
16292 `(("r-ggplot2" ,r-ggplot2)
16293 ("r-shiny" ,r-shiny)))
16294 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
16295 (synopsis "Apps-based activities for communicating and understanding statistics")
16297 "This package provides a set of Shiny apps for effective communication
16298 and understanding in statistics. The current version includes properties of
16299 normal distribution, properties of sampling distribution, one-sample z and t
16300 tests, two samples independent (unpaired) t test and analysis of variance.")
16301 (license license:gpl3)))
16303 (define-public r-abc-rap
16310 (uri (cran-uri "ABC.RAP" version))
16313 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
16314 (properties `((upstream-name . "ABC.RAP")))
16315 (build-system r-build-system)
16316 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
16317 (synopsis "Array-based CpG region analysis pipeline")
16319 "This package aims to identify candidate genes that are differentially
16320 methylated between cases and controls. It applies Student's t-test and delta
16321 beta analysis to identify candidate genes containing multiple CpG sites.")
16322 (license license:gpl3)))
16324 (define-public r-abcadm
16331 (uri (cran-uri "abcADM" version))
16334 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
16335 (properties `((upstream-name . "abcADM")))
16336 (build-system r-build-system)
16339 ("r-rcpp" ,r-rcpp)))
16340 (home-page "https://cran.r-project.org/web/packages/abcADM/")
16341 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
16343 "This package provides tools to estimate parameters of accumulated
16344 damage (load duration) models based on failure time data under a Bayesian
16345 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
16346 long-term reliability under stochastic load profiles.")
16347 (license license:gpl3)))
16349 (define-public r-rglpk
16356 (uri (cran-uri "Rglpk" version))
16359 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
16360 (properties `((upstream-name . "Rglpk")))
16361 (build-system r-build-system)
16363 `(("r-slam" ,r-slam)))
16366 (home-page "https://r-forge.r-project.org/projects/rglp/")
16367 (synopsis "R interface to the GNU Linear Programming Kit")
16369 "This package provides an R interface to the GNU Linear Programming Kit,
16370 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
16371 integer linear programming} (MILP) and other related problems.")
16373 (license (list license:gpl2 license:gpl3))))
16375 (define-public r-abcdefba
16377 (name "r-abcdefba")
16382 (uri (cran-uri "abcdeFBA" version))
16385 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
16386 (properties `((upstream-name . "abcdeFBA")))
16387 (build-system r-build-system)
16389 `(("r-corrplot" ,r-corrplot)
16390 ("r-lattice" ,r-lattice)
16392 ("r-rglpk" ,r-rglpk)))
16393 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
16394 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
16396 "This package provides functions for Constraint Based Simulation using
16397 Flux Balance Analysis and informative analysis of the data generated during
16399 (license license:gpl2)))
16401 (define-public r-abcrlda
16408 (uri (cran-uri "abcrlda" version))
16411 "0j29ifsvmxfx2g6v4bpbb4s6miwfpf4vlkpbgj6f2q078s4clc85"))))
16412 (properties `((upstream-name . "abcrlda")))
16413 (build-system r-build-system)
16414 (home-page "https://ieeexplore.ieee.org/document/8720003/")
16415 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
16417 "This package offers methods to perform @dfn{asymptotically
16418 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
16419 cost-sensitive binary classification. The bias-correction is an estimate of
16420 the bias term added to regularized discriminant analysis that minimizes the
16422 (license license:gpl3)))
16424 (define-public r-abemus
16431 (uri (cran-uri "abemus" version))
16434 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
16435 (properties `((upstream-name . "abemus")))
16436 (build-system r-build-system)
16438 `(("r-data-table" ,r-data-table)))
16439 (home-page "https://cran.r-project.org/web/packages/abemus/")
16440 (synopsis "Adaptive base error model in ultra-deep sequencing data")
16442 "This package provides an implementation of @dfn{Adaptive Base Error
16443 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
16444 platform-specific genetic knowledge and empirical signal to readily detect and
16445 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
16446 cell free DNA} (cfDNA).")
16447 (license license:gpl3)))
16449 ;; This package includes minified JavaScript files. When upgrading please
16450 ;; check that there are no new minified JavaScript files.
16451 (define-public r-rintrojs
16453 (name "r-rintrojs")
16458 (uri (cran-uri "rintrojs" version))
16461 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
16462 (properties `((upstream-name . "rintrojs")))
16463 (build-system r-build-system)
16465 `(#:modules ((guix build utils)
16466 (guix build r-build-system)
16470 (modify-phases %standard-phases
16471 (add-after 'unpack 'process-javascript
16472 (lambda* (#:key inputs #:allow-other-keys)
16473 (with-directory-excursion "inst/javascript/introjs/"
16477 `((,(assoc-ref inputs "intro.js")
16479 (lambda (sources targets)
16480 (for-each (lambda (source target)
16481 (format #t "Processing ~a --> ~a~%"
16483 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16484 (call-with-output-file target
16486 (dump-port minified port)))))
16487 sources targets))))
16490 `(("uglify-js" ,uglify-js)
16494 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
16497 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
16499 `(("r-jsonlite" ,r-jsonlite)
16500 ("r-shiny" ,r-shiny)))
16501 (home-page "https://github.com/carlganz/rintrojs")
16502 (synopsis "Wrapper for the Intro.js library")
16504 "This package provides a wrapper for the @url{http://www.introjs.com,
16505 Intro.js} library. This package makes it easy to include step-by-step
16506 introductions, and clickable hints in a Shiny application. It supports both
16507 static introductions in the UI, and programmatic introductions from the
16509 (license license:agpl3+)))
16511 (define-public r-sysfonts
16513 (name "r-sysfonts")
16518 (uri (cran-uri "sysfonts" version))
16521 "0wng902plryf2d8fc7k7m3jx11acz51kb2d91cqbyhq7xpk06z43"))))
16522 (properties `((upstream-name . "sysfonts")))
16523 (build-system r-build-system)
16525 `(("freetype" ,freetype)
16529 `(("pkg-config" ,pkg-config)))
16530 (home-page "https://github.com/yixuan/sysfonts")
16531 (synopsis "Loading fonts into R")
16533 "This is a package to simplify loading of system fonts and Google Fonts
16534 into R, in order to support other packages.")
16535 (license license:gpl2)))
16537 (define-public r-showtextdb
16539 (name "r-showtextdb")
16544 (uri (cran-uri "showtextdb" version))
16547 "1qwwj9x2jvadvwn60h75k99c9xi7yhqjsgaakahz5paxgj583bsh"))))
16548 (properties `((upstream-name . "showtextdb")))
16549 (build-system r-build-system)
16551 `(("r-sysfonts" ,r-sysfonts)))
16552 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
16553 (synopsis "Font files for the 'showtext' package")
16555 "This package provides font files that can be used by the @code{showtext}
16557 (license license:asl2.0)))
16559 (define-public r-showtext
16561 (name "r-showtext")
16566 (uri (cran-uri "showtext" version))
16569 "1ihgqzfia36b0n9aa41p1w98wxxvs1lxh1zz0570hbfqmph1sk73"))))
16570 (properties `((upstream-name . "showtext")))
16571 (build-system r-build-system)
16573 `(("freetype" ,freetype)
16577 `(("r-showtextdb" ,r-showtextdb)
16578 ("r-sysfonts" ,r-sysfonts)))
16579 (native-inputs `(("pkg-config" ,pkg-config)))
16580 (home-page "https://github.com/yixuan/showtext")
16581 (synopsis "Using fonts more easily in R graphs")
16583 "This package aims to make it easy to use various types of
16584 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
16585 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
16586 will be converted into polygons or raster images, hence after the plot has
16587 been created, it no longer relies on the font files. No external software
16588 such as Ghostscript is needed to use this package.")
16589 (license license:asl2.0)))
16591 (define-public r-emojifont
16593 (name "r-emojifont")
16598 (uri (cran-uri "emojifont" version))
16601 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
16602 (properties `((upstream-name . "emojifont")))
16603 (build-system r-build-system)
16605 `(("r-ggplot2" ,r-ggplot2)
16606 ("r-proto" ,r-proto)
16607 ("r-showtext" ,r-showtext)
16608 ("r-sysfonts" ,r-sysfonts)))
16609 (home-page "https://guangchuangyu.github.io/emojifont")
16610 (synopsis "Emoji and Font Awesome in R graphics")
16612 "This package enables the use of emoji and the Font Awesome glyphs in
16613 both base and ggplot2 graphics.")
16614 (license license:artistic2.0)))
16616 (define-public r-abstractr
16618 (name "r-abstractr")
16623 (uri (cran-uri "abstractr" version))
16626 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
16627 (properties `((upstream-name . "abstractr")))
16628 (build-system r-build-system)
16630 `(("r-colourpicker" ,r-colourpicker)
16631 ("r-emojifont" ,r-emojifont)
16632 ("r-ggplot2" ,r-ggplot2)
16633 ("r-gridextra" ,r-gridextra)
16634 ("r-rintrojs" ,r-rintrojs)
16635 ("r-shiny" ,r-shiny)
16636 ("r-shinythemes" ,r-shinythemes)))
16637 (home-page "https://matt-kumar.shinyapps.io/portfolio")
16638 (synopsis "R-Shiny application for creating visual abstracts")
16640 "This package provides an R Shiny application to create visual abstracts
16641 for original research. A variety of user defined options and formatting are
16643 (license license:gpl3)))
16645 (define-public r-abtest
16652 (uri (cran-uri "abtest" version))
16655 "1ky3cf827kj24bhcpk00v5zl5jdkii1gca0x81ay1cjkzfispgws"))))
16656 (properties `((upstream-name . "abtest")))
16657 (build-system r-build-system)
16659 `(("r-matrix" ,r-matrix)
16660 ("r-mvtnorm" ,r-mvtnorm)
16661 ("r-plotrix" ,r-plotrix)
16662 ("r-rcolorbrewer" ,r-rcolorbrewer)
16665 ("r-truncnorm" ,r-truncnorm)
16666 ("r-vgam" ,r-vgam)))
16667 (home-page "https://cran.r-project.org/web/packages/abtest/")
16668 (synopsis "Bayesian A/B testing")
16670 "This package provides functions for Bayesian A/B testing including prior
16671 elicitation options based on Kass and Vaidyanathan (1992)
16672 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
16673 (license license:gpl2+)))
16675 (define-public r-accept
16682 (uri (cran-uri "accept" version))
16685 "1r4mhy9g4wjcjgdd0gwdarmr09292il3vdkmx0hz7vh9mffyr9kx"))))
16686 (properties `((upstream-name . "accept")))
16687 (build-system r-build-system)
16689 `(("r-dplyr" ,r-dplyr)
16690 ("r-extrafont" ,r-extrafont)
16692 ("r-plotly" ,r-plotly)
16693 ("r-stringr" ,r-stringr)
16694 ("r-viridis" ,r-viridis)))
16695 (home-page "https://cran.r-project.org/web/packages/accept/")
16696 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
16698 "This package allows clinicians to predict the rate and severity of
16699 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
16700 Disease} (COPD) patients, based on the clinical prediction model published in
16701 Adibi et al. (2019) @url{doi:10.1101/651901}.")
16702 (license license:gpl3)))
16704 (define-public r-smpracticals
16706 (name "r-smpracticals")
16711 (uri (cran-uri "SMPracticals" version))
16714 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
16715 (properties `((upstream-name . "SMPracticals")))
16716 (build-system r-build-system)
16718 `(("r-ellipse" ,r-ellipse)
16721 ("r-survival" ,r-survival)))
16722 (home-page "http://statwww.epfl.ch/davison/SM/")
16723 (synopsis "Practicals for use with Davison (2003) Statistical Models")
16725 "This package contains the datasets and a few functions for use with the
16726 practicals outlined in Appendix A of the book Statistical Models (Davison,
16727 2003, Cambridge University Press). The practicals themselves can be found at
16728 @url{http://statwww.epfl.ch/davison/SM/}.")
16729 (license license:gpl2+)))
16731 (define-public r-fgui
16738 (uri (cran-uri "fgui" version))
16741 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
16742 (properties `((upstream-name . "fgui")))
16743 (build-system r-build-system)
16745 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
16746 (synopsis "Create GUI for R functions")
16748 "Rapidly create a GUI for a function you created by automatically
16749 creating widgets for arguments of the function. This package automatically
16750 parses help routines for context-sensitive help to these arguments. The
16751 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
16752 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
16753 incorporated into the interface for greater customization for the more
16755 ;; Any version of the GPL.
16756 (license (list license:gpl2+ license:gpl3+))))
16758 (define-public r-tcltk2
16765 (uri (cran-uri "tcltk2" version))
16768 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
16769 (properties `((upstream-name . "tcltk2")))
16770 (build-system r-build-system)
16774 (home-page "https://www.sciviews.org/SciViews-R")
16775 (synopsis "Tcl/Tk additions")
16777 "This package provides a series of additional Tcl commands and Tk widgets
16778 with style and various functions to supplement the tcltk package")
16779 (license license:lgpl3)))
16781 (define-public r-accrual
16788 (uri (cran-uri "accrual" version))
16791 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
16792 (properties `((upstream-name . "accrual")))
16793 (build-system r-build-system)
16795 `(("r-fgui" ,r-fgui)
16796 ("r-smpracticals" ,r-smpracticals)
16797 ("r-tcltk2" ,r-tcltk2)))
16798 (home-page "https://cran.r-project.org/web/packages/accrual/")
16799 (synopsis "Bayesian accrual prediction")
16801 "Subject recruitment for medical research is challenging. Slow patient
16802 accrual leads to delay in research. Accrual monitoring during the process of
16803 recruitment is critical. Researchers need reliable tools to manage the
16804 accrual rate. This package provides an implementation of a Bayesian method
16805 that integrates researcher's experience on previous trials and data from the
16806 current study, providing reliable prediction on accrual rate for clinical
16807 studies. It provides functions for Bayesian accrual prediction which can be
16808 easily used by statisticians and clinical researchers.")
16809 (license license:gpl2)))
16811 (define-public r-accrued
16818 (uri (cran-uri "accrued" version))
16821 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
16822 (properties `((upstream-name . "accrued")))
16823 (build-system r-build-system)
16824 (home-page "https://cran.r-project.org/web/packages/accrued/")
16825 (synopsis "Data quality visualization tools for partially accruing data")
16827 "This is a package for visualizing data quality of partially accruing
16829 (license license:gpl3)))
16831 (define-public r-mda
16838 (uri (cran-uri "mda" version))
16841 "19g6kn6g0shidrjfffklbmzc5w7mcimrxhagx4nmpslg59ibqdkh"))))
16842 (properties `((upstream-name . "mda")))
16843 (build-system r-build-system)
16844 (propagated-inputs `(("r-class" ,r-class)))
16845 (native-inputs `(("gfortran" ,gfortran)))
16846 (home-page "https://cran.r-project.org/web/packages/mda/")
16847 (synopsis "Mixture and flexible discriminant analysis")
16849 "This is a package for mixture and flexible discriminant analysis,
16850 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
16851 (license license:gpl2)))
16853 (define-public r-elasticnet
16855 (name "r-elasticnet")
16860 (uri (cran-uri "elasticnet" version))
16863 "0p9dplnsp28z4s2fl6afbwrgd0aj339fak8mmndicmrh7bb7rpmb"))))
16864 (properties `((upstream-name . "elasticnet")))
16865 (build-system r-build-system)
16867 `(("r-lars" ,r-lars)))
16868 (home-page "http://www.stat.umn.edu/~hzou")
16869 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
16871 "This package provides functions for fitting the entire solution path of
16872 the Elastic-Net and also provides functions for estimating sparse Principal
16873 Components. The Lasso solution paths can be computed by the same function.")
16874 (license license:gpl2+)))
16876 (define-public r-sparselda
16878 (name "r-sparselda")
16883 (uri (cran-uri "sparseLDA" version))
16886 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
16887 (properties `((upstream-name . "sparseLDA")))
16888 (build-system r-build-system)
16890 `(("r-elasticnet" ,r-elasticnet)
16893 (home-page "http://www.imm.dtu.dk/~lhc")
16894 (synopsis "Sparse discriminant analysis")
16896 "This package performs sparse linear discriminant analysis for Gaussians
16897 and mixture of Gaussian models.")
16898 (license license:gpl2+)))
16900 (define-public r-accsda
16907 (uri (cran-uri "accSDA" version))
16910 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
16911 (properties `((upstream-name . "accSDA")))
16912 (build-system r-build-system)
16914 `(("r-ggplot2" ,r-ggplot2)
16915 ("r-ggthemes" ,r-ggthemes)
16916 ("r-gridextra" ,r-gridextra)
16918 ("r-rarpack" ,r-rarpack)
16919 ("r-sparselda" ,r-sparselda)))
16920 (home-page "https://github.com/gumeo/accSDA/wiki")
16921 (synopsis "Accelerated sparse discriminant analysis")
16923 "This package provides an implementation of sparse linear discriminant
16924 analysis, which is a supervised classification method for multiple classes.
16925 Various novel optimization approaches to this problem are implemented
16926 including @dfn{alternating direction method of multipliers} (ADMM),
16927 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
16928 Functions for performing cross validation are also supplied along with basic
16929 prediction and plotting functions. @dfn{Sparse zero variance
16930 discriminant} (SZVD) analysis is also included in the package.")
16931 (license license:gpl2+)))
16933 (define-public r-ace2fastq
16935 (name "r-ace2fastq")
16940 (uri (cran-uri "ace2fastq" version))
16943 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
16944 (properties `((upstream-name . "ace2fastq")))
16945 (build-system r-build-system)
16947 `(("r-stringr" ,r-stringr)))
16948 (home-page "https://github.com/c5sire/ace2fastq")
16949 (synopsis "ACE file to FASTQ converter")
16951 "The ACE file format is used in genomics to store contigs from sequencing
16952 machines. This tools converts it into FASTQ format. Both formats contain the
16953 sequence characters and their corresponding quality information. Unlike the
16954 FASTQ file, the ACE file stores the quality values numerically. The
16955 conversion algorithm uses the standard Sanger formula. The package
16956 facilitates insertion into pipelines, and content inspection.")
16957 (license license:gpl3)))
16959 (define-public r-rngwell
16966 (uri (cran-uri "rngWELL" version))
16969 "0pjjcs9pqj7mf0mhb2cwd0aanqpwnm65bm86hk6mi2vw8rgnj2vv"))))
16970 (properties `((upstream-name . "rngWELL")))
16971 (build-system r-build-system)
16972 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
16973 (synopsis "Toolbox for WELL random number generators")
16975 "This is a dedicated package to WELL pseudo random generators, which were
16976 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
16977 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
16978 (license license:bsd-3)))
16980 (define-public r-randtoolbox
16982 (name "r-randtoolbox")
16987 (uri (cran-uri "randtoolbox" version))
16990 "141p13ajgzmb2s89rlac7zrra92mi1izvpfrngb4kqzlf3igdsqd"))))
16991 (properties `((upstream-name . "randtoolbox")))
16992 (build-system r-build-system)
16994 `(("r-rngwell" ,r-rngwell)))
16996 `(("gfortran" ,gfortran)))
16997 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
16998 (synopsis "Toolbox for pseudo and quasi random number generation")
17000 "This package provides
17003 @item pseudo random generators, such as general linear
17004 congruential generators, multiple recursive generators and generalized
17005 feedback shift register (SF-Mersenne Twister algorithm and WELL
17008 @item quasi random generators, such as the Torus algorithm, the Sobol
17009 sequence, the Halton sequence (including the Van der Corput sequence), and
17011 @item some generator tests: the gap test, the serial test, the poker test.
17014 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
17015 (license license:bsd-3)))
17017 (define-public r-lhs
17024 (uri (cran-uri "lhs" version))
17027 "0lzaqr7xi3ckln5nglv5xf5njm359slpz1jc6s02hpsqdw6armd4"))))
17028 (properties `((upstream-name . "lhs")))
17029 (build-system r-build-system)
17030 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
17031 (home-page "https://github.com/bertcarnell/lhs")
17032 (synopsis "Latin Hypercube Samples")
17034 "This package provides a number of methods for creating and augmenting
17035 Latin Hypercube Samples.")
17036 (license license:gpl3)))
17038 (define-public r-acebayes
17040 (name "r-acebayes")
17045 (uri (cran-uri "acebayes" version))
17048 "1xm6bw0qm2vlcrk274x0bawzb2lnacb1wsmzba5mg3i75a55pqln"))))
17049 (properties `((upstream-name . "acebayes")))
17050 (build-system r-build-system)
17052 `(("r-compare" ,r-compare)
17054 ("r-randtoolbox" ,r-randtoolbox)
17056 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17057 (home-page "https://cran.r-project.org/web/packages/acebayes/")
17058 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
17060 "Finding an optimal Bayesian experimental design involves maximizing an
17061 objective function given by the expectation of some appropriately chosen
17062 utility function with respect to the joint distribution of unknown
17063 quantities (including responses). This objective function is usually not
17064 available in closed form and the design space can be continuous and of high
17065 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
17066 to maximise an approximation to the expectation of the utility function.")
17067 (license license:gpl2)))
17069 (define-public r-acet
17076 (uri (cran-uri "ACEt" version))
17079 "0626d6kg485xjya164wagrr5z223jvi93ywbwpdns7fkm03c0dlq"))))
17080 (properties `((upstream-name . "ACEt")))
17081 (build-system r-build-system)
17086 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17087 (home-page "https://cran.r-project.org/web/packages/ACEt/")
17088 (synopsis "Estimating dynamic heritability and twin model comparison")
17090 "This package supports twin models that are able to estimate the dynamic
17091 behaviour of the variance components in the classical twin models with respect
17092 to age using B-splines and P-splines.")
17093 (license license:gpl2+)))
17095 (define-public r-acfmperiod
17097 (name "r-acfmperiod")
17102 (uri (cran-uri "acfMPeriod" version))
17105 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
17106 (properties `((upstream-name . "acfMPeriod")))
17107 (build-system r-build-system)
17109 `(("r-mass" ,r-mass)))
17110 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
17111 (synopsis "Estimation of the ACF from the M-periodogram")
17113 "This package support non-robust and robust computations of the sample
17114 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
17115 univariate and multivariate processes. The methodology consists in reversing
17116 the diagonalization procedure involving the periodogram or the
17117 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
17118 ACOVF or the ACF as discussed in Fuller (1995)
17119 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
17120 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
17121 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
17122 (license license:gpl2+)))
17124 (define-public r-gamlss-data
17126 (name "r-gamlss-data")
17131 (uri (cran-uri "gamlss.data" version))
17134 "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
17135 (properties `((upstream-name . "gamlss.data")))
17136 (build-system r-build-system)
17137 (home-page "http://www.gamlss.org/")
17138 (synopsis "GAMLSS data")
17140 "This package provides data used as examples to demonstrate GAMLSS
17142 ;; Either version of the license
17143 (license (list license:gpl2 license:gpl3))))
17145 (define-public r-gamlss
17152 (uri (cran-uri "gamlss" version))
17155 "0gcngfck0dk2rhjg0z1fnc61dqs0s049jy2rkywaf57531s2k8bc"))))
17156 (properties `((upstream-name . "gamlss")))
17157 (build-system r-build-system)
17159 `(("r-gamlss-data" ,r-gamlss-data)
17160 ("r-gamlss-dist" ,r-gamlss-dist)
17163 ("r-survival" ,r-survival)))
17164 (home-page "http://www.gamlss.org/")
17165 (synopsis "Generalized additive models for location scale and shape")
17167 "This package provides functions for fitting the generalized additive
17168 models for location scale and shape introduced by Rigby and
17169 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
17170 use a distributional regression approach where all the parameters of the
17171 conditional distribution of the response variable are modelled using
17172 explanatory variables.")
17173 ;; Either version of the license
17174 (license (list license:gpl2 license:gpl3))))
17176 (define-public r-acid
17183 (uri (cran-uri "acid" version))
17186 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
17187 (properties `((upstream-name . "acid")))
17188 (build-system r-build-system)
17190 `(("r-gamlss" ,r-gamlss)
17191 ("r-gamlss-dist" ,r-gamlss-dist)
17192 ("r-hmisc" ,r-hmisc)))
17193 (home-page "https://cran.r-project.org/web/packages/acid/")
17194 (synopsis "Analysing conditional income distributions")
17196 "This package provides functions for the analysis of income distributions
17197 for subgroups of the population as defined by a set of variables like age,
17198 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
17199 distribution as well as functions for moments, inequality measures, entropy
17200 measures and polarisation measures of income distributions. This package thus
17201 aides the analysis of income inequality by offering tools for the exploratory
17202 analysis of income distributions at the disaggregated level.")
17203 (license license:gpl3)))
17205 (define-public r-acm4r
17212 (uri (cran-uri "acm4r" version))
17215 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
17216 (properties `((upstream-name . "acm4r")))
17217 (build-system r-build-system)
17218 (propagated-inputs `(("r-mass" ,r-mass)))
17219 (home-page "https://cran.r-project.org/web/packages/acm4r/")
17220 (synopsis "Align-and-count method comparisons of RFLP data")
17222 "This is a package to compare sequence fragment lengths or molecular
17223 weights from pairs of lanes. The number of matching bands in the
17224 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
17225 the align-and-count method.")
17226 ;; Any version of the GPL
17227 (license (list license:gpl2+ license:gpl3+))))
17229 (define-public r-filematrix
17231 (name "r-filematrix")
17236 (uri (cran-uri "filematrix" version))
17239 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
17240 (properties `((upstream-name . "filematrix")))
17241 (build-system r-build-system)
17242 ;; These inputs are needed for vignettes
17244 `(("r-knitr" ,r-knitr)
17245 ("r-rmarkdown" ,r-rmarkdown)
17246 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
17247 (home-page "https://github.com/andreyshabalin/filematrix")
17248 (synopsis "File-backed matrix class with convenient read and write access")
17250 "This package provides an interface for working with large matrices
17251 stored in files, not in computer memory. It supports multiple non-character
17252 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
17253 byte real values). Access to parts of the matrix is done by indexing, exactly
17254 as with usual R matrices. It supports very large matrices; the package has
17255 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
17256 columns, ad allows for quick addition of extra columns to a filematrix.")
17257 (license license:lgpl3)))
17259 (define-public r-acmeeqtl
17261 (name "r-acmeeqtl")
17266 (uri (cran-uri "ACMEeqtl" version))
17269 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
17270 (properties `((upstream-name . "ACMEeqtl")))
17271 (build-system r-build-system)
17273 `(("r-filematrix" ,r-filematrix)))
17274 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
17275 (synopsis "Estimation of interpretable eQTL effect sizes")
17277 "This package provides a non-linear model, termed ACME, that reflects a
17278 parsimonious biological model for allelic contributions of cis-acting eQTLs.
17279 With non-linear least-squares algorithm the maximum likelihood parameters can
17280 be estimated. The ACME model provides interpretable effect size estimates and
17281 p-values with well controlled Type-I error.")
17282 (license license:lgpl3)))
17284 (define-public r-acmer
17291 (uri (cran-uri "acmeR" version))
17294 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
17295 (properties `((upstream-name . "acmeR")))
17296 (build-system r-build-system)
17297 (propagated-inputs `(("r-foreign" ,r-foreign)))
17298 (home-page "https://cran.r-project.org/web/packages/acmeR/")
17299 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
17301 "This package provides an implementation of the ACME estimator, described
17302 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
17303 Mortality at Wind Turbines. Unlike most other models, this estimator supports
17304 decreasing-hazard Weibull model for persistence; decreasing search proficiency
17305 as carcasses age; variable bleed-through at successive searches; and interval
17306 mortality estimates. The package provides, based on search data, functions
17307 for estimating the mortality inflation factor in Frequentist and Bayesian
17309 (license license:expat)))
17311 (define-public r-r-huge
17318 (uri (cran-uri "R.huge" version))
17321 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
17322 (properties `((upstream-name . "R.huge")))
17323 (build-system r-build-system)
17325 `(("r-r-methodss3" ,r-r-methodss3)
17327 ("r-r-utils" ,r-r-utils)))
17328 (home-page "https://github.com/HenrikBengtsson/R.huge")
17329 (synopsis "Methods for accessing huge amounts of data")
17331 "This is a deprecated package for accessing huge amounts of data.
17332 Cross-platform alternatives are the following packages: bigmemory (CRAN),
17333 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
17334 the @code{aroma.affymetrix} package.")
17335 (license license:lgpl2.1+)))
17337 (define-public r-r-filesets
17339 (name "r-r-filesets")
17344 (uri (cran-uri "R.filesets" version))
17347 "124rygq0bl9n4akxcm868nl30cyk3rz0iprb98zlpk62gci9f5fg"))))
17348 (properties `((upstream-name . "R.filesets")))
17349 (build-system r-build-system)
17351 `(("r-digest" ,r-digest)
17352 ("r-r-cache" ,r-r-cache)
17353 ("r-r-methodss3" ,r-r-methodss3)
17355 ("r-r-utils" ,r-r-utils)))
17356 (home-page "https://github.com/HenrikBengtsson/R.filesets")
17357 (synopsis "Easy handling of and access to files")
17359 "This package provides classes and methods to locate, setup, subset,
17360 navigate and iterate file sets, i.e. sets of files located in one or more
17361 directories on the file system. The API is designed such that these classes
17362 can be extended via inheritance to provide a richer API for special file
17363 formats. Moreover, a specific name format is defined such that filenames and
17364 directories can be considered to have full names which consists of a name
17365 followed by comma-separated tags. This adds additional flexibility to
17366 identify file sets and individual files.")
17367 (license license:lgpl2.1+)))
17369 (define-public r-r-devices
17371 (name "r-r-devices")
17376 (uri (cran-uri "R.devices" version))
17379 "15zlnq3g27whq26fbcy5zfl5hiddm256h4rga4frblg6wqlbkvdd"))))
17380 (properties `((upstream-name . "R.devices")))
17381 (build-system r-build-system)
17383 `(("r-base64enc" ,r-base64enc)
17384 ("r-r-methodss3" ,r-r-methodss3)
17386 ("r-r-utils" ,r-r-utils)))
17387 (home-page "https://github.com/HenrikBengtsson/R.devices")
17388 (synopsis "Unified handling of graphics devices")
17390 "This package provides functions for creating plots and image files in a
17391 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
17392 Default device options as well as scales and aspect ratios are controlled in a
17393 uniform way across all device types. Switching output format requires minimal
17394 changes in code. This package is ideal for large-scale batch processing,
17395 because it will never leave open graphics devices or incomplete image files
17396 behind, even on errors or user interrupts.")
17397 (license license:lgpl2.1+)))
17399 (define-public r-acnr
17406 (uri (cran-uri "acnr" version))
17409 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
17410 (properties `((upstream-name . "acnr")))
17411 (build-system r-build-system)
17412 (home-page "https://github.com/mpierrejean/acnr")
17413 (synopsis "Annotated copy-number regions")
17415 "This package provides SNP array data from different types of copy-number
17416 regions. These regions were identified manually by the authors of the package
17417 and may be used to generate realistic data sets with known truth.")
17418 (license license:lgpl2.1+)))
17420 (define-public r-acopula
17427 (uri (cran-uri "acopula" version))
17430 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
17431 (properties `((upstream-name . "acopula")))
17432 (build-system r-build-system)
17433 (home-page "https://cran.r-project.org/web/packages/acopula/")
17434 (synopsis "Modelling dependence with multivariate Archimax copulas")
17436 "Archimax copulas are a mixture of Archimedean and EV copulas. This
17437 package provides definitions of several parametric families of generator and
17438 dependence function, computes CDF and PDF, estimates parameters, tests for
17439 goodness of fit, generates random sample and checks copula properties for
17440 custom constructs. In the 2-dimensional case explicit formulas for density
17441 are used, contrary to higher dimensions when all derivatives are linearly
17442 approximated. Several non-archimax families (normal, FGM, Plackett) are
17443 provided as well.")
17444 (license license:gpl2)))
17446 (define-public r-tuner
17453 (uri (cran-uri "tuneR" version))
17456 "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
17457 (properties `((upstream-name . "tuneR")))
17458 (build-system r-build-system)
17459 (propagated-inputs `(("r-signal" ,r-signal)))
17460 (home-page "https://cran.r-project.org/web/packages/tuneR/")
17461 (synopsis "Analysis of music and speech")
17463 "This is a package for the analysis of music and speech. Analyze music
17464 and speech, extract features like MFCCs, handle wave files and their
17465 representation in various ways, read MP3, read MIDI, perform steps of a
17466 transcription, ...")
17467 ;; Either of these versions.
17468 (license (list license:gpl2 license:gpl3))))
17470 (define-public r-seewave
17477 (uri (cran-uri "seewave" version))
17480 "1qg8f5gik9pw6f9mcxqmrc9x3003s8vdm6g01pjjpyc9qaqiz2vi"))))
17481 (properties `((upstream-name . "seewave")))
17482 (build-system r-build-system)
17484 `(("r-tuner" ,r-tuner)))
17485 (home-page "http://rug.mnhn.fr/seewave")
17486 (synopsis "Sound analysis and synthesis")
17488 "This package provides functions for analysing, manipulating, displaying,
17489 editing and synthesizing time waves (particularly sound). This package
17490 processes time analysis (oscillograms and envelopes), spectral content,
17491 resonance quality factor, entropy, cross correlation and autocorrelation,
17492 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
17493 and 3D spectrograms and many other analyses.")
17494 (license license:gpl2+)))
17496 (define-public r-acousticndlcoder
17498 (name "r-acousticndlcoder")
17503 (uri (cran-uri "AcousticNDLCodeR" version))
17506 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
17508 `((upstream-name . "AcousticNDLCodeR")))
17509 (build-system r-build-system)
17511 `(("r-seewave" ,r-seewave)
17512 ("r-tuner" ,r-tuner)
17514 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
17515 (synopsis "Coding sound files for use with NDL")
17517 "Make acoustic cues to use with the R package @code{ndl}.
17518 The package implements functions used in the PLoS ONE paper \"Words from
17519 spontaneous conversational speech can be recognized with human-like accuracy
17520 by an error-driven learning algorithm that discriminates between meanings
17521 straight from smart acoustic features, bypassing the phoneme as recognition
17522 unit.\" @url{doi:10.1371/journal.pone.0174623}")
17523 (license license:gpl2+)))
17525 (define-public r-acp
17532 (uri (cran-uri "acp" version))
17535 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
17536 (properties `((upstream-name . "acp")))
17537 (build-system r-build-system)
17539 `(("r-quantmod" ,r-quantmod)
17540 ("r-tseries" ,r-tseries)))
17541 (home-page "https://cran.r-project.org/web/packages/acp/")
17542 (synopsis "Autoregressive conditional Poisson")
17544 "This package supports the analysis of count data exhibiting
17545 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
17546 model (ACP(p,q)) proposed by Heinen (2003).")
17547 (license license:gpl2)))
17549 (define-public r-ada
17556 (uri (cran-uri "ada" version))
17559 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
17560 (properties `((upstream-name . "ada")))
17561 (build-system r-build-system)
17562 (propagated-inputs `(("r-rpart" ,r-rpart)))
17563 (home-page "https://cran.r-project.org/web/packages/ada/")
17564 (synopsis "Stochastic boosting")
17566 "This package provides a straightforward, well-documented, and broad
17567 boosting routine for classification, ideally suited for small to
17568 moderate-sized data sets. It performs discrete, real, and gentle boost under
17569 both exponential and logistic loss on a given data set.")
17570 ;; Any version of the GPL.
17571 (license (list license:gpl2+ license:gpl3+))))
17573 (define-public r-genalg
17580 (uri (cran-uri "genalg" version))
17583 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
17584 (properties `((upstream-name . "genalg")))
17585 (build-system r-build-system)
17586 (home-page "https://github.com/egonw/genalg")
17587 (synopsis "R based genetic algorithm")
17589 "This package provides an R based genetic algorithm for binary and
17590 floating point chromosomes.")
17591 (license license:gpl2)))
17593 (define-public r-kernelfactory
17595 (name "r-kernelfactory")
17600 (uri (cran-uri "kernelFactory" version))
17603 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
17604 (properties `((upstream-name . "kernelFactory")))
17605 (build-system r-build-system)
17608 ("r-genalg" ,r-genalg)
17609 ("r-kernlab" ,r-kernlab)
17610 ("r-randomforest" ,r-randomforest)))
17611 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
17612 (synopsis "Ensemble of kernel machines")
17614 "Kernel factory is an ensemble method where each base classifier (random
17615 forest) is fit on the kernel matrix of a subset of the training data.")
17616 (license license:gpl2+)))
17618 (define-public r-dummies
17625 (uri (cran-uri "dummies" version))
17628 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
17629 (properties `((upstream-name . "dummies")))
17630 (build-system r-build-system)
17631 (home-page "https://decisionpatterns.com")
17632 (synopsis "Create dummy/indicator variables flexibly and efficiently")
17634 "This package lets you expand factors, characters and other eligible
17635 classes into dummy/indicator variables.")
17636 (license license:gpl2+)))
17638 (define-public r-acrm
17645 (uri (cran-uri "aCRM" version))
17648 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
17649 (properties `((upstream-name . "aCRM")))
17650 (build-system r-build-system)
17653 ("r-dummies" ,r-dummies)
17654 ("r-kernelfactory" ,r-kernelfactory)
17655 ("r-randomforest" ,r-randomforest)))
17656 (home-page "https://cran.r-project.org/web/packages/aCRM/")
17657 (synopsis "Convenience functions for analytical customer relationship management")
17659 "This package provides convenience functions for data preparation and
17660 modeling often used in @dfn{analytical customer relationship
17661 management} (aCRM).")
17662 (license license:gpl2+)))
17664 (define-public r-treeclust
17666 (name "r-treeclust")
17671 (uri (cran-uri "treeClust" version))
17674 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
17675 (properties `((upstream-name . "treeClust")))
17676 (build-system r-build-system)
17678 `(("r-cluster" ,r-cluster)
17679 ("r-rpart" ,r-rpart)))
17680 (home-page "https://cran.r-project.org/web/packages/treeClust/")
17681 (synopsis "Cluster distances through trees")
17683 "This package provides tools to create a measure of inter-point
17684 dissimilarity useful for clustering mixed data, and, optionally, perform the
17686 (license license:gpl2+)))
17688 (define-public r-acrosstic
17690 (name "r-acrosstic")
17695 (uri (cran-uri "AcrossTic" version))
17698 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
17699 (properties `((upstream-name . "AcrossTic")))
17700 (build-system r-build-system)
17702 `(("r-lpsolve" ,r-lpsolve)
17703 ("r-treeclust" ,r-treeclust)))
17704 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
17705 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
17707 "This is a package for constructing minimum-cost regular spanning
17708 subgraph as part of a non-parametric two-sample test for equality of
17710 (license license:gpl2+)))
17712 (define-public r-acrt
17719 (uri (cran-uri "acrt" version))
17722 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
17723 (properties `((upstream-name . "acrt")))
17724 (build-system r-build-system)
17726 `(("r-rcpp" ,r-rcpp)
17727 ("r-rcppeigen" ,r-rcppeigen)
17728 ("r-sandwich" ,r-sandwich)))
17729 (home-page "https://cran.r-project.org/web/packages/acrt/")
17730 (synopsis "Autocorrelation robust testing")
17732 "This package provides functions for testing affine hypotheses on the
17733 regression coefficient vector in regression models with autocorrelated
17735 (license license:gpl2)))
17737 (define-public r-acs
17744 (uri (cran-uri "acs" version))
17747 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
17748 (properties `((upstream-name . "acs")))
17749 (build-system r-build-system)
17751 `(("r-httr" ,r-httr)
17754 ("r-stringr" ,r-stringr)
17756 (home-page "http://dusp.mit.edu/faculty/ezra-glenn")
17757 (synopsis "Work with data from the US Census")
17759 "This package provides a general toolkit for downloading, managing,
17760 analyzing, and presenting data from the
17761 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
17762 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
17763 American Community Survey (ACS). Confidence intervals provided with ACS data
17764 are converted to standard errors to be bundled with estimates in complex
17765 @code{acs} objects. The package provides new methods to conduct standard
17766 operations on @code{acs} objects and present/plot data in statistically
17767 appropriate ways.")
17768 (license license:gpl3)))
17770 (define-public r-acss-data
17772 (name "r-acss-data")
17777 (uri (cran-uri "acss.data" version))
17780 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
17781 (properties `((upstream-name . "acss.data")))
17782 (build-system r-build-system)
17783 (home-page "http://complexitycalculator.com/methodology.html")
17784 (synopsis "Data for algorithmic complexity of short strings")
17786 "This is a data only package providing the algorithmic complexity of
17787 short strings, computed using the coding theorem method. For a given set of
17788 symbols in a string, all possible or a large number of random samples of
17789 Turing machines with a given number of states (e.g., 5) and number of symbols
17790 corresponding to the number of symbols in the strings were simulated until
17791 they reached a halting state or failed to end. This package contains data on
17792 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
17793 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
17794 distribution of the halting states.")
17795 (license license:gpl2+)))
17797 (define-public r-acss
17804 (uri (cran-uri "acss" version))
17807 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
17808 (properties `((upstream-name . "acss")))
17809 (build-system r-build-system)
17811 `(("r-acss-data" ,r-acss-data)
17813 (home-page "http://complexitycalculator.com/methodology.html")
17814 (synopsis "Algorithmic complexity for short strings")
17816 "The main purpose of this package is to provide the algorithmic
17817 complexity for short strings, an approximation of the Kolmogorov Complexity of
17818 a short string using the coding theorem method. While the database containing
17819 the complexity is provided in the data only package @code{acss.data}, this
17820 package provides functions accessing the data such as @code{prob_random}
17821 returning the posterior probability that a given string was produced by a
17822 random process. In addition, two traditional (but problematic) measures of
17823 complexity are also provided: entropy and change complexity.")
17824 (license license:gpl2+)))
17826 (define-public r-acswr
17833 (uri (cran-uri "ACSWR" version))
17836 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
17837 (properties `((upstream-name . "ACSWR")))
17838 (build-system r-build-system)
17840 `(("r-mass" ,r-mass)))
17841 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
17842 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
17844 "This is a companion package for the book \"A Course in Statistics with
17845 R\" (ISBN 978-1-119-15272-9.)")
17846 (license license:gpl2)))
17848 (define-public r-alabama
17851 (version "2015.3-1")
17855 (uri (cran-uri "alabama" version))
17858 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
17859 (properties `((upstream-name . "alabama")))
17860 (build-system r-build-system)
17861 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
17862 (home-page "https://cran.r-project.org/web/packages/alabama/")
17863 (synopsis "Constrained nonlinear optimization")
17865 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
17866 Algorithm; it is used for optimizing smooth nonlinear objective functions with
17867 constraints. Linear or nonlinear equality and inequality constraints are
17869 (license license:gpl2+)))
17871 (define-public r-gdina
17878 (uri (cran-uri "GDINA" version))
17881 "1aj2ssd7vpszl7p22srkkkpx4a7gkc38vrv3bq7j1zr32096y4zj"))))
17882 (properties `((upstream-name . "GDINA")))
17883 (build-system r-build-system)
17885 `(("r-alabama" ,r-alabama)
17886 ("r-ggplot2" ,r-ggplot2)
17888 ("r-nloptr" ,r-nloptr)
17889 ("r-numderiv" ,r-numderiv)
17891 ("r-rcpparmadillo" ,r-rcpparmadillo)
17892 ("r-rsolnp" ,r-rsolnp)
17893 ("r-shiny" ,r-shiny)
17894 ("r-shinydashboard" ,r-shinydashboard)))
17895 (home-page "https://github.com/Wenchao-Ma/GDINA")
17896 (synopsis "Generalized DINA model framework")
17898 "This package provides a set of psychometric tools for cognitive
17899 diagnosis modeling based on the generalized deterministic inputs, noisy and
17900 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
17901 and its extensions, including the sequential G-DINA model by Ma and de la
17902 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
17903 polytomous G-DINA model by Chen and de la Torre
17904 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
17905 distribution can be independent, saturated, higher-order, loglinear smoothed
17906 or structured. Q-matrix validation, item and model fit statistics, model
17907 comparison at test and item level and differential item functioning can also
17908 be conducted. A graphical user interface is also provided.")
17909 (license license:gpl3)))
17911 (define-public r-actcd
17918 (uri (cran-uri "ACTCD" version))
17921 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
17922 (properties `((upstream-name . "ACTCD")))
17923 (build-system r-build-system)
17925 `(("r-gdina" ,r-gdina)
17926 ("r-r-methodss3" ,r-r-methodss3)))
17928 `(("gfortran" ,gfortran)))
17929 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
17930 (synopsis "Asymptotic classification theory for cognitive diagnosis")
17932 "This is a package supporting cluster analysis for cognitive diagnosis
17933 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
17934 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
17935 sum-scores, cluster analysis techniques can be used to classify examinees into
17936 latent classes based on their attribute patterns. In addition to the
17937 algorithms used to classify data, three labeling approaches are proposed to
17938 label clusters so that examinees' attribute profiles can be obtained.")
17939 (license license:gpl2+)))
17941 (define-public r-ineq
17948 (uri (cran-uri "ineq" version))
17951 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
17952 (properties `((upstream-name . "ineq")))
17953 (build-system r-build-system)
17954 (home-page "https://cran.r-project.org/web/packages/ineq/")
17955 (synopsis "Measuring inequality, concentration, and poverty")
17957 "This package provides tools for measuring inequality, concentration, and
17958 poverty measures. It provides both empirical and theoretical Lorenz curves.")
17959 ;; Either of these two versions.
17960 (license (list license:gpl2 license:gpl3))))
17962 (define-public r-actfrag
17969 (uri (cran-uri "ActFrag" version))
17972 "06l5a679j6289008ls57v420mnzpq9a4ln7svi5bh0vpvws7sr9d"))))
17973 (properties `((upstream-name . "ActFrag")))
17974 (build-system r-build-system)
17976 `(("r-accelerometry" ,r-accelerometry)
17977 ("r-dplyr" ,r-dplyr)
17979 ("r-survival" ,r-survival)
17980 ("r-tidyr" ,r-tidyr)))
17981 (home-page "https://github.com/junruidi/ActFrag")
17982 (synopsis "Activity fragmentation metrics extraction")
17984 "This package provides functions to extract commonly used fragmentation
17985 metrics to quantify time accumulation strategies based on minute level
17986 actigraphy-measured activity counts data.")
17987 (license license:gpl3)))
17989 (define-public r-fda
17996 (uri (cran-uri "fda" version))
17999 "0n39rzbhg1hipzn51rzmbchn2358qgapg08iv7lmiqj5y7i9qns2"))))
18000 (properties `((upstream-name . "fda")))
18001 (build-system r-build-system)
18003 `(("r-matrix" ,r-matrix)))
18004 (home-page "http://www.functionaldata.org")
18005 (synopsis "Functional data analysis")
18007 "These functions were developed to support functional data analysis as
18008 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
18009 Analysis. The package includes data sets and script files working many
18011 (license license:gpl2+)))
18013 (define-public r-actigraphy
18015 (name "r-actigraphy")
18020 (uri (cran-uri "Actigraphy" version))
18023 "0y0ccmxhdfhdmi4k6pbfvnqknkqbgvfsf2qf7z7rc4xpfgym6574"))))
18024 (properties `((upstream-name . "Actigraphy")))
18025 (build-system r-build-system)
18028 ("r-sdmtools" ,r-sdmtools)))
18029 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
18030 (synopsis "Actigraphy data analysis")
18032 "This package provides tools for functional linear modeling and analysis
18033 of actigraphy data.")
18034 (license license:asl2.0)))
18036 (define-public r-activedriver
18038 (name "r-activedriver")
18043 (uri (cran-uri "ActiveDriver" version))
18046 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
18047 (properties `((upstream-name . "ActiveDriver")))
18048 (build-system r-build-system)
18050 `(("r-mass" ,r-mass)))
18051 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
18052 (synopsis "Tools for finding cancer driver proteins")
18054 "This package provides a mutation analysis tool that discovers cancer
18055 driver genes with frequent mutations in protein signalling sites such as
18056 post-translational modifications (phosphorylation, ubiquitination, etc). The
18057 Poisson generalized linear regression model identifies genes where cancer
18058 mutations in signalling sites are more frequent than expected from the
18059 sequence of the entire gene. Integration of mutations with signalling
18060 information helps find new driver genes and propose candidate mechanisms to
18062 (license license:gpl2+)))
18064 (define-public r-activitycounts
18066 (name "r-activitycounts")
18071 (uri (cran-uri "activityCounts" version))
18074 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
18076 `((upstream-name . "activityCounts")))
18077 (build-system r-build-system)
18079 `(("r-lubridate" ,r-lubridate)
18080 ("r-magrittr" ,r-magrittr)
18081 ("r-seewave" ,r-seewave)
18082 ("r-signal" ,r-signal)
18083 ("r-tibble" ,r-tibble)))
18084 (home-page "https://github.com/walkabillylab/activityCounts")
18085 (synopsis "Generate ActiLife counts")
18087 "ActiLife generates activity counts from data collected by Actigraph
18088 accelerometers. Actigraph is one of the most common research-grade
18089 accelerometers. There is considerable research validating and developing
18090 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
18091 counts are proprietary and difficult to implement if researchers use different
18092 accelerometer brands. The code creates ActiLife counts from raw acceleration
18093 data for different accelerometer brands.")
18094 (license license:gpl3)))
18096 (define-public r-activityindex
18098 (name "r-activityindex")
18103 (uri (cran-uri "ActivityIndex" version))
18106 "14k6d78s15j7kb7jhixf4msrdjdl28d0r264cbvy41p8dkq7ysvk"))))
18107 (properties `((upstream-name . "ActivityIndex")))
18108 (build-system r-build-system)
18110 `(("r-data-table" ,r-data-table)
18111 ("r-matrixstats" ,r-matrixstats)
18112 ("r-r-utils" ,r-r-utils)))
18113 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
18114 (synopsis "Activity Index calculation using raw accelerometry data")
18116 "This is a package to read raw accelerometry from GT3X+ accelerometry
18117 data and plain table data to calculate the Activity Index from Bai et
18118 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
18119 (license license:gpl3)))
18121 (define-public r-activpal
18123 (name "r-activpal")
18128 (uri (cran-uri "activPAL" version))
18131 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
18132 (properties `((upstream-name . "activPAL")))
18133 (build-system r-build-system)
18135 `(("r-devtools" ,r-devtools)
18136 ("r-dplyr" ,r-dplyr)
18137 ("r-ggplot2" ,r-ggplot2)
18138 ("r-lubridate" ,r-lubridate)
18139 ("r-magrittr" ,r-magrittr)
18140 ("r-tidyr" ,r-tidyr)))
18141 (home-page "https://cran.r-project.org/web/packages/activPAL")
18142 (synopsis "Processing and chart generation from activPAL events files")
18144 "This package contains functions to generate pre-defined summary
18145 statistics from activPAL events files. The package also contains functions to
18146 produce informative graphics that visualize physical activity behaviour and
18147 trends. This includes generating graphs that align physical activity
18148 behaviour with additional time based observations described by other data
18149 sets, such as sleep diaries and continuous glucose monitoring data.")
18150 (license license:gpl3)))
18152 (define-public r-activpalprocessing
18154 (name "r-activpalprocessing")
18159 (uri (cran-uri "activpalProcessing" version))
18162 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
18164 `((upstream-name . "activpalProcessing")))
18165 (build-system r-build-system)
18167 `(("r-chron" ,r-chron)))
18168 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
18169 (synopsis "Process activPAL events files")
18171 "This package performs estimation of physical activity and sedentary
18172 behavior variables from activPAL events files.")
18173 ;; Either version of the GPL.
18174 (license (list license:gpl2 license:gpl3))))
18176 (define-public r-actogrammr
18178 (name "r-actogrammr")
18183 (uri (cran-uri "actogrammr" version))
18186 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
18187 (properties `((upstream-name . "actogrammr")))
18188 (build-system r-build-system)
18190 `(("r-dplyr" ,r-dplyr)
18191 ("r-ggplot2" ,r-ggplot2)
18192 ("r-lubridate" ,r-lubridate)
18193 ("r-readr" ,r-readr)
18194 ("r-tidyr" ,r-tidyr)))
18195 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
18196 (synopsis "Read in activity data and plot actograms")
18198 "Read in activity measurements from standard file formats used by
18199 circadian rhythm researchers, currently only ClockLab format, and process and
18200 plot the data. The central type of plot is the actogram, as first described
18201 in \"Activity and distribution of certain wild mice in relation to biotic
18202 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
18203 (license license:gpl3)))
18205 (define-public r-expint
18212 (uri (cran-uri "expint" version))
18215 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
18216 (properties `((upstream-name . "expint")))
18217 (build-system r-build-system)
18218 (home-page "https://gitlab.com/vigou3/expint")
18219 (synopsis "Exponential integral and incomplete Gamma function")
18221 "This package provides the exponential integrals @code{E_1(x)},
18222 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
18223 function @code{G(a, x)} defined for negative values of its first argument.
18224 The package also gives easy access to the underlying C routines through an
18225 API; see the package vignette for details.")
18226 (license license:gpl2+)))
18228 (define-public r-actuar
18235 (uri (cran-uri "actuar" version))
18238 "0aw3hlan5y22mdqk1wvnw9ksqhwp4yy5hi0dpv21p7s0hyxhphih"))))
18239 (properties `((upstream-name . "actuar")))
18240 (build-system r-build-system)
18241 (propagated-inputs `(("r-expint" ,r-expint)))
18242 (home-page "https://gitlab.com/vigou3/actuar")
18243 (synopsis "Actuarial functions and heavy tailed distributions")
18245 "This package provides functions and data sets for actuarial science:
18246 modeling of loss distributions; risk theory and ruin theory; simulation of
18247 compound models, discrete mixtures and compound hierarchical models;
18248 credibility theory. It boasts support for many additional probability
18249 distributions to model insurance loss amounts and loss frequency: 19
18250 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
18251 distribution; zero-truncated and zero-modified extensions of the standard
18252 discrete distributions. It also supports phase-type distributions commonly
18253 used to compute ruin probabilities.")
18254 (license license:gpl2+)))
18256 (define-public r-bmp
18263 (uri (cran-uri "bmp" version))
18266 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
18267 (properties `((upstream-name . "bmp")))
18268 (build-system r-build-system)
18269 (home-page "https://cran.r-project.org/web/packages/bmp/")
18270 (synopsis "Read Bitmap (BMP) images")
18272 "This package provides pure R tools to read BMP format images. It is
18273 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
18274 (license license:gpl2+)))
18276 (define-public r-readbitmap
18278 (name "r-readbitmap")
18283 (uri (cran-uri "readbitmap" version))
18286 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
18287 (properties `((upstream-name . "readbitmap")))
18288 (build-system r-build-system)
18290 `(("libjpeg" ,libjpeg)
18291 ("libpng" ,libpng)))
18296 ("r-tiff" ,r-tiff)))
18297 (home-page "https://github.com/jefferis/readbitmap")
18298 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
18300 "This package provides tools to identify and read BMP, JPEG, PNG, and
18301 TIFF format bitmap images. Identification defaults to the use of the magic
18302 number embedded in the file rather than the file extension.")
18303 (license license:gpl2+)))
18305 (define-public r-imager
18312 (uri (cran-uri "imager" version))
18315 "19fqgjhg04garbipx20g72h9dd6k0jj4ac48nby6km4h665vrs4v"))))
18316 (properties `((upstream-name . "imager")))
18317 (build-system r-build-system)
18320 ("libtiff" ,libtiff)
18324 `(("r-cairo" ,r-cairo)
18325 ("r-downloader" ,r-downloader)
18326 ("r-igraph" ,r-igraph)
18328 ("r-magrittr" ,r-magrittr)
18331 ("r-purrr" ,r-purrr)
18333 ("r-readbitmap" ,r-readbitmap)
18334 ("r-stringr" ,r-stringr)))
18335 (native-inputs `(("pkg-config" ,pkg-config)))
18336 (home-page "http://dahtah.github.io/imager")
18337 (synopsis "Image processing library")
18339 "This is a package for fast image processing for images in up to 4
18340 dimensions (two spatial dimensions, one time/depth dimension, one color
18341 dimension). It provides most traditional image processing tools (filtering,
18342 morphology, transformations, etc.) as well as various functions for easily
18343 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
18344 simple, modern C++ library for image processing.")
18345 (license license:lgpl3)))
18347 (define-public r-acuityview
18349 (name "r-acuityview")
18354 (uri (cran-uri "AcuityView" version))
18357 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
18358 (properties `((upstream-name . "AcuityView")))
18359 (build-system r-build-system)
18361 `(("r-fftwtools" ,r-fftwtools)
18362 ("r-imager" ,r-imager)
18363 ("r-plotrix" ,r-plotrix)))
18364 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
18365 (synopsis "Display scenes as seen by an animal with less acute vision")
18367 "This package provides a simple method for representing a visual scene as
18368 it may be seen by an animal with less acute vision.")
18369 (license license:gpl2+)))
18371 (define-public r-caret
18378 (uri (cran-uri "caret" version))
18381 "0jxbf2zcvbb5s2pnjzg182awjvylc57q7z5plx6gs6gm62zxjafs"))))
18382 (build-system r-build-system)
18384 `(("r-foreach" ,r-foreach)
18385 ("r-ggplot2" ,r-ggplot2)
18386 ("r-lattice" ,r-lattice)
18387 ("r-modelmetrics" ,r-modelmetrics)
18391 ("r-recipes" ,r-recipes)
18392 ("r-reshape2" ,r-reshape2)
18393 ("r-withr" ,r-withr)))
18394 (home-page "https://github.com/topepo/caret")
18395 (synopsis "Classification and regression training")
18397 "This package provides miscellaneous functions for training and plotting
18398 classification and regression models.")
18399 (license license:gpl2+)))
18401 (define-public r-adabag
18408 (uri (cran-uri "adabag" version))
18411 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
18412 (properties `((upstream-name . "adabag")))
18413 (build-system r-build-system)
18415 `(("r-caret" ,r-caret)
18416 ("r-doparallel" ,r-doparallel)
18417 ("r-foreach" ,r-foreach)
18418 ("r-rpart" ,r-rpart)))
18419 (home-page "https://cran.r-project.org/web/packages/adabag/")
18420 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
18422 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
18423 Breiman's Bagging algorithm using classification trees as individual
18424 classifiers. Once these classifiers have been trained, they can be used to
18425 predict on new data. Also, cross validation estimation of the error can be
18427 (license license:gpl2+)))
18429 (define-public r-adagio
18436 (uri (cran-uri "adagio" version))
18439 "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
18440 (properties `((upstream-name . "adagio")))
18441 (build-system r-build-system)
18442 (native-inputs `(("gfortran" ,gfortran)))
18443 (home-page "https://cran.r-project.org/web/packages/adagio/")
18444 (synopsis "Discrete and global optimization routines")
18446 "This package provides methods and algorithms for discrete optimization,
18447 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
18448 Hooke-Jeeves minimization, and some (evolutionary) global optimization
18450 (license license:gpl3+)))
18452 (define-public r-univoutl
18454 (name "r-univoutl")
18459 (uri (cran-uri "univOutl" version))
18462 "193wrpkvgmlrx43nag8w3ivrlqm37nm6g86wcvd3bgw3hchs70gi"))))
18463 (properties `((upstream-name . "univOutl")))
18464 (build-system r-build-system)
18466 `(("r-hmisc" ,r-hmisc)
18467 ("r-robustbase" ,r-robustbase)))
18468 (home-page "https://github.com/marcellodo/univOutl")
18469 (synopsis "Detection of univariate outliers")
18471 "This package provides well-known outlier detection techniques in the
18472 univariate case. Methods to deal with skewed distribution are included too.
18473 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
18474 historical data is implemented as well. When available, survey weights can be
18475 used in outliers detection.")
18476 (license license:gpl2+)))
18478 (define-public r-tolerance
18480 (name "r-tolerance")
18485 (uri (cran-uri "tolerance" version))
18488 "17qh4ad1f3fbcpwlxxqh8qr9bnwjcl4yxk0l3fkbr6b2l4rc5p86"))))
18489 (properties `((upstream-name . "tolerance")))
18490 (build-system r-build-system)
18492 `(("r-rgl" ,r-rgl)))
18493 (home-page "https://cran.r-project.org/web/packages/tolerance/")
18494 (synopsis "Statistical tolerance intervals and regions")
18496 "This package provides functions for estimating tolerance
18497 limits (intervals) for various univariate distributions (binomial, Cauchy,
18498 discrete Pareto, exponential, two-parameter exponential, extreme value,
18499 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
18500 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
18501 Bayesian normal tolerance limits, multivariate normal tolerance regions,
18502 nonparametric tolerance intervals, tolerance bands for regression
18503 settings (linear regression, nonlinear regression, nonparametric regression,
18504 and multivariate regression), and analysis of variance tolerance intervals.
18505 Visualizations are also available for most of these settings.")
18506 (license license:gpl2+)))
18508 (define-public r-additivitytests
18510 (name "r-additivitytests")
18515 (uri (cran-uri "additivityTests" version))
18518 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
18520 `((upstream-name . "additivityTests")))
18521 (build-system r-build-system)
18522 (home-page "https://github.com/simecek/additivityTests")
18523 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
18525 "This package provides an implementation of the Tukey, Mandel,
18526 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
18527 (license license:gpl3)))
18529 (define-public r-flexclust
18531 (name "r-flexclust")
18536 (uri (cran-uri "flexclust" version))
18539 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
18540 (properties `((upstream-name . "flexclust")))
18541 (build-system r-build-system)
18543 `(("r-class" ,r-class)
18544 ("r-lattice" ,r-lattice)
18545 ("r-modeltools" ,r-modeltools)))
18546 (home-page "https://cran.r-project.org/web/packages/flexclust/")
18547 (synopsis "Flexible cluster algorithms")
18549 "The main function @code{kcca} implements a general framework for
18550 k-centroids cluster analysis supporting arbitrary distance measures and
18551 centroid computation. Further cluster methods include hard competitive
18552 learning, neural gas, and QT clustering. There are numerous visualization
18553 methods for cluster results (neighborhood graphs, convex cluster hulls,
18554 barcharts of centroids, ...), and bootstrap methods for the analysis of
18555 cluster stability.")
18556 (license license:gpl2)))
18558 (define-public r-biclust
18565 (uri (cran-uri "biclust" version))
18568 "1y5n6wfa1lx88ck3x09rcg0dh3pw89225h85hmq2la1s1fpa48i0"))))
18569 (properties `((upstream-name . "biclust")))
18570 (build-system r-build-system)
18572 `(("r-additivitytests" ,r-additivitytests)
18573 ("r-colorspace" ,r-colorspace)
18574 ("r-flexclust" ,r-flexclust)
18575 ("r-ggplot2" ,r-ggplot2)
18576 ("r-lattice" ,r-lattice)
18578 ("r-tidyr" ,r-tidyr)))
18579 (home-page "https://cran.r-project.org/web/packages/biclust/")
18580 (synopsis "BiCluster algorithms")
18582 "The main function @code{biclust()} provides several algorithms to find
18583 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
18584 In addition, the package provides methods for data
18585 preprocessing (normalization and discretization), visualization, and
18586 validation of bicluster solutions.")
18587 (license license:gpl3)))
18589 (define-public r-icge
18596 (uri (cran-uri "ICGE" version))
18599 "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
18600 (properties `((upstream-name . "ICGE")))
18601 (build-system r-build-system)
18603 `(("r-cluster" ,r-cluster)
18604 ("r-mass" ,r-mass)))
18605 (home-page "https://cran.r-project.org/web/packages/ICGE/")
18606 (synopsis "Cluster estimation and identification of atypical units")
18608 "ICGE is a package that helps to estimate the number of real clusters in
18609 data as well as to identify atypical units. The underlying methods are based
18610 on distances rather than on unit x variables.")
18611 (license license:gpl2+)))
18613 (define-public r-depth
18616 (version "2.1-1.1")
18620 (uri (cran-uri "depth" version))
18623 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
18624 (properties `((upstream-name . "depth")))
18625 (build-system r-build-system)
18627 `(("r-abind" ,r-abind)
18628 ("r-circular" ,r-circular)
18631 `(("gfortran" ,gfortran)))
18632 (home-page "https://cran.r-project.org/web/packages/depth/")
18633 (synopsis "Nonparametric depth functions for multivariate analysis")
18635 "This package provides tools for depth functions methodology applied to
18636 multivariate analysis. Besides allowing calculation of depth values and
18637 depth-based location estimators, the package includes functions or drawing
18638 contour plots and perspective plots of depth functions. Euclidian and
18639 spherical depths are supported.")
18640 (license license:gpl2)))
18642 (define-public r-archetypes
18644 (name "r-archetypes")
18645 (version "2.2-0.1")
18649 (uri (cran-uri "archetypes" version))
18652 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
18653 (properties `((upstream-name . "archetypes")))
18654 (build-system r-build-system)
18656 `(("r-modeltools" ,r-modeltools)
18657 ("r-nnls" ,r-nnls)))
18658 (home-page "https://cran.r-project.org/web/packages/archetypes")
18659 (synopsis "Archetypal analysis")
18661 "The main function @code{archetypes} implements a framework for
18662 archetypal analysis supporting arbitrary problem solving mechanisms for the
18663 different conceptual parts of the algorithm.")
18664 (license license:gpl2+)))
18666 (define-public r-shapes
18673 (uri (cran-uri "shapes" version))
18676 "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s"))))
18677 (properties `((upstream-name . "shapes")))
18678 (build-system r-build-system)
18680 `(("r-mass" ,r-mass)
18681 ("r-minpack-lm" ,r-minpack-lm)
18683 ("r-scatterplot3d" ,r-scatterplot3d)))
18684 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
18685 (synopsis "Statistical shape analysis")
18687 "This package provides routines for the statistical analysis of landmark
18688 shapes, including Procrustes analysis, graphical displays, principal
18689 components analysis, permutation and bootstrap tests, thin-plate spline
18690 transformation grids and comparing covariance matrices. See Dryden, I.L. and
18691 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
18692 Edition), John Wiley and Sons.")
18693 (license license:gpl2)))
18695 (define-public r-anthropometry
18697 (name "r-anthropometry")
18702 (uri (cran-uri "Anthropometry" version))
18705 "1f568ri1s6psaby8y737vrkarbjg64v89d4jyw23hy17apdmszr8"))))
18706 (properties `((upstream-name . "Anthropometry")))
18707 (build-system r-build-system)
18709 `(("r-archetypes" ,r-archetypes)
18710 ("r-biclust" ,r-biclust)
18711 ("r-cluster" ,r-cluster)
18712 ("r-depth" ,r-depth)
18717 ("r-shapes" ,r-shapes)))
18718 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
18719 (synopsis "Statistical methods for anthropometric data")
18721 "This package provides statistical methods especially developed to
18722 analyze anthropometric data. These methods are aimed at providing effective
18723 solutions to some commons problems related to Ergonomics and Anthropometry.
18724 They are based on clustering, the statistical concept of data depth,
18725 statistical shape analysis and archetypal analysis.")
18726 (license license:gpl2+)))
18728 (define-public r-adamethods
18730 (name "r-adamethods")
18735 (uri (cran-uri "adamethods" version))
18738 "0mp73zh5x6h18gv29v981kb9n632kb58lvlcxwr6vcvrx393nrxh"))))
18739 (properties `((upstream-name . "adamethods")))
18740 (build-system r-build-system)
18742 `(("r-anthropometry" ,r-anthropometry)
18743 ("r-archetypes" ,r-archetypes)
18745 ("r-foreach" ,r-foreach)
18747 ("r-tolerance" ,r-tolerance)
18748 ("r-univoutl" ,r-univoutl)))
18749 (home-page "https://cran.r-project.org/web/packages/adamethods/")
18750 (synopsis "Archetypoid algorithms and anomaly detection")
18752 "This package is a collection of several algorithms to obtain
18753 archetypoids with small and large databases and with both classical
18754 multivariate data and functional data (univariate and multivariate). Some of
18755 these algorithms also allow to detect anomalies (outliers).")
18756 (license license:gpl2+)))
18758 (define-public r-idpmisc
18765 (uri (cran-uri "IDPmisc" version))
18768 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
18769 (properties `((upstream-name . "IDPmisc")))
18770 (build-system r-build-system)
18772 `(("r-lattice" ,r-lattice)))
18773 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
18774 (synopsis "Functions for data analyses and visualization")
18776 "This package provides different high-level graphics functions for
18777 displaying large datasets, displaying circular data in a very flexible way,
18778 finding local maxima, brewing color ramps, drawing nice arrows, zooming
18779 2D-plots, creating figures with differently colored margin and plot region.
18780 In addition, the package contains auxiliary functions for data manipulation
18781 like omitting observations with irregular values or selecting data by logical
18782 vectors, which include NAs. Other functions are especially useful in
18783 spectroscopy and analyses of environmental data: robust baseline fitting,
18784 finding peaks in spectra, converting humidity measures.")
18785 (license license:gpl3+)))
18787 (define-public r-qqman
18794 (uri (cran-uri "qqman" version))
18797 "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
18798 (properties `((upstream-name . "qqman")))
18799 (build-system r-build-system)
18801 `(("r-calibrate" ,r-calibrate)))
18802 (home-page "https://cran.r-project.org/web/packages/qqman/")
18803 (synopsis "Q-Q and Manhattan plots for GWAS data")
18805 "This package allows you to create Q-Q and Manhattan plots for GWAS data
18806 from PLINK results.")
18807 (license license:gpl3)))
18809 (define-public r-ggplot-multistats
18811 (name "r-ggplot-multistats")
18816 (uri (cran-uri "ggplot.multistats" version))
18819 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
18821 `((upstream-name . "ggplot.multistats")))
18822 (build-system r-build-system)
18824 `(("r-ggplot2" ,r-ggplot2)
18825 ("r-hexbin" ,r-hexbin)
18826 ("r-rlang" ,r-rlang)
18827 ("r-scales" ,r-scales)))
18828 (home-page "https://github.com/flying-sheep/ggplot.multistats")
18829 (synopsis "Multiple summary statistics for binned stats/geometries")
18831 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
18832 which functions similar to its singular form, but allows the use of multiple
18833 statistics per bin. Those statistics can be mapped to multiple bin
18835 (license license:gpl3)))
18837 (define-public r-knn-covertree
18839 (name "r-knn-covertree")
18844 (uri (cran-uri "knn.covertree" version))
18847 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
18848 (properties `((upstream-name . "knn.covertree")))
18849 (build-system r-build-system)
18851 `(("r-matrix" ,r-matrix)
18853 ("r-rcppeigen" ,r-rcppeigen)))
18854 (home-page "https://github.com/flying-sheep/knn.covertree")
18855 (synopsis "Accurate kNN Implementation with multiple distance measures")
18857 "Similarly to the FNN package, this package allows calculation of the k
18858 nearest neighbors (kNN) of a data matrix. The implementation is based on
18859 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
18860 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
18861 (license license:agpl3+)))
18863 (define-public r-poibin
18870 (uri (cran-uri "poibin" version))
18873 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
18874 (properties `((upstream-name . "poibin")))
18875 (build-system r-build-system)
18876 (home-page "https://cran.r-project.org/web/packages/poibin/")
18877 (synopsis "Poisson binomial distribution")
18879 "This package provides an implementation of both the exact and
18880 approximation methods for computing the @dfn{cumulative distribution
18881 function} (CDF) of the Poisson binomial distribution. It also provides the
18882 @dfn{probability mass function} (PMF), quantile function, and random number
18883 generation for the Poisson binomial distribution.")
18884 (license license:gpl2)))
18886 (define-public r-diagram
18893 (uri (cran-uri "diagram" version))
18896 "0f6ffprn5k0ir1s7m9s7izc64aa17r3gnygagz5bihrlsvawaavw"))))
18897 (properties `((upstream-name . "diagram")))
18898 (build-system r-build-system)
18900 `(("r-shape" ,r-shape)))
18901 (home-page "https://cran.r-project.org/web/packages/diagram/")
18902 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
18904 "This package provides tools to visualize simple graphs (networks) based
18905 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
18906 electrical networks, etc. It also includes supporting material for the book
18907 \"A practical guide to ecological modelling - using R as a simulation
18908 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
18909 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
18910 Francesca Mazzia (2012).")
18911 (license license:gpl2+)))
18913 (define-public r-lim
18920 (uri (cran-uri "LIM" version))
18923 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
18924 (properties `((upstream-name . "LIM")))
18925 (build-system r-build-system)
18927 `(("r-diagram" ,r-diagram)
18928 ("r-limsolve" ,r-limsolve)))
18929 (home-page "https://cran.r-project.org/web/packages/LIM/")
18930 (synopsis "Linear inverse model examples and solution methods")
18932 "This package provides functions that read and solve linear inverse
18933 problems (food web problems, linear programming problems).")
18934 (license license:gpl2+)))
18936 (define-public r-shinycssloaders
18938 (name "r-shinycssloaders")
18943 (uri (cran-uri "shinycssloaders" version))
18946 "1gzq1lhcnhqd145ys3ixf0l13l560fiqr2sc3m2nrijwxlgcw54d"))))
18948 `((upstream-name . "shinycssloaders")))
18949 (build-system r-build-system)
18951 `(("r-digest" ,r-digest)
18953 ("r-shiny" ,r-shiny)))
18954 (home-page "https://github.com/andrewsali/shinycssloaders")
18955 (synopsis "Add CSS loading animations to Shiny outputs")
18957 "This package provides tools to create a lightweight Shiny wrapper for
18958 the css-loaders created by Luke Hass
18959 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
18960 automatically show a loader when the output is (re)calculating.")
18961 (license license:gpl3)))
18963 (define-public r-rsvg
18970 (uri (cran-uri "rsvg" version))
18973 "11mccgf6hfskg45wqc114sx3qy2r494y6axdf73z6xwhs1wpm97g"))))
18974 (properties `((upstream-name . "rsvg")))
18975 (build-system r-build-system)
18977 `(("librsvg" ,librsvg)
18980 `(("pkg-config" ,pkg-config)))
18981 (home-page "https://github.com/jeroen/rsvg#readme")
18982 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
18984 "This package allows you to render vector-based SVG images into
18985 high-quality custom-size bitmap arrays using the librsvg2 library. The
18986 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
18987 addition, the package can convert images directly to various formats such as
18988 PDF or PostScript.")
18989 (license license:expat)))
18991 (define-public r-influencer
18993 (name "r-influencer")
18998 (uri (cran-uri "influenceR" version))
19001 "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
19002 (properties `((upstream-name . "influenceR")))
19003 (build-system r-build-system)
19005 `(("r-igraph" ,r-igraph)
19006 ("r-matrix" ,r-matrix)))
19007 (home-page "https://github.com/rcc-uchicago/influenceR")
19008 (synopsis "Tools to quantify structural importance of nodes in a network")
19010 "This package provides functionality to compute various node centrality
19011 measures on networks. Included are functions to compute betweenness
19012 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
19013 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
19014 algorithm to identify key players, and Valente's bridging metric. The
19015 betweenness, Key Players, and bridging implementations are parallelized with
19017 (license license:gpl2)))
19019 (define-public r-emplik
19022 (version "1.0-4.3")
19026 (uri (cran-uri "emplik" version))
19029 "1g4hz85bvw29c77zs0ig487z92jjl682vv457x81l077h0psvk7c"))))
19030 (properties `((upstream-name . "emplik")))
19031 (build-system r-build-system)
19033 `(("r-quantreg" ,r-quantreg)))
19034 (home-page "http://www.ms.uky.edu/~mai/EmpLik.html")
19035 (synopsis "Empirical likelihood ratio for censored/truncated data")
19037 "This package provides empirical likelihood ratio tests for
19038 means/quantiles/hazards from possibly censored and/or truncated data. It also
19040 (license license:gpl2+)))
19042 (define-public r-imputeyn
19044 (name "r-imputeyn")
19049 (uri (cran-uri "imputeYn" version))
19052 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
19053 (properties `((upstream-name . "imputeYn")))
19054 (build-system r-build-system)
19056 `(("r-boot" ,r-boot)
19057 ("r-emplik" ,r-emplik)
19058 ("r-mvtnorm" ,r-mvtnorm)
19059 ("r-quadprog" ,r-quadprog)
19060 ("r-survival" ,r-survival)))
19061 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
19062 (synopsis "Impute last largest censored observation under weighted least squares")
19064 "This package allows for the imputation of the last largest censored
19065 observantions. This method brings less bias and more efficient estimates for
19067 (license license:gpl2)))
19069 (define-public r-adapenetclass
19071 (name "r-adapenetclass")
19076 (uri (cran-uri "AdapEnetClass" version))
19079 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
19080 (properties `((upstream-name . "AdapEnetClass")))
19081 (build-system r-build-system)
19083 `(("r-glmnet" ,r-glmnet)
19084 ("r-imputeyn" ,r-imputeyn)
19086 ("r-quadprog" ,r-quadprog)))
19087 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
19088 (synopsis "Class of adaptive elastic net methods for censored data")
19090 "This package provides methods for variable selection for AFT models.")
19091 (license license:gpl2)))
19093 (define-public r-flock
19100 (uri (cran-uri "flock" version))
19103 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
19104 (properties `((upstream-name . "flock")))
19105 (build-system r-build-system)
19106 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
19107 (home-page "https://cran.r-project.org/web/packages/flock/")
19108 (synopsis "Process synchronization using file locks")
19110 "This package implements synchronization between R processes (spawned by
19111 using the @code{parallel} package for instance) using file locks. It supports
19112 both exclusive and shared locking.")
19113 (license license:asl2.0)))
19115 (define-public r-archivist
19117 (name "r-archivist")
19122 (uri (cran-uri "archivist" version))
19125 "1i11hrcq1910jgd6diw6h3sxx624v57zjianm49pqvb2dvd0b8y7"))))
19126 (properties `((upstream-name . "archivist")))
19127 (build-system r-build-system)
19130 ("r-digest" ,r-digest)
19131 ("r-flock" ,r-flock)
19133 ("r-lubridate" ,r-lubridate)
19134 ("r-magrittr" ,r-magrittr)
19135 ("r-rcurl" ,r-rcurl)
19136 ("r-rsqlite" ,r-rsqlite)))
19137 (home-page "https://pbiecek.github.io/archivist/")
19138 (synopsis "Tools for storing, restoring and searching for R objects")
19140 "Data exploration and modelling is a process in which a lot of data
19141 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
19142 statistical models, different versions of data sets and different versions of
19143 results. Archivist helps to store and manage artifacts created in R. It
19144 allows you to store selected artifacts as binary files together with their
19145 metadata and relations. Archivist allows sharing artifacts with others. It
19146 can look for already created artifacts by using its class, name, date of the
19147 creation or other properties. It also makes it easy to restore such
19149 (license license:gpl2)))
19151 (define-public r-versions
19153 (name "r-versions")
19158 (uri (cran-uri "versions" version))
19161 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
19162 (properties `((upstream-name . "versions")))
19163 (build-system r-build-system)
19164 (home-page "https://cran.r-project.org/web/packages/versions/")
19165 (synopsis "Query and install specific versions of CRAN packages")
19167 "This package allows you to install specified versions of R packages
19168 hosted on CRAN and provides functions to list available versions and the
19169 versions of currently installed packages.")
19170 (license license:bsd-3)))
19172 (define-public r-adapr
19179 (uri (cran-uri "adapr" version))
19182 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
19183 (properties `((upstream-name . "adapr")))
19184 (build-system r-build-system)
19186 `(("r-archivist" ,r-archivist)
19187 ("r-devtools" ,r-devtools)
19188 ("r-digest" ,r-digest)
19189 ("r-doparallel" ,r-doparallel)
19190 ("r-gdata" ,r-gdata)
19191 ("r-ggplot2" ,r-ggplot2)
19192 ("r-git2r" ,r-git2r)
19193 ("r-igraph" ,r-igraph)
19194 ("r-knitr" ,r-knitr)
19195 ("r-plotly" ,r-plotly)
19197 ("r-rmarkdown" ,r-rmarkdown)
19198 ("r-shiny" ,r-shiny)
19199 ("r-shinydashboard" ,r-shinydashboard)
19200 ("r-versions" ,r-versions)))
19201 (home-page "https://cran.r-project.org/web/packages/adapr/")
19202 (synopsis "Implementation of an accountable data analysis process")
19204 "This package tracks reading and writing within R scripts that are
19205 organized into a directed acyclic graph. It contains an interactive Shiny
19206 application @code{adaprApp()}. It uses Git and file hashes to track version
19207 histories of inputs and outputs.")
19208 (license license:lgpl2.0)))
19210 (define-public r-adapsamp
19212 (name "r-adapsamp")
19217 (uri (cran-uri "AdapSamp" version))
19220 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
19221 (properties `((upstream-name . "AdapSamp")))
19222 (build-system r-build-system)
19223 (propagated-inputs `(("r-pracma" ,r-pracma)))
19224 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
19225 (synopsis "Adaptive sampling algorithms")
19227 "For distributions whose probability density functions are log-concave,
19228 the adaptive rejection sampling algorithm can be used to build envelope
19229 functions for sampling. For others, the modified adaptive rejection sampling
19230 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
19231 adaptive slice sampling algorithm can be used. This R package mainly includes
19232 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
19233 @code{rASS()}. These functions can realize sampling based on the algorithms
19235 (license license:gpl2)))
19237 (define-public r-adaptalint
19239 (name "r-adaptalint")
19244 (uri (cran-uri "adaptalint" version))
19247 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
19248 (properties `((upstream-name . "adaptalint")))
19249 (build-system r-build-system)
19251 `(("r-dplyr" ,r-dplyr)
19252 ("r-lintr" ,r-lintr)
19253 ("r-purrr" ,r-purrr)))
19254 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
19255 (synopsis "Check R code style")
19257 "This package provides tools to infer the code style (which style rules
19258 are followed and which ones are not) from one package and use it to check
19259 another. This makes it easier to find and correct the most important problems
19261 (license license:gpl3)))