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 "1hvxw2glizq8g0qnxakcxh8jc5scn0hp1x8i70fdpqwwbgx49slr"))))
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 "0lyvhnr6n57h3a89bvipii7x17nvfaycm9j5j50bfrlr48jv9ic8"))))
539 (build-system r-build-system)
540 (home-page "http://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 "1rggww8cbwv0vzlj5afzhbsbngg4bzj5znbkz7wmxsbshfbsm9b2"))))
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 "1acf0qc9597apcidjzrpvwhg9ihypr38jigc10jvqn33qbn1i9s7"))))
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 "http://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 "1fl3w2n602ldybc5qj7qw4xmzzb804bsjkqwf6dswzj0vf0qiadr"))))
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 "0p3z42hnk53x7ky4d1dr2brf7p8gv3agxr71i99m01n2hq2ri91m"))))
2045 (build-system r-build-system)
2047 `(("r-assertthat" ,r-assertthat)
2048 ("r-magrittr" ,r-magrittr)))
2049 (home-page "https://github.com/gaborcsardi/prettyunits")
2050 (synopsis "Pretty, human readable formatting of quantities")
2052 "This package provides tools for pretty, human readable formatting of
2054 (license license:expat)))
2056 (define-public r-reshape
2063 (uri (cran-uri "reshape" version))
2066 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
2067 (build-system r-build-system)
2069 `(("r-plyr" ,r-plyr)
2070 ("r-rcpp" ,r-rcpp)))
2071 (home-page "http://had.co.nz/reshape")
2072 (synopsis "Flexibly reshape data")
2074 "Flexibly restructure and aggregate data using just two functions:
2075 @code{melt} and @code{cast}. This package provides them.")
2076 (license license:expat)))
2078 (define-public r-progress
2085 (uri (cran-uri "progress" version))
2088 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
2089 (build-system r-build-system)
2091 `(("r-crayon" ,r-crayon)
2093 ("r-prettyunits" ,r-prettyunits)
2095 (home-page "https://github.com/gaborcsardi/progress")
2096 (synopsis "Terminal progress bars")
2098 "This package provides configurable progress bars. They may include
2099 percentage, elapsed time, and/or the estimated completion time. They work in
2100 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
2101 package also provides a C++ API, that works with or without Rcpp.")
2102 (license license:expat)))
2104 (define-public r-ggally
2111 (uri (cran-uri "GGally" version))
2114 "1zjmcc5bzagvy7c5cmdcl39xmx07fwi98yrj4i05w7y40kqcsiws"))))
2115 (properties `((upstream-name . "GGally")))
2116 (build-system r-build-system)
2118 `(("libressl" ,libressl)))
2120 `(("r-ggplot2" ,r-ggplot2)
2121 ("r-gtable" ,r-gtable)
2123 ("r-progress" ,r-progress)
2124 ("r-rcolorbrewer" ,r-rcolorbrewer)
2125 ("r-reshape" ,r-reshape)
2126 ("r-rlang" ,r-rlang)))
2127 (home-page "https://ggobi.github.io/ggally")
2128 (synopsis "Extension to ggplot2")
2130 "The R package ggplot2 is a plotting system based on the grammar of
2131 graphics. GGally extends ggplot2 by adding several functions to reduce the
2132 complexity of combining geometric objects with transformed data. Some of
2133 these functions include a pairwise plot matrix, a two group pairwise plot
2134 matrix, a parallel coordinates plot, a survival plot, and several functions to
2136 (license license:gpl2+)))
2138 (define-public r-proxy
2145 (uri (cran-uri "proxy" version))
2148 "17b6qfllqrhzrxqgx7dccffgybnkcria5a68ap5ly3plg04ypm4x"))))
2149 (build-system r-build-system)
2150 (home-page "https://cran.r-project.org/web/packages/proxy")
2151 (synopsis "Distance and similarity measures")
2153 "This package provides an extensible framework for the efficient
2154 calculation of auto- and cross-proximities, along with implementations of the
2155 most popular ones.")
2156 (license license:gpl2)))
2165 (uri (cran-uri "sp" version))
2167 (base32 "0kpjsqh3lzqp1m0avsvm54lazlgwfx3hyf0av3mvbyslsanj42ll"))))
2168 (build-system r-build-system)
2170 `(("r-lattice" ,r-lattice)))
2171 (home-page "https://cran.r-project.org/web/packages/sp")
2172 (synopsis "Classes and methods for spatial data")
2174 "This package provides classes and methods for spatial data; the classes
2175 document where the spatial location information resides, for 2D or 3D data.
2176 Utility functions are provided, e.g. for plotting data as maps, spatial
2177 selection, as well as methods for retrieving coordinates, for subsetting,
2178 print, summary, etc.")
2179 (license license:gpl2+)))
2181 (define-public r-rmtstat
2188 (uri (cran-uri "RMTstat" version))
2191 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
2192 (properties `((upstream-name . "RMTstat")))
2193 (build-system r-build-system)
2194 (home-page "https://cran.r-project.org/web/packages/RMTstat")
2195 (synopsis "Distributions, statistics and tests derived from random matrix theory")
2197 "This package provides functions for working with the Tracy-Widom laws
2198 and other distributions related to the eigenvalues of large Wishart
2200 (license license:bsd-3)))
2202 (define-public r-rmpi
2208 (uri (cran-uri "Rmpi" version))
2211 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
2212 (properties `((upstream-name . "Rmpi")))
2213 (build-system r-build-system)
2215 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
2216 #:phases (modify-phases %standard-phases
2217 (add-before 'install 'mpi-setup
2220 `(("openmpi" ,openmpi)))
2222 `(("pkg-config" ,pkg-config)))
2223 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
2224 (synopsis "R interface to message-passing interface (MPI)")
2226 "This package provides an interface (wrapper) to MPI APIs. It also
2227 provides an interactive R manager and worker environment.")
2228 (license license:gpl2+)))
2230 (define-public r-lmoments
2237 (uri (cran-uri "Lmoments" version))
2240 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
2241 (properties `((upstream-name . "Lmoments")))
2242 (build-system r-build-system)
2244 `(("r-rcpp" ,r-rcpp)
2245 ("r-rcpparmadillo" ,r-rcpparmadillo)))
2246 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
2247 (synopsis "L-moments and quantile mixtures")
2249 "This package contains functions to estimate L-moments and trimmed
2250 L-moments from the data. It also contains functions to estimate the
2251 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
2252 quantile mixture from L-moments and trimmed L-moments.")
2253 (license license:gpl2)))
2255 (define-public r-distillery
2257 (name "r-distillery")
2262 (uri (cran-uri "distillery" version))
2265 "1mi3ig9jq0kd7yrwc5m37lmrw04p1b4lirnbsxi10z3n5yay4429"))))
2266 (build-system r-build-system)
2267 (home-page "http://www.ral.ucar.edu/staff/ericg")
2268 (synopsis "Functions for confidence intervals and object information")
2270 "This package provides some very simple method functions for confidence
2271 interval calculation and to distill pertinent information from a potentially
2272 complex object; primarily used in common with the packages extRemes and
2274 (license license:gpl2+)))
2276 (define-public r-extremes
2283 (uri (cran-uri "extRemes" version))
2286 "0hmgynxhzswqnhwb2sxrkczgam8c17s3vpxqc5bcz0bwczpxxyvm"))))
2287 (properties `((upstream-name . "extRemes")))
2288 (build-system r-build-system)
2290 `(("r-distillery" ,r-distillery)
2291 ("r-lmoments" ,r-lmoments)))
2292 (home-page "http://www.assessment.ucar.edu/toolkit/")
2293 (synopsis "Extreme value analysis")
2295 "ExtRemes is a suite of functions for carrying out analyses on the
2296 extreme values of a process of interest; be they block maxima over long blocks
2297 or excesses over a high threshold.")
2298 (license license:gpl2+)))
2300 (define-public r-lmtest
2307 (uri (cran-uri "lmtest" version))
2310 "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx"))))
2311 (build-system r-build-system)
2313 `(("r-zoo" ,r-zoo)))
2315 `(("gfortran" ,gfortran)))
2316 (home-page "https://cran.r-project.org/web/packages/lmtest")
2317 (synopsis "Testing linear regression models")
2319 "This package provides a collection of tests, data sets, and examples for
2320 diagnostic checking in linear regression models. Furthermore, some generic
2321 tools for inference in parametric models are provided.")
2322 ;; Either version is okay
2323 (license (list license:gpl2 license:gpl3))))
2325 (define-public r-idr
2331 (uri (cran-uri "idr" version))
2334 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
2335 (build-system r-build-system)
2336 (home-page "https://cran.r-project.org/web/packages/idr/")
2337 (synopsis "Irreproducible discovery rate")
2339 "This is a package for estimating the copula mixture model and plotting
2340 correspondence curves in \"Measuring reproducibility of high-throughput
2341 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
2342 by Li, Brown, Huang, and Bickel")
2343 (license license:gpl2+)))
2345 (define-public r-inline
2351 (uri (cran-uri "inline" version))
2354 "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
2355 (build-system r-build-system)
2356 (home-page "https://cran.r-project.org/web/packages/inline")
2357 (synopsis "Functions to inline C, C++, Fortran function calls from R")
2359 "This package provides functionality to dynamically define R functions
2360 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
2361 @code{.Call} calling conventions.")
2362 ;; Any version of the LGPL.
2363 (license license:lgpl3+)))
2365 (define-public r-bdsmatrix
2367 (name "r-bdsmatrix")
2372 (uri (cran-uri "bdsmatrix" version))
2375 "17ddvz4gnih7rx0lr1gzk280xyh6x796cf2x794dvplpiiq83skh"))))
2376 (properties `((upstream-name . "bdsmatrix")))
2377 (build-system r-build-system)
2378 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
2379 (synopsis "Routines for block diagonal symmetric matrices")
2381 "This package provides procedures to work with block diagonal symmetric
2382 matrices, a special case of sparse matrices.")
2383 (license license:lgpl2.0)))
2385 (define-public r-bbmle
2392 (uri (cran-uri "bbmle" version))
2395 "1idn55w5f3iw4r0ydyww8xyinninw07sxlwfqb565vmdrs87dwl4"))))
2396 (build-system r-build-system)
2398 `(("r-bdsmatrix" ,r-bdsmatrix)
2399 ("r-lattice" ,r-lattice)
2401 ("r-matrix" ,r-matrix)
2402 ("r-mvtnorm" ,r-mvtnorm)
2403 ("r-numderiv" ,r-numderiv)))
2404 (home-page "https://cran.r-project.org/web/packages/bbmle")
2405 (synopsis "Tools for General Maximum Likelihood Estimation")
2407 "This package provides methods and functions for fitting maximum
2408 likelihood models in R. This package modifies and extends the @code{mle}
2409 classes in the @code{stats4} package.")
2410 ;; Any version of the GPL
2411 (license license:gpl2+)))
2413 (define-public r-emdbook
2420 (uri (cran-uri "emdbook" version))
2423 "0a515jdzvg87npvrh7md7zp0v5nlz7c2jr7pba5dql6slb0d8j7q"))))
2424 (build-system r-build-system)
2426 `(("r-bbmle" ,r-bbmle)
2428 ("r-lattice" ,r-lattice)
2431 ("r-rcpp" ,r-rcpp)))
2432 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
2433 (synopsis "Support functions and data for \"Ecological Models and Data\"")
2435 "This package provides auxiliary functions and data sets for \"Ecological
2436 Models and Data\", a book presenting maximum likelihood estimation and related
2437 topics for ecologists (ISBN 978-0-691-12522-0).")
2439 (license (list license:gpl2 license:gpl3))))
2441 (define-public r-lpsolve
2444 (version "5.6.13.3")
2448 (uri (cran-uri "lpSolve" version))
2451 "1xazby8amb47vw5n12k13awv7x3bjci3q8vdd3vk1ms0ii16ahg6"))))
2452 (properties `((upstream-name . "lpSolve")))
2453 (build-system r-build-system)
2454 (home-page "https://cran.r-project.org/web/packages/lpSolve")
2455 (synopsis "R interface to Lp_solve to solve linear/integer programs")
2457 "Lp_solve is software for solving linear, integer and mixed integer
2458 programs. This implementation supplies a \"wrapper\" function in C and some R
2459 functions that solve general linear/integer problems, assignment problems, and
2460 transportation problems.")
2461 (license license:lgpl2.0)))
2463 (define-public r-limsolve
2470 (uri (cran-uri "limSolve" version))
2473 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
2474 (properties `((upstream-name . "limSolve")))
2475 (build-system r-build-system)
2477 `(("r-lpsolve" ,r-lpsolve)
2479 ("r-quadprog" ,r-quadprog)))
2480 (native-inputs `(("gfortran" ,gfortran)))
2481 (home-page "https://cran.r-project.org/web/packages/limSolve")
2482 (synopsis "Solving linear inverse models")
2484 "This package provides functions that:
2487 @item find the minimum/maximum of a linear or quadratic function,
2488 @item sample an underdetermined or overdetermined system,
2489 @item solve a linear system Ax=B for the unknown x.
2492 It includes banded and tridiagonal linear systems. The package calls Fortran
2493 functions from LINPACK.")
2495 (license (list license:gpl2+ license:gpl3+))))
2497 (define-public r-fitdistrplus
2499 (name "r-fitdistrplus")
2504 (uri (cran-uri "fitdistrplus" version))
2507 "10q08wsv8v3w7797jdvvv60bgrf1bi6438wf0jcqv81ays82a245"))))
2508 (build-system r-build-system)
2510 `(("r-mass" ,r-mass)
2511 ("r-npsurv" ,r-npsurv)
2512 ("r-survival" ,r-survival)))
2513 (home-page "http://riskassessment.r-forge.r-project.org")
2514 (synopsis "Fitting a parametric distribution from data")
2516 "This package extends the @code{fitdistr} function of the MASS package
2517 with several functions to help the fit of a parametric distribution to
2518 non-censored or censored data. Censored data may contain left-censored,
2519 right-censored and interval-censored values, with several lower and upper
2520 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
2521 provides moment matching (MME), quantile matching (QME) and maximum
2522 goodness-of-fit estimation (MGE) methods (available only for non-censored
2523 data). Weighted versions of MLE, MME and QME are available.")
2524 (license license:gpl2+)))
2526 (define-public r-energy
2533 (uri (cran-uri "energy" version))
2536 "13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37"))))
2537 (build-system r-build-system)
2539 `(("r-boot" ,r-boot)
2540 ("r-rcpp" ,r-rcpp)))
2541 (home-page "https://cran.r-project.org/web/packages/energy")
2542 (synopsis "Multivariate inference via the energy of data")
2544 "This package provides e-statistics (energy) tests and statistics for
2545 multivariate and univariate inference, including distance correlation,
2546 one-sample, two-sample, and multi-sample tests for comparing multivariate
2547 distributions, are implemented. Measuring and testing multivariate
2548 independence based on distance correlation, partial distance correlation,
2549 multivariate goodness-of-fit tests, clustering based on energy distance,
2550 testing for multivariate normality, distance components (disco) for
2551 non-parametric analysis of structured data, and other energy
2552 statistics/methods are implemented.")
2553 (license license:gpl2+)))
2555 (define-public r-suppdists
2557 (name "r-suppdists")
2562 (uri (cran-uri "SuppDists" version))
2565 "1ffx8wigqqvz2pnh06jjc0fnf4vq9z2rhwk2y3f9aszn18ap3dgw"))))
2566 (properties `((upstream-name . "SuppDists")))
2567 (build-system r-build-system)
2568 (home-page "https://cran.r-project.org/web/packages/SuppDists")
2569 (synopsis "Supplementary distributions")
2571 "This package provides ten distributions supplementing those built into
2572 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
2573 Spearman's rho, maximum F ratio, the Pearson product moment correlation
2574 coefficient, Johnson distributions, normal scores and generalized
2575 hypergeometric distributions. In addition two random number generators of
2576 George Marsaglia are included.")
2577 (license license:gpl2+)))
2579 (define-public r-ksamples
2586 (uri (cran-uri "kSamples" version))
2589 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
2590 (properties `((upstream-name . "kSamples")))
2591 (build-system r-build-system)
2593 `(("r-suppdists" ,r-suppdists)))
2594 (home-page "https://cran.r-project.org/web/packages/kSamples")
2595 (synopsis "K-Sample rank tests and their combinations")
2597 "This package provides tools to compares k samples using the
2598 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
2599 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
2600 test. It computes asymptotic, simulated or (limited) exact P-values, all
2601 valid under randomization, with or without ties, or conditionally under random
2602 sampling from populations, given the observed tie pattern. Except for Steel's
2603 test and the JT test it also combines these tests across several blocks of
2605 (license license:gpl2+)))
2607 (define-public r-cvst
2614 (uri (cran-uri "CVST" version))
2617 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
2618 (properties `((upstream-name . "CVST")))
2619 (build-system r-build-system)
2621 `(("r-kernlab" ,r-kernlab)
2622 ("r-matrix" ,r-matrix)))
2623 (home-page "https://cran.r-project.org/web/packages/CVST")
2624 (synopsis "Fast cross-validation via sequential testing")
2626 "This package implements the fast cross-validation via sequential
2627 testing (CVST) procedure. CVST is an improved cross-validation procedure
2628 which uses non-parametric testing coupled with sequential analysis to
2629 determine the best parameter set on linearly increasing subsets of the data.
2630 Additionally to the CVST the package contains an implementation of the
2631 ordinary k-fold cross-validation with a flexible and powerful set of helper
2632 objects and methods to handle the overall model selection process. The
2633 implementations of the Cochran's Q test with permutations and the sequential
2634 testing framework of Wald are generic and can therefore also be used in other
2636 (license license:gpl2+)))
2638 (define-public r-squarem
2641 (version "2017.10-1")
2645 (uri (cran-uri "SQUAREM" version))
2648 "10xj26x7qjyvzndnbjl5krr9wabnb9cbrnp3m7xg673g8ddr12cv"))))
2649 (properties `((upstream-name . "SQUAREM")))
2650 (build-system r-build-system)
2651 (home-page "http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.html")
2652 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
2654 "This package provides algorithms for accelerating the convergence of
2655 slow, monotone sequences from smooth, contraction mapping such as the EM
2656 algorithm. It can be used to accelerate any smooth, linearly convergent
2657 acceleration scheme. A tutorial style introduction to this package is
2658 available in a vignette.")
2659 (license license:gpl2+)))
2661 (define-public r-lava
2668 (uri (cran-uri "lava" version))
2671 "0nfab5fgnmxh8cplg8rd8cp34fny5j0k5wn4baj51r6ck7fq9g3s"))))
2672 (build-system r-build-system)
2674 `(("r-numderiv" ,r-numderiv)
2675 ("r-squarem" ,r-squarem)
2676 ("r-survival" ,r-survival)))
2677 (home-page "https://github.com/kkholst/lava")
2678 (synopsis "Latent variable models")
2680 "This package provides tools for the estimation and simulation of latent
2682 (license license:gpl3)))
2684 (define-public r-drr
2691 (uri (cran-uri "DRR" version))
2694 "1yd1fvllfkcrwg9v322n4wkk4q4q84nvy58y4vac9pdr3yf3i4vl"))))
2695 (properties `((upstream-name . "DRR")))
2696 (build-system r-build-system)
2698 `(("r-cvst" ,r-cvst)
2699 ("r-kernlab" ,r-kernlab)
2700 ("r-matrix" ,r-matrix)))
2701 (home-page "https://cran.r-project.org/web/packages/DRR")
2702 (synopsis "Dimensionality reduction via regression")
2704 "This package provides an implementation of dimensionality reduction via
2705 regression using Kernel Ridge Regression.")
2706 (license license:gpl3)))
2708 (define-public r-prodlim
2711 (version "2019.11.13")
2715 (uri (cran-uri "prodlim" version))
2718 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
2719 (build-system r-build-system)
2721 `(("r-kernsmooth" ,r-kernsmooth)
2724 ("r-survival" ,r-survival)))
2725 (home-page "https://cran.r-project.org/web/packages/prodlim")
2726 (synopsis "Product-limit estimation for censored event history analysis")
2728 "This package provides a fast and user-friendly implementation of
2729 nonparametric estimators for censored event history (survival) analysis with
2730 the Kaplan-Meier and Aalen-Johansen methods.")
2731 (license license:gpl2+)))
2733 (define-public r-dimred
2740 (uri (cran-uri "dimRed" version))
2743 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
2744 (properties `((upstream-name . "dimRed")))
2745 (build-system r-build-system)
2748 ("r-magrittr" ,r-magrittr)))
2749 (home-page "https://github.com/gdkrmr/dimRed")
2750 (synopsis "Framework for dimensionality reduction")
2752 "This package provides a collection of dimensionality reduction
2753 techniques from R packages and provides a common interface for calling the
2755 (license license:gpl3)))
2757 (define-public r-timedate
2760 (version "3043.102")
2764 (uri (cran-uri "timeDate" version))
2767 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
2768 (properties `((upstream-name . "timeDate")))
2769 (build-system r-build-system)
2770 (home-page "https://www.rmetrics.org")
2771 (synopsis "Chronological and calendar objects")
2773 "This package provides an environment for teaching \"Financial
2774 Engineering and Computational Finance\" and for managing chronological and
2776 (license license:gpl2+)))
2778 (define-public r-magic
2785 (uri (cran-uri "magic" version))
2788 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
2789 (build-system r-build-system)
2791 `(("r-abind" ,r-abind)))
2792 (home-page "https://github.com/RobinHankin/magic.git")
2793 (synopsis "Create and investigate magic squares")
2795 "This package provides a collection of efficient, vectorized algorithms
2796 for the creation and investigation of magic squares and hypercubes, including
2797 a variety of functions for the manipulation and analysis of arbitrarily
2798 dimensioned arrays.")
2799 (license license:gpl2)))
2801 (define-public r-rmysql
2808 (uri (cran-uri "RMySQL" version))
2811 "0r4626sk78fhlgivr0c7mwg9mj29ayr0iz5x90rdl4d5nc2r6kq4"))))
2812 (properties `((upstream-name . "RMySQL")))
2813 (build-system r-build-system)
2815 `(("mariadb" ,mariadb "lib")
2816 ("mariadb-dev" ,mariadb "dev")
2819 `(("r-dbi" ,r-dbi)))
2820 (home-page "https://github.com/r-dbi/RMySQL")
2821 (synopsis "Database interface and MySQL driver for R")
2823 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
2824 package contains an old implementation based on legacy code from S-PLUS which
2825 is being phased out. A modern MySQL client based on Rcpp is available from
2826 the RMariaDB package.")
2827 (license license:gpl2)))
2829 (define-public r-rpostgresql
2831 (name "r-rpostgresql")
2836 (uri (cran-uri "RPostgreSQL" version))
2839 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
2840 (properties `((upstream-name . "RPostgreSQL")))
2841 (build-system r-build-system)
2843 `(("postgresql" ,postgresql)))
2845 `(("r-dbi" ,r-dbi)))
2846 (home-page "https://github.com/tomoakin/RPostgreSQL")
2847 (synopsis "R interface to the PostgreSQL database system")
2849 "This package provides a Database Interface (DBI) compliant driver for R
2850 to access PostgreSQL database systems.")
2851 ;; The whole package is released under GPL version 2. It includes code
2852 ;; under the PostgreSQL license.
2853 (license license:gpl2)))
2855 (define-public r-linprog
2862 (uri (cran-uri "linprog" version))
2865 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
2866 (build-system r-build-system)
2867 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
2868 (home-page "http://linprog.r-forge.r-project.org/")
2869 (synopsis "Linear programming and optimization")
2871 "This package can be used to solve Linear Programming / Linear
2872 Optimization problems by using the simplex algorithm.")
2873 (license license:gpl2+)))
2875 (define-public r-geometry
2882 (uri (cran-uri "geometry" version))
2885 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
2886 (build-system r-build-system)
2888 `(("r-magic" ,r-magic)
2889 ("r-linprog" ,r-linprog)
2890 ("r-lpsolve" ,r-lpsolve)
2892 ("r-rcppprogress" ,r-rcppprogress)))
2893 (home-page "http://geometry.r-forge.r-project.org/")
2894 (synopsis "Mesh generation and surface tesselation")
2896 "This package makes the qhull library available in R, in a similar manner
2897 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
2898 intersections about a point, Voronoi diagrams, furthest-site Delaunay
2899 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
2900 and higher dimensions. It implements the Quickhull algorithm for computing
2901 the convex hull. Qhull does not support constrained Delaunay triangulations,
2902 or mesh generation of non-convex objects, but the package does include some R
2903 functions that allow for this. Currently the package only gives access to
2904 Delaunay triangulation and convex hull computation.")
2905 ;; The Qhull sources are included and are distributed under a custom
2906 ;; non-copyleft license. The R sources are released under GPL version 2.
2907 (license (list license:gpl2
2908 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
2910 (define-public r-ddalpha
2917 (uri (cran-uri "ddalpha" version))
2920 "1064g7y8d7kmvd5kjc2m48yvidmh2ci1y0xgil3pcx4ix6mf0ljz"))))
2921 (build-system r-build-system)
2924 ("r-class" ,r-class)
2925 ("r-geometry" ,r-geometry)
2928 ("r-robustbase" ,r-robustbase)
2929 ("r-sfsmisc" ,r-sfsmisc)))
2931 `(("gfortran" ,gfortran)))
2932 (home-page "https://cran.r-project.org/web/packages/ddalpha")
2933 (synopsis "Depth-Based classification and calculation of data depth")
2935 "This package contains procedures for depth-based supervised learning,
2936 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
2937 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
2938 statistical depth function to a compact low-dimensional space, where the final
2939 classification is done. It also offers an extension to functional data and
2940 routines for calculating certain notions of statistical depth functions. 50
2941 multivariate and 5 functional classification problems are included.")
2942 (license license:gpl2)))
2944 (define-public r-gower
2951 (uri (cran-uri "gower" version))
2954 "007ivwn1nagpi26qq8iih1c2l61c53glvv60n90hi341ry8vwgxg"))))
2955 (build-system r-build-system)
2956 (home-page "https://github.com/markvanderloo/gower")
2957 (synopsis "Gower's distance")
2959 "This package provides tools to compute Gower's distance (or similarity)
2960 coefficient between records, and to compute the top-n matches between records.
2961 Core algorithms are executed in parallel on systems supporting OpenMP.")
2962 (license license:gpl3)))
2964 (define-public r-rcpproll
2971 (uri (cran-uri "RcppRoll" version))
2974 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
2975 (properties `((upstream-name . "RcppRoll")))
2976 (build-system r-build-system)
2978 `(("r-rcpp" ,r-rcpp)))
2979 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
2980 (synopsis "Efficient rolling and windowed operations")
2982 "This package provides fast and efficient routines for common rolling /
2983 windowed operations. Routines for the efficient computation of windowed mean,
2984 median, sum, product, minimum, maximum, standard deviation and variance are
2986 (license license:gpl2+)))
2988 (define-public r-ipred
2995 (uri (cran-uri "ipred" version))
2998 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
2999 (build-system r-build-system)
3001 `(("r-class" ,r-class)
3004 ("r-prodlim" ,r-prodlim)
3005 ("r-rpart" ,r-rpart)
3006 ("r-survival" ,r-survival)))
3007 (home-page "https://cran.r-project.org/web/packages/ipred")
3008 (synopsis "Improved predictors")
3010 "This package provides improved predictive models by indirect
3011 classification and bagging for classification, regression and survival
3012 problems as well as resampling based estimators of prediction error.")
3013 (license license:gpl2+)))
3015 (define-public r-psych
3022 (uri (cran-uri "psych" version))
3025 "13r7fyjsl93m121awnwfhya8a0lw0l2byn60yqdbf9gp3lmb9ny0"))))
3026 (build-system r-build-system)
3028 `(("r-foreign" ,r-foreign)
3029 ("r-lattice" ,r-lattice)
3030 ("r-mnormt" ,r-mnormt)
3031 ("r-nlme" ,r-nlme)))
3032 (home-page "https://cran.r-project.org/web/packages/psych/")
3033 (synopsis "Procedures for psychological, psychometric, and personality research")
3035 "This package provides a general purpose toolbox for personality,
3036 psychometric theory and experimental psychology. Functions are primarily for
3037 multivariate analysis and scale construction using factor analysis, principal
3038 component analysis, cluster analysis and reliability analysis, although others
3039 provide basic descriptive statistics. Item Response Theory is done using
3040 factor analysis of tetrachoric and polychoric correlations. Functions for
3041 analyzing data at multiple levels include within and between group statistics,
3042 including correlations and factor analysis. Functions for simulating and
3043 testing particular item and test structures are included. Several functions
3044 serve as a useful front end for structural equation modeling. Graphical
3045 displays of path diagrams, factor analysis and structural equation models are
3046 created using basic graphics.")
3047 (license license:gpl2+)))
3049 (define-public r-generics
3056 (uri (cran-uri "generics" version))
3059 "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi"))))
3060 (build-system r-build-system)
3061 (home-page "https://github.com/r-lib/generics")
3062 (synopsis "Common S3 generics not provided by base R methods")
3064 "In order to reduce potential package dependencies and conflicts,
3065 generics provides a number of commonly used S3 generics that are not provided
3066 by base R methods related to model fitting.")
3067 (license license:gpl2)))
3069 (define-public r-broom
3076 (uri (cran-uri "broom" version))
3079 "177m249dxbf9pf249610qrl58v025ws41ipfihy66751pwsv2n8d"))))
3080 (build-system r-build-system)
3082 `(("r-backports" ,r-backports)
3083 ("r-dplyr" ,r-dplyr)
3084 ("r-generics" ,r-generics)
3086 ("r-purrr" ,r-purrr)
3087 ("r-reshape2" ,r-reshape2)
3088 ("r-stringr" ,r-stringr)
3089 ("r-tibble" ,r-tibble)
3090 ("r-tidyr" ,r-tidyr)))
3091 (home-page "https://github.com/tidyverse/broom")
3092 (synopsis "Convert statistical analysis objects into tidy data frames")
3094 "This package provides tools to convert statistical analysis objects from
3095 R into tidy data frames, so that they can more easily be combined, reshaped
3096 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
3097 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
3098 summarizes a model's statistical findings such as coefficients of a
3099 regression; @code{augment}, which adds columns to the original data such as
3100 predictions, residuals and cluster assignments; and @code{glance}, which
3101 provides a one-row summary of model-level statistics.")
3102 (license license:expat)))
3104 (define-public r-recipes
3111 (uri (cran-uri "recipes" version))
3114 "1n32qc2a3n9cykm8dv9qcr77kdhqfsjiqf6kgfk9s0lnpx2zaldm"))))
3115 (build-system r-build-system)
3117 `(("r-dplyr" ,r-dplyr)
3118 ("r-generics" ,r-generics)
3120 ("r-gower" ,r-gower)
3121 ("r-ipred" ,r-ipred)
3122 ("r-lubridate" ,r-lubridate)
3123 ("r-magrittr" ,r-magrittr)
3124 ("r-matrix" ,r-matrix)
3125 ("r-purrr" ,r-purrr)
3126 ("r-rlang" ,r-rlang)
3127 ("r-tibble" ,r-tibble)
3128 ("r-tidyr" ,r-tidyr)
3129 ("r-tidyselect" ,r-tidyselect)
3130 ("r-timedate" ,r-timedate)
3131 ("r-withr" ,r-withr)))
3132 (home-page "https://github.com/topepo/recipes")
3133 (synopsis "Preprocessing tools to create design matrices")
3135 "Recipes is an extensible framework to create and preprocess design
3136 matrices. Recipes consist of one or more data manipulation and analysis
3137 \"steps\". Statistical parameters for the steps can be estimated from an
3138 initial data set and then applied to other data sets. The resulting design
3139 matrices can then be used as inputs into statistical or machine learning
3141 (license license:gpl2)))
3143 (define-public r-pdist
3150 (uri (cran-uri "pdist" version))
3153 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
3154 (build-system r-build-system)
3155 (home-page "https://github.com/jeffwong/pdist")
3156 (synopsis "Partitioned distance function")
3158 "Pdist computes the euclidean distance between rows of a matrix X and
3159 rows of another matrix Y. Previously, this could be done by binding the two
3160 matrices together and calling @code{dist}, but this creates unnecessary
3161 computation by computing the distances between a row of X and another row of
3162 X, and likewise for Y. Pdist strictly computes distances across the two
3163 matrices, not within the same matrix, making computations significantly faster
3164 for certain use cases.")
3165 (license license:gpl3+)))
3167 (define-public r-ggrepel
3174 (uri (cran-uri "ggrepel" version))
3177 "10vjrcmx8yknfbx93d9a4y3z8gafri0fhimw6hcq733dmdvkml6m"))))
3178 (build-system r-build-system)
3180 `(("r-ggplot2" ,r-ggplot2)
3182 ("r-scales" ,r-scales)))
3183 (home-page "http://github.com/slowkow/ggrepel")
3184 (synopsis "Repulsive text and label geometries for ggplot2")
3186 "This package provides text and label geometries for ggplot2 that help to
3187 avoid overlapping text labels. Labels repel away from each other and away
3188 from the data points.")
3189 (license license:gpl3)))
3191 (define-public r-corrplot
3198 (uri (cran-uri "corrplot" version))
3201 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
3202 (build-system r-build-system)
3203 (home-page "https://github.com/taiyun/corrplot")
3204 (synopsis "Visualization of a correlation matrix")
3206 "This package provides a graphical display of a correlation matrix or
3207 general matrix. It also contains some algorithms to do matrix reordering. In
3208 addition, corrplot is good at details, including choosing color, text labels,
3209 color labels, layout, etc.")
3210 ;; Any version of the GPL
3211 (license license:gpl2+)))
3213 (define-public r-stringdist
3215 (name "r-stringdist")
3220 (uri (cran-uri "stringdist" version))
3222 (base32 "1dqfakclzaf878x7mhwmqrcpcql2h9cv19fz5f3ygpajf3si5kqi"))))
3223 (build-system r-build-system)
3224 (home-page "https://github.com/markvanderloo/stringdist")
3225 (synopsis "Approximate string matching and string distance functions")
3227 "This package implements an approximate string matching version of R's
3228 native @code{match} function. It can calculate various string distances based
3229 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
3230 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
3231 Jaro-Winkler). An implementation of soundex is provided as well. Distances
3232 can be computed between character vectors while taking proper care of encoding
3233 or between integer vectors representing generic sequences.")
3234 (license license:gpl3+)))
3236 (define-public r-ucminf
3243 (uri (cran-uri "ucminf" version))
3246 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
3247 (build-system r-build-system)
3248 (native-inputs `(("gfortran" ,gfortran)))
3249 (home-page "https://cran.r-project.org/web/packages/ucminf/")
3250 (synopsis "General-purpose unconstrained non-linear optimization")
3252 "This package provides an implementation of an algorithm for
3253 general-purpose unconstrained non-linear optimization. The algorithm is of
3254 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
3255 search with a trust region type monitoring of the input to the line search
3256 algorithm. The interface of @code{ucminf} is designed for easy interchange
3257 with the package @code{optim}.")
3258 (license license:gpl2+)))
3260 (define-public r-ordinal
3263 (version "2019.12-10")
3267 (uri (cran-uri "ordinal" version))
3270 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
3271 (build-system r-build-system)
3273 `(("r-mass" ,r-mass)
3274 ("r-matrix" ,r-matrix)
3275 ("r-numderiv" ,r-numderiv)
3276 ("r-ucminf" ,r-ucminf)))
3277 (home-page "https://github.com/runehaubo/ordinal")
3278 (synopsis "Regression models for ordinal data")
3280 "This package provides an implementation of cumulative link (mixed)
3281 models also known as ordered regression models, proportional odds models,
3282 proportional hazards models for grouped survival times and ordered models.
3283 Estimation is via maximum likelihood and mixed models are fitted with the
3284 Laplace approximation and adaptive Gauss-Hermite quadrature.")
3285 (license license:gpl2+)))
3287 (define-public r-jomo
3294 (uri (cran-uri "jomo" version))
3297 "1k9l4290g350zbw1pjs871q9bxj3j2h1dilxpp06v4wy4n7d8qs0"))))
3298 (build-system r-build-system)
3300 `(("r-lme4" ,r-lme4)
3302 ("r-ordinal" ,r-ordinal)
3303 ("r-survival" ,r-survival)))
3304 (home-page "https://cran.r-project.org/web/packages/jomo/")
3305 (synopsis "Multilevel Joint Modelling Multiple Imputation")
3307 "Similarly to Schafer's package pan, jomo is a package for multilevel
3308 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
3309 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
3310 possibility of handling binary and categorical data through latent normal
3311 variables, the option to use cluster-specific covariance matrices and to
3312 impute compatibly with the substantive model.")
3313 (license license:gpl2)))
3315 (define-public r-pan
3322 (uri (cran-uri "pan" version))
3325 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
3326 (build-system r-build-system)
3327 (native-inputs `(("gfortran" ,gfortran)))
3328 (home-page "https://cran.r-project.org/web/packages/pan/")
3329 (synopsis "Multiple imputation for multivariate panel or clustered data")
3331 "This package implements multiple imputation for multivariate panel or
3333 (license license:gpl3)))
3335 (define-public r-mitml
3342 (uri (cran-uri "mitml" version))
3345 "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
3346 (build-system r-build-system)
3348 `(("r-haven" ,r-haven)
3351 (home-page "https://cran.r-project.org/web/packages/mitml/")
3352 (synopsis "Tools for multiple imputation in multilevel modeling")
3354 "This package provides tools for multiple imputation of missing data in
3355 multilevel modeling. It includes a user-friendly interface to the packages
3356 pan and jomo, and several functions for visualization, data management and the
3357 analysis of multiply imputed data sets.")
3358 (license license:gpl2+)))
3360 (define-public r-mice
3367 (uri (cran-uri "mice" version))
3370 "1wx1s1gc07iz63w4m8z0i1n5mc273f89grp5d3hfla7ypicjkasf"))))
3371 (build-system r-build-system)
3373 `(("r-broom" ,r-broom)
3374 ("r-dplyr" ,r-dplyr)
3375 ("r-lattice" ,r-lattice)
3377 ("r-mitml" ,r-mitml)
3380 ("r-rlang" ,r-rlang)
3381 ("r-rpart" ,r-rpart)
3382 ("r-survival" ,r-survival)))
3383 (home-page "https://cran.r-project.org/web/packages/mice/")
3384 (synopsis "Multivariate imputation by chained equations")
3386 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
3387 implemented by the MICE algorithm as described in @url{Van Buuren and
3388 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
3389 variable has its own imputation model. Built-in imputation models are
3390 provided for continuous data (predictive mean matching, normal), binary
3391 data (logistic regression), unordered categorical data (polytomous logistic
3392 regression) and ordered categorical data (proportional odds). MICE can also
3393 impute continuous two-level data (normal model, pan, second-level variables).
3394 Passive imputation can be used to maintain consistency between variables.
3395 Various diagnostic plots are available to inspect the quality of the
3397 ;; Any of these two versions.
3398 (license (list license:gpl2 license:gpl3))))
3400 (define-public r-truncnorm
3402 (name "r-truncnorm")
3407 (uri (cran-uri "truncnorm" version))
3410 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
3411 (build-system r-build-system)
3412 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
3413 (synopsis "Truncated normal distribution")
3414 (description "This package provides functions for the truncated normal
3415 distribution with mean equal to @code{mean} and standard deviation equal to
3416 @code{sd}. It includes density, distribution, quantile, and expected value
3417 functions, as well as a random generation function.")
3418 (license license:gpl2)))
3420 (define-public r-rsolnp
3427 (uri (cran-uri "Rsolnp" version))
3430 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
3431 (properties `((upstream-name . "Rsolnp")))
3432 (build-system r-build-system)
3434 `(("r-truncnorm" ,r-truncnorm)))
3435 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
3436 (synopsis "General non-linear optimization")
3437 (description "The Rsolnp package implements a general non-linear augmented
3438 Lagrange multiplier method solver, a @dfn{sequential quadratic
3439 programming} (SQP) based solver).")
3440 ;; Any version of the GPL.
3441 (license license:gpl2+)))
3443 (define-public r-hardyweinberg
3445 (name "r-hardyweinberg")
3450 (uri (cran-uri "HardyWeinberg" version))
3453 "1irz44q6nf95h37av868f47aakwv3jgwgw217xfsfw0afkm7s25f"))))
3454 (properties `((upstream-name . "HardyWeinberg")))
3455 (build-system r-build-system)
3457 `(("r-mice" ,r-mice)
3459 ("r-rsolnp" ,r-rsolnp)))
3460 (home-page "https://cran.r-project.org/package=HardyWeinberg")
3461 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
3463 "This package contains tools for exploring Hardy-Weinberg equilibrium for
3464 diallelic genetic marker data. All classical tests (chi-square, exact,
3465 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
3466 included in the package, as well as functions for power computation and for
3467 the simulation of marker data under equilibrium and disequilibrium. Routines
3468 for dealing with markers on the X-chromosome are included. Functions for
3469 testing equilibrium in the presence of missing data by using multiple
3470 imputation are also provided. Implements several graphics for exploring the
3471 equilibrium status of a large set of diallelic markers: ternary plots with
3472 acceptance regions, log-ratio plots and Q-Q plots.")
3473 (license license:gpl2+)))
3482 (uri (cran-uri "sm" version))
3485 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
3486 (build-system r-build-system)
3487 (native-inputs `(("gfortran" ,gfortran)))
3488 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
3489 (synopsis "Smoothing methods for nonparametric regression and density estimation")
3491 "This is software accompanying the book 'Applied Smoothing Techniques for
3492 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
3493 University Press. It provides smoothing methods for nonparametric regression
3494 and density estimation")
3495 (license license:gpl2+)))
3497 (define-public r-venndiagram
3499 (name "r-venndiagram")
3503 (uri (cran-uri "VennDiagram" version))
3506 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
3507 (properties `((upstream-name . "VennDiagram")))
3508 (build-system r-build-system)
3510 `(("r-futile-logger" ,r-futile-logger)))
3511 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
3512 (synopsis "Generate High-Resolution Venn and Euler Plots")
3514 "This package provides a set of functions to generate high-resolution
3515 Venn and Euler plots. It includes handling for several special cases,
3516 including two-case scaling, and extensive customization of plot shape and
3518 (license license:gpl2+)))
3520 (define-public r-vioplot
3527 (uri (cran-uri "vioplot" version))
3530 "1fsklymilspzz5fzlj7666x09aglaw0v4x0yfjjzy4vr5qpjc529"))))
3531 (build-system r-build-system)
3535 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
3536 (synopsis "Violin plot")
3538 "This package provides a violin plot, which is a combination of a box
3539 plot and a kernel density plot.")
3540 (license license:bsd-3)))
3542 (define-public r-rsofia
3548 ;; This package has been removed from CRAN, so we can
3549 ;; only fetch it from the archives.
3550 (uri (string-append "https://cran.r-project.org/src/"
3551 "contrib/Archive/RSofia/RSofia_"
3555 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
3556 (properties `((upstream-name . "RSofia")))
3557 (build-system r-build-system)
3559 `(("r-rcpp" ,r-rcpp)))
3560 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
3561 (synopsis "Port of sofia-ml to R")
3562 (description "This package is a port of sofia-ml to R. Sofia-ml is a
3563 suite of fast incremental algorithms for machine learning that can be used for
3564 training models for classification or ranking.")
3565 (license license:asl2.0)))
3567 (define-public r-xts
3574 (uri (cran-uri "xts" version))
3577 "1f0kxrvn13py3hk2gh2m56cqm39x3bqp1i350r5viddacrm2yxqj"))))
3578 (build-system r-build-system)
3579 (propagated-inputs `(("r-zoo" ,r-zoo)))
3580 (home-page "https://github.com/joshuaulrich/xts")
3581 (synopsis "Extensible time series")
3583 "This package provides for uniform handling of R's different time-based
3584 data classes by extending @code{zoo}, maximizing native format information
3585 preservation and allowing for user-level customization and extension, while
3586 simplifying cross-class interoperability.")
3587 (license license:gpl2+)))
3589 (define-public r-performanceanalytics
3591 (name "r-performanceanalytics")
3596 (uri (cran-uri "PerformanceAnalytics" version))
3599 "0jhjldwyxwq7a47zmk5y1jjck7hvq92p8rlgjvdfy51hx2dmlqqd"))))
3601 `((upstream-name . "PerformanceAnalytics")))
3602 (build-system r-build-system)
3604 `(("r-quadprog" ,r-quadprog)
3607 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
3608 (synopsis "Econometric tools for performance and risk analysis")
3609 (description "This is a collection of econometric functions for
3610 performance and risk analysis. This package aims to aid practitioners and
3611 researchers in utilizing the latest research in analysis of non-normal return
3612 streams. In general, it is most tested on return (rather than price) data on
3613 a regular scale, but most functions will work with irregular return data as
3614 well, and increasing numbers of functions will work with P&L or price data
3616 ;; Either version may be picked.
3617 (license (list license:gpl2 license:gpl3))))
3619 (define-public r-laeken
3626 (uri (cran-uri "laeken" version))
3629 "1g9r3y7b0gl91hijk9awa8rjk97mqpkxinzq2cgmx0m38ng9ylpa"))))
3630 (build-system r-build-system)
3632 `(("r-boot" ,r-boot)
3633 ("r-mass" ,r-mass)))
3634 (home-page "https://cran.r-project.org/web/packages/laeken/")
3635 (synopsis "Estimation of indicators on social exclusion and poverty")
3636 (description "This package provides tools for the estimation of indicators
3637 on social exclusion and poverty, as well as an implementation of Pareto tail
3638 modeling for empirical income distributions.")
3639 (license license:gpl2+)))
3641 (define-public r-vcd
3648 (uri (cran-uri "vcd" version))
3651 "1lp99h0wvsc61l1dgcqjxdrcgpgw88ak430cdsv43kmm43qssqd5"))))
3652 (build-system r-build-system)
3654 `(("r-colorspace" ,r-colorspace)
3655 ("r-lmtest" ,r-lmtest)
3656 ("r-mass" ,r-mass)))
3657 (home-page "https://cran.r-project.org/web/packages/vcd/")
3658 (synopsis "Visualizing categorical data")
3659 (description "This package provides visualization techniques, data sets,
3660 summary and inference procedures aimed particularly at categorical data.
3661 Special emphasis is given to highly extensible grid graphics. The package was
3662 originally inspired by the book \"Visualizing Categorical Data\" by Michael
3663 Friendly and is now the main support package for a new book, \"Discrete Data
3664 Analysis with R\" by Michael Friendly and David Meyer (2015).")
3665 (license license:gpl2)))
3667 (define-public r-ica
3674 (uri (cran-uri "ica" version))
3677 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
3678 (build-system r-build-system)
3679 (home-page "https://cran.r-project.org/web/packages/ica/")
3680 (synopsis "Independent component analysis")
3681 (description "This package provides tools for @dfn{Independent Component
3682 Analysis} (ICA) using various algorithms: FastICA,
3683 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
3684 of Eigenmatrices} (JADE).")
3685 (license license:gpl2+)))
3687 (define-public r-dtw
3694 (uri (cran-uri "dtw" version))
3697 "02hyhx1sy5h3vzh9zixy18a7d47df4k5d0wyflcvlcbsbcl6p90s"))))
3698 (build-system r-build-system)
3699 (propagated-inputs `(("r-proxy" ,r-proxy)))
3700 (home-page "http://dtw.r-forge.r-project.org/")
3701 (synopsis "Dynamic Time Warping Algorithms")
3702 (description "This package provides a comprehensive implementation of
3703 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
3704 optimal (least cumulative distance) alignment between points of two time
3705 series. Common DTW variants covered include local (slope) and global (window)
3706 constraints, subsequence matches, arbitrary distance definitions,
3707 normalizations, minimum variance matching, and so on.")
3708 (license license:gpl2+)))
3710 (define-public r-sdmtools
3713 (version "1.1-221.2")
3717 (uri (cran-uri "SDMTools" version))
3720 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
3721 (properties `((upstream-name . "SDMTools")))
3722 (build-system r-build-system)
3723 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
3724 (home-page "http://www.rforge.net/SDMTools/")
3725 (synopsis "Species distribution modelling tools")
3726 (description "This package provides a set of tools for post processing
3727 the outcomes of species distribution modeling exercises. It includes novel
3728 methods for comparing models and tracking changes in distributions through
3729 time. It further includes methods for visualizing outcomes, selecting
3730 thresholds, calculating measures of accuracy and landscape fragmentation
3732 (license license:gpl3+)))
3734 (define-public r-scatterplot3d
3736 (name "r-scatterplot3d")
3741 (uri (cran-uri "scatterplot3d" version))
3744 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
3745 (build-system r-build-system)
3746 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
3747 (synopsis "3D scatter plot")
3748 (description "This package provides an implementation of scatter plots for
3749 plotting. a three dimensional point cloud.")
3750 (license license:gpl2)))
3752 (define-public r-ggridges
3759 (uri (cran-uri "ggridges" version))
3762 "0dhwcpy785ac2ny5bjp284595nnybi3554wd0yffsli0vzf7ry01"))))
3763 (build-system r-build-system)
3765 `(("r-ggplot2" ,r-ggplot2)
3767 ("r-scales" ,r-scales)
3768 ("r-withr" ,r-withr)))
3769 (home-page "https://github.com/clauswilke/ggridges")
3770 (synopsis "Ridgeline plots in ggplot2")
3772 "Ridgeline plots provide a convenient way of visualizing changes in
3773 distributions over time or space. This package enables the creation of such
3774 plots in @code{ggplot2}.")
3775 (license license:gpl2)))
3777 (define-public r-ggjoy
3784 (uri (cran-uri "ggjoy" version))
3787 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
3788 (build-system r-build-system)
3790 `(("r-ggplot2" ,r-ggplot2)
3791 ("r-ggridges" ,r-ggridges)))
3792 (home-page "https://github.com/clauswilke/ggjoy")
3793 (synopsis "Joyplots in ggplot2")
3794 (description "Joyplots provide a convenient way of visualizing changes in
3795 distributions over time or space. This package enables the creation of such
3796 plots in @code{ggplot2}.")
3797 (license license:gpl2)))
3799 (define-public r-cli
3806 (uri (cran-uri "cli" version))
3809 "1gv3zqdipj29ivkw5dsi1qdlra7q4lcrcqvlg9fns7d670yglfki"))))
3810 (build-system r-build-system)
3812 `(("r-assertthat" ,r-assertthat)
3813 ("r-crayon" ,r-crayon)
3814 ("r-fansi" ,r-fansi)
3815 ("r-glue" ,r-glue)))
3816 (home-page "https://github.com/r-lib/cli#readme")
3817 (synopsis "Helpers for developing command line interfaces")
3818 (description "This package provides a suite of tools designed to build
3819 attractive command line interfaces (CLIs). It includes tools for drawing
3820 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
3821 (license license:expat)))
3823 (define-public r-argparser
3825 (name "r-argparser")
3830 (uri (cran-uri "argparser" version))
3833 "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x"))))
3834 (build-system r-build-system)
3835 (home-page "https://bitbucket.org/djhshih/argparser")
3836 (synopsis "Command-line argument parser")
3838 "This package provides a cross-platform command-line argument parser
3839 written purely in R with no external dependencies. It is useful with the
3840 Rscript front-end and facilitates turning an R script into an executable
3842 (license license:gpl3+)))
3844 (define-public r-debugme
3851 (uri (cran-uri "debugme" version))
3854 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
3855 (build-system r-build-system)
3856 (propagated-inputs `(("r-crayon" ,r-crayon)))
3857 (home-page "https://github.com/r-lib/debugme#readme")
3858 (synopsis "Debug R packages")
3860 "This package allows the user to specify debug messages as special string
3861 constants, and control debugging of packages via environment variables.")
3862 (license license:expat)))
3864 (define-public r-processx
3871 (uri (cran-uri "processx" version))
3874 "1g6ipcaxg9y94lyrnbp7kkbqfkcdh1fyrqjjclbjp3x7iysdvazi"))))
3875 (build-system r-build-system)
3879 (home-page "https://github.com/r-lib/processx3")
3880 (synopsis "Execute and control system processes")
3882 "This package provides portable tools to run system processes in the
3883 background. It can check if a background process is running; wait on a
3884 background process to finish; get the exit status of finished processes; kill
3885 background processes and their children; restart processes. It can read the
3886 standard output and error of the processes, using non-blocking connections.
3887 @code{processx} can poll a process for standard output or error, with a
3888 timeout. It can also poll several processes at once.")
3889 (license license:expat)))
3891 (define-public r-tsp
3898 (uri (cran-uri "TSP" version))
3901 "0rxxhvqi55869dg2p82hzg5kvgcqf9h60cjcg00k3pv9aw4x07kb"))))
3902 (properties `((upstream-name . "TSP")))
3903 (build-system r-build-system)
3904 (propagated-inputs `(("r-foreach" ,r-foreach)))
3905 (home-page "https://cran.r-project.org/web/packages/TSP/")
3906 (synopsis "Traveling salesperson problem (TSP)")
3907 (description "This package provides basic infrastructure and some
3908 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
3909 traveling salesman problem).")
3910 (license license:gpl3)))
3912 (define-public r-qap
3919 (uri (cran-uri "qap" version))
3922 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
3923 (build-system r-build-system)
3924 (native-inputs `(("gfortran" ,gfortran)))
3925 (home-page "https://cran.r-project.org/web/packages/qap/")
3926 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
3927 (description "This package implements heuristics for the @dfn{quadratic
3928 assignment problem} (QAP). Currently only a simulated annealing heuristic is
3930 (license license:gpl3)))
3932 (define-public r-gclus
3939 (uri (cran-uri "gclus" version))
3942 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
3943 (build-system r-build-system)
3944 (propagated-inputs `(("r-cluster" ,r-cluster)))
3945 (home-page "https://cran.r-project.org/web/packages/gclus/")
3946 (synopsis "Clustering graphics")
3947 (description "This package orders panels in scatterplot matrices and
3948 parallel coordinate displays by some merit index. It contains various indices
3949 of merit, ordering functions, and enhanced versions of @code{pairs} and
3950 @code{parcoord} which color panels according to their merit level.")
3951 (license license:gpl2+)))
3953 (define-public r-webshot
3960 (uri (cran-uri "webshot" version))
3963 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
3964 (build-system r-build-system)
3966 `(("r-callr" ,r-callr)
3967 ("r-jsonlite" ,r-jsonlite)
3968 ("r-magrittr" ,r-magrittr)))
3969 (home-page "https://github.com/wch/webshot/")
3970 (synopsis "Take screenshots of web pages")
3972 "Webshot makes it easy to take screenshots of web pages from within R.
3973 It can also run Shiny applications locally and take screenshots of the
3974 application; and it can render and screenshot static as well as interactive R
3975 Markdown documents.")
3976 (license license:gpl2)))
3978 (define-public r-seriation
3980 (name "r-seriation")
3985 (uri (cran-uri "seriation" version))
3988 "1zbdxq0s5rc5v307b69fw9k52m0654ls7pf22lh35ggirig6lwsk"))))
3989 (build-system r-build-system)
3991 `(("r-cluster" ,r-cluster)
3992 ("r-colorspace" ,r-colorspace)
3993 ("r-dendextend" ,r-dendextend)
3994 ("r-gclus" ,r-gclus)
3995 ("r-gplots" ,r-gplots)
3998 ("r-registry" ,r-registry)
4000 (native-inputs `(("gfortran" ,gfortran)))
4001 (home-page "http://s2.smu.edu/IDA/seriation/")
4002 (synopsis "Infrastructure for ordering objects using seriation")
4004 "This package provides infrastructure for seriation with an
4005 implementation of several seriation/sequencing techniques to reorder matrices,
4006 dissimilarity matrices, and dendrograms. It also provides (optimally)
4007 reordered heatmaps, color images and clustering visualizations like
4008 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
4010 (license license:gpl3)))
4012 (define-public r-xfun
4019 (uri (cran-uri "xfun" version))
4021 (base32 "0dncw6bqkal7nyarrrrj9arxy0y3nkdzmrbibcjh84m1cxd4phiw"))))
4022 (build-system r-build-system)
4023 (home-page "https://github.com/yihui/xfun")
4024 (synopsis "Miscellaneous functions")
4026 "This package provides miscellaneous functions commonly used in other
4027 packages maintained by Yihui Xie.")
4028 (license license:expat)))
4030 (define-public r-utf8
4037 (uri (cran-uri "utf8" version))
4040 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
4041 (build-system r-build-system)
4042 (home-page "https://github.com/patperry/r-utf8")
4043 (synopsis "Unicode text processing")
4045 "This package provides tools to process and print UTF-8 encoded
4046 international text (Unicode). Input, validate, normalize, encode, format, and
4048 (license license:asl2.0)))
4050 (define-public r-zeallot
4057 (uri (cran-uri "zeallot" version))
4060 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
4061 (build-system r-build-system)
4062 (home-page "https://github.com/nteetor/zeallot")
4063 (synopsis "Multiple, unpacking, and destructuring assignment")
4065 "This package provides a @code{%<-%} operator to perform multiple,
4066 unpacking, and destructuring assignment in R. The operator unpacks the
4067 right-hand side of an assignment into multiple values and assigns these values
4068 to variables on the left-hand side of the assignment.")
4069 (license license:expat)))
4071 (define-public r-vctrs
4078 (uri (cran-uri "vctrs" version))
4081 "0rlwjfvvhv3s5mj4lqhwlqwddpizyp46i1qbcvw0mzb5q8b0nkz0"))))
4082 (build-system r-build-system)
4084 `(("r-backports" ,r-backports)
4085 ("r-digest" ,r-digest)
4086 ("r-ellipsis" ,r-ellipsis)
4088 ("r-rlang" ,r-rlang)
4089 ("r-zeallot" ,r-zeallot)))
4090 (home-page "https://github.com/r-lib/vctrs")
4091 (synopsis "Vector helpers")
4093 "There are three main goals to the @code{vctrs} package:
4096 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
4097 @code{length()} and @code{class()}. These definitions are paired with a
4098 framework for type-coercion and size-recycling.
4099 @item To define type- and size-stability as desirable function properties, use
4100 them to analyse existing base function, and to propose better alternatives.
4101 This work has been particularly motivated by thinking about the ideal
4102 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
4103 @item To provide a new @code{vctr} base class that makes it easy to create new
4104 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
4105 a few new @code{vctrs} generics, making implementation considerably simpler
4108 (license license:gpl3)))
4110 (define-public r-pillar
4117 (uri (cran-uri "pillar" version))
4120 "02sn7zw80wq33jgxk2i6m5jb83sk7y72dfhgyy0apfinv05w92ss"))))
4121 (build-system r-build-system)
4124 ("r-crayon" ,r-crayon)
4125 ("r-fansi" ,r-fansi)
4126 ("r-rlang" ,r-rlang)
4128 ("r-vctrs" ,r-vctrs)))
4129 (home-page "https://github.com/r-lib/pillar")
4130 (synopsis "Coloured formatting for columns")
4132 "This package provides a @code{pillar} generic designed for formatting
4133 columns of data using the full range of colours provided by modern
4135 (license license:gpl3)))
4137 (define-public r-uuid
4144 (uri (cran-uri "uuid" version))
4147 "1gmisd630fc8ybg845hbg13wmm3pk3npaamrh5wqbc1nqd6p0wfx"))))
4148 (build-system r-build-system)
4149 (home-page "http://www.rforge.net/uuid")
4150 (synopsis "Tools for generating and handling of UUIDs")
4152 "This package provides tools for generating and handling of
4153 @dfn{Universally Unique Identifiers} (UUIDs).")
4154 (license license:expat)))
4156 (define-public r-tinytex
4163 (uri (cran-uri "tinytex" version))
4166 "04mpbhadixbxmnazj0q6cj973cajchscvyh1k6a5b3qk26dp5krr"))))
4167 (build-system r-build-system)
4169 `(("r-xfun" ,r-xfun)))
4170 (home-page "https://github.com/yihui/tinytex")
4171 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
4173 "This package provides helper functions to install and maintain the LaTeX
4174 distribution named TinyTeX, a lightweight, cross-platform, portable, and
4175 easy-to-maintain version of TeX Live. This package also contains helper
4176 functions to compile LaTeX documents, and install missing LaTeX packages
4178 (license license:expat)))
4180 (define-public r-network
4187 (uri (cran-uri "network" version))
4190 "0dnf1wl3za2lhx2lwd8smhlijl1cfhckgr8zz9piiirrfi2m2kx2"))))
4191 (build-system r-build-system)
4193 `(("r-magrittr" ,r-magrittr)
4194 ("r-tibble" ,r-tibble)))
4195 (home-page "https://statnet.org/")
4196 (synopsis "Classes for relational data")
4198 "This package provides tools to create and modify network objects. The
4199 @code{network} class can represent a range of relational data types, and
4200 supports arbitrary vertex/edge/graph attributes.")
4201 (license license:gpl2+)))
4203 (define-public r-statnet-common
4205 (name "r-statnet-common")
4210 (uri (cran-uri "statnet.common" version))
4213 "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3"))))
4215 `((upstream-name . "statnet.common")))
4216 (build-system r-build-system)
4218 `(("r-coda" ,r-coda)))
4219 (home-page "https://statnet.org")
4220 (synopsis "R scripts and utilities used by the Statnet software")
4221 (description "This package provides non-statistical utilities used by the
4222 software developed by the Statnet Project.")
4223 (license license:gpl3)))
4225 (define-public r-statcheck
4227 (name "r-statcheck")
4232 (uri (cran-uri "statcheck" version))
4235 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
4236 (build-system r-build-system)
4238 `(("r-ggplot2" ,r-ggplot2)
4240 ("r-rmarkdown" ,r-rmarkdown)))
4241 (home-page "https://cran.r-project.org/web/packages/statcheck/")
4242 (synopsis "Extract statistics from articles and recompute p-values")
4243 (description "This package can automatically extract statistical
4244 null-hypothesis significant testing (NHST) results from articles and recompute
4245 the p-values based on the reported test statistic and degrees of freedom to
4246 detect possible inconsistencies.")
4247 (license license:gpl2)))
4249 (define-public r-sna
4256 (uri (cran-uri "sna" version))
4259 "1j3i6300m686qqfmyvadim377cd3mplzgj6mandygw8brg50id8k"))))
4260 (build-system r-build-system)
4262 `(("r-network" ,r-network)
4263 ("r-statnet-common" ,r-statnet-common)))
4264 (home-page "https://statnet.org")
4265 (synopsis "Tools for social network analysis")
4267 "This package provides a range of tools for social network analysis,
4268 including node and graph-level indices, structural distance and covariance
4269 methods, structural equivalence detection, network regression, random graph
4270 generation, and 2D/3D network visualization.")
4271 (license license:gpl2+)))
4273 (define-public r-tfisher
4280 (uri (cran-uri "TFisher" version))
4283 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
4284 (properties `((upstream-name . "TFisher")))
4285 (build-system r-build-system)
4287 `(("r-matrix" ,r-matrix)
4288 ("r-mvtnorm" ,r-mvtnorm)
4290 (home-page "https://cran.r-project.org/web/packages/TFisher/")
4291 (synopsis "Optimal thresholding Fisher's p-value combination method")
4293 "This package provides the @dfn{cumulative distribution function} (CDF),
4294 quantile, and statistical power calculator for a collection of thresholding
4295 Fisher's p-value combination methods, including Fisher's p-value combination
4296 method, truncated product method and, in particular, soft-thresholding
4297 Fisher's p-value combination method which is proven to be optimal in some
4298 context of signal detection. The p-value calculator for the omnibus version
4299 of these tests are also included.")
4300 (license license:gpl2)))
4302 (define-public r-ttr
4309 (uri (cran-uri "TTR" version))
4312 "0rg22ma3x07s9djlxscfw5jcq1gbir05cwhgvwfi53x1sf4hmhdg"))))
4313 (properties `((upstream-name . "TTR")))
4314 (build-system r-build-system)
4316 `(("r-curl" ,r-curl)
4319 (home-page "https://github.com/joshuaulrich/TTR")
4320 (synopsis "Technical trading rules")
4322 "This package provides functions and data to construct technical trading
4324 (license license:gpl2)))
4326 (define-public r-leaps
4333 (uri (cran-uri "leaps" version))
4336 "11gjmn1azrjw5xlvdb4gknj9985kck9x8zb9np1rnk2smp6pka2m"))))
4337 (build-system r-build-system)
4338 (native-inputs `(("gfortran" ,gfortran)))
4339 (home-page "https://cran.r-project.org/web/packages/leaps/")
4340 (synopsis "Regression subset selection")
4342 "This package provides tools for regression subset selection, including
4343 exhaustive search.")
4344 (license license:gpl2+)))
4346 (define-public r-splus2r
4353 (uri (cran-uri "splus2R" version))
4356 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
4357 (properties `((upstream-name . "splus2R")))
4358 (build-system r-build-system)
4359 (native-inputs `(("gfortran" ,gfortran)))
4360 (home-page "https://cran.r-project.org/web/packages/splus2R/")
4361 (synopsis "Supplemental S-PLUS functionality in R")
4363 "Currently there are many functions in S-PLUS that are missing in R. To
4364 facilitate the conversion of S-PLUS packages to R packages, this package
4365 provides some missing S-PLUS functionality in R.")
4366 (license license:gpl2)))
4368 (define-public r-ifultools
4370 (name "r-ifultools")
4375 (uri (cran-uri "ifultools" version))
4378 "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j"))))
4379 (build-system r-build-system)
4381 `(("r-mass" ,r-mass)
4382 ("r-splus2r" ,r-splus2r)))
4383 (home-page "https://cran.r-project.org/web/packages/ifultools/")
4384 (synopsis "Insightful research tools")
4385 (description "This package provides C code used by the wmtsa, fractal, and
4387 (license license:gpl2)))
4389 (define-public r-sapa
4396 (uri (cran-uri "sapa" version))
4399 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
4400 (build-system r-build-system)
4402 `(("r-ifultools" ,r-ifultools)
4403 ("r-splus2r" ,r-splus2r)))
4404 (home-page "https://cran.r-project.org/web/packages/sapa/")
4405 (synopsis "Spectral analysis for physical applications")
4406 (description "This package provides software for the book Spectral
4407 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
4408 Cambridge University Press, 1993.")
4409 (license license:gpl2)))
4411 (define-public r-aggregation
4413 (name "r-aggregation")
4418 (uri (cran-uri "aggregation" version))
4421 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
4422 (build-system r-build-system)
4423 (home-page "https://cran.r-project.org/web/packages/aggregation/")
4424 (synopsis "Methods for p-value aggregation")
4426 "This package contains functionality for performing the following methods
4427 of p-value aggregation: Fisher's method, the Lancaster method (weighted
4428 Fisher's method), and Sidak correction.")
4429 (license license:gpl3)))
4431 (define-public r-quantmod
4438 (uri (cran-uri "quantmod" version))
4441 "0lyzaf5ypk93v6zj9gdghy05cc7cxgn9yasv1apx5r6qsjcfgwky"))))
4442 (build-system r-build-system)
4444 `(("r-curl" ,r-curl)
4448 (home-page "https://cran.r-project.org/web/packages/quantmod/")
4449 (synopsis "Quantitative financial modelling framework")
4450 (description "This package provides a quantitative financial modelling
4451 framework to allow users to specify, build, trade, and analyse quantitative
4452 financial trading strategies.")
4453 (license license:gpl3)))
4455 (define-public r-tseries
4462 (uri (cran-uri "tseries" version))
4465 "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
4466 (build-system r-build-system)
4468 `(("r-quadprog" ,r-quadprog)
4469 ("r-quantmod" ,r-quantmod)
4472 `(("gfortran" ,gfortran)))
4473 (home-page "https://cran.r-project.org/web/packages/tseries/")
4474 (synopsis "Time series analysis and computational finance")
4476 "This package provides functions relating to time series analysis and
4477 computational finance.")
4478 (license license:gpl2)))
4480 (define-public r-wmtsa
4487 (uri (cran-uri "wmtsa" version))
4490 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
4491 (build-system r-build-system)
4493 `(("r-ifultools" ,r-ifultools)
4495 ("r-splus2r" ,r-splus2r)))
4496 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
4497 (synopsis "Wavelet methods for time series analysis")
4499 "This package provides software to accompany the book \"Wavelet Methods
4500 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
4501 University Press, 2000.")
4502 (license license:gpl2)))
4504 (define-public r-tsa
4511 (uri (cran-uri "TSA" version))
4514 "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q"))))
4515 (properties `((upstream-name . "TSA")))
4516 (build-system r-build-system)
4518 `(("r-leaps" ,r-leaps)
4519 ("r-locfit" ,r-locfit)
4520 ("r-mgcv" ,r-mgcv)))
4521 (home-page "http://www.stat.uiowa.edu/~kchan/TSA.htm")
4522 (synopsis "Time series analysis")
4524 "This package contains R functions and datasets detailed in the book
4525 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
4526 Cryer and Kung-Sik Chan.")
4527 (license license:gpl2+)))
4529 (define-public r-extradistr
4531 (name "r-extradistr")
4536 (uri (cran-uri "extraDistr" version))
4539 "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3"))))
4540 (properties `((upstream-name . "extraDistr")))
4541 (build-system r-build-system)
4543 `(("r-rcpp" ,r-rcpp)))
4544 (home-page "https://github.com/twolodzko/extraDistr")
4545 (synopsis "Additional univariate and multivariate distributions")
4547 "This package implements density, distribution functions, quantile
4548 functions and random generation functions for a large number of univariate and
4549 multivariate distributions.")
4550 (license license:gpl2)))
4552 (define-public r-fractal
4559 (uri (cran-uri "fractal" version))
4562 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
4563 (build-system r-build-system)
4565 `(("r-ifultools" ,r-ifultools)
4568 ("r-scatterplot3d" ,r-scatterplot3d)
4569 ("r-splus2r" ,r-splus2r)
4570 ("r-wmtsa" ,r-wmtsa)))
4571 (home-page "https://cran.r-project.org/web/packages/fractal/")
4572 (synopsis "Fractal time series modeling and analysis")
4574 "This package provides tools for stochastic fractal and deterministic
4575 chaotic time series analysis.")
4576 (license license:gpl2)))
4578 (define-public r-urca
4585 (uri (cran-uri "urca" version))
4588 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
4589 (build-system r-build-system)
4590 (propagated-inputs `(("r-nlme" ,r-nlme)))
4591 (native-inputs `(("gfortran" ,gfortran)))
4592 (home-page "https://cran.r-project.org/web/packages/urca/")
4593 (synopsis "Unit root and cointegration tests for time series data")
4595 "This package provides unit root and cointegration tests encountered in
4596 applied econometric analysis.")
4597 (license license:gpl2+)))
4599 (define-public r-cubature
4606 (uri (cran-uri "cubature" version))
4609 "0jpyq8j7x06dpiz29w48av879ygldzgls9z810192hsymkmfaz6r"))))
4610 (build-system r-build-system)
4612 `(("r-rcpp" ,r-rcpp)))
4613 (home-page "https://github.com/bnaras/cubature")
4614 (synopsis "Adaptive multivariate integration over hypercubes")
4616 "This package is an R wrapper around the cubature C library for adaptive
4617 multivariate integration over hypercubes. This version provides both
4618 @code{hcubature} and @code{pcubature} routines in addition to a vector
4620 ;; The included cubature C library is released under GPLv2+, but the
4621 ;; wrapper declares the license to be GPLv3+.
4622 (license (list license:gpl2+ license:gpl3+))))
4624 (define-public r-trend
4631 (uri (cran-uri "trend" version))
4634 "1bd567n15k2vpmgbx02584k5kglrc58mlb5kgd07wdss3knpa48q"))))
4635 (build-system r-build-system)
4637 `(("r-extradistr" ,r-extradistr)))
4639 `(("gfortran" ,gfortran)))
4640 (home-page "https://cran.r-project.org/web/packages/trend/")
4641 (synopsis "Non-parametric trend tests and change-point detection")
4643 "The analysis of environmental data often requires the detection of
4644 trends and change-points. This package includes tests for trend
4645 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
4646 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
4647 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
4648 correlation trend test), change-point detection (Lanzante's test procedures,
4649 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
4650 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
4651 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
4652 sample Robust Rank-Order Distributional Test.")
4653 (license license:gpl3)))
4655 (define-public r-expm
4662 (uri (cran-uri "expm" version))
4665 "15k0acg2aqb2ajhwal6l7vhhp03m4lg579805d34554cl0kn9l2q"))))
4666 (build-system r-build-system)
4667 (propagated-inputs `(("r-matrix" ,r-matrix)))
4668 (native-inputs `(("gfortran" ,gfortran)))
4669 (home-page "https://r-forge.r-project.org/projects/expm/")
4670 (synopsis "Tools for matrix exponentials and related quantities")
4672 "This package provides tools for the computation of the matrix
4673 exponential, logarithm, square root, and related quantities.")
4674 (license license:gpl2+)))
4676 (define-public r-complexplus
4678 (name "r-complexplus")
4683 (uri (cran-uri "complexplus" version))
4686 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
4687 (build-system r-build-system)
4689 `(("r-expm" ,r-expm)
4690 ("r-matrix" ,r-matrix)))
4691 (home-page "https://cran.r-project.org/web/packages/complexplus/")
4692 (synopsis "Functions of complex or real variables")
4694 "This package extends several functions to the complex domain, including
4695 the matrix exponential and logarithm, and the determinant.")
4696 (license license:gpl2)))
4698 (define-public r-phontools
4700 (name "r-phontools")
4705 (uri (cran-uri "phonTools" version))
4708 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
4709 (properties `((upstream-name . "phonTools")))
4710 (build-system r-build-system)
4711 (home-page "http://www.santiagobarreda.com/rscripts.html")
4712 (synopsis "Tools for phonetic and acoustic analyses")
4714 "This package contains tools for the organization, display, and analysis
4715 of the sorts of data frequently encountered in phonetics research and
4716 experimentation, including the easy creation of IPA vowel plots, and the
4717 creation and manipulation of WAVE audio files.")
4718 (license license:bsd-2)))
4727 (uri (cran-uri "np" version))
4730 "1z4jcpx8bbgwslv42wrphfd1qfq965qjn0kmfxm5f6hbbycahcgy"))))
4731 (build-system r-build-system)
4733 `(("r-boot" ,r-boot)
4734 ("r-cubature" ,r-cubature)
4735 ("r-quadprog" ,r-quadprog)
4736 ("r-quantreg" ,r-quantreg)))
4737 (home-page "https://github.com/JeffreyRacine/R-Package-np")
4738 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
4739 (description "This package provides non-parametric (and semi-parametric)
4740 kernel methods that seamlessly handle a mix of continuous, unordered, and
4741 ordered factor data types.")
4742 ;; Any version of the GPL.
4743 (license license:gpl3+)))
4745 (define-public r-powerplus
4747 (name "r-powerplus")
4752 (uri (cran-uri "powerplus" version))
4755 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
4756 (build-system r-build-system)
4758 `(("r-complexplus" ,r-complexplus)
4761 ("r-matrix" ,r-matrix)
4762 ("r-phontools" ,r-phontools)))
4763 (home-page "https://cran.r-project.org/web/packages/powerplus/")
4764 (synopsis "Exponentiation operations")
4766 "This package provides tools for the computation of matrix and scalar
4768 (license license:gpl2)))
4770 (define-public r-egg
4777 (uri (cran-uri "egg" version))
4780 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
4781 (properties `((upstream-name . "egg")))
4782 (build-system r-build-system)
4784 `(("r-ggplot2" ,r-ggplot2)
4785 ("r-gridextra" ,r-gridextra)
4786 ("r-gtable" ,r-gtable)))
4787 (home-page "https://cran.r-project.org/web/packages/egg")
4788 (synopsis "Extensions for ggplot2")
4790 "This package provides miscellaneous functions to help customize ggplot2
4791 objects. High-level functions are provided to post-process ggplot2 layouts
4792 and allow alignment between plot panels, as well as setting panel sizes to
4793 fixed values. Other functions include a custom @code{geom}, and helper
4794 functions to enforce symmetric scales or add tags to facetted plots.")
4795 (license license:gpl3)))
4797 (define-public r-heatmaply
4799 (name "r-heatmaply")
4804 (uri (cran-uri "heatmaply" version))
4807 "0576gml3bcl7r1biigzj1rag2xzz422knbw7arc8d2gsakjj757g"))))
4808 (build-system r-build-system)
4810 `(("r-assertthat" ,r-assertthat)
4811 ("r-colorspace" ,r-colorspace)
4812 ("r-dendextend" ,r-dendextend)
4814 ("r-ggplot2" ,r-ggplot2)
4815 ("r-htmlwidgets" ,r-htmlwidgets)
4816 ("r-magrittr" ,r-magrittr)
4817 ("r-plotly" ,r-plotly)
4818 ("r-rcolorbrewer" ,r-rcolorbrewer)
4819 ("r-reshape2" ,r-reshape2)
4820 ("r-scales" ,r-scales)
4821 ("r-seriation" ,r-seriation)
4822 ("r-viridis" ,r-viridis)
4823 ("r-webshot" ,r-webshot)))
4824 (home-page "https://cran.r-project.org/package=heatmaply")
4825 (synopsis "Interactive cluster heat maps using plotly")
4827 "This package enables you to create interactive cluster heatmaps that can
4828 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
4829 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
4830 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
4831 a popular graphical method for visualizing high-dimensional data, in which a
4832 table of numbers is encoded as a grid of colored cells. The rows and columns
4833 of the matrix are ordered to highlight patterns and are often accompanied by
4835 ;; Either version of the license.
4836 (license (list license:gpl2 license:gpl3))))
4845 (uri (cran-uri "h5" version))
4848 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
4849 (build-system r-build-system)
4854 `(("which" ,which)))
4856 `(("r-rcpp" ,r-rcpp)))
4857 (home-page "https://github.com/mannau/h5")
4858 (synopsis "Interface to the HDF5 Library")
4860 "This package provides an S4 interface to the HDF5 library supporting
4861 fast storage and retrieval of R-objects like vectors, matrices and arrays to
4862 binary files in a language independent format. The HDF5 format can therefore
4863 be used as an alternative to R's save/load mechanism. Since h5 is able to
4864 access only subsets of stored data it can also handle data sets which do not
4866 (license license:bsd-2)))
4868 (define-public r-cgdsr
4875 (uri (cran-uri "cgdsr" version))
4878 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
4879 (build-system r-build-system)
4881 `(("r-httr" ,r-httr)
4882 ("r-r-methodss3" ,r-r-methodss3)
4883 ("r-r-oo" ,r-r-oo)))
4884 (home-page "https://github.com/cBioPortal/cgdsr")
4885 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
4887 "This package provides a basic set of R functions for querying the Cancer
4888 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
4889 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
4890 (license license:lgpl3)))
4892 (define-public r-import
4899 (uri (cran-uri "import" version))
4902 "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
4903 (build-system r-build-system)
4904 (home-page "https://github.com/smbache/import")
4905 (synopsis "Import mechanism for R")
4907 "This is an alternative mechanism for importing objects from packages.
4908 The syntax allows for importing multiple objects from a package with a single
4909 command in an expressive way. The import package bridges some of the gap
4910 between using @code{library} (or @code{require}) and direct (single-object)
4911 imports. Furthermore the imported objects are not placed in the current
4912 environment. It is also possible to import objects from stand-alone @code{.R}
4914 (license license:expat)))
4916 (define-public r-shinyace
4923 (uri (cran-uri "shinyAce" version))
4926 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
4927 (properties `((upstream-name . "shinyAce")))
4928 (build-system r-build-system)
4930 `(("r-shiny" ,r-shiny)
4931 ("r-jsonlite" ,r-jsonlite)))
4932 (home-page "http://cran.r-project.org/web/packages/shinyAce")
4933 (synopsis "Ace editor bindings for Shiny")
4935 "This package provides Ace editor bindings to enable a rich text editing
4936 environment within Shiny.")
4937 (license license:expat)))
4939 (define-public r-base64url
4941 (name "r-base64url")
4946 (uri (cran-uri "base64url" version))
4949 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
4950 (build-system r-build-system)
4952 `(("r-backports" ,r-backports)))
4953 (home-page "https://github.com/mllg/base64url")
4954 (synopsis "Fast and URL-safe base64 encoder and decoder")
4956 "This package provides a URL-safe base64 encoder and decoder. In
4957 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
4958 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
4959 encoder does not fill the string with trailing @code{=}. The resulting
4960 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
4961 and thus are safe to use in URLs or for file names. The package also comes
4962 with a simple base32 encoder/decoder suited for case insensitive file
4964 (license license:gpl3)))
4966 (define-public r-radiant-data
4968 (name "r-radiant-data")
4973 (uri (cran-uri "radiant.data" version))
4976 "08x7zasxf429m021482p86lx3zc6dqz2mih0id8s34isg4gafapg"))
4977 (modules '((guix build utils)))
4980 ;; Delete files that are under CC-NC-SA.
4981 (delete-file-recursively "inst/app/tools/help")
4983 (properties `((upstream-name . "radiant.data")))
4984 (build-system r-build-system)
4986 `(("r-base64enc" ,r-base64enc)
4987 ("r-broom" ,r-broom)
4990 ("r-dplyr" ,r-dplyr)
4993 ("r-ggplot2" ,r-ggplot2)
4994 ("r-gridextra" ,r-gridextra)
4995 ("r-import" ,r-import)
4996 ("r-jsonlite" ,r-jsonlite)
4997 ("r-knitr" ,r-knitr)
4998 ("r-lubridate" ,r-lubridate)
4999 ("r-magrittr" ,r-magrittr)
5000 ("r-markdown" ,r-markdown)
5001 ("r-plotly" ,r-plotly)
5002 ("r-psych" ,r-psych)
5003 ("r-readr" ,r-readr)
5004 ("r-readxl" ,r-readxl)
5005 ("r-rlang" ,r-rlang)
5006 ("r-rmarkdown" ,r-rmarkdown)
5007 ("r-rstudioapi" ,r-rstudioapi)
5008 ("r-scales" ,r-scales)
5009 ("r-shiny" ,r-shiny)
5010 ("r-shinyfiles" ,r-shinyfiles)
5011 ("r-shinyace" ,r-shinyace)
5012 ("r-stringi" ,r-stringi)
5013 ("r-tibble" ,r-tibble)
5014 ("r-tidyr" ,r-tidyr)
5015 ("r-writexl" ,r-writexl)))
5016 (home-page "https://github.com/radiant-rstats/radiant.data")
5017 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
5019 "The Radiant Data menu includes interfaces for loading, saving, viewing,
5020 visualizing, summarizing, transforming, and combining data. It also contains
5021 functionality to generate reproducible reports of the analyses conducted in
5023 (license license:agpl3)))
5025 (define-public r-algdesign
5027 (name "r-algdesign")
5032 (uri (cran-uri "AlgDesign" version))
5034 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
5035 (properties `((upstream-name . "AlgDesign")))
5036 (build-system r-build-system)
5037 (home-page "https://github.com/jvbraun/AlgDesign")
5038 (synopsis "Algorithmic experimental design")
5040 "This package provides tools to calculate exact and approximate theory
5041 experimental designs for D, A, and I criteria. Very large designs may be
5042 created. Experimental designs may be blocked or blocked designs created from
5043 a candidate list, using several criteria. The blocking can be done when whole
5044 and within plot factors interact.")
5045 (license license:gpl2+)))
5047 (define-public r-signal
5054 (uri (cran-uri "signal" version))
5057 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
5058 (build-system r-build-system)
5059 (propagated-inputs `(("r-mass" ,r-mass)))
5060 (native-inputs `(("gfortran" ,gfortran)))
5061 (home-page "https://cran.r-project.org/web/packages/signal/")
5062 (synopsis "Signal processing")
5064 "This package provides a set of signal processing functions originally
5065 written for Matlab and GNU Octave. It includes filter generation utilities,
5066 filtering functions, resampling routines, and visualization of filter models.
5067 It also includes interpolation functions.")
5068 (license license:gpl2)))
5070 (define-public r-gsubfn
5077 (uri (cran-uri "gsubfn" version))
5080 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
5081 (build-system r-build-system)
5082 (propagated-inputs `(("r-proto" ,r-proto)))
5083 (home-page "http://gsubfn.googlecode.com")
5084 (synopsis "Utilities for strings and function arguments.")
5086 "This package provides @code{gsubfn} which is like @code{gsub} but can
5087 take a replacement function or certain other objects instead of the
5088 replacement string. Matches and back references are input to the replacement
5089 function and replaced by the function output. @code{gsubfn} can be used to
5090 split strings based on content rather than delimiters and for quasi-perl-style
5091 string interpolation. The package also has facilities for translating
5092 formulas to functions and allowing such formulas in function calls instead of
5094 (license license:gpl2+)))
5096 (define-public r-sqldf
5103 (uri (cran-uri "sqldf" version))
5106 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
5107 (build-system r-build-system)
5109 `(("r-chron" ,r-chron)
5111 ("r-gsubfn" ,r-gsubfn)
5112 ("r-proto" ,r-proto)
5113 ("r-rsqlite" ,r-rsqlite)))
5114 (home-page "https://github.com/ggrothendieck/sqldf")
5115 (synopsis "Manipulate R data frames using SQL")
5117 "The @code{sqldf} function is typically passed a single argument which is
5118 an SQL select statement where the table names are ordinary R data frame names.
5119 @code{sqldf} transparently sets up a database, imports the data frames into
5120 that database, performs the SQL statement and returns the result using a
5121 heuristic to determine which class to assign to each column of the returned
5122 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
5123 used to read filtered files into R even if the original files are larger than
5124 R itself can handle.")
5125 (license license:gpl2)))
5127 (define-public r-abind
5134 (uri (cran-uri "abind" version))
5137 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
5138 (build-system r-build-system)
5139 (home-page "https://cran.r-project.org/web/packages/abind/")
5140 (synopsis "Combine multidimensional arrays")
5142 "This package provides tools to combine multidimensional arrays into a
5143 single array. This is a generalization of @code{cbind} and @code{rbind}. It
5144 works with vectors, matrices, and higher-dimensional arrays. It also provides
5145 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
5146 extracting and replacing data in arrays.")
5147 (license license:lgpl2.0+)))
5149 (define-public r-prroc
5156 (uri (cran-uri "PRROC" version))
5159 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
5160 (properties `((upstream-name . "PRROC")))
5161 (build-system r-build-system)
5162 (home-page "https://cran.r-project.org/web/packages/PRROC/")
5163 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
5165 "This package computes the areas under the @dfn{precision-recall} (PR)
5166 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
5167 contrast to other implementations, the interpolation between points of the PR
5168 curve is done by a non-linear piecewise function. In addition to the areas
5169 under the curves, the curves themselves can also be computed and plotted by a
5170 specific S3-method.")
5171 (license license:gpl3)))
5173 (define-public r-vim
5180 (uri (cran-uri "VIM" version))
5183 "08x4a4yzgp8adgrv7a3666yma4b60n64mcsnvhzmwdy023f4ysrw"))))
5184 (properties `((upstream-name . "VIM")))
5185 (build-system r-build-system)
5188 ("r-colorspace" ,r-colorspace)
5189 ("r-data-table" ,r-data-table)
5190 ("r-e1071" ,r-e1071)
5191 ("r-laeken" ,r-laeken)
5194 ("r-ranger" ,r-ranger)
5196 ("r-robustbase" ,r-robustbase)
5199 (home-page "https://github.com/alexkowa/VIM")
5200 (synopsis "Visualization and imputation of missing values")
5202 "This package provides tools for the visualization of missing and/or
5203 imputed values are introduced, which can be used for exploring the data and
5204 the structure of the missing and/or imputed values. Depending on this
5205 structure of the missing values, the corresponding methods may help to
5206 identify the mechanism generating the missing values and allows to explore the
5207 data including missing values. In addition, the quality of imputation can be
5208 visually explored using various univariate, bivariate, multiple and
5209 multivariate plot methods.")
5210 (license license:gpl2+)))
5212 (define-public r-fnn
5219 (uri (cran-uri "FNN" version))
5222 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
5223 (properties `((upstream-name . "FNN")))
5224 (build-system r-build-system)
5225 (home-page "https://cran.r-project.org/web/packages/FNN")
5226 (synopsis "Fast nearest neighbor search algorithms and applications")
5228 "This package provides cover-tree and kd-tree fast k-nearest neighbor
5229 search algorithms. Related applications including KNN classification,
5230 regression and information measures are implemented.")
5231 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
5232 ;; later can be used.
5233 (license license:gpl2+)))
5235 (define-public r-smoother
5242 (uri (cran-uri "smoother" version))
5245 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
5246 (build-system r-build-system)
5248 `(("r-ttr" ,r-ttr)))
5249 (home-page "http://cran.r-project.org/web/packages/smoother")
5250 (synopsis "Functions relating to the smoothing of numerical data")
5252 "This package provides a collection of methods for smoothing numerical
5253 data, commencing with a port of the Matlab gaussian window smoothing function.
5254 In addition, several functions typically used in smoothing of financial data
5256 (license license:gpl2)))
5258 (define-public r-riverplot
5260 (name "r-riverplot")
5265 (uri (cran-uri "riverplot" version))
5268 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
5269 (build-system r-build-system)
5270 (home-page "https://logfc.wordpress.com")
5271 (synopsis "Sankey or ribbon plots")
5273 "Sankey plots are a type of diagram that is convenient to illustrate how
5274 flow of information, resources etc. separates and joins, much like observing
5275 how rivers split and merge. For example, they can be used to compare
5276 different clusterings. This package provides an implementation of Sankey
5278 (license license:gpl2+)))
5280 (define-public r-dyn
5287 (uri (cran-uri "dyn" version))
5290 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
5291 (build-system r-build-system)
5293 `(("r-zoo" ,r-zoo)))
5294 (home-page "https://cran.r-project.org/web/packages/dyn")
5295 (synopsis "Time series regression")
5297 "This package provides the dyn class interfaces @code{ts}, @code{irts},
5298 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
5299 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
5300 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
5301 @code{randomForest::randomForest()} and other regression functions, allowing
5302 those functions to be used with time series including specifications that may
5303 contain lags, diffs and missing values.")
5305 (license license:gpl2+)))
5307 (define-public r-catdap
5314 (uri (cran-uri "catdap" version))
5317 "0i877l61f6c75pczi235rzci67w29zv1d7z5zn5p5ymndclvlpl2"))))
5318 (build-system r-build-system)
5320 `(("gfortran" ,gfortran)))
5321 (home-page "https://cran.r-project.org/web/packages/catdap/")
5322 (synopsis "Tools for categorical data analysis")
5324 "This package provides functions for analyzing multivariate data.
5325 Dependencies of the distribution of the specified variable (response
5326 variable) to other variables (explanatory variables) are derived and
5327 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
5328 (license license:gpl2+)))
5330 (define-public r-arules
5337 (uri (cran-uri "arules" version))
5340 "003c5cd3xzq39h7c19px077ygm0n1v7k83icy5zzrnkagyds2p8n"))))
5341 (build-system r-build-system)
5343 `(("r-matrix" ,r-matrix)))
5344 (home-page "https://github.com/mhahsler/arules")
5345 (synopsis "Mining association rules and frequent itemsets")
5347 "This package provides an infrastructure for representing, manipulating
5348 and analyzing transaction data and patterns (frequent itemsets and association rules).
5349 It also provides C implementations of the association mining algorithms Apriori
5351 (license license:gpl3)))
5353 (define-public r-parsedate
5355 (name "r-parsedate")
5360 (uri (cran-uri "parsedate" version))
5363 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
5364 (build-system r-build-system)
5366 `(("r-rematch2" ,r-rematch2)))
5367 (home-page "https://github.com/gaborcsardi/parsedate")
5369 "Recognize and parse dates in various formats")
5371 "This package provides three functions for dealing with dates:
5372 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
5373 time formats, @code{parse_date} parses dates in unspecified formats,
5374 and @code{format_iso_8601} formats a date in ISO 8601 format.")
5375 (license license:gpl2)))
5377 (define-public r-abc-data
5384 (uri (cran-uri "abc.data" version))
5387 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
5388 (properties `((upstream-name . "abc.data")))
5389 (build-system r-build-system)
5390 (home-page "https://cran.r-project.org/web/packages/abc.data/")
5391 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
5393 "This package contains data which are used by functions of the abc
5394 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
5395 algorithms for performing parameter estimation, model selection, and
5397 (license license:gpl3+)))
5399 (define-public r-abc
5406 (uri (cran-uri "abc" version))
5409 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
5410 (build-system r-build-system)
5412 `(("r-abc-data" ,r-abc-data)
5413 ("r-locfit" ,r-locfit)
5416 ("r-quantreg" ,r-quantreg)))
5417 (home-page "https://cran.r-project.org/web/packages/abc/")
5418 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
5420 "This package implements several @dfn{Approximate Bayesian
5421 Computation} (ABC) algorithms for performing parameter estimation, model
5422 selection, and goodness-of-fit. Cross-validation tools are also available for
5423 measuring the accuracy of ABC estimates, and to calculate the
5424 misclassification probabilities of different models.")
5425 (license license:gpl3+)))
5427 (define-public r-zip
5434 (uri (cran-uri "zip" version))
5437 "1c02amk3pl6xir5jnbfiwiv2wvpkpbkkb1w71y6lf2yk7g3d0pdb"))))
5438 (build-system r-build-system)
5439 (home-page "https://github.com/gaborcsardi/zip")
5440 (synopsis "Cross-platform Zip compression")
5442 "This package provides a cross-platform Zip compression library for R.
5443 It is a replacement for the @code{zip} function, that does not require any
5444 additional external tools on any platform.")
5445 (license license:cc0)))
5447 (define-public r-openxlsx
5454 (uri (cran-uri "openxlsx" version))
5457 "1mwxldw9i9nfksx1i6h1kfs7vmsz9fgyllbsipar4vnfyqhqp8q7"))))
5458 (build-system r-build-system)
5460 `(("r-rcpp" ,r-rcpp)
5461 ("r-stringi" ,r-stringi)
5463 (home-page "https://github.com/awalker89/openxlsx")
5464 (synopsis "Read, write and edit XLSX files")
5466 "This package simplifies the creation of Excel @code{.xlsx} files by
5467 providing a high level interface to writing, styling and editing worksheets.
5468 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
5469 and @code{XLConnect} packages with the added benefit of removing the
5470 dependency on Java.")
5471 (license license:gpl3)))
5473 (define-public r-rio
5480 (uri (cran-uri "rio" version))
5483 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
5484 (build-system r-build-system)
5486 `(("r-curl" ,r-curl)
5487 ("r-data-table" ,r-data-table)
5488 ("r-foreign" ,r-foreign)
5489 ("r-haven" ,r-haven)
5490 ("r-openxlsx" ,r-openxlsx)
5491 ("r-readxl" ,r-readxl)
5492 ("r-tibble" ,r-tibble)))
5493 (home-page "https://github.com/leeper/rio")
5494 (synopsis "Swiss-army knife for data I/O")
5496 "This package provides streamlined data import and export infrastructure
5497 by making assumptions that the user is probably willing to make: @code{import}
5498 and @code{export} determine the data structure from the file extension,
5499 reasonable defaults are used for data import and export (e.g.,
5500 @code{stringsAsFactors=FALSE}), web-based import is natively
5501 supported (including from SSL/HTTPS), compressed files can be read directly
5502 without explicit decompression, and fast import packages are used where
5503 appropriate. An additional convenience function, @code{convert}, provides a
5504 simple method for converting between file types.")
5505 (license license:gpl2)))
5507 (define-public r-maptools
5514 (uri (cran-uri "maptools" version))
5517 "0v4llkxk8qs61vq4ykvaim4k23aagdaz0p62ns7zfq02sln3pfk9"))))
5518 (build-system r-build-system)
5520 `(("r-foreign" ,r-foreign)
5521 ("r-lattice" ,r-lattice)
5523 (home-page "http://r-forge.r-project.org/projects/maptools/")
5524 (synopsis "Tools for reading and handling spatial objects")
5526 "This package provides a set of tools for manipulating and reading
5527 geographic data, in particular ESRI Shapefiles. It includes binary access to
5528 GSHHG shoreline files. The package also provides interface wrappers for
5529 exchanging spatial objects with other R packages.")
5530 ;; The C source files from shapelib are released under the Expat license.
5531 ;; The R code is released under GPL version 2 or later.
5532 (license (list license:gpl2+
5535 (define-public r-later
5542 (uri (cran-uri "later" version))
5545 "11xjavj7siz0xv2ffq1ld4bwl35jyrcfpvvs4p3ilpifxx49hyr7"))))
5546 (build-system r-build-system)
5550 ("r-rlang" ,r-rlang)))
5551 (home-page "https://github.com/r-lib/later")
5552 (synopsis "Utilities for delaying function execution")
5554 "This package provides tools to execute arbitrary R or C functions some
5555 time after the current time, after the R execution stack has emptied.")
5556 (license license:gpl2+)))
5558 (define-public r-promises
5565 (uri (cran-uri "promises" version))
5568 "01l0ydjvvy6afcg5d6pzvk1ikd3djq8n2flv8c831ksn68z0zsn8"))))
5569 (build-system r-build-system)
5571 `(("r-later" ,r-later)
5572 ("r-magrittr" ,r-magrittr)
5575 ("r-rlang" ,r-rlang)))
5576 (home-page "https://rstudio.github.io/promises")
5577 (synopsis "Abstractions for promise-based asynchronous programming")
5579 "This package provides fundamental abstractions for doing asynchronous
5580 programming in R using promises. Asynchronous programming is useful for
5581 allowing a single R process to orchestrate multiple tasks in the background
5582 while also attending to something else. Semantics are similar to JavaScript
5583 promises, but with a syntax that is idiomatic R.")
5584 (license license:expat)))
5586 (define-public r-dosnow
5593 (uri (cran-uri "doSNOW" version))
5596 "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh"))))
5597 (properties `((upstream-name . "doSNOW")))
5598 (build-system r-build-system)
5600 `(("r-foreach" ,r-foreach)
5601 ("r-iterators" ,r-iterators)
5602 ("r-snow" ,r-snow)))
5603 (home-page "https://cran.r-project.org/web/packages/doSNOW")
5604 (synopsis "Foreach parallel adaptor for the snow package")
5606 "This package provides a parallel backend for the @code{%dopar%} function
5607 using the @code{snow} package.")
5608 (license license:gpl2)))
5610 (define-public r-snowfall
5613 (version "1.84-6.1")
5616 (uri (cran-uri "snowfall" version))
5618 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
5619 (build-system r-build-system)
5621 `(("r-snow" ,r-snow)))
5622 (home-page "http://cran.r-project.org/web/packages/snowfall/")
5623 (synopsis "Easier cluster computing")
5624 (description "This package is a usability wrapper around snow for easier
5625 development of parallel R programs. This package offers e.g. extended error
5626 checks, and additional functions. All functions work in sequential mode, too,
5627 if no cluster is present or wished. The package is also designed as connector
5628 to the cluster management tool @code{sfCluster}, but can also used without
5630 (license license:gpl2+)))
5632 (define-public r-rappdirs
5639 (uri (cran-uri "rappdirs" version))
5642 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
5643 (build-system r-build-system)
5644 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
5645 (synopsis "Determine where to save data, caches, and logs")
5647 "This package provides an easy way to determine which directories on the
5648 user's computer should be used to save data, caches and logs. It is a port of
5649 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
5650 (license license:expat)))
5652 (define-public r-renv
5659 (uri (cran-uri "renv" version))
5662 "1jwnabryn77s29ybwdfzlnd7c8m05xmi69kp5qbvdxy2gjwjzcdr"))))
5663 (properties `((upstream-name . "renv")))
5664 (build-system r-build-system)
5665 (home-page "https://rstudio.github.io/renv")
5666 (synopsis "Project environments")
5668 "This package provides a dependency management toolkit for R. Using
5669 renv, you can create and manage project-local R libraries, save the state of
5670 these libraries to a lockfile, and later restore your library as required.
5671 Together, these tools can help make your projects more isolated, portable, and
5673 (license license:expat)))
5675 (define-public r-learnr
5682 (uri (cran-uri "learnr" version))
5685 "0278q9nbkc4nb0rp930kjrwyidf0v7y38d1s187m4f4bs7ha82k6"))))
5686 (build-system r-build-system)
5688 `(("r-checkmate" ,r-checkmate)
5689 ("r-ellipsis" ,r-ellipsis)
5690 ("r-evaluate" ,r-evaluate)
5691 ("r-htmltools" ,r-htmltools)
5692 ("r-htmlwidgets" ,r-htmlwidgets)
5693 ("r-jsonlite" ,r-jsonlite)
5694 ("r-knitr" ,r-knitr)
5695 ("r-markdown" ,r-markdown)
5696 ("r-rappdirs" ,r-rappdirs)
5698 ("r-rmarkdown" ,r-rmarkdown)
5699 ("r-rprojroot" ,r-rprojroot)
5700 ("r-shiny" ,r-shiny)
5701 ("r-withr" ,r-withr)))
5702 (home-page "https://rstudio.github.io/learnr/")
5703 (synopsis "Interactive tutorials for R")
5705 "This package provides tools to create interactive tutorials using R
5706 Markdown. Use a combination of narrative, figures, videos, exercises, and
5707 quizzes to create self-paced tutorials for learning about R and R packages.")
5708 (license license:asl2.0)))
5710 (define-public r-analytics
5712 (name "r-analytics")
5717 (uri (cran-uri "analytics" version))
5720 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
5721 (build-system r-build-system)
5724 ("r-cluster" ,r-cluster)
5725 ("r-fractal" ,r-fractal)
5726 ("r-lmtest" ,r-lmtest)
5729 ("r-powerplus" ,r-powerplus)
5730 ("r-robust" ,r-robust)
5731 ("r-trend" ,r-trend)
5735 (home-page "https://cran.r-project.org/web/packages/analytics/")
5736 (synopsis "Collection of data analysis tools")
5738 "This package is a collection of data analysis tools. It includes tools
5739 for regression outlier detection in a fitted linear model, stationary
5740 bootstrap using a truncated geometric distribution, a comprehensive test for
5741 weak stationarity, column means by group, weighted biplots, and a heuristic to
5742 obtain a better initial configuration in non-metric MDS.")
5743 (license license:gpl2)))
5745 (define-public r-reticulate
5747 (name "r-reticulate")
5752 (uri (cran-uri "reticulate" version))
5755 "0icb9zl9zlx75njv7y1dr450k0yw2n3q2jkr4nicnphdyfn69gkn"))))
5756 (build-system r-build-system)
5757 (inputs `(("python" ,python)))
5759 `(("r-rappdirs" ,r-rappdirs)
5760 ("r-jsonlite" ,r-jsonlite)
5761 ("r-matrix" ,r-matrix)
5762 ("r-rcpp" ,r-rcpp)))
5763 (home-page "https://github.com/rstudio/reticulate")
5764 (synopsis "R interface to Python")
5766 "This package provides an interface from R to Python modules, classes,
5767 and functions. When calling into Python, R data types are automatically
5768 converted to their equivalent Python types. When values are returned from
5769 Python to R they are converted back to R types.")
5770 (license license:asl2.0)))
5772 (define-public r-bibtex
5779 (uri (cran-uri "bibtex" version))
5782 "1ks1w59ldwmfd1sj8ap7smyhf8dhykv7xnwrl8z9xzkcfpv1rbc0"))))
5783 (build-system r-build-system)
5784 (propagated-inputs `(("r-stringr" ,r-stringr)))
5785 (home-page "https://github.com/romainfrancois/bibtex")
5786 (synopsis "Bibtex parser")
5787 (description "This package provides a utility for R to parse a bibtex
5789 (license license:gpl2+)))
5791 (define-public r-ggseqlogo
5793 (name "r-ggseqlogo")
5798 (uri (cran-uri "ggseqlogo" version))
5801 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
5802 (build-system r-build-system)
5803 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
5804 (home-page "https://github.com/omarwagih/ggseqlogo")
5805 (synopsis "ggplot2 extension for drawing genetic sequence logos")
5807 "The range of functions provided by this package makes it possible to
5808 draw highly versatile genomic sequence logos. Features include, but are not
5809 limited to, modifying colour schemes and fonts used to draw the logo,
5810 generating multiple logo plots, and aiding the visualisation with annotations.
5811 Sequence logos can easily be combined with other ggplot2 plots.")
5812 ;; Unspecified version of the LGPL.
5813 (license license:lgpl3+)))
5815 (define-public r-ggsci
5822 (uri (cran-uri "ggsci" version))
5825 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
5826 (build-system r-build-system)
5828 `(("r-ggplot2" ,r-ggplot2)
5829 ("r-scales" ,r-scales)))
5830 (home-page "https://nanx.me/ggsci/")
5831 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
5833 "This package provides a collection of ggplot2 color palettes inspired by
5834 plots in scientific journals, data visualization libraries, science fiction
5835 movies, and TV shows.")
5836 (license license:gpl3)))
5838 (define-public r-ggsignif
5845 (uri (cran-uri "ggsignif" version))
5848 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
5849 (build-system r-build-system)
5851 `(("r-ggplot2" ,r-ggplot2)))
5852 (home-page "https://github.com/const-ae/ggsignif")
5853 (synopsis "Significance brackets for ggplot2")
5855 "Enrich your ggplots with group-wise comparisons. This package provides
5856 an easy way to indicate if two groups are significantly different. Commonly
5857 this is shown by a bracket on top connecting the groups of interest which
5858 itself is annotated with the level of significance. The package provides a
5859 single layer that takes the groups for comparison and the test as arguments
5860 and adds the annotation to the plot.")
5861 (license license:gpl3)))
5863 (define-public r-ggpubr
5870 (uri (cran-uri "ggpubr" version))
5873 "0ln1gh3zlfx5s7zqcpvfdiksq74v1pma5kwkhc6r0riqnjjd19pf"))))
5874 (build-system r-build-system)
5876 `(("r-cowplot" ,r-cowplot)
5877 ("r-dplyr" ,r-dplyr)
5878 ("r-ggplot2" ,r-ggplot2)
5879 ("r-ggrepel" ,r-ggrepel)
5880 ("r-ggsci" ,r-ggsci)
5881 ("r-ggsignif" ,r-ggsignif)
5883 ("r-gridextra" ,r-gridextra)
5884 ("r-magrittr" ,r-magrittr)
5885 ("r-polynom" ,r-polynom)
5886 ("r-purrr" ,r-purrr)
5887 ("r-rlang" ,r-rlang)
5888 ("r-scales" ,r-scales)
5889 ("r-tidyr" ,r-tidyr)))
5890 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
5891 (synopsis "ggplot2-based publication-ready plots")
5893 "The ggplot2 package is an excellent and flexible package for elegant
5894 data visualization in R. However the default generated plots require some
5895 formatting before we can send them for publication. The ggpubr package
5896 provides some easy-to-use functions for creating and customizing ggplot2-based
5897 publication-ready plots.")
5898 (license license:gpl2)))
5900 (define-public r-ellipse
5907 (uri (cran-uri "ellipse" version))
5910 "0g82vc51m3c1k0hnpp2zla6amxxgk2mmkl8ssnsc49jv3599r6hs"))))
5911 (build-system r-build-system)
5912 (home-page "https://cran.r-project.org/web/packages/ellipse/")
5913 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
5915 "This package contains various routines for drawing ellipses and
5916 ellipse-like confidence regions, implementing the plots described in Murdoch
5917 and Chow (1996), A graphical display of large correlation matrices, The
5918 American Statistician 50, 178-180. There are also routines implementing the
5919 profile plots described in Bates and Watts (1988), Nonlinear Regression
5920 Analysis and its Applications.")
5921 (license license:gpl2+)))
5923 (define-public r-flashclust
5925 (name "r-flashclust")
5930 (uri (cran-uri "flashClust" version))
5933 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
5934 (properties `((upstream-name . "flashClust")))
5935 (build-system r-build-system)
5936 (native-inputs `(("gfortran" ,gfortran)))
5937 (home-page "https://cran.r-project.org/web/packages/flashClust/")
5938 (synopsis "Implementation of optimal hierarchical clustering")
5940 "This package provides a fast implementation of hierarchical
5942 (license license:gpl2+)))
5944 (define-public r-factominer
5946 (name "r-factominer")
5951 (uri (cran-uri "FactoMineR" version))
5954 "0qiw60ypf3bf5xsqz2b9l82i4jvprjm8lzpp12lhl8d9j5s8m0j8"))))
5955 (properties `((upstream-name . "FactoMineR")))
5956 (build-system r-build-system)
5959 ("r-cluster" ,r-cluster)
5960 ("r-ellipse" ,r-ellipse)
5961 ("r-flashclust" ,r-flashclust)
5962 ("r-ggplot2" ,r-ggplot2)
5963 ("r-ggrepel" ,r-ggrepel)
5964 ("r-lattice" ,r-lattice)
5965 ("r-leaps" ,r-leaps)
5967 ("r-scatterplot3d" ,r-scatterplot3d)))
5968 (home-page "http://factominer.free.fr")
5969 (synopsis "Multivariate exploratory data analysis and data mining")
5971 "This package provides exploratory data analysis methods to summarize,
5972 visualize and describe datasets. The main principal component methods are
5973 available, those with the largest potential in terms of applications:
5974 principal component analysis (PCA) when variables are quantitative,
5975 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
5976 variables are categorical, Multiple Factor Analysis when variables are
5977 structured in groups, etc. and hierarchical cluster analysis.")
5978 (license license:gpl2+)))
5980 (define-public r-factoextra
5982 (name "r-factoextra")
5987 (uri (cran-uri "factoextra" version))
5990 "0bpsbcmp6jpa9qk53dhfzghrz98dh0h0n68brl7rjz724yjbvhn8"))))
5991 (build-system r-build-system)
5993 `(("r-abind" ,r-abind)
5994 ("r-cluster" ,r-cluster)
5995 ("r-dendextend" ,r-dendextend)
5996 ("r-factominer" ,r-factominer)
5997 ("r-ggplot2" ,r-ggplot2)
5998 ("r-ggpubr" ,r-ggpubr)
5999 ("r-ggrepel" ,r-ggrepel)
6000 ("r-reshape2" ,r-reshape2)
6001 ("r-tidyr" ,r-tidyr)))
6002 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
6003 (synopsis "Extract and visualize the results of multivariate data analyses")
6005 "This package provides some easy-to-use functions to extract and
6006 visualize the output of multivariate data analyses, including
6007 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
6008 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
6009 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
6010 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
6011 packages. It contains also functions for simplifying some clustering analysis
6012 steps and provides ggplot2-based elegant data visualization.")
6013 (license license:gpl2)))
6015 (define-public r-fansi
6022 (uri (cran-uri "fansi" version))
6025 "02f2rx7v7wz6w97m2slwky2i5y8f9iafycmkyr3siy3z3k8fj171"))))
6026 (build-system r-build-system)
6028 `(("r-knitr" ,r-knitr))) ; for vignettes
6029 (home-page "https://github.com/brodieG/fansi")
6030 (synopsis "ANSI control sequence aware string functions")
6032 "This package provides counterparts to R string manipulation functions
6033 that account for the effects of ANSI text formatting control sequences.")
6034 (license license:gpl2+)))
6036 (define-public r-nbclust
6043 (uri (cran-uri "NbClust" version))
6046 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
6047 (properties `((upstream-name . "NbClust")))
6048 (build-system r-build-system)
6049 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
6050 (synopsis "Determine the best number of clusters in a data set")
6052 "NbClust provides 30 indexes for determining the optimal number of
6053 clusters in a data set and offers the best clustering scheme from different
6054 results to the user.")
6055 (license license:gpl2)))
6057 (define-public r-hdf5r
6064 (uri (cran-uri "hdf5r" version))
6067 "1pq12vkfqxvcaznwaxvjdg3acimk5a20m8h18sixvxc34vnqxw8f"))))
6068 (build-system r-build-system)
6073 `(("r-bit64" ,r-bit64)
6075 (home-page "https://hhoeflin.github.io/hdf5r")
6076 (synopsis "Interface to the HDF5 binary data format")
6078 "HDF5 is a data model, library and file format for storing and managing
6079 large amounts of data. This package provides a nearly feature complete,
6080 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
6081 functionality is added so that HDF5 objects behave very similar to their
6082 corresponding R counterparts.")
6083 (license license:asl2.0)))
6085 (define-public r-itertools
6087 (name "r-itertools")
6092 (uri (cran-uri "itertools" version))
6095 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
6096 (build-system r-build-system)
6098 `(("r-iterators" ,r-iterators)))
6099 (home-page "https://cran.r-project.org/web/packages/itertools/")
6100 (synopsis "Iterator tools")
6102 "This package provides various tools for creating iterators, many
6103 patterned after functions in the Python @code{itertools} module, and others
6104 patterned after functions in the snow package.")
6105 (license license:gpl2)))
6107 (define-public r-polynom
6114 (uri (cran-uri "polynom" version))
6117 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
6118 (build-system r-build-system)
6119 (home-page "https://cran.r-project.org/web/packages/polynom/")
6120 (synopsis "Functions for univariate polynomial manipulations")
6122 "This package provides a collection of functions to implement a class for
6123 univariate polynomial manipulations.")
6124 (license license:gpl2)))
6126 (define-public r-gbrd
6133 (uri (cran-uri "gbRd" version))
6136 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
6137 (properties `((upstream-name . "gbRd")))
6138 (build-system r-build-system)
6139 (home-page "https://cran.r-project.org/web/packages/gbRd/")
6140 (synopsis "Utilities for processing Rd objects and files")
6142 "This package provides utilities for processing Rd objects and files.
6143 Extract argument descriptions and other parts of the help pages of
6145 (license license:gpl2+)))
6147 (define-public r-rjags
6154 (uri (cran-uri "rjags" version))
6157 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
6158 (build-system r-build-system)
6160 `(("r-coda" ,r-coda)))
6164 `(("pkg-config" ,pkg-config)))
6165 (home-page "http://mcmc-jags.sourceforge.net")
6166 (synopsis "Bayesian graphical models using MCMC")
6168 "This package provides an R interface to the JAGS MCMC library. JAGS is
6169 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
6170 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
6171 (license license:gpl2)))
6173 (define-public r-rdpack
6180 (uri (cran-uri "Rdpack" version))
6183 "080y15p2hl4jsq91ak2f1y2kx1iqq5c5wzyx3zyhjwp01cahy0jq"))))
6184 (properties `((upstream-name . "Rdpack")))
6185 (build-system r-build-system)
6187 `(("r-bibtex" ,r-bibtex)
6188 ("r-gbrd" ,r-gbrd)))
6189 (home-page "https://github.com/GeoBosh/Rdpack")
6190 (synopsis "Update and manipulate Rd documentation objects")
6192 "This package provides functions for manipulation of R documentation
6193 objects, including functions @code{reprompt()} and @code{ereprompt()} for
6194 updating Rd documentation for functions, methods and classes; it also includes
6195 Rd macros for citations and import of references from bibtex files for use in
6196 Rd files and roxygen2 comments, as well as many functions for manipulation of
6197 references and Rd files.")
6198 (license license:gpl2+)))
6200 (define-public r-officer
6207 (uri (cran-uri "officer" version))
6210 "1i6jmnbkx7gd0qyf6akhizmxp7y1dh3h7a886mcbmrzka9d60zh4"))))
6211 (build-system r-build-system)
6213 `(("r-base64enc" ,r-base64enc)
6214 ("r-digest" ,r-digest)
6215 ("r-htmltools" ,r-htmltools)
6216 ("r-magrittr" ,r-magrittr)
6219 ("r-rlang" ,r-rlang)
6223 (home-page "https://davidgohel.github.io/officer")
6224 (synopsis "Manipulation of Word and PowerPoint documents")
6226 "This package provides tools to access and manipulate Word and PowerPoint
6227 documents from R. The package focuses on tabular and graphical reporting from
6228 R; it also provides two functions that let users get document content into
6229 data objects. A set of functions lets add and remove images, tables and
6230 paragraphs of text in new or existing documents. When working with PowerPoint
6231 presentations, slides can be added or removed; shapes inside slides can also
6232 be added or removed. When working with Word documents, a cursor can be used
6233 to help insert or delete content at a specific location in the document.")
6234 (license license:gpl3)))
6236 (define-public r-abn
6243 (uri (cran-uri "abn" version))
6246 "19w6bdjyp4zwqs6p0flry4qxqynf9rh8ykdrfrp61wrdf7kysw0d"))))
6247 (build-system r-build-system)
6251 `(("r-lme4" ,r-lme4)
6255 ("r-rcpparmadillo" ,r-rcpparmadillo)
6256 ("r-rjags" ,r-rjags)))
6257 (home-page "http://www.r-bayesian-networks.org")
6258 (synopsis "Modelling multivariate data with additive bayesian networks")
6260 "Bayesian network analysis is a form of probabilistic graphical models
6261 which derives from empirical data a directed acyclic graph, DAG, describing
6262 the dependency structure between random variables. An additive Bayesian
6263 network model consists of a form of a DAG where each node comprises a
6264 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
6265 equivalent to Bayesian multivariate regression using graphical modelling, they
6266 generalises the usual multivariable regression, GLM, to multiple dependent
6267 variables. This package provides routines to help determine optimal Bayesian
6268 network models for a given data set, where these models are used to identify
6269 statistical dependencies in messy, complex data.")
6270 (license license:gpl2+)))
6272 (define-public r-acd
6279 (uri (cran-uri "ACD" version))
6282 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
6283 (properties `((upstream-name . "ACD")))
6284 (build-system r-build-system)
6285 (home-page "https://cran.r-project.org/web/packages/ACD/")
6286 (synopsis "Categorical data analysis with complete or missing responses")
6288 "This package provides tools for categorical data analysis with complete
6289 or missing responses.")
6290 (license license:gpl2+)))
6292 (define-public r-acdm
6299 (uri (cran-uri "ACDm" version))
6302 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
6303 (properties `((upstream-name . "ACDm")))
6304 (build-system r-build-system)
6306 `(("r-dplyr" ,r-dplyr)
6307 ("r-ggplot2" ,r-ggplot2)
6309 ("r-rsolnp" ,r-rsolnp)
6311 (home-page "https://cran.r-project.org/web/packages/ACDm/")
6312 (synopsis "Tools for Autoregressive Conditional Duration Models")
6314 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
6315 and Russell, 1998) models. It creates trade, price or volume durations from
6316 transactions (tic) data, performs diurnal adjustments, fits various ACD models
6318 (license license:gpl2+)))
6320 (define-public r-overlap
6327 (uri (cran-uri "overlap" version))
6330 "1j3m6ir1chdz0si2fhcw6gs7c9h09bv0chz18rpzxsywww6d4rzy"))))
6331 (build-system r-build-system)
6332 (home-page "https://cran.r-project.org/web/packages/overlap/")
6333 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
6335 "This package provides functions to fit kernel density functions to data
6336 on temporal activity patterns of animals; estimate coefficients of overlapping
6337 of densities for two species; and calculate bootstrap estimates of confidence
6339 (license license:gpl3+)))
6341 (define-public r-snakecase
6343 (name "r-snakecase")
6348 (uri (cran-uri "snakecase" version))
6351 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
6352 (build-system r-build-system)
6354 `(("r-stringi" ,r-stringi)
6355 ("r-stringr" ,r-stringr)))
6356 (home-page "https://github.com/Tazinho/snakecase")
6357 (synopsis "Convert strings into any case")
6359 "This package provides a consistent, flexible and easy to use tool to
6360 parse and convert strings into cases like snake or camel among others.")
6361 (license license:gpl3)))
6363 (define-public r-prediction
6365 (name "r-prediction")
6370 (uri (cran-uri "prediction" version))
6373 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
6374 (build-system r-build-system)
6376 `(("r-data-table" ,r-data-table)))
6377 (home-page "https://github.com/leeper/prediction")
6378 (synopsis "Tidy, type-safe prediction methods")
6380 "This package provides the @code{prediction()} function, a type-safe
6381 alternative to @code{predict()} that always returns a data frame. The package
6382 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
6383 from the @code{stats} package, as well as numerous other model classes from
6384 other add-on packages.")
6385 (license license:expat)))
6387 (define-public r-insight
6394 (uri (cran-uri "insight" version))
6397 "0scjmr8qvwaswb9wfq2lxp1v5fl72way8cid9agrf0z1agp0adad"))))
6398 (build-system r-build-system)
6399 (home-page "https://easystats.github.io/insight/")
6400 (synopsis "Easy access to model information for various model objects")
6402 "This package provides a tool to provide an easy, intuitive and
6403 consistent access to information contained in various R models, like model
6404 formulas, model terms, information about random effects, data that was used to
6405 fit the model or data from response variables. The package mainly revolves
6406 around two types of functions: Functions that find (the names of) information,
6407 starting with @code{find_}, and functions that get the underlying data,
6408 starting with @code{get_}. The package has a consistent syntax and works with
6409 many different model objects, where otherwise functions to access these
6410 information are missing.")
6411 (license license:gpl3)))
6413 (define-public r-sjlabelled
6415 (name "r-sjlabelled")
6420 (uri (cran-uri "sjlabelled" version))
6423 "0c9wy0gsr2sbkrv2638xbi7qm0gl6jyr6sfricavhkm7l4hljjkz"))))
6424 (build-system r-build-system)
6426 `(("r-haven" ,r-haven)
6427 ("r-insight" ,r-insight)
6428 ("r-magrittr" ,r-magrittr)
6429 ("r-purrr" ,r-purrr)
6430 ("r-rlang" ,r-rlang)
6431 ("r-tidyselect" ,r-tidyselect)))
6432 (home-page "https://github.com/strengejacke/sjlabelled")
6433 (synopsis "Labelled data utility functions")
6435 "This package provides a collection of functions dealing with labelled
6436 data, like reading and writing data between R and other statistical software
6437 packages. This includes easy ways to get, set or change value and variable
6438 label attributes, to convert labelled vectors into factors or numeric (and
6439 vice versa), or to deal with multiple declared missing values.")
6440 (license license:gpl3)))
6442 (define-public r-sjmisc
6449 (uri (cran-uri "sjmisc" version))
6452 "0rl0bmk91wc4dxdgy008fl0dwkx3ffvys30vgpnr78lb4pk45nb2"))))
6453 (build-system r-build-system)
6455 `(("r-dplyr" ,r-dplyr)
6456 ("r-insight" ,r-insight)
6457 ("r-magrittr" ,r-magrittr)
6458 ("r-purrr" ,r-purrr)
6459 ("r-rlang" ,r-rlang)
6460 ("r-sjlabelled" ,r-sjlabelled)
6461 ("r-tidyselect" ,r-tidyselect)))
6462 (home-page "https://github.com/strengejacke/sjmisc")
6463 (synopsis "Data and variable transformation functions")
6465 "This package is a collection of miscellaneous utility functions,
6466 supporting data transformation tasks like recoding, dichotomizing or grouping
6467 variables, setting and replacing missing values. The data transformation
6468 functions also support labelled data, and all integrate seamlessly into a
6469 tidyverse workflow.")
6470 (license license:gpl3)))
6472 (define-public r-nortest
6479 (uri (cran-uri "nortest" version))
6482 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
6483 (build-system r-build-system)
6484 (home-page "https://cran.r-project.org/web/packages/nortest/")
6485 (synopsis "Tests for normality")
6487 "This package provides five omnibus tests for testing the composite
6488 hypothesis of normality.")
6489 (license license:gpl2+)))
6491 (define-public r-moonbook
6498 (uri (cran-uri "moonBook" version))
6501 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
6502 (properties `((upstream-name . "moonBook")))
6503 (build-system r-build-system)
6505 `(("r-magrittr" ,r-magrittr)
6506 ("r-nortest" ,r-nortest)
6507 ("r-purrr" ,r-purrr)
6508 ("r-sjmisc" ,r-sjmisc)
6509 ("r-stringr" ,r-stringr)
6510 ("r-survival" ,r-survival)))
6511 (home-page "https://github.com/cardiomoon/moonBook")
6512 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
6514 "This package provides several analysis-related functions for the book
6515 entitled \"R statistics and graph for medical articles\" (written in Korean),
6516 version 1, by Keon-Woong Moon with Korean demographic data with several plot
6518 (license license:gpl2)))
6520 (define-public r-flextable
6522 (name "r-flextable")
6527 (uri (cran-uri "flextable" version))
6530 "1f869f2dfqkzhf6yix7xcbs8rn1nwq3sg623h74zg6h1pl6px66w"))))
6531 (build-system r-build-system)
6533 `(("r-base64enc" ,r-base64enc)
6534 ("r-data-table" ,r-data-table)
6535 ("r-gdtools" ,r-gdtools)
6536 ("r-htmltools" ,r-htmltools)
6537 ("r-knitr" ,r-knitr)
6538 ("r-officer" ,r-officer)
6539 ("r-rlang" ,r-rlang)
6540 ("r-rmarkdown" ,r-rmarkdown)
6541 ("r-xml2" ,r-xml2)))
6542 (home-page "https://davidgohel.github.io/flextable")
6543 (synopsis "Functions for tabular reporting")
6545 "This package provides tools to create pretty tables for HTML documents
6546 and other formats. Functions are provided to let users create tables, modify
6547 and format their content. It extends the @code{officer} package and can be
6548 used within R markdown documents when rendering to HTML and to Word
6550 (license license:gpl3)))
6552 (define-public r-writexl
6559 (uri (cran-uri "writexl" version))
6562 "09fhdip6igcg97fjx4c7727cx2lb49l4d74l4i8rg2bag2s5lrj3"))))
6563 (build-system r-build-system)
6564 (inputs `(("zlib" ,zlib)))
6565 (home-page "https://github.com/ropensci/writexl")
6566 (synopsis "Export data frames to xlsx format")
6568 "This package provides a data frame to xlsx exporter based on
6570 (license license:bsd-2)))
6572 (define-public r-biasedurn
6574 (name "r-biasedurn")
6579 (uri (cran-uri "BiasedUrn" version))
6582 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
6583 (properties `((upstream-name . "BiasedUrn")))
6584 (build-system r-build-system)
6585 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
6586 (synopsis "Biased Urn model distributions")
6588 "This package provides statistical models of biased sampling in the form
6589 of univariate and multivariate noncentral hypergeometric distributions,
6590 including Wallenius' noncentral hypergeometric distribution and Fisher's
6591 noncentral hypergeometric distribution (also called extended hypergeometric
6593 (license license:gpl3)))
6595 (define-public r-goplot
6602 (uri (cran-uri "GOplot" version))
6605 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
6606 (properties `((upstream-name . "GOplot")))
6607 (build-system r-build-system)
6609 `(("r-ggdendro" ,r-ggdendro)
6610 ("r-ggplot2" ,r-ggplot2)
6611 ("r-gridextra" ,r-gridextra)
6612 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6613 (home-page "https://github.com/wencke/wencke.github.io")
6614 (synopsis "Visualization of functional analysis data")
6616 "This package provides an implementation of multilayered visualizations
6617 for enhanced graphical representation of functional analysis data. It
6618 combines and integrates omics data derived from expression and functional
6619 annotation enrichment analyses. Its plotting functions have been developed
6620 with an hierarchical structure in mind: starting from a general overview to
6621 identify the most enriched categories (modified bar plot, bubble plot) to a
6622 more detailed one displaying different types of relevant information for the
6623 molecules in a given set of categories (circle plot, chord plot, cluster plot,
6624 Venn diagram, heatmap).")
6625 (license license:gpl2)))
6627 (define-public r-getopt
6634 (uri (cran-uri "getopt" version))
6637 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
6638 (build-system r-build-system)
6639 (home-page "https://github.com/trevorld/getopt")
6640 (synopsis "Command-line option processor for R")
6642 "This package is designed to be used with Rscript to write shebang
6643 scripts that accept short and long options. Many users will prefer to
6644 use the packages @code{optparse} or @code{argparse} which add extra
6645 features like automatically generated help options and usage texts,
6646 support for default values, positional argument support, etc.")
6647 (license license:gpl2+)))
6649 (define-public r-findpython
6651 (name "r-findpython")
6656 (uri (cran-uri "findpython" version))
6659 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
6660 (build-system r-build-system)
6661 (home-page "https://github.com/trevorld/findpython")
6662 (synopsis "Functions to find an acceptable Python binary")
6664 "This package was designed to find an acceptable Python binary that
6665 matches version and feature constraints.")
6666 (license license:expat)))
6668 ;; This in not the same as "r-argparser"
6669 (define-public r-argparse
6676 (uri (cran-uri "argparse" version))
6679 "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l"))))
6680 (build-system r-build-system)
6681 (inputs `(("python" ,python)))
6683 `(("r-findpython" ,r-findpython)
6684 ("r-jsonlite" ,r-jsonlite)
6686 (home-page "https://github.com/trevorld/argparse")
6687 (synopsis "Command line optional and positional argument parser")
6689 "This package provides a command line parser to be used with Rscript to
6690 write shebang scripts that gracefully accept positional and optional arguments
6691 and automatically generate usage notices.")
6692 (license license:gpl2+)))
6694 (define-public r-hash
6701 (uri (cran-uri "hash" version))
6704 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
6705 (build-system r-build-system)
6706 (home-page "https://cran.r-project.org/web/packages/hash/")
6707 (synopsis "Implementation of hash/associated arrays/dictionaries")
6709 "This package implements a data structure similar to hashes in Perl and
6710 dictionaries in Python but with a purposefully R flavor. For objects of
6711 appreciable size, access using hashes outperforms native named lists and
6713 (license license:gpl2+)))
6715 (define-public r-orddom
6722 (uri (cran-uri "orddom" version))
6725 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
6726 (build-system r-build-system)
6727 (propagated-inputs `(("r-psych" ,r-psych)))
6728 (home-page "https://cran.r-project.org/web/packages/orddom/")
6729 (synopsis "Ordinal dominance statistics")
6731 "This package provides tools to compute ordinal, statistics and effect
6732 sizes as an alternative to mean comparison: Cliff's delta or success rate
6733 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
6734 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
6735 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
6736 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
6737 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
6738 Group (Non-)Overlap considerations.")
6739 (license license:gpl2)))
6741 (define-public r-deriv
6748 (uri (cran-uri "Deriv" version))
6751 "03mlfy8jzzzbh2l18gnmw0a71n9savx4cw72yhkxq93v2xj8fy3n"))))
6752 (properties `((upstream-name . "Deriv")))
6753 (build-system r-build-system)
6754 (home-page "https://cran.r-project.org/web/packages/Deriv")
6755 (synopsis "Symbolic differentiation")
6757 "This package provides an R-based solution for symbolic differentiation.
6758 It admits user-defined functions as well as function substitution in arguments
6759 of functions to be differentiated. Some symbolic simplification is part of
6761 (license license:gpl3+)))
6763 (define-public r-doby
6770 (uri (cran-uri "doBy" version))
6773 "1d0d6pwai1g4i5jls0jm9va29ci5hy92n5957608f3fzi1jwy635"))))
6774 (properties `((upstream-name . "doBy")))
6775 (build-system r-build-system)
6777 `(("r-broom" ,r-broom)
6778 ("r-deriv" ,r-deriv)
6779 ("r-dplyr" ,r-dplyr)
6780 ("r-magrittr" ,r-magrittr)
6782 ("r-matrix" ,r-matrix)
6784 ("r-pbkrtest" ,r-pbkrtest)
6785 ("r-tibble" ,r-tibble)))
6786 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
6787 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
6789 "This package contains:
6792 @item facilities for working with grouped data: @code{do}
6793 something to data stratified @code{by} some variables.
6794 @item implementations of least-squares means, general linear contrasts, and
6795 @item miscellaneous other utilities.
6797 (license license:gpl2+)))
6799 (define-public r-refgenome
6801 (name "r-refgenome")
6806 (uri (cran-uri "refGenome" version))
6809 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
6810 (properties `((upstream-name . "refGenome")))
6811 (build-system r-build-system)
6815 ("r-rsqlite" ,r-rsqlite)))
6816 (home-page "https://cran.r-project.org/web/packages/refGenome/")
6818 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
6820 "This package contains functionality for importing and managing of
6821 downloaded genome annotation data from the Ensembl genome browser (European
6822 Bioinformatics Institute) and from the UCSC genome browser (University of
6823 California, Santa Cruz) and annotation routines for genomic positions and
6824 splice site positions.")
6825 (license license:gpl2)))
6827 (define-public r-basix
6834 (uri (cran-uri "BASIX" version))
6837 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
6838 (properties `((upstream-name . "BASIX")))
6839 (build-system r-build-system)
6840 (home-page "https://cran.r-project.org/web/packages/BASIX/")
6841 (synopsis "Efficient C/C++ toolset for R")
6843 "BASIX provides some efficient C/C++ implementations of native R
6844 procedures to speed up calculations in R.")
6845 (license license:gpl2)))
6847 (define-public r-blockfest
6849 (name "r-blockfest")
6854 (uri (cran-uri "BlockFeST" version))
6857 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
6858 (properties `((upstream-name . "BlockFeST")))
6859 (build-system r-build-system)
6860 (propagated-inputs `(("r-basix" ,r-basix)))
6861 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
6862 (synopsis "Bayesian calculation of region-specific fixation index")
6864 "This package provides an R implementation of an extension of the
6865 BayeScan software for codominant markers, adding the option to group
6866 individual SNPs into pre-defined blocks. A typical application of this new
6867 approach is the identification of genomic regions, genes, or gene sets
6868 containing one or more SNPs that evolved under directional selection.")
6869 (license license:gpl2)))
6871 (define-public r-proc
6878 (uri (cran-uri "pROC" version))
6881 "1jx8af9p6sxbypqvj1cci7q9sbyaw310inbjxibjcr3acj59h45h"))))
6882 (properties `((upstream-name . "pROC")))
6883 (build-system r-build-system)
6885 `(("r-plyr" ,r-plyr)
6886 ("r-rcpp" ,r-rcpp)))
6887 (home-page "http://expasy.org/tools/pROC/")
6888 (synopsis "Display and analyze ROC curves")
6890 "This package provides tools for visualizing, smoothing and comparing
6891 receiver operating characteristic (ROC curves). The area under the
6892 curve (AUC) can be compared with statistical tests based on U-statistics or
6893 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
6894 (license license:gpl3+)))
6896 (define-public r-rootsolve
6898 (name "r-rootsolve")
6903 (uri (cran-uri "rootSolve" version))
6906 "0rj7c4zcrzgz7sb0vgvh7swpfafnw4040cxp7ypas3s8fnihn54l"))))
6907 (properties `((upstream-name . "rootSolve")))
6908 (build-system r-build-system)
6909 (native-inputs `(("gfortran" ,gfortran)))
6910 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
6911 (synopsis "Tools for the analysis of ordinary differential equations")
6913 "This package provides routines to find the root of nonlinear functions,
6914 and to perform steady-state and equilibrium analysis of @dfn{ordinary
6915 differential equations} (ODE). It includes routines that:
6918 @item generate gradient and jacobian matrices (full and banded),
6919 @item find roots of non-linear equations by the Newton-Raphson method,
6920 @item estimate steady-state conditions of a system of (differential) equations
6921 in full, banded or sparse form, using the Newton-Raphson method, or by
6922 dynamically running,
6923 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
6924 and 3-D partial differential equations, that have been converted to ordinary
6925 differential equations by numerical differencing (using the method-of-lines
6928 (license license:gpl2+)))
6930 (define-public r-abcanalysis
6932 (name "r-abcanalysis")
6937 (uri (cran-uri "ABCanalysis" version))
6939 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
6940 (properties `((upstream-name . "ABCanalysis")))
6941 (build-system r-build-system)
6942 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
6943 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
6944 (synopsis "Computed ABC Analysis")
6946 "Multivariate data sets often differ in several factors or derived statistical
6947 parameters, which have to be selected for a valid interpretation. Basing this
6948 selection on traditional statistical limits leads occasionally to the perception
6949 of losing information from a data set. This package provides tools to calculate
6950 these limits on the basis of the mathematical properties of the distribution of
6951 the analyzed items.")
6952 (license license:gpl3)))
6954 (define-public r-slam
6961 (uri (cran-uri "slam" version))
6963 (base32 "12fggw2c7hz3bpvsaqm24g3r6lbpq6jgli24g7x5j859iak5cqv9"))))
6964 (build-system r-build-system)
6965 (home-page "https://cran.r-project.org/web/packages/slam/")
6966 (synopsis "Sparse lightweight arrays and matrices")
6968 "This package contains data structures and algorithms for sparse arrays and matrices,
6969 based on index arrays and simple triplet representations, respectively.")
6970 (license license:gpl2)))
6972 (define-public r-manipulatewidget
6974 (name "r-manipulatewidget")
6979 (uri (cran-uri "manipulateWidget" version))
6981 (base32 "1zagrbwkn2d50zzw8i2vyb1hsq4cydmfsqiy1a2qlp6zrv8a6q9x"))))
6983 `((upstream-name . "manipulateWidget")))
6984 (build-system r-build-system)
6986 `(("r-base64enc" ,r-base64enc)
6987 ("r-codetools" ,r-codetools)
6988 ("r-htmltools" ,r-htmltools)
6989 ("r-htmlwidgets" ,r-htmlwidgets)
6990 ("r-knitr" ,r-knitr)
6991 ("r-miniui" ,r-miniui)
6992 ("r-shiny" ,r-shiny)
6993 ("r-webshot" ,r-webshot)))
6994 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
6995 (synopsis "Add even more interactivity to interactive charts")
6997 "This package lets you create in just a few lines of R code a nice user interface to
6998 modify the data or the graphical parameters of one or multiple interactive
6999 charts. It is useful to quickly explore visually some data or for package
7000 developers to generate user interfaces easy to maintain.")
7001 (license license:gpl2+)))
7010 (uri (cran-uri "A3" version))
7012 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
7013 (properties `((upstream-name . "A3")))
7014 (build-system r-build-system)
7016 `(("r-pbapply" ,r-pbapply)
7017 ("r-xtable" ,r-xtable)))
7018 (home-page "https://cran.r-project.org/web/packages/A3/")
7019 (synopsis "Error metrics for predictive models")
7021 "This package supplies tools for tabulating and analyzing the results of predictive
7022 models. The methods employed are applicable to virtually any predictive model
7023 and make comparisons between different methodologies straightforward.")
7024 (license license:gpl2+)))
7026 (define-public r-infotheo
7033 (uri (cran-uri "infotheo" version))
7036 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
7037 (build-system r-build-system)
7038 (home-page "http://homepage.meyerp.com/software")
7039 (synopsis "Information-theoretic measures")
7041 "This package implements various measures of information theory based on
7042 several entropy estimators.")
7043 (license license:gpl3+)))
7045 (define-public r-abcoptim
7052 (uri (cran-uri "ABCoptim" version))
7054 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
7055 (properties `((upstream-name . "ABCoptim")))
7056 (build-system r-build-system)
7057 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
7058 (home-page "https://github.com/gvegayon/ABCoptim/")
7059 (synopsis "Optimization of Artificial Bee Colony algorithm")
7061 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
7062 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
7063 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
7064 algorithms, and uses only common control parameters such as colony size and
7065 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
7066 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
7067 This version is a work-in-progress and is written in R code.")
7068 (license license:expat)))
7070 (define-public r-abcp2
7077 (uri (cran-uri "ABCp2" version))
7079 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
7080 (properties `((upstream-name . "ABCp2")))
7081 (build-system r-build-system)
7082 (propagated-inputs `(("r-mass" ,r-mass)))
7083 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
7084 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
7086 "This package tests the goodness of fit of a distribution of offspring to the Normal,
7087 Poisson, and Gamma distribution and estimates the proportional paternity of the
7088 second male (P2) based on the best fit distribution.")
7089 (license license:gpl2)))
7091 (define-public r-abcrf
7098 (uri (cran-uri "abcrf" version))
7100 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
7101 (build-system r-build-system)
7103 `(("r-doparallel" ,r-doparallel)
7104 ("r-foreach" ,r-foreach)
7106 ("r-matrixstats" ,r-matrixstats)
7107 ("r-ranger" ,r-ranger)
7109 ("r-rcpparmadillo" ,r-rcpparmadillo)
7110 ("r-readr" ,r-readr)
7111 ("r-stringr" ,r-stringr)))
7112 (home-page "https://cran.r-project.org/web/packages/abcrf/")
7113 (synopsis "Approximate bayesian computation via random forests")
7115 "This package performs approximate bayesian computation (ABC) model choice and
7116 parameter inference via random forests. This machine learning tool named random
7117 forests (RF) can conduct selection among the highly complex models covered by
7119 (license license:gpl2+)))
7121 (define-public r-abctools
7128 (uri (cran-uri "abctools" version))
7130 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
7131 (build-system r-build-system)
7134 ("r-abind" ,r-abind)
7135 ("r-hmisc" ,r-hmisc)
7136 ("r-plyr" ,r-plyr)))
7137 (home-page "https://github.com/dennisprangle/abctools/")
7138 (synopsis "Tools for ABC analyses")
7140 "This @code{r-abctools} package provides tools for approximate Bayesian computation
7141 including summary statistic selection and assessing coverage. This includes
7142 recent dimension reduction algorithms to tune the choice of summary statistics,
7143 and coverage methods to tune the choice of threshold.")
7144 (license license:gpl2+)))
7146 (define-public r-ggstance
7153 (uri (cran-uri "ggstance" version))
7155 (base32 "0kdksay61hyb6612b07r84chh7a9aibjyclk3qcypvr9aang8hkh"))))
7156 (build-system r-build-system)
7158 `(("r-ggplot2" ,r-ggplot2)
7160 ("r-rlang" ,r-rlang)
7161 ("r-withr" ,r-withr)))
7162 (home-page "https://cran.r-project.org/web/packages/ggstance/")
7163 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
7165 "This package is a @code{r-ggplot2} extension that provides flipped components:
7167 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
7168 @item vertical versions of @code{r-ggplot2} positions.
7170 (license license:gpl3)))
7172 (define-public r-mosaiccore
7174 (name "r-mosaiccore")
7179 (uri (cran-uri "mosaicCore" version))
7181 (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
7182 (properties `((upstream-name . "mosaicCore")))
7183 (build-system r-build-system)
7185 `(("r-dplyr" ,r-dplyr)
7186 ("r-lazyeval" ,r-lazyeval)
7188 ("r-rlang" ,r-rlang)
7189 ("r-tidyr" ,r-tidyr)))
7190 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
7191 (synopsis "Common utilities for mosaic family packages")
7193 "Common utilities used in other Mosaic family packages are collected here.")
7194 (license license:gpl2+)))
7196 (define-public r-ggformula
7198 (name "r-ggformula")
7203 (uri (cran-uri "ggformula" version))
7205 (base32 "16ycabhnp78fsiv1dc63ccgh9gmpsy2683vbmq0fdzl6w3pd87sr"))))
7206 (build-system r-build-system)
7208 `(("r-ggplot2" ,r-ggplot2)
7209 ("r-ggstance" ,r-ggstance)
7210 ("r-magrittr" ,r-magrittr)
7211 ("r-mosaiccore" ,r-mosaiccore)
7212 ("r-rlang" ,r-rlang)
7213 ("r-stringr" ,r-stringr)
7214 ("r-tibble" ,r-tibble)
7215 ("r-tidyr" ,r-tidyr)))
7216 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
7217 (synopsis "Formula interface for the @code{r-ggplot2}")
7219 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
7220 gf_density(), and so on, bring the formula interface to ggplot(). This captures
7221 and extends the excellent simplicity of the lattice-graphics formula interface,
7222 while providing the intuitive capabilities of @code{r-ggplot2}.")
7223 (license license:expat)))
7225 (define-public r-mosaicdata
7227 (name "r-mosaicdata")
7232 (uri (cran-uri "mosaicData" version))
7234 (base32 "04z0mdm52mykqsxsinhmsihn181zf6cw321gayk2rjp7lj7mwdq9"))))
7235 (properties `((upstream-name . "mosaicData")))
7236 (build-system r-build-system)
7237 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
7238 (synopsis "Data sets for project Mosaic")
7240 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
7241 used to teach mathematics, statistics, computation and modeling.")
7242 (license license:gpl2+)))
7244 (define-public r-raster
7251 (uri (cran-uri "raster" version))
7254 "0faxv71hlxkblvbi3ps1vfzm3wwi0brwzmpsr5114bddcqyiqkvn"))))
7255 (build-system r-build-system)
7257 `(("r-rcpp" ,r-rcpp)
7259 (home-page "https://www.rspatial.org/")
7260 (synopsis "Geographic data analysis and modeling")
7262 "The package implements basic and high-level functions for reading,
7263 writing, manipulating, analyzing and modeling of gridded spatial data.
7264 Processing of very large files is supported.")
7265 (license license:gpl3+)))
7267 (define-public r-mosaic
7274 (uri (cran-uri "mosaic" version))
7276 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
7277 (build-system r-build-system)
7279 `(("r-broom" ,r-broom)
7280 ("r-dplyr" ,r-dplyr)
7281 ("r-ggdendro" ,r-ggdendro)
7282 ("r-ggformula" ,r-ggformula)
7283 ("r-ggplot2" ,r-ggplot2)
7284 ("r-ggrepel" ,r-ggrepel)
7286 ("r-gridextra" ,r-gridextra)
7287 ("r-lattice" ,r-lattice)
7288 ("r-latticeextra" ,r-latticeextra)
7289 ("r-lazyeval" ,r-lazyeval)
7291 ("r-matrix" ,r-matrix)
7292 ("r-mosaiccore" ,r-mosaiccore)
7293 ("r-mosaicdata" ,r-mosaicdata)
7294 ("r-readr" ,r-readr)
7295 ("r-tidyr" ,r-tidyr)))
7296 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
7297 (synopsis "Mathematics, statistics, and computation teaching utilities")
7299 "This package contain data sets and utilities from
7300 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
7301 statistics, computation and modeling. Project MOSAIC is a community of
7302 educators working to tie together aspects of quantitative work that students
7303 in science, technology, engineering and mathematics will need in their
7304 professional lives, but which are usually taught in isolation, if at all.")
7305 (license license:gpl2+)))
7307 (define-public r-abd
7314 (uri (cran-uri "abd" version))
7316 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
7317 (build-system r-build-system)
7319 `(("r-lattice" ,r-lattice)
7320 ("r-mosaic" ,r-mosaic)
7321 ("r-nlme" ,r-nlme)))
7322 (home-page "https://cran.r-project.org/web/packages/abd/")
7323 (synopsis "Analysis of biological data")
7325 "The @code{r-abd} package contains data sets and sample code for the Analysis of
7326 biological data by Michael Whitlock and Dolph Schluter.")
7327 (license license:gpl2)))
7329 (define-public r-svgui
7336 (uri (cran-uri "svGUI" version))
7338 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
7339 (properties `((upstream-name . "svGUI")))
7340 (build-system r-build-system)
7341 (home-page "https://github.com/SciViews/svGUI/")
7342 (synopsis "Functions for managing GUI clients in R")
7344 "The SciViews @code{svGUI} package eases the management of Graphical User
7345 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
7346 centralizes info about GUI elements currently used, and it dispatches GUI
7347 calls to the particular toolkits in use in function of the context.")
7348 (license license:gpl2)))
7350 (define-public r-svdialogs
7352 (name "r-svdialogs")
7357 (uri (cran-uri "svDialogs" version))
7359 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
7360 (properties `((upstream-name . "svDialogs")))
7361 (build-system r-build-system)
7364 ("zenity" ,zenity)))
7366 `(("r-rstudioapi" ,r-rstudioapi)
7367 ("r-svgui" ,r-svgui)))
7368 (home-page "https://github.com/SciViews/svDialogs/")
7369 (synopsis "Portable dialog boxes")
7371 "This package helps to construct standard dialog boxes for your GUI, including
7372 message boxes, input boxes, list, file or directory selection, and others. In
7373 case R cannot display GUI dialog boxes, a simpler command line version of these
7374 interactive elements is also provided as a fallback solution.")
7375 (license license:gpl2)))
7377 (define-public r-abe
7384 (uri (cran-uri "abe" version))
7387 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
7388 (build-system r-build-system)
7389 (home-page "https://cran.r-project.org/web/packages/abe/")
7390 (synopsis "Augmented backward elimination")
7392 "This package performs augmented backward elimination and checks the
7393 stability of the obtained model. Augmented backward elimination combines
7394 significance or information based criteria with the change in estimate to
7395 either select the optimal model for prediction purposes or to serve as a tool
7396 to obtain a practically sound, highly interpretable model.")
7397 (license license:gpl2+)))
7399 (define-public r-abf2
7406 (uri (cran-uri "abf2" version))
7408 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
7409 (build-system r-build-system)
7410 (home-page "https://cran.r-project.org/web/packages/abf2/")
7411 (synopsis "Load gap-free axon @code{r-abf2} files")
7413 "This package loads electrophysiology data from ABF2 files, as created by
7414 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
7415 mode are currently supported.")
7416 (license license:artistic2.0)))
7418 (define-public r-abhgenotyper
7420 (name "r-abhgenotyper")
7425 (uri (cran-uri "ABHgenotypeR" version))
7427 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
7428 (properties `((upstream-name . "ABHgenotypeR")))
7429 (build-system r-build-system)
7431 `(("r-ggplot2" ,r-ggplot2)
7432 ("r-reshape2" ,r-reshape2)))
7433 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
7434 (synopsis "Visualize and manipulate ABH genotypes")
7436 "The @code{r-abhgenotyper} package provides simple imputation,
7437 error-correction and plotting capacities for genotype data. The package is
7438 supposed to serve as an intermediate but independent analysis tool between the
7439 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
7440 not found in either TASSEL or @code{r-qtl} in addition to visualization of
7441 genotypes as \"graphical genotypes\".")
7442 (license license:gpl3)))
7444 (define-public r-furrr
7451 (uri (cran-uri "furrr" version))
7454 "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx"))))
7455 (build-system r-build-system)
7457 `(("r-future" ,r-future)
7458 ("r-globals" ,r-globals)
7459 ("r-purrr" ,r-purrr)
7460 ("r-rlang" ,r-rlang)))
7461 (home-page "https://github.com/DavisVaughan/furrr")
7462 (synopsis "Apply mapping functions in parallel using futures")
7464 "This package provides implementations of the family of @code{map()}
7465 functions from the @code{purrr} package that can be resolved using any
7466 @code{future}-supported backend, e.g. parallel on the local machine or
7467 distributed on a compute cluster.")
7468 (license license:lgpl2.1+)))
7470 (define-public r-abjutils
7477 (uri (cran-uri "abjutils" version))
7479 (base32 "0n4zps65y3zg0gfzlv97w91si52a9izkncirskbkj5x9hk0nhxcv"))))
7480 (build-system r-build-system)
7482 `(("r-devtools" ,r-devtools)
7483 ("r-dplyr" ,r-dplyr)
7484 ("r-furrr" ,r-furrr)
7485 ("r-future" ,r-future)
7488 ("r-magrittr" ,r-magrittr)
7489 ("r-progress" ,r-progress)
7490 ("r-purrr" ,r-purrr)
7491 ("r-readr" ,r-readr)
7492 ("r-rlang" ,r-rlang)
7493 ("r-rstudioapi" ,r-rstudioapi)
7494 ("r-scales" ,r-scales)
7495 ("r-stringi" ,r-stringi)
7496 ("r-stringr" ,r-stringr)
7497 ("r-tibble" ,r-tibble)
7498 ("r-tidyr" ,r-tidyr)))
7499 (home-page "https://github.com/abjur/abjutils/")
7500 (synopsis "Collection of tools for jurimetrical analysis")
7502 "This package implements general purpose tools, such as functions for
7503 sampling and basic manipulation of Brazilian lawsuits identification number.
7504 It also implements functions for text cleaning, such as accentuation
7506 (license license:expat)))
7508 (define-public r-abnormality
7510 (name "r-abnormality")
7515 (uri (cran-uri "abnormality" version))
7517 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
7518 (build-system r-build-system)
7520 `(("r-mass" ,r-mass)
7521 ("r-matrix" ,r-matrix)))
7522 (home-page "https://cran.r-project.org/web/packages/abnormality/")
7523 (synopsis "Measure a subject's abnormality with respect to a reference population")
7525 "This package contains functions to implement the methodology and
7526 considerations laid out by Marks et al. in the article \"Measuring abnormality
7527 in high dimensional spaces: applications in biomechanical gait analysis\".
7528 Using high-dimensional datasets to measure a subject's overall level of
7529 abnormality as compared to a reference population is often needed in outcomes
7531 (license license:expat)))
7533 (define-public r-abodoutlier
7535 (name "r-abodoutlier")
7540 (uri (cran-uri "abodOutlier" version))
7542 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
7543 (properties `((upstream-name . "abodOutlier")))
7544 (build-system r-build-system)
7546 `(("r-cluster" ,r-cluster)))
7547 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
7548 (synopsis "Angle-based outlier detection")
7550 "This package performs angle-based outlier detection on a given data
7551 frame. It offers three methods to process data:
7553 @item full but slow implementation using all the data that has cubic
7555 @item a fully randomized method;
7556 @item a method using k-nearest neighbours.
7558 These algorithms are well suited for high dimensional data outlier
7560 (license license:expat)))
7562 (define-public r-abps
7569 (uri (cran-uri "ABPS" version))
7571 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
7572 (properties `((upstream-name . "ABPS")))
7573 (build-system r-build-system)
7574 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
7575 (home-page "https://cran.r-project.org/web/packages/ABPS/")
7576 (synopsis "Abnormal blood profile score to detect blood doping")
7578 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
7579 The ABPS is a part of the Athlete biological passport program of the World
7580 anti-doping agency, which combines several blood parameters into a single
7581 score in order to detect blood doping. The package also contains functions to
7582 calculate other scores used in anti-doping programs, such as the ratio of
7583 hemoglobin to reticulocytes (OFF-score), as well as example data.")
7584 (license license:gpl2+)))
7586 (define-public r-parmigene
7588 (name "r-parmigene")
7593 (uri (cran-uri "parmigene" version))
7596 "1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d"))))
7597 (build-system r-build-system)
7598 (home-page "https://cran.r-project.org/web/packages/parmigene/")
7599 (synopsis "Mutual information estimation for gene network reconstruction")
7601 "This package provides a parallel estimation of the mutual information
7602 based on entropy estimates from k-nearest neighbors distances and algorithms
7603 for the reconstruction of gene regulatory networks.")
7604 (license license:agpl3+)))
7606 (define-public r-pscl
7613 (uri (cran-uri "pscl" version))
7615 (base32 "1phf3awsfr4ncqfqzin5m1pz0g7y1zhbcm2sz7358ssw914fd7rc"))))
7616 (build-system r-build-system)
7618 `(("r-mass" ,r-mass)))
7619 (home-page "https://github.com/atahk/pscl/")
7620 (synopsis "Political science computational laboratory")
7622 "The @code{pscl} is an R package providing classes and methods for:
7624 @item Bayesian analysis of roll call data (item-response models);
7625 @item elementary Bayesian statistics;
7626 @item maximum likelihood estimation of zero-inflated and hurdle models for count
7628 @item utility functions.
7630 (license license:gpl2)))
7632 (define-public r-accelmissing
7634 (name "r-accelmissing")
7639 (uri (cran-uri "accelmissing" version))
7641 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
7642 (build-system r-build-system)
7644 `(("r-mice" ,r-mice)
7645 ("r-pscl" ,r-pscl)))
7646 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
7647 (synopsis "Missing value imputation for accelerometer data")
7649 "This package provides a statistical method to impute the missing values in
7650 accelerometer data. The methodology includes both parametric and
7651 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
7652 model. It also provides multiple functions to preprocess the accelerometer data
7653 previous to the missing data imputation. These include detecting the wearing
7654 and the non-wearing time, selecting valid days and subjects, and creating plots.")
7655 (license license:gpl2+)))
7657 (define-public r-mhsmm
7664 (uri (cran-uri "mhsmm" version))
7666 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
7667 (build-system r-build-system)
7668 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
7669 (home-page "https://github.com/jaredo/mhsmm/")
7670 (synopsis "Inference for hidden Markov and semi-Markov models")
7672 "The @code{r-mhsmm} package implements estimation and prediction methods for
7673 hidden Markov and semi-Markov models for multiple observation sequences. Such
7674 techniques are of interest when observed data is thought to be dependent on some
7675 unobserved (or hidden) state. Also, this package is suitable for equidistant
7676 time series data, with multivariate and/or missing data. Allows user defined
7677 emission distributions.")
7678 (license license:gpl2+)))
7680 (define-public r-nleqslv
7687 (uri (cran-uri "nleqslv" version))
7689 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
7690 (build-system r-build-system)
7691 (native-inputs `(("gfortran" ,gfortran)))
7692 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
7693 (synopsis "Solve systems of nonlinear equations")
7695 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
7696 Broyden or a Newton method with a choice of global strategies such as line
7697 search and trust region. There are options for using a numerical or user
7698 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
7699 singular or ill-conditioned Jacobian.")
7700 (license license:gpl2+)))
7702 (define-public r-physicalactivity
7704 (name "r-physicalactivity")
7709 (uri (cran-uri "PhysicalActivity" version))
7711 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
7713 `((upstream-name . "PhysicalActivity")))
7714 (build-system r-build-system)
7715 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
7716 (synopsis "Procesing accelerometer data for physical activity measurement")
7718 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
7719 for classification of monitor wear and nonwear time intervals in accelerometer
7720 data collected to assess physical activity. The package also contains functions
7721 for making plots of accelerometer data and obtaining the summary of various
7722 information including daily monitor wear time and the mean monitor wear time
7723 during valid days. The revised package version 0.2-1 improved the functions
7724 regarding speed, robustness and add better support for time zones and daylight
7725 saving. In addition, several functions were added:
7727 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
7728 @item the @code{markPAI} can categorize physical activity intensity level based
7729 on user-defined cut-points of accelerometer counts.
7731 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
7732 @code{queryActigraph} functions.")
7733 (license license:gpl3+)))
7735 (define-public r-acc
7742 (uri (cran-uri "acc" version))
7744 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
7745 (build-system r-build-system)
7747 `(("r-circlize" ,r-circlize)
7749 ("r-ggplot2" ,r-ggplot2)
7750 ("r-iterators" ,r-iterators)
7751 ("r-mhsmm" ,r-mhsmm)
7752 ("r-nleqslv" ,r-nleqslv)
7753 ("r-physicalactivity" ,r-physicalactivity)
7755 ("r-r-utils" ,r-r-utils)
7757 ("r-rcpparmadillo" ,r-rcpparmadillo)
7758 ("r-rsqlite" ,r-rsqlite)
7760 (home-page "https://cran.r-project.org/web/packages/acc/")
7761 (synopsis "Exploring accelerometer data")
7763 "This package processes accelerometer data from uni-axial and tri-axial devices
7764 and generates data summaries. Also, includes functions to plot, analyze, and
7765 simulate accelerometer data.")
7766 (license license:gpl2+)))
7768 (define-public r-rbenchmark
7770 (name "r-rbenchmark")
7775 (uri (cran-uri "rbenchmark" version))
7777 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
7778 (build-system r-build-system)
7779 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
7780 (synopsis "Benchmarking routine for R")
7782 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
7783 and is intended to facilitate benchmarking of arbitrary R code. The library
7784 consists of just one function, benchmark, which is a simple wrapper around
7785 system.time. Given a specification of the benchmarking process (counts of
7786 replications, evaluation environment) and an arbitrary number of expressions,
7787 benchmark evaluates each of the expressions in the specified environment,
7788 replicating the evaluation as many times as specified, and returning the results
7789 conveniently wrapped into a data frame.")
7790 (license license:gpl2+)))
7792 (define-public r-mitools
7799 (uri (cran-uri "mitools" version))
7802 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
7803 (build-system r-build-system)
7804 (propagated-inputs `(("r-dbi" ,r-dbi)))
7805 (home-page "https://cran.r-project.org/web/packages/mitools/")
7806 (synopsis "Tools for multiple imputation of missing data")
7808 "This package provides tools to perform analyses and combine results from
7809 multiple-imputation datasets.")
7810 (license license:gpl2)))
7812 (define-public r-magick
7819 (uri (cran-uri "magick" version))
7822 "1xh5mhaks3wk1iwqs9d3lnbfv121lc1yz5fqdzk5il9ppr831l85"))))
7823 (build-system r-build-system)
7825 `(("imagemagick" ,imagemagick)
7828 `(("r-curl" ,r-curl)
7829 ("r-magrittr" ,r-magrittr)
7830 ("r-rcpp" ,r-rcpp)))
7832 `(("pkg-config" ,pkg-config)))
7833 (home-page "https://github.com/ropensci/magick")
7834 (synopsis "Advanced graphics and image-processing in R")
7836 "This package provides bindings to ImageMagick, a comprehensive image
7837 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
7838 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
7839 operations are vectorized via the Magick++ STL meaning they operate either on
7840 a single frame or a series of frames for working with layers, collages, or
7841 animation. In RStudio, images are automatically previewed when printed to the
7842 console, resulting in an interactive editing environment.")
7843 (license license:expat)))
7845 (define-public r-survey
7852 (uri (cran-uri "survey" version))
7855 "0xclsy4ram4k48vzh5m5bpmknnpwxnss85v73s4czsjj5ffjxwwh"))))
7856 (build-system r-build-system)
7858 `(("r-lattice" ,r-lattice)
7859 ("r-matrix" ,r-matrix)
7860 ("r-minqa" ,r-minqa)
7861 ("r-mitools" ,r-mitools)
7862 ("r-numderiv" ,r-numderiv)
7863 ("r-survival" ,r-survival)))
7864 (home-page "http://r-survey.r-forge.r-project.org/survey/")
7865 (synopsis "Analysis of complex survey samples")
7867 "This package provides tools for the analysis of complex survey samples.
7868 The provided features include: summary statistics, two-sample tests, rank
7869 tests, generalised linear models, cumulative link models, Cox models,
7870 loglinear models, and general maximum pseudolikelihood estimation for
7871 multistage stratified, cluster-sampled, unequally weighted survey samples;
7872 variances by Taylor series linearisation or replicate weights;
7873 post-stratification, calibration, and raking; two-phase subsampling designs;
7874 graphics; PPS sampling without replacement; principal components, and factor
7876 ;; Either version of the GPL.
7877 (license (list license:gpl2 license:gpl3))))
7879 (define-public r-gee
7886 (uri (cran-uri "gee" version))
7889 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
7890 (properties `((upstream-name . "gee")))
7891 (build-system r-build-system)
7893 `(("gfortran" ,gfortran)))
7894 (home-page "https://cran.r-project.org/web/packages/gee/")
7895 (synopsis "Generalized estimation equation solver")
7897 "This package provides a solver for generalized estimation equations.")
7898 (license license:gpl2)))
7900 (define-public r-tab
7907 (uri (cran-uri "tab" version))
7910 "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
7911 (properties `((upstream-name . "tab")))
7912 (build-system r-build-system)
7914 `(("r-dplyr" ,r-dplyr)
7916 ("r-knitr" ,r-knitr)
7918 ("r-survey" ,r-survey)
7919 ("r-survival" ,r-survival)
7920 ("r-xtable" ,r-xtable)))
7921 (home-page "https://cran.r-project.org/web/packages/tab/")
7922 (synopsis "Create summary tables for statistical reports")
7924 "This package contains functions for creating various types of summary
7925 tables, e.g. comparing characteristics across levels of a categorical variable
7926 and summarizing fitted generalized linear models, generalized estimating
7927 equations, and Cox proportional hazards models. Functions are available to
7928 handle data from simple random samples as well as complex surveys.")
7929 (license license:gpl3+)))
7931 (define-public r-dvmisc
7938 (uri (cran-uri "dvmisc" version))
7940 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
7941 (build-system r-build-system)
7943 `(("r-cubature" ,r-cubature)
7944 ("r-data-table" ,r-data-table)
7945 ("r-dplyr" ,r-dplyr)
7946 ("r-ggplot2" ,r-ggplot2)
7948 ("r-mvtnorm" ,r-mvtnorm)
7949 ("r-pracma" ,r-pracma)
7950 ("r-rbenchmark" ,r-rbenchmark)
7952 ("r-survey" ,r-survey)
7954 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
7955 (synopsis "Faster computation of common statistics and miscellaneous functions")
7957 "This package implements faster versions of base R functions (e.g. mean, standard
7958 deviation, covariance, weighted mean), mostly written in C++, along with
7959 miscellaneous functions for various purposes (e.g. create the histogram with
7960 fitted probability density function or probability mass function curve, create
7961 the body mass index groups, assess the linearity assumption in logistic
7963 (license license:gpl2)))
7965 (define-public r-accelerometry
7967 (name "r-accelerometry")
7972 (uri (cran-uri "accelerometry" version))
7974 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
7975 (build-system r-build-system)
7977 `(("r-dvmisc" ,r-dvmisc)
7978 ("r-rcpp" ,r-rcpp)))
7979 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
7980 (synopsis "Functions for processing accelerometer data")
7982 "This package provides a collection of functions that perform operations on
7983 time-series accelerometer data, such as identify the non-wear time, flag minutes
7984 that are part of an activity bout, and find the maximum 10-minute average count
7985 value. The functions are generally very flexible, allowing for a variety of
7986 algorithms to be implemented.")
7987 (license license:gpl3)))
7989 (define-public r-absim
7996 (uri (cran-uri "AbSim" version))
7998 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
7999 (properties `((upstream-name . "AbSim")))
8000 (build-system r-build-system)
8003 ("r-powerlaw" ,r-powerlaw)))
8004 (home-page "https://cran.r-project.org/web/packages/AbSim/")
8005 (synopsis "Time resolved simulations of antibody repertoires")
8007 "This package provides simulation methods for the evolution of antibody repertoires.
8008 The heavy and light chain variable region of both human and C57BL/6 mice can
8009 be simulated in a time-dependent fashion. Both single lineages using one set of
8010 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
8011 with an initial V-D-J recombination event, starting the first phylogenetic tree.
8012 Upon completion, the main loop of the algorithm begins, with each iteration
8013 representing one simulated time step. Various mutation events are possible at
8014 each time step, contributing to a diverse final repertoire.")
8015 (license license:gpl2)))
8017 (define-public r-quic
8024 (uri (cran-uri "QUIC" version))
8026 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
8027 (properties `((upstream-name . "QUIC")))
8028 (build-system r-build-system)
8029 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
8030 (synopsis "Regularized sparse inverse covariance matrix estimation")
8032 "This package implements the regularized Gaussian maximum likelihood
8033 estimation of the inverse of a covariance matrix. It uses Newton's method and
8034 coordinate descent to solve the regularized inverse covariance matrix
8035 estimation problem.")
8036 ;; The project home page states that the release is under GPLv3 or later.
8037 ;; The CRAN page only says GPL-3.
8038 (license license:gpl3+)))
8040 (define-public r-abundant
8047 (uri (cran-uri "abundant" version))
8049 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
8050 (build-system r-build-system)
8052 `(("r-quic" ,r-quic)))
8053 (home-page "https://cran.r-project.org/web/packages/abundant/")
8054 (synopsis "Abundant regression and high-dimensional principal fitted components")
8056 "This package provides tools to fit and predict with the high-dimensional
8057 principal fitted components model. This model is described by Cook, Forzani,
8058 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
8059 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
8060 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
8061 (license license:gpl2+)))
8063 (define-public r-ac3net
8070 (uri (cran-uri "Ac3net" version))
8072 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
8073 (properties `((upstream-name . "Ac3net")))
8074 (build-system r-build-system)
8076 `(("r-data-table" ,r-data-table)))
8077 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
8078 (synopsis "Inferring directional conservative causal core gene networks")
8079 (description "This package infers directional Conservative causal core
8080 (gene) networks (C3NET). This is a version of the algorithm C3NET with
8081 directional network.")
8082 (license license:gpl3+)))
8084 (define-public r-aca
8091 (uri (cran-uri "ACA" version))
8093 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
8094 (properties `((upstream-name . "ACA")))
8095 (build-system r-build-system)
8096 (home-page "https://cran.r-project.org/web/packages/ACA/")
8097 (synopsis "Abrupt change-point or aberration detection in point series")
8099 "This package offers an interactive function for the detection of breakpoints in
8101 ;; Any version of the GPL
8102 (license (list license:gpl2+ license:gpl3+))))
8104 (define-public r-acceptancesampling
8106 (name "r-acceptancesampling")
8111 (uri (cran-uri "AcceptanceSampling" version))
8113 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
8115 `((upstream-name . "AcceptanceSampling")))
8116 (build-system r-build-system)
8117 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
8118 (synopsis "Creation and evaluation of acceptance sampling plans")
8120 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
8121 acceptance sampling plans. Acceptance sampling is a methodology commonly used
8122 in quality control and improvement. International standards of acceptance
8123 sampling provide sampling plans for specific circumstances. The aim of this
8124 package is to provide an easy-to-use interface to visualize single, double or
8125 multiple sampling plans. In addition, methods have been provided to enable the
8126 user to assess sampling plans against pre-specified levels of performance, as
8127 measured by the probability of acceptance for a given level of quality in the
8129 (license license:gpl3+)))
8131 (define-public r-acclma
8138 (uri (cran-uri "ACCLMA" version))
8140 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
8141 (properties `((upstream-name . "ACCLMA")))
8142 (build-system r-build-system)
8143 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
8144 (synopsis "ACC & LMA graph plotting")
8146 "This package contains a function that imports data from a @acronym{CSV,
8147 Comma-Separated Values} file, or uses manually entered data from the format (x,
8148 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
8149 Curve} vs @acronym{LOI, Line of Independence} graph and
8150 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
8151 function is @code{plotLMA} (source file, header) that takes a data set and plots the
8152 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
8153 string) was passed, a manual data entry window is opened. The header parameter
8154 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
8155 a header row or not. The dataset should contain only one independent variable
8156 (x) and one dependent variable (y) and can contain a weight for each
8158 (license license:gpl2)))
8160 (define-public r-aspi
8167 (uri (cran-uri "aspi" version))
8169 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
8170 (build-system r-build-system)
8172 "https://cran.r-project.org/web/packages/aspi/")
8174 "Analysis of symmetry of parasitic infections")
8176 "This package provides tools for the analysis and visualization of bilateral
8177 asymmetry in parasitic infections.")
8178 (license license:gpl3+)))
8180 (define-public r-sandwich
8187 (uri (cran-uri "sandwich" version))
8190 "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv"))))
8191 (build-system r-build-system)
8193 `(("r-zoo" ,r-zoo)))
8194 (home-page "https://cran.r-project.org/web/packages/sandwich/")
8195 (synopsis "Robust Covariance Matrix Estimators")
8197 "This package provides model-robust standard error estimators for
8198 cross-sectional, time series, clustered, panel, and longitudinal data.")
8199 ;; Either version of the license.
8200 (license (list license:gpl2 license:gpl3))))
8202 (define-public r-th-data
8209 (uri (cran-uri "TH.data" version))
8212 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
8213 (properties `((upstream-name . "TH.data")))
8214 (build-system r-build-system)
8216 `(("r-mass" ,r-mass)
8217 ("r-survival" ,r-survival)))
8218 (home-page "https://cran.r-project.org/web/packages/TH.data/")
8219 (synopsis "Shared data sets")
8221 "This package contains supporting data sets that are used in other
8222 packages maintained by Torsten Hothorn.")
8223 (license license:gpl3)))
8225 (define-public r-multcomp
8232 (uri (cran-uri "multcomp" version))
8235 "0jw9661hs4396wz9vflk3rak0ryzj1cg2pnndsn1gb4fjyf2vlhb"))))
8236 (build-system r-build-system)
8238 `(("r-codetools" ,r-codetools)
8239 ("r-mvtnorm" ,r-mvtnorm)
8240 ("r-sandwich" ,r-sandwich)
8241 ("r-survival" ,r-survival)
8242 ("r-th-data" ,r-th-data)))
8243 (home-page "https://cran.r-project.org/web/packages/multcomp/")
8244 (synopsis "Simultaneous inference in general parametric models")
8246 "Simultaneous tests and confidence intervals for general linear
8247 hypotheses in parametric models, including linear, generalized linear, linear
8248 mixed effects, and survival models. The package includes demos reproducing
8249 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
8250 Hothorn, Westfall, 2010, CRC Press).")
8251 (license license:gpl2)))
8253 (define-public r-emmeans
8256 (version "1.4.3.01")
8260 (uri (cran-uri "emmeans" version))
8263 "16v5j31516nbqnj2zhgqvyp5yxd4zcs5zi0aspa5plr2qikvrkmg"))))
8264 (build-system r-build-system)
8266 `(("r-estimability" ,r-estimability)
8267 ("r-mvtnorm" ,r-mvtnorm)
8268 ("r-numderiv" ,r-numderiv)
8270 ("r-xtable" ,r-xtable)))
8271 (home-page "https://github.com/rvlenth/emmeans")
8272 (synopsis "Estimated marginal means, aka least-squares means")
8274 "This package provides tools to obtain @dfn{estimated marginal
8275 means} (EMMs) for many linear, generalized linear, and mixed models. It can
8276 be used to compute contrasts or linear functions of EMMs, trends, and
8277 comparisons of slopes.")
8278 ;; Either version of the license.
8279 (license (list license:gpl2 license:gpl3))))
8281 (define-public r-pwr
8288 (uri (cran-uri "pwr" version))
8291 "0r5g781lr677vp3zyhgmi7r68c87l8gd05l1s3ffnxgn5wf043sm"))))
8292 (build-system r-build-system)
8294 `(("r-knitr" ,r-knitr)))
8295 (home-page "https://github.com/heliosdrm/pwr")
8296 (synopsis "Basic functions for power analysis")
8298 "This package provides power analysis functions along the lines of
8300 (license license:gpl3+)))
8302 (define-public r-libcoin
8309 (uri (cran-uri "libcoin" version))
8312 "1cm9x1dlg9f7fh7n5nw3x4a7rl88c7ylrlc8x3rx4mq5w1j42x0a"))))
8313 (build-system r-build-system)
8314 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8315 (home-page "https://cran.r-project.org/web/packages/libcoin")
8316 (synopsis "Linear test statistics for permutation inference")
8318 "This package provides basic infrastructure for linear test statistics
8319 and permutation inference in the framework of Strasser and Weber (1999).")
8320 (license license:gpl2)))
8322 (define-public r-coin
8329 (uri (cran-uri "coin" version))
8332 "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx"))))
8333 (build-system r-build-system)
8335 `(("r-libcoin" ,r-libcoin)
8336 ("r-matrixstats" ,r-matrixstats)
8337 ("r-modeltools" ,r-modeltools)
8338 ("r-multcomp" ,r-multcomp)
8339 ("r-mvtnorm" ,r-mvtnorm)
8340 ("r-survival" ,r-survival)))
8341 (home-page "http://coin.r-forge.r-project.org")
8342 (synopsis "Conditional inference procedures in a permutation test framework")
8344 "This package provides conditional inference procedures for the general
8345 independence problem including two-sample, K-sample (non-parametric ANOVA),
8346 correlation, censored, ordered and multivariate problems.")
8347 (license license:gpl2)))
8349 (define-public r-bayesplot
8351 (name "r-bayesplot")
8356 (uri (cran-uri "bayesplot" version))
8359 "0sq0ajnm96hmlqf1cv5n2gshh3qdij4n1zbm7qrniz2q6b5aj342"))))
8360 (build-system r-build-system)
8362 `(("pandoc" ,ghc-pandoc)
8363 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
8365 `(("r-dplyr" ,r-dplyr)
8366 ("r-ggplot2" ,r-ggplot2)
8367 ("r-ggridges" ,r-ggridges)
8369 ("r-reshape2" ,r-reshape2)
8370 ("r-rlang" ,r-rlang)
8371 ("r-tibble" ,r-tibble)
8372 ("r-tidyselect" ,r-tidyselect)))
8373 (home-page "http://mc-stan.org/bayesplot")
8374 (synopsis "Plotting for Bayesian models")
8376 "This package provides plotting functions for posterior analysis, model
8377 checking, and MCMC diagnostics. The package is designed not only to provide
8378 convenient functionality for users, but also a common set of functions that
8379 can be easily used by developers working on a variety of R packages for
8380 Bayesian modeling.")
8381 (license license:gpl3+)))
8383 (define-public r-tmb
8390 (uri (cran-uri "TMB" version))
8393 "1r2d8c5iazihba42sn33yarv0dcfiy989sx64zcf14zr8k6cgjzs"))))
8394 (properties `((upstream-name . "TMB")))
8395 (build-system r-build-system)
8397 `(("r-matrix" ,r-matrix)
8398 ("r-rcppeigen" ,r-rcppeigen)))
8399 (home-page "http://tmb-project.org")
8400 (synopsis "Template model builder: a general random effect tool")
8402 "With this tool, a user should be able to quickly implement complex
8403 random effect models through simple C++ templates. The package combines
8404 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
8405 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
8406 from R) to obtain an efficient implementation of the applied Laplace
8407 approximation with exact derivatives. Key features are: Automatic sparseness
8408 detection, parallelism through BLAS and parallel user templates.")
8409 (license license:gpl2)))
8411 (define-public r-sjstats
8418 (uri (cran-uri "sjstats" version))
8420 (base32 "029rl05p88bp01favz300m980r1khcx2a2kn88yqbnbgkjjgqqc6"))))
8421 (build-system r-build-system)
8423 `(("r-bayestestr" ,r-bayestestr)
8424 ("r-broom" ,r-broom)
8425 ("r-dplyr" ,r-dplyr)
8426 ("r-emmeans" ,r-emmeans)
8427 ("r-insight" ,r-insight)
8429 ("r-magrittr" ,r-magrittr)
8431 ("r-modelr" ,r-modelr)
8432 ("r-parameters" ,r-parameters)
8433 ("r-performance" ,r-performance)
8434 ("r-purrr" ,r-purrr)
8435 ("r-rlang" ,r-rlang)
8436 ("r-sjlabelled" ,r-sjlabelled)
8437 ("r-sjmisc" ,r-sjmisc)
8438 ("r-tidyr" ,r-tidyr)))
8439 (home-page "https://github.com/strengejacke/sjstats")
8440 (synopsis "Functions for common statistical computations")
8442 "This package provides a collection of convenient functions for common
8443 statistical computations, which are not directly provided by R's @code{base}
8444 or @code{stats} packages. This package aims at providing, first, shortcuts
8445 for statistical measures, which otherwise could only be calculated with
8446 additional effort. Second, these shortcut functions are generic, and can be
8447 applied not only to vectors, but also to other objects as well. The focus of
8448 most functions lies on summary statistics or fit measures for regression
8449 models, including generalized linear models, mixed effects models and Bayesian
8451 (license license:gpl3)))
8453 (define-public r-glmmtmb
8460 (uri (cran-uri "glmmTMB" version))
8463 "035hkywa37bz555fv6znxd4hfcs5w884365wfnwk4jx5vann4vvb"))))
8464 (properties `((upstream-name . "glmmTMB")))
8465 (build-system r-build-system)
8467 `(("r-lme4" ,r-lme4)
8468 ("r-matrix" ,r-matrix)
8470 ("r-rcppeigen" ,r-rcppeigen)
8473 `(("r-knitr" ,r-knitr))) ; for vignettes
8474 (home-page "https://github.com/glmmTMB")
8475 (synopsis "Generalized linear mixed models")
8477 "Fit linear and generalized linear mixed models with various extensions,
8478 including zero-inflation. The models are fitted using maximum likelihood
8479 estimation via the Template Model Builder. Random effects are assumed to be
8480 Gaussian on the scale of the linear predictor and are integrated out using the
8481 Laplace approximation. Gradients are calculated using automatic
8483 (license license:agpl3+)))
8485 (define-public r-bayestestr
8487 (name "r-bayestestr")
8492 (uri (cran-uri "bayestestR" version))
8495 "1d3f50rzjzgzclwd6j887dssyhv7hdq7pik9nnlr3w775v3f69zc"))))
8496 (properties `((upstream-name . "bayestestR")))
8497 (build-system r-build-system)
8499 `(("r-insight" ,r-insight)))
8500 (home-page "https://github.com/easystats/bayestestR")
8501 (synopsis "Describe Bayesian models and posterior distributions")
8503 "This package provides utilities to understand and describe posterior
8504 distributions and Bayesian models. It includes point-estimates such as
8505 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
8506 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
8507 ROPE percentage and pd).")
8508 (license license:gpl3)))
8510 (define-public r-performance
8512 (name "r-performance")
8517 (uri (cran-uri "performance" version))
8520 "1pcjmqqm178dvdcpzkv5p4sj7glsppcny7znljb2nqkxh539a59p"))))
8521 (build-system r-build-system)
8523 `(("r-bayestestr" ,r-bayestestr)
8524 ("r-insight" ,r-insight)))
8525 (home-page "https://easystats.github.io/performance/")
8526 (synopsis "Assessment of regression models performance")
8528 "This package provides utilities for computing measures to assess model
8529 quality, which are not directly provided by R's @code{base} or @code{stats}
8530 packages. These include e.g. measures like r-squared, intraclass correlation
8531 coefficient, root mean squared error or functions to check models for
8532 overdispersion, singularity or zero-inflation and more. Functions apply to a
8533 large variety of regression models, including generalized linear models, mixed
8534 effects models and Bayesian models.")
8535 (license license:gpl3)))
8537 (define-public r-ggeffects
8539 (name "r-ggeffects")
8544 (uri (cran-uri "ggeffects" version))
8547 "1djz82xww86h8f33m2vm40lliicppgyhm6hyn3h6rzrqjrlrsmdw"))))
8548 (build-system r-build-system)
8550 `(("r-insight" ,r-insight)
8551 ("r-magrittr" ,r-magrittr)
8553 ("r-purrr" ,r-purrr)
8554 ("r-sjlabelled" ,r-sjlabelled)
8555 ("r-sjmisc" ,r-sjmisc)))
8556 (home-page "https://github.com/strengejacke/ggeffects")
8557 (synopsis "Create tidy data frames of marginal effects for ggplot")
8559 "This package provides tools to compute marginal effects from statistical
8560 models and return the result as tidy data frames. These data frames are ready
8561 to use with the @code{ggplot2} package. Marginal effects can be calculated
8562 for many different models. Interaction terms, splines and polynomial terms
8563 are also supported. The two main functions are @code{ggpredict()} and
8564 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
8565 results using @code{ggplot2}.")
8566 (license license:gpl3)))
8568 (define-public r-effectsize
8570 (name "r-effectsize")
8575 (uri (cran-uri "effectsize" version))
8578 "07vgmxdl75798hgdh90zysafjh97rmmj2wjjyr6xff4fbhi8rlkb"))))
8579 (properties `((upstream-name . "effectsize")))
8580 (build-system r-build-system)
8582 `(("r-bayestestr" ,r-bayestestr)
8583 ("r-insight" ,r-insight)
8584 ("r-parameters" ,r-parameters)))
8585 (home-page "https://github.com/easystats/effectsize")
8586 (synopsis "Indices of effect size and standardized parameters")
8588 "This package provides utilities to work with indices of effect size and
8589 standardized parameters for a wide variety of models, allowing computation and
8590 conversion of indices such as Cohen's d, r, odds, etc.")
8591 (license license:gpl3)))
8593 (define-public r-sjplot
8600 (uri (cran-uri "sjPlot" version))
8602 (base32 "0rmfc2pq80w0kxh6icljhqm31q580s0czvllsfxk6crmpyfgxkp7"))))
8603 (properties `((upstream-name . "sjPlot")))
8604 (build-system r-build-system)
8606 `(("r-bayestestr" ,r-bayestestr)
8607 ("r-dplyr" ,r-dplyr)
8608 ("r-effectsize" ,r-effectsize)
8609 ("r-forcats" ,r-forcats)
8610 ("r-ggeffects" ,r-ggeffects)
8611 ("r-ggplot2" ,r-ggplot2)
8612 ("r-ggrepel" ,r-ggrepel)
8613 ("r-glmmtmb" ,r-glmmtmb)
8614 ("r-insight" ,r-insight)
8615 ("r-knitr" ,r-knitr)
8617 ("r-magrittr" ,r-magrittr)
8619 ("r-modelr" ,r-modelr)
8620 ("r-parameters" ,r-parameters)
8621 ("r-performance" ,r-performance)
8622 ("r-psych" ,r-psych)
8623 ("r-purrr" ,r-purrr)
8624 ("r-rlang" ,r-rlang)
8625 ("r-scales" ,r-scales)
8626 ("r-sjlabelled" ,r-sjlabelled)
8627 ("r-sjmisc" ,r-sjmisc)
8628 ("r-sjstats" ,r-sjstats)
8629 ("r-tidyr" ,r-tidyr)))
8630 (home-page "https://strengejacke.github.io/sjPlot/")
8631 (synopsis "Data visualization for statistics in social science")
8633 "This package represents a collection of plotting and table output
8634 functions for data visualization. Results of various statistical
8635 analyses (that are commonly used in social sciences) can be visualized using
8636 this package, including simple and cross tabulated frequencies, histograms,
8637 box plots, (generalized) linear models, mixed effects models, principal
8638 component analysis and correlation matrices, cluster analyses, scatter plots,
8639 stacked scales, effects plots of regression models (including interaction
8640 terms) and much more. This package supports labelled data.")
8641 (license license:gpl3)))
8643 (define-public r-ini
8650 (uri (cran-uri "ini" version))
8653 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
8654 (build-system r-build-system)
8655 (home-page "https://github.com/dvdscripter/ini")
8656 (synopsis "Read and write configuration files")
8658 "This package provides tools to parse simple @code{.ini} configuration
8659 files to an structured list. Users can manipulate this resulting list with
8660 @code{lapply()} functions. This same structured list can be used to write
8661 back to file after modifications.")
8662 (license license:gpl3)))
8671 (uri (cran-uri "gh" version))
8674 "1llinfajb0g7006jd2w1hpskxpmkjhnqarcjb71r1qvsccb2ph7k"))))
8675 (build-system r-build-system)
8677 `(("r-httr" ,r-httr)
8679 ("r-jsonlite" ,r-jsonlite)))
8680 (home-page "https://github.com/r-lib/gh#readme")
8681 (synopsis "Access the GitHub API via R")
8683 "This package provides a minimal R client to access the GitHub API.")
8684 (license license:expat)))
8693 (uri (cran-uri "fs" version))
8696 "1g26rgx13dzigp2vrlld6h28q33lwbax97zvwdrq2pc3iz54v4yn"))))
8697 (build-system r-build-system)
8699 `(("r-rcpp" ,r-rcpp)))
8701 `(("pkg-config" ,pkg-config)))
8702 (home-page "http://fs.r-lib.org")
8703 (synopsis "Cross-platform file system operations based on libuv")
8705 "This package provides a cross-platform interface to file system
8706 operations, built on top of the libuv C library.")
8707 (license license:gpl3)))
8709 (define-public r-clisymbols
8711 (name "r-clisymbols")
8716 (uri (cran-uri "clisymbols" version))
8719 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
8720 (build-system r-build-system)
8721 (home-page "https://github.com/gaborcsardi/clisymbols")
8722 (synopsis "Unicode symbols at the R prompt")
8724 "This package provides a small subset of Unicode symbols, that are useful
8725 when building command line applications. They fall back to alternatives on
8726 terminals that do not support Unicode.")
8727 (license license:expat)))
8729 (define-public r-usethis
8736 (uri (cran-uri "usethis" version))
8739 "07an5wbikilg7cb3q6x5aykw8dfqnjrc3wpfb7gjmy0d9fh20fcy"))))
8740 (build-system r-build-system)
8742 `(("r-clipr" ,r-clipr)
8743 ("r-clisymbols" ,r-clisymbols)
8744 ("r-crayon" ,r-crayon)
8749 ("r-git2r" ,r-git2r)
8751 ("r-purrr" ,r-purrr)
8752 ("r-rlang" ,r-rlang)
8753 ("r-rprojroot" ,r-rprojroot)
8754 ("r-rstudioapi" ,r-rstudioapi)
8755 ("r-whisker" ,r-whisker)
8756 ("r-withr" ,r-withr)
8757 ("r-yaml" ,r-yaml)))
8758 (home-page "https://github.com/r-lib/usethis")
8759 (synopsis "Automate R package and project setup")
8761 "This package helps you to automate R package and project setup tasks
8762 that are otherwise performed manually. This includes setting up unit testing,
8763 test coverage, continuous integration, Git, GitHub integration, licenses,
8764 Rcpp, RStudio projects, and more.")
8765 (license license:gpl3)))
8767 (define-public r-sessioninfo
8769 (name "r-sessioninfo")
8774 (uri (cran-uri "sessioninfo" version))
8777 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
8778 (build-system r-build-system)
8781 ("r-withr" ,r-withr)))
8782 (home-page "https://github.com/r-lib/sessioninfo#readme")
8783 (synopsis "R session information")
8785 "This package provides tools to query and print information about the
8786 current R session. It is similar to @code{utils::sessionInfo()}, but includes
8787 more information about packages, and where they were installed from.")
8788 (license license:gpl2)))
8790 (define-public r-remotes
8797 (uri (cran-uri "remotes" version))
8800 "19v8dmnk9l4i9m64p7zgmj7y1vhnnwhi5kyn0k5d034zzkvchi49"))))
8801 (build-system r-build-system)
8802 (home-page "https://github.com/r-lib/remotes#readme")
8803 (synopsis "R package installation from remote repositories")
8805 "Download and install R packages stored in GitHub, BitBucket, or plain
8806 subversion or git repositories. This package is a lightweight replacement of
8807 the @code{install_*} functions in the @code{devtools} package. Indeed most of
8808 the code was copied over from @code{devtools}.")
8809 (license license:gpl2+)))
8811 (define-public r-xopen
8818 (uri (cran-uri "xopen" version))
8821 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
8822 (build-system r-build-system)
8824 `(("r-processx" ,r-processx)))
8825 (home-page "https://github.com/r-lib/xopen#readme")
8826 (synopsis "Open system files, URLs, anything")
8828 "This package provides a cross-platform solution to open files,
8829 directories or URLs with their associated programs.")
8830 (license license:expat)))
8832 (define-public r-rcmdcheck
8834 (name "r-rcmdcheck")
8839 (uri (cran-uri "rcmdcheck" version))
8842 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
8843 (build-system r-build-system)
8845 `(("r-callr" ,r-callr)
8847 ("r-crayon" ,r-crayon)
8849 ("r-digest" ,r-digest)
8850 ("r-pkgbuild" ,r-pkgbuild)
8851 ("r-prettyunits" ,r-prettyunits)
8853 ("r-rprojroot" ,r-rprojroot)
8854 ("r-sessioninfo" ,r-sessioninfo)
8855 ("r-withr" ,r-withr)
8856 ("r-xopen" ,r-xopen)))
8857 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
8858 (synopsis "Run R CMD check from R and capture results")
8860 "Run @code{R CMD check} from R programmatically, and capture the results
8861 of the individual checks.")
8862 (license license:expat)))
8864 (define-public r-rapportools
8866 (name "r-rapportools")
8871 (uri (cran-uri "rapportools" version))
8874 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
8875 (build-system r-build-system)
8877 `(("r-pander" ,r-pander)
8879 ("r-reshape" ,r-reshape)))
8880 (home-page "https://cran.r-project.org/web/packages/rapportools/")
8881 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
8883 "This package provides helper functions that act as wrappers to more
8884 advanced statistical methods with the advantage of having sane defaults for
8886 (license license:agpl3+)))
8888 (define-public r-pander
8895 (uri (cran-uri "pander" version))
8898 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
8899 (build-system r-build-system)
8901 `(("r-digest" ,r-digest)
8902 ("r-rcpp" ,r-rcpp)))
8903 (home-page "https://rapporter.github.io/pander")
8904 (synopsis "Render R objects into Pandoc's markdown")
8906 "The main aim of the pander R package is to provide a minimal and easy
8907 tool for rendering R objects into Pandoc's markdown. The package is also
8908 capable of exporting/converting complex Pandoc documents (reports) in various
8910 ;; This package is licensed under either the AGPLv3+ or the very rarely
8912 (license license:agpl3+)))
8914 (define-public r-summarytools
8916 (name "r-summarytools")
8921 (uri (cran-uri "summarytools" version))
8924 "1n695baz56mg4f13xjjadfq0xalw5xsn6xicil0yap5hgi8fsr3a"))))
8925 (build-system r-build-system)
8927 `(("r-checkmate" ,r-checkmate)
8928 ("r-dplyr" ,r-dplyr)
8929 ("r-htmltools" ,r-htmltools)
8930 ("r-lubridate" ,r-lubridate)
8931 ("r-magick" ,r-magick)
8932 ("r-matrixstats" ,r-matrixstats)
8933 ("r-pander" ,r-pander)
8935 ("r-rapportools" ,r-rapportools)
8936 ("r-rcurl" ,r-rcurl)
8937 ("r-tibble" ,r-tibble)
8938 ("r-tidyr" ,r-tidyr)))
8939 (home-page "https://github.com/dcomtois/summarytools")
8940 (synopsis "Tools to quickly and neatly summarize data")
8942 "This package provides tools for data frame summaries, cross-tabulations,
8943 weight-enabled frequency tables and common univariate statistics in concise
8944 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
8945 good point-of-entry for exploring data, both for experienced and new R
8947 (license license:gpl2)))
8949 (define-public r-lsei
8956 (uri (cran-uri "lsei" version))
8959 "1xl06fb3is744pxlh42wx5hn1h0ab1k31wnmsmh0524kxzcyp0a7"))))
8960 (build-system r-build-system)
8962 `(("gfortran" ,gfortran)))
8963 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
8964 (synopsis "Solve regression problems under equality/inequality constraints")
8966 "It contains functions that solve least squares linear regression
8967 problems under linear equality/inequality constraints. Functions for solving
8968 quadratic programming problems are also available, which transform such
8969 problems into least squares ones first.")
8970 (license license:gpl2+)))
8972 (define-public r-npsurv
8979 (uri (cran-uri "npsurv" version))
8982 "1wq4c9yfha5azjhrn40iiqkshmvh611sa90jp3lh82n4bl9zfk20"))))
8983 (build-system r-build-system)
8985 `(("r-lsei" ,r-lsei)))
8986 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
8987 (synopsis "Nonparametric survival analysis")
8989 "This package contains functions for non-parametric survival analysis of
8990 exact and interval-censored observations.")
8991 (license license:gpl2+)))
8993 (define-public r-clusteval
8995 (name "r-clusteval")
9000 (uri (cran-uri "clusteval" version))
9003 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
9004 (build-system r-build-system)
9006 `(("r-mvtnorm" ,r-mvtnorm)
9007 ("r-rcpp" ,r-rcpp)))
9008 (home-page "https://cran.r-project.org/web/packages/clusteval/")
9009 (synopsis "Evaluation of clustering algorithms")
9011 "This R package provides a suite of tools to evaluate clustering
9012 algorithms, clusterings, and individual clusters.")
9013 (license license:expat)))
9015 (define-public r-tweedie
9022 (uri (cran-uri "tweedie" version))
9025 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
9026 (build-system r-build-system)
9027 (native-inputs `(("gfortran" ,gfortran)))
9028 (home-page "https://cran.r-project.org/web/packages/tweedie/")
9029 (synopsis "Evaluation of Tweedie exponential family models")
9031 "Maximum likelihood computations for Tweedie families, including the
9032 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
9033 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
9034 and related methods.")
9035 (license license:gpl2+)))
9037 (define-public r-rcppgsl
9044 (uri (cran-uri "RcppGSL" version))
9046 (base32 "0cnw2k7cfqrm79r6j283aybflxig80x4n4rjkfp2317wf10mrsa5"))))
9047 (properties `((upstream-name . "RcppGSL")))
9048 (build-system r-build-system)
9050 `(("r-rcpp" ,r-rcpp)
9053 `(("r-knitr" ,r-knitr))) ; for vignettes
9054 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
9055 (synopsis "Rcpp integration for GSL vectors and matrices")
9057 "The GNU Scientific Library (or GSL) is a collection of numerical
9058 routines for scientific computing. It is particularly useful for C and C++
9059 programs as it provides a standard C interface to a wide range of mathematical
9060 routines. There are over 1000 functions in total with an extensive test
9061 suite. The RcppGSL package provides an easy-to-use interface between GSL data
9062 structures and R using concepts from Rcpp which is itself a package that eases
9063 the interfaces between R and C++.")
9064 (license license:gpl2+)))
9066 (define-public r-mvabund
9073 (uri (cran-uri "mvabund" version))
9076 "0la935gsiryfc0zixxr1dqj0av271x96pqxbi3bp6dksbw5gm68k"))))
9077 (build-system r-build-system)
9079 `(("r-mass" ,r-mass)
9081 ("r-rcppgsl" ,r-rcppgsl)
9082 ("r-statmod" ,r-statmod)
9083 ("r-tweedie" ,r-tweedie)))
9084 (home-page "https://cran.r-project.org/web/packages/mvabund/")
9085 (synopsis "Statistical methods for analysing multivariate abundance data")
9087 "This package provides a set of tools for displaying, modeling and
9088 analysing multivariate abundance data in community ecology.")
9089 (license license:lgpl2.1+)))
9091 (define-public r-afex
9098 (uri (cran-uri "afex" version))
9101 "12n020y7rjm7402940gkqxa5j901p093f381i23p66fa3fyrshkf"))))
9102 (build-system r-build-system)
9106 ("r-lmertest" ,r-lmertest)
9107 ("r-pbkrtest" ,r-pbkrtest)
9108 ("r-reshape2" ,r-reshape2)))
9109 (home-page "https://afex.singmann.science/")
9110 (synopsis "Analysis of factorial experiments")
9112 "This package provides convenience functions for analyzing factorial
9113 experiments using ANOVA or mixed models.")
9114 (license license:gpl2+)))
9116 (define-public r-lmertest
9123 (uri (cran-uri "lmerTest" version))
9126 "0r2vvs3nl6p8xla3gd943khb4ixp0alvspqpnz2y6n3wk8zgh3jj"))))
9127 (properties `((upstream-name . "lmerTest")))
9128 (build-system r-build-system)
9130 `(("r-ggplot2" ,r-ggplot2)
9133 ("r-numderiv" ,r-numderiv)))
9134 (home-page "https://github.com/runehaubo/lmerTestR")
9135 (synopsis "Tests in linear mixed effects models")
9137 "This package provides p-values in type I, II or III anova and summary
9138 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
9139 method. A Kenward-Roger method is also available via the @code{pbkrtest}
9140 package. Model selection methods include step, drop1 and anova-like tables
9141 for random effects (ranova). Methods for Least-Square means (LS-means) and
9142 tests of linear contrasts of fixed effects are also available.")
9143 (license license:gpl2+)))
9145 (define-public r-r2glmm
9152 (uri (cran-uri "r2glmm" version))
9155 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
9156 (build-system r-build-system)
9158 `(("r-afex" ,r-afex)
9159 ("r-data-table" ,r-data-table)
9160 ("r-dplyr" ,r-dplyr)
9161 ("r-ggplot2" ,r-ggplot2)
9162 ("r-gridextra" ,r-gridextra)
9163 ("r-lmertest" ,r-lmertest)
9165 ("r-matrix" ,r-matrix)
9167 ("r-pbkrtest" ,r-pbkrtest)))
9168 (home-page "https://github.com/bcjaeger/r2glmm")
9169 (synopsis "Compute R squared for mixed (multilevel) models")
9171 "This package computes model and semi partial R squared with confidence
9172 limits for the linear and generalized linear mixed model (LMM and GLMM). The
9173 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
9174 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
9176 (license license:gpl2)))
9178 (define-public r-weights
9185 (uri (cran-uri "weights" version))
9188 "0186bfpkhxngrshac6bpg37alp6slwhwd43inrm8hqg0vhpfgc4c"))))
9189 (build-system r-build-system)
9191 `(("r-gdata" ,r-gdata)
9192 ("r-hmisc" ,r-hmisc)
9193 ("r-mice" ,r-mice)))
9195 "https://cran.r-project.org/web/packages/weights/")
9196 (synopsis "Weighting and weighted statistics")
9197 (description "This package Provides a variety of functions for producing
9198 simple weighted statistics, such as weighted Pearson's correlations, partial
9199 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
9200 includes some software for quickly recoding survey data and plotting point
9201 estimates from interaction terms in regressions (and multiply imputed
9202 regressions). NOTE: Weighted partial correlation calculations pulled to
9204 (license license:gpl2+)))
9206 (define-public r-rcppannoy
9208 (name "r-rcppannoy")
9213 (uri (cran-uri "RcppAnnoy" version))
9216 "1wiigx5g5788j6lyc3f6bs1rsvc4alyc3052g35hxl1giinxmhn4"))))
9217 (properties `((upstream-name . "RcppAnnoy")))
9218 (build-system r-build-system)
9220 `(("r-rcpp" ,r-rcpp)))
9222 `(("r-knitr" ,r-knitr))) ; for vignettes
9223 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
9224 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
9226 "Annoy is a small C++ library for Approximate Nearest Neighbors written
9227 for efficient memory usage as well an ability to load from and save to disk.
9228 This package provides an R interface.")
9229 ;; Annoy is released under ASL 2.0, but this wrapper is released under
9231 (license (list license:gpl2+ license:asl2.0))))
9233 (define-public r-rcpphnsw
9240 (uri (cran-uri "RcppHNSW" version))
9243 "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv"))))
9244 (properties `((upstream-name . "RcppHNSW")))
9245 (build-system r-build-system)
9246 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9247 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
9248 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
9250 "Hnswlib is a C++ library for approximate nearest neighbors. This
9251 package provides a minimal R interface by relying on the Rcpp package.")
9252 ;; hnswlib is released under Version 2.0 of the Apache License.
9253 (license (list license:gpl3 license:asl2.0))))
9255 (define-public r-rcppparallel
9257 (name "r-rcppparallel")
9262 (uri (cran-uri "RcppParallel" version))
9265 "0p13f2mywjr7gmskf8ri4y8p5yr1bvr4xrpw2w11vdvafwz1vcia"))))
9266 (properties `((upstream-name . "RcppParallel")))
9267 (build-system r-build-system)
9268 (home-page "http://rcppcore.github.io/RcppParallel")
9269 (synopsis "Parallel programming tools for Rcpp")
9271 "This package provides high level functions for parallel programming with
9272 Rcpp. For example, the @code{parallelFor()} function can be used to convert
9273 the work of a standard serial @code{for} loop into a parallel one and the
9274 @code{parallelReduce()} function can be used for accumulating aggregates or
9276 (license license:gpl2)))
9278 (define-public r-ncdf4
9285 (uri (cran-uri "ncdf4" version))
9288 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
9289 (build-system r-build-system)
9291 `(("netcdf" ,netcdf)
9293 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
9294 (synopsis "R interface to Unidata netCDF format data files")
9296 "This package provides a high-level R interface to data files written
9297 using Unidata's netCDF library (version 4 or earlier), which are binary data
9298 files that are portable across platforms and include metadata information in
9299 addition to the data sets. Using this package, netCDF files can be opened and
9300 data sets read in easily. It is also easy to create new netCDF dimensions,
9301 variables, and files, in either version 3 or 4 format, and manipulate existing
9303 (license license:gpl3+)))
9305 (define-public r-biocmanager
9307 (name "r-biocmanager")
9312 (uri (cran-uri "BiocManager" version))
9314 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
9315 (properties `((upstream-name . "BiocManager")))
9316 (build-system r-build-system)
9317 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
9318 (synopsis "Access the Bioconductor project package repository")
9320 "This package provides a convenient tool to install and update
9321 Bioconductor packages.")
9322 (license license:artistic2.0)))
9324 (define-public r-rgl
9327 (version "0.100.30")
9331 (uri (cran-uri "rgl" version))
9334 "0rzqzskcwf2ah4yr62x5rjwf7yh90d43h39gk7jmfc5lc08zaxc5"))))
9335 (build-system r-build-system)
9337 `(("pkg-config" ,pkg-config)))
9339 `(("freetype" ,freetype)
9343 ("ghc-pandoc" ,ghc-pandoc)
9346 `(("r-crosstalk" ,r-crosstalk)
9347 ("r-htmltools" ,r-htmltools)
9348 ("r-htmlwidgets" ,r-htmlwidgets)
9349 ("r-jsonlite" ,r-jsonlite)
9350 ("r-knitr" ,r-knitr)
9351 ("r-magrittr" ,r-magrittr)
9352 ("r-manipulatewidget" ,r-manipulatewidget)
9353 ("r-shiny" ,r-shiny)))
9354 (home-page "https://r-forge.r-project.org/projects/rgl/")
9355 (synopsis "3D visualization using OpenGL")
9357 "This package provides medium to high level functions for 3D interactive graphics,
9358 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
9359 as functions for constructing representations of geometric
9360 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
9361 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
9362 image formats, including PNG, Postscript, SVG, PGF.")
9363 ;; Any version of the GPL.
9364 (license (list license:gpl2+ license:gpl3+))))
9366 (define-public r-multicool
9368 (name "r-multicool")
9373 (uri (cran-uri "multicool" version))
9376 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
9377 (build-system r-build-system)
9378 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9379 (home-page "https://cran.r-project.org/web/packages/multicool/")
9380 (synopsis "Permutations of multisets in cool-lex order")
9382 "This package provides a set of tools to permute multisets without loops
9383 or hash tables and to generate integer partitions. Cool-lex order is similar
9384 to colexicographical order.")
9385 (license license:gpl2)))
9387 (define-public r-misc3d
9394 (uri (cran-uri "misc3d" version))
9397 "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
9398 (build-system r-build-system)
9399 (home-page "https://cran.r-project.org/web/packages/misc3d/")
9400 (synopsis "Miscellaneous 3D Plots")
9402 "This package provides a collection of miscellaneous 3d plots, including
9404 ;; Any version of the GPL.
9405 (license (list license:gpl2+ license:gpl3+))))
9414 (uri (cran-uri "ks" version))
9416 (base32 "0hcccjfqnzdxkmnfzq8c5a7yhc138azwyl7rp29d1vl1jawwrwfq"))))
9417 (build-system r-build-system)
9420 ("r-kernlab" ,r-kernlab)
9421 ("r-kernsmooth" ,r-kernsmooth)
9422 ("r-matrix" ,r-matrix)
9423 ("r-mclust" ,r-mclust)
9425 ("r-multicool" ,r-multicool)
9426 ("r-mvtnorm" ,r-mvtnorm)))
9427 (home-page "http://www.mvstat.net/tduong/")
9428 (synopsis "Kernel smoothing")
9430 "This package provides kernel smoothers for univariate and multivariate
9431 data, including density functions, density derivatives, cumulative
9432 distributions, modal clustering, discriminant analysis, and two-sample
9433 hypothesis testing.")
9434 ;; Either version of the GPL.
9435 (license (list license:gpl2 license:gpl3))))
9437 (define-public r-feature
9444 (uri (cran-uri "feature" version))
9447 "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
9448 (build-system r-build-system)
9451 ("r-misc3d" ,r-misc3d)
9453 (home-page "http://www.mvstat.net/tduong/")
9454 (synopsis "Inferential feature significance for kernel density estimation")
9456 "The feature package contains functions to display and compute kernel
9457 density estimates, significant gradient and significant curvature regions.
9458 Significant gradient and/or curvature regions often correspond to significant
9459 features (e.g. local modes).")
9460 ;; Either version of the GPL.
9461 (license (list license:gpl2 license:gpl3))))
9463 (define-public r-arm
9470 (uri (cran-uri "arm" version))
9473 "0vvp90jygajd6ydky57z66wqjq9msfbl88irj5jbsray574mh4bg"))))
9474 (build-system r-build-system)
9476 `(("r-abind" ,r-abind)
9480 ("r-matrix" ,r-matrix)
9481 ("r-nlme" ,r-nlme)))
9482 (home-page "https://cran.r-project.org/web/packages/arm/")
9483 (synopsis "Data analysis using regression and multilevel/hierarchical models")
9485 "This package provides functions to accompany A. Gelman and J. Hill,
9486 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
9487 University Press, 2007.")
9488 (license license:gpl3+)))
9490 (define-public r-circular
9497 (uri (cran-uri "circular" version))
9500 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
9501 (build-system r-build-system)
9503 `(("r-boot" ,r-boot)
9504 ("r-mvtnorm" ,r-mvtnorm)))
9506 `(("gfortran" ,gfortran)))
9507 (home-page "https://cran.r-project.org/web/packages/circular/")
9508 (synopsis "Circular statistics")
9510 "This package provides tools for circular statistics, from \"Topics in
9511 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
9513 (license license:gpl2+)))
9515 (define-public r-activity
9522 (uri (cran-uri "activity" version))
9525 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
9526 (build-system r-build-system)
9528 `(("r-circular" ,r-circular)
9529 ("r-insol" ,r-insol)
9530 ("r-pbapply" ,r-pbapply)))
9531 (home-page "https://cran.r-project.org/web/packages/activity/")
9532 (synopsis "Animal activity statistics")
9534 "This package provides functions to fit kernel density functions to
9535 animal activity time data; plot activity distributions; quantify overall
9536 levels of activity; statistically compare activity metrics through
9537 bootstrapping; and evaluate variation in linear variables with time (or other
9538 circular variables).")
9539 (license license:gpl3)))
9541 (define-public r-ouch
9548 (uri (cran-uri "ouch" version))
9551 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
9552 (build-system r-build-system)
9553 (propagated-inputs `(("r-subplex" ,r-subplex)))
9554 (home-page "http://kingaa.github.io/ouch/")
9555 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
9557 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
9558 for evolution along a phylogenetic tree.")
9559 (license license:gpl2+)))
9561 (define-public r-fmsb
9568 (uri (cran-uri "fmsb" version))
9571 "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
9572 (build-system r-build-system)
9573 (home-page "http://minato.sip21c.org/msb/")
9574 (synopsis "Functions for medical statistics book with demographic data")
9576 "This package provides several utility functions for the book entitled
9577 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
9578 Japan, 2007) with Japanese demographic data and some demographic analysis
9579 related functions.")
9580 (license license:gpl2+)))
9582 (define-public r-stabledist
9584 (name "r-stabledist")
9589 (uri (cran-uri "stabledist" version))
9592 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
9593 (build-system r-build-system)
9594 (home-page "http://www.rmetrics.org")
9595 (synopsis "Stable distribution functions")
9597 "This package provides density, probability and quantile functions, and
9598 random number generation for (skew) stable distributions, using the
9599 parametrizations of Nolan.")
9600 (license license:gpl2+)))
9602 (define-public r-gsl
9609 (uri (cran-uri "gsl" version))
9612 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
9613 (build-system r-build-system)
9616 (home-page "https://cran.r-project.org/web/packages/gsl")
9617 (synopsis "Wrapper for the GNU Scientific Library")
9619 "This package provides an R wrapper for the special functions and quasi
9620 random number generators of the GNU Scientific Library.")
9621 (license license:gpl2+)))
9623 (define-public r-adgoftest
9625 (name "r-adgoftest")
9630 (uri (cran-uri "ADGofTest" version))
9633 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
9634 (properties `((upstream-name . "ADGofTest")))
9635 (build-system r-build-system)
9636 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
9637 (synopsis "Anderson-Darling GoF test")
9639 "This package provides an implementation of the Anderson-Darling GoF test
9640 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
9641 Anderson-Darling Distribution\".")
9642 ;; Any version of the GPL.
9643 (license license:gpl3+)))
9645 (define-public r-softimpute
9647 (name "r-softimpute")
9652 (uri (cran-uri "softImpute" version))
9655 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
9656 (properties `((upstream-name . "softImpute")))
9657 (build-system r-build-system)
9659 `(("r-matrix" ,r-matrix)))
9661 `(("gfortran" ,gfortran)))
9662 (home-page "https://cran.r-project.org/web/packages/softImpute")
9663 (synopsis "Matrix completion via iterative soft-thresholded SVD")
9665 "This package provides iterative methods for matrix completion that use
9666 nuclear-norm regularization. The package includes procedures for centering
9667 and scaling rows, columns or both, and for computing low-rank @dfn{single
9668 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
9670 (license license:gpl2)))
9672 (define-public r-fftwtools
9674 (name "r-fftwtools")
9679 (uri (cran-uri "fftwtools" version))
9682 "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6"))))
9683 (build-system r-build-system)
9684 (inputs `(("fftw" ,fftw)))
9685 (home-page "https://github.com/krahim/fftwtools")
9686 (synopsis "Wrapper for FFTW3")
9688 "This package provides a wrapper for several FFTW functions. It provides
9689 access to the two-dimensional FFT, the multivariate FFT, and the
9690 one-dimensional real to complex FFT using the FFTW3 library. The package
9691 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
9692 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
9693 The FFT functions have a parameter that allows them to not return the
9694 redundant complex conjugate when the input is real data.")
9695 (license license:gpl2+)))
9697 (define-public r-tiff
9704 (uri (cran-uri "tiff" version))
9707 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
9708 (build-system r-build-system)
9710 `(("libtiff" ,libtiff)
9711 ("libjpeg" ,libjpeg)
9713 (home-page "http://www.rforge.net/tiff/")
9714 (synopsis "Read and write TIFF images")
9716 "This package provides an easy and simple way to read, write and display
9717 bitmap images stored in the TIFF format. It can read and write both files and
9718 in-memory raw vectors.")
9719 ;; Either of these two license versions.
9720 (license (list license:gpl2 license:gpl3))))
9722 (define-public r-nlp
9729 (uri (cran-uri "NLP" version))
9732 "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w"))))
9733 (properties `((upstream-name . "NLP")))
9734 (build-system r-build-system)
9735 (home-page "https://cran.r-project.org/web/packages/NLP/")
9736 (synopsis "Natural language processing infrastructure")
9738 "This package provides basic classes and methods for Natural Language
9740 (license license:gpl3)))
9749 (uri (cran-uri "tm" version))
9752 "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh"))))
9753 (properties `((upstream-name . "tm")))
9754 (build-system r-build-system)
9760 ("r-xml2" ,r-xml2)))
9761 (home-page "http://tm.r-forge.r-project.org/")
9762 (synopsis "Text mining package")
9764 "This package provides a framework for text mining applications within R.")
9765 (license license:gpl3)))
9767 (define-public r-waveslim
9774 (uri (cran-uri "waveslim" version))
9777 "0mky0nb4xxp8rybp87mxw2f1q6k400wpxv01zr4injv7ja6028xk"))))
9778 (build-system r-build-system)
9780 `(("gfortran" ,gfortran)))
9781 (home-page "http://waveslim.blogspot.com")
9782 (synopsis "Basic wavelet routines for signal processing")
9784 "This package provides basic wavelet routines for time series (1D),
9785 image (2D) and array (3D) analysis. The code provided here is based on
9786 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
9787 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
9788 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
9789 pairs (Selesnick 2001, 2002).")
9790 (license license:bsd-3)))
9792 (define-public r-wordcloud
9794 (name "r-wordcloud")
9799 (uri (cran-uri "wordcloud" version))
9802 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
9803 (build-system r-build-system)
9805 `(("r-rcolorbrewer" ,r-rcolorbrewer)
9807 ;; The "tm" package is only "suggested" according to CRAN, but the
9808 ;; wordcloud package cannot be loaded without it.
9810 (home-page "https://cran.r-project.org/web/packages/wordcloud")
9811 (synopsis "Word clouds")
9813 "This package provides functionality to create pretty word clouds,
9814 visualize differences and similarity between documents, and avoid
9815 over-plotting in scatter plots with text.")
9816 (license license:lgpl2.1)))
9818 (define-public r-colorramps
9820 (name "r-colorramps")
9825 (uri (cran-uri "colorRamps" version))
9828 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
9829 (properties `((upstream-name . "colorRamps")))
9830 (build-system r-build-system)
9831 (home-page "https://cran.r-project.org/web/packages/colorRamps")
9832 (synopsis "Build color tables")
9833 (description "This package provides features to build gradient color
9835 ;; Any version of the GPL
9836 (license license:gpl3+)))
9838 (define-public r-tidytree
9845 (uri (cran-uri "tidytree" version))
9847 (base32 "1bnzs62z2l8ck2h9gabmxvayizv4nfn8dmyzry83fv0cspjbyiv7"))))
9848 (build-system r-build-system)
9851 ("r-dplyr" ,r-dplyr)
9852 ("r-lazyeval" ,r-lazyeval)
9853 ("r-magrittr" ,r-magrittr)
9854 ("r-rlang" ,r-rlang)
9855 ("r-tibble" ,r-tibble)))
9856 (home-page "https://github.com/GuangchuangYu/tidytree")
9857 (synopsis "Tidy tool for phylogenetic tree data manipulation")
9859 "Phylogenetic trees generally contain multiple components including nodes,
9860 edges, branches and associated data. This package provides an approach to
9861 convert tree objects to tidy data frames. It also provides tidy interfaces to
9862 manipulate tree data.")
9863 (license license:artistic2.0)))
9865 (define-public r-rvcheck
9872 (uri (cran-uri "rvcheck" version))
9874 (base32 "1a3xlzi4n1rqiapfa180aif7n7nws8pbg8k3nk7ccaczvmni38aw"))))
9875 (build-system r-build-system)
9877 `(("r-biocmanager" ,r-biocmanager)
9878 ("r-rlang" ,r-rlang)))
9879 (home-page "https://cran.r-project.org/web/packages/rvcheck")
9880 (synopsis "R package version check")
9882 "This package provides tools to check the latest release version of R and
9883 R packages (on CRAN, Bioconductor or Github).")
9884 (license license:artistic2.0)))
9886 (define-public r-docopt
9893 (uri (cran-uri "docopt" version))
9896 "06zknnd0c5s2y0hbddzdlr3m63ib783izpck6pgz7sjbab5pd068"))))
9897 (build-system r-build-system)
9898 (home-page "https://github.com/docopt/docopt.R")
9899 (synopsis "Command-line interface specification language")
9901 "This package enables you to define a command-line interface by just
9902 giving it a description in the specific format.")
9903 (license license:expat)))
9905 (define-public r-sparsesvd
9907 (name "r-sparsesvd")
9912 (uri (cran-uri "sparsesvd" version))
9915 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
9916 (build-system r-build-system)
9917 (propagated-inputs `(("r-matrix" ,r-matrix)))
9918 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
9919 (synopsis "Sparse truncated singular value decomposition")
9921 "This package provides a Wrapper around the SVDLIBC library
9922 for (truncated) singular value decomposition of a sparse matrix. Currently,
9923 only sparse real matrices in Matrix package format are supported.")
9924 ;; SVDLIBC is released under BSD-2. The R interface is released under
9926 (license (list license:bsd-3 license:bsd-2))))
9928 (define-public r-speedglm
9935 (uri (cran-uri "speedglm" version))
9938 "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz"))))
9939 (build-system r-build-system)
9941 `(("r-mass" ,r-mass)
9942 ("r-matrix" ,r-matrix)))
9943 (home-page "https://cran.r-project.org/web/packages/speedglm")
9944 (synopsis "Fit linear and generalized linear models to large data sets")
9946 "This package provides tools for fitting linear models and generalized
9947 linear models to large data sets by updating algorithms.")
9948 ;; Any version of the GPL
9949 (license license:gpl2+)))
9951 (define-public r-densityclust
9953 (name "r-densityclust")
9958 (uri (cran-uri "densityClust" version))
9961 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
9962 (properties `((upstream-name . "densityClust")))
9963 (build-system r-build-system)
9966 ("r-ggplot2" ,r-ggplot2)
9967 ("r-ggrepel" ,r-ggrepel)
9968 ("r-gridextra" ,r-gridextra)
9969 ("r-rcolorbrewer" ,r-rcolorbrewer)
9971 ("r-rtsne" ,r-rtsne)))
9972 (home-page "https://cran.r-project.org/web/packages/densityClust")
9973 (synopsis "Clustering by fast search and find of density peaks")
9975 "This package provides an improved implementation (based on k-nearest
9976 neighbors) of the density peak clustering algorithm, originally described by
9977 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
9978 large datasets (> 100,000 samples) very efficiently.")
9979 (license license:gpl2+)))
9981 (define-public r-combinat
9988 (uri (cran-uri "combinat" version))
9991 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
9992 (build-system r-build-system)
9993 (home-page "https://cran.r-project.org/web/packages/combinat")
9994 (synopsis "Combinatorics utilities")
9995 (description "This package provides assorted routines for combinatorics.")
9996 (license license:gpl2)))
9998 (define-public r-qlcmatrix
10000 (name "r-qlcmatrix")
10005 (uri (cran-uri "qlcMatrix" version))
10008 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
10009 (properties `((upstream-name . "qlcMatrix")))
10010 (build-system r-build-system)
10012 `(("r-docopt" ,r-docopt)
10013 ("r-matrix" ,r-matrix)
10015 ("r-sparsesvd" ,r-sparsesvd)))
10016 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
10017 (synopsis "Sparse matrix functions for quantitative language comparison")
10019 "This package provides an extension of the functionality of the Matrix
10020 package for using sparse matrices. Some of the functions are very general,
10021 while other are highly specific for the special data format used for
10022 @dfn{quantitative language comparison} (QLC).")
10023 (license license:gpl3)))
10025 (define-public r-ddrtree
10032 (uri (cran-uri "DDRTree" version))
10035 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
10036 (properties `((upstream-name . "DDRTree")))
10037 (build-system r-build-system)
10040 ("r-irlba" ,r-irlba)
10042 ("r-rcppeigen" ,r-rcppeigen)))
10043 (home-page "https://cran.r-project.org/web/packages/DDRTree")
10044 (synopsis "Learning principal graphs with DDRTree")
10046 "This package provides an implementation of the framework of
10047 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
10048 dimensional space while constructs a principal tree which passes through the
10049 middle of the data simultaneously. DDRTree shows superiority to
10050 alternatives (Wishbone, DPT) for inferring the ordering as well as the
10051 intrinsic structure of single cell genomics data. In general, it could be
10052 used to reconstruct the temporal progression as well as the bifurcation
10053 structure of any data type.")
10054 (license license:asl2.0)))
10056 (define-public r-corpcor
10063 (uri (cran-uri "corpcor" version))
10066 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
10067 (build-system r-build-system)
10068 (home-page "http://strimmerlab.org/software/corpcor/")
10069 (synopsis "Efficient estimation of covariance and (partial) correlation")
10071 "This package implements a James-Stein-type shrinkage estimator for the
10072 covariance matrix, with separate shrinkage for variances and correlations.
10073 Furthermore, functions are available for fast singular value decomposition,
10074 for computing the pseudoinverse, and for checking the rank and positive
10075 definiteness of a matrix.")
10076 (license license:gpl3+)))
10078 (define-public r-rspectra
10080 (name "r-rspectra")
10085 (uri (cran-uri "RSpectra" version))
10088 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
10089 (properties `((upstream-name . "RSpectra")))
10090 (build-system r-build-system)
10092 `(("r-matrix" ,r-matrix)
10094 ("r-rcppeigen" ,r-rcppeigen)))
10095 (home-page "https://github.com/yixuan/RSpectra")
10096 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
10098 "This package provides an R interface to the Spectra library for
10099 large-scale eigenvalue and SVD problems. It is typically used to compute a
10100 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
10101 which is usually more efficient than @code{eigen()} if k << n.")
10103 (license license:mpl2.0)))
10105 (define-public r-vbsr
10112 (uri (cran-uri "vbsr" version))
10115 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
10116 (build-system r-build-system)
10117 (home-page "https://cran.r-project.org/web/packages/vbsr")
10118 (synopsis "Variational Bayes spike regression regularized linear models")
10120 "This package provides an efficient algorithm for solving ultra-sparse
10121 regularized regression models using a variational Bayes algorithm with a spike
10122 prior. The algorithm is solved on a path, with coordinate updates, and is
10123 capable of generating very sparse models. Very general model
10124 diagnostics for controlling type-1 errors are also provided.")
10125 (license license:gpl2)))
10127 (define-public r-flare
10130 (version "1.6.0.2")
10134 (uri (cran-uri "flare" version))
10137 "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
10138 (build-system r-build-system)
10140 `(("r-igraph" ,r-igraph)
10141 ("r-lattice" ,r-lattice)
10143 ("r-matrix" ,r-matrix)))
10144 (home-page "https://cran.r-project.org/web/packages/flare")
10145 (synopsis "Family of Lasso regression implementations")
10147 "This package provides implementations of a family of Lasso variants
10148 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
10149 high dimensional sparse linear models.")
10150 (license license:gpl2)))
10152 (define-public r-lassopv
10159 (uri (cran-uri "lassopv" version))
10162 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
10163 (build-system r-build-system)
10164 (propagated-inputs `(("r-lars" ,r-lars)))
10165 (home-page "https://github.com/lingfeiwang/lassopv")
10166 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
10168 "This package enables you to estimate the p-values for predictors x
10169 against target variable y in Lasso regression, using the regularization
10170 strength when each predictor enters the active set of regularization path for
10171 the first time as the statistic.")
10172 (license license:gpl3)))
10174 (define-public r-splitstackshape
10176 (name "r-splitstackshape")
10181 (uri (cran-uri "splitstackshape" version))
10184 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
10185 (build-system r-build-system)
10187 `(("r-data-table" ,r-data-table)))
10188 (home-page "https://github.com/mrdwab/splitstackshape")
10189 (synopsis "Stack and reshape datasets after splitting concatenated values")
10191 "Online data collection tools like Google Forms often export
10192 multiple-response questions with data concatenated in cells. The
10193 @code{concat.split} (cSplit) family of functions provided by this package
10194 splits such data into separate cells. This package also includes functions to
10195 stack groups of columns and to reshape wide data, even when the data are
10196 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
10197 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
10199 (license license:gpl3)))
10201 (define-public r-tfmpvalue
10203 (name "r-tfmpvalue")
10208 (uri (cran-uri "TFMPvalue" version))
10211 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
10212 (properties `((upstream-name . "TFMPvalue")))
10213 (build-system r-build-system)
10214 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10215 (home-page "https://github.com/ge11232002/TFMPvalue")
10216 (synopsis "P-value computation for position weight matrices")
10218 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
10219 identification from sequence/alignments, we are interested in the significance
10220 of certain match scores. TFMPvalue provides the accurate calculation of a
10221 p-value with a score threshold for position weight matrices, or the score with
10222 a given p-value. It is an interface to code originally made available by
10223 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
10224 Touzet and Varre (2007).")
10225 (license license:gpl2)))
10227 (define-public r-rnifti
10234 (uri (cran-uri "RNifti" version))
10237 "0hfid40pgfi1ykqka8y3v0m7h0iyd6fbvycvqlad3ibmbg621f0w"))))
10238 (properties `((upstream-name . "RNifti")))
10239 (build-system r-build-system)
10240 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10241 (home-page "https://github.com/jonclayden/RNifti")
10242 (synopsis "Fast R and C++ access to NIfTI images")
10244 "This package provides very fast read and write access to images stored
10245 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
10246 compiled C and interpreted R code. It also provides a C/C++ API that can be
10247 used by other packages.")
10248 (license license:gpl2)))
10250 (define-public r-shades
10257 (uri (cran-uri "shades" version))
10260 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
10261 (build-system r-build-system)
10262 (home-page "https://github.com/jonclayden/shades")
10263 (synopsis "Simple color manipulation")
10265 "This package provides functions for easily manipulating colors,
10266 creating color scales and calculating color distances.")
10267 (license license:bsd-3)))
10269 (define-public r-ore
10276 (uri (cran-uri "ore" version))
10278 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
10279 (build-system r-build-system)
10280 (home-page "https://github.com/jonclayden/ore")
10281 (synopsis "R interface to the Onigmo regular expression library")
10283 "This package provides an alternative to R's built-in functionality for
10284 handling regular expressions, based on the Onigmo library. It offers
10285 first-class compiled regex objects, partial matching and function-based
10286 substitutions, amongst other features.")
10287 (license license:bsd-3)))
10289 (define-public r-reportr
10296 (uri (cran-uri "reportr" version))
10299 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
10300 (build-system r-build-system)
10301 (propagated-inputs `(("r-ore" ,r-ore)))
10302 (home-page "https://github.com/jonclayden/reportr")
10303 (synopsis "General message and error reporting system")
10305 "This package provides a system for reporting messages, which offers
10306 certain useful features over the standard R system, such as the incorporation
10307 of output consolidation, message filtering, assertions, expression
10308 substitution, automatic generation of stack traces for debugging, and
10309 conditional reporting based on the current \"output level\".")
10310 (license license:gpl2)))
10312 (define-public r-tractor-base
10314 (name "r-tractor-base")
10319 (uri (cran-uri "tractor.base" version))
10322 "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i"))))
10323 (properties `((upstream-name . "tractor.base")))
10324 (build-system r-build-system)
10327 ("r-reportr" ,r-reportr)
10328 ("r-rnifti" ,r-rnifti)
10329 ("r-shades" ,r-shades)))
10330 (home-page "http://www.tractor-mri.org.uk")
10331 (synopsis "Read, manipulate and visualize magnetic resonance images")
10333 "This package provides functions for working with magnetic resonance
10334 images. It supports reading and writing of popular file formats (DICOM,
10335 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
10336 visualization; flexible image manipulation; metadata and sparse image
10338 (license license:gpl2)))
10340 (define-public r-grimport
10342 (name "r-grimport")
10347 (uri (cran-uri "grImport" version))
10350 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
10351 (properties `((upstream-name . "grImport")))
10352 (build-system r-build-system)
10354 `(("ghostscript" ,ghostscript)))
10356 `(("r-xml" ,r-xml)))
10357 (home-page "https://cran.r-project.org/web/packages/grImport")
10358 (synopsis "Convert, import, and draw PostScript pictures")
10360 "This package provides functions for converting, importing, and drawing
10361 PostScript pictures in R plots.")
10362 (license license:gpl2+)))
10364 (define-public r-grimport2
10366 (name "r-grimport2")
10371 (uri (cran-uri "grImport2" version))
10374 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
10375 (properties `((upstream-name . "grImport2")))
10376 (build-system r-build-system)
10378 `(("r-base64enc" ,r-base64enc)
10382 (home-page "https://cran.r-project.org/web/packages/grImport2/")
10383 (synopsis "Import SVG graphics")
10385 "This package provides functions for importing external vector images and
10386 drawing them as part of R plots. This package is different from the
10387 @code{grImport} package because, where that package imports PostScript format
10388 images, this package imports SVG format images. Furthermore, this package
10389 imports a specific subset of SVG, so external images must be preprocessed
10390 using a package like @code{rsvg} to produce SVG that this package can import.
10391 SVG features that are not supported by R graphics, such as gradient fills, can
10392 be imported and then exported via the @code{gridSVG} package.")
10393 (license license:gpl2+)))
10395 (define-public r-kohonen
10402 (uri (cran-uri "kohonen" version))
10405 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
10406 (build-system r-build-system)
10408 `(("r-rcpp" ,r-rcpp)))
10409 (home-page "https://cran.r-project.org/web/packages/kohonen")
10410 (synopsis "Supervised and unsupervised self-organising maps")
10412 "This package provides functions to train @dfn{self-organising
10413 maps} (SOMs). Also interrogation of the maps and prediction using trained
10414 maps are supported. The name of the package refers to Teuvo Kohonen, the
10415 inventor of the SOM.")
10416 (license license:gpl2+)))
10418 (define-public r-nnls
10425 (uri (cran-uri "nnls" version))
10428 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
10429 (build-system r-build-system)
10430 (native-inputs `(("gfortran" ,gfortran)))
10431 (home-page "https://cran.r-project.org/web/packages/nnls")
10432 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
10434 "This package provides an R interface to the Lawson-Hanson implementation
10435 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
10436 the combination of non-negative and non-positive constraints.")
10437 (license license:gpl2+)))
10439 (define-public r-iso
10446 (uri (cran-uri "Iso" version))
10449 "014mm5b1f7i6nwlz3kyg1biph0y542kcx5bd13p68cv5a928qzid"))))
10450 (properties `((upstream-name . "Iso")))
10451 (build-system r-build-system)
10452 (native-inputs `(("gfortran" ,gfortran)))
10453 (home-page "http://www.stat.auckland.ac.nz/~rolf/")
10454 (synopsis "Functions to perform isotonic regression")
10456 "This package provides support for linear order and unimodal
10457 order (univariate) isotonic regression and bivariate isotonic regression with
10458 linear order on both variables.")
10459 (license license:gpl2+)))
10461 (define-public r-chemometricswithr
10463 (name "r-chemometricswithr")
10468 (uri (cran-uri "ChemometricsWithR" version))
10471 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
10473 `((upstream-name . "ChemometricsWithR")))
10474 (build-system r-build-system)
10476 `(("r-devtools" ,r-devtools)
10477 ("r-kohonen" ,r-kohonen)
10480 (home-page "https://github.com/rwehrens/CWR")
10481 (synopsis "Chemometrics with R")
10483 "This package provides functions and scripts used in the book
10484 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
10485 Life Sciences\" by Ron Wehrens, Springer (2011).")
10486 (license license:gpl2+)))
10488 (define-public r-als
10495 (uri (cran-uri "ALS" version))
10498 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
10499 (properties `((upstream-name . "ALS")))
10500 (build-system r-build-system)
10503 ("r-nnls" ,r-nnls)))
10504 (home-page "https://cran.r-project.org/web/packages/ALS")
10505 (synopsis "Multivariate curve resolution alternating least squares")
10507 "Alternating least squares is often used to resolve components
10508 contributing to data with a bilinear structure; the basic technique may be
10509 extended to alternating constrained least squares. This package provides an
10510 implementation of @dfn{multivariate curve resolution alternating least
10511 squares} (MCR-ALS).
10513 Commonly applied constraints include unimodality, non-negativity, and
10514 normalization of components. Several data matrices may be decomposed
10515 simultaneously by assuming that one of the two matrices in the bilinear
10516 decomposition is shared between datasets.")
10517 (license license:gpl2+)))
10519 (define-public r-strucchange
10521 (name "r-strucchange")
10526 (uri (cran-uri "strucchange" version))
10529 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
10530 (build-system r-build-system)
10532 `(("r-sandwich" ,r-sandwich)
10534 (home-page "https://cran.r-project.org/web/packages/strucchange")
10535 (synopsis "Testing, monitoring, and dating structural changes")
10537 "This package provides tools for testing, monitoring and dating
10538 structural changes in (linear) regression models. It features tests/methods
10539 from the generalized fluctuation test framework as well as from the F
10540 test (Chow test) framework. This includes methods to fit, plot and test
10541 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
10542 statistics, respectively. It is possible to monitor incoming data online
10543 using fluctuation processes. Finally, the breakpoints in regression models
10544 with structural changes can be estimated together with confidence intervals.
10545 Emphasis is always given to methods for visualizing the data.")
10546 ;; Either of these two GPL versions
10547 (license (list license:gpl2 license:gpl3))))
10549 (define-public r-pixmap
10556 (uri (cran-uri "pixmap" version))
10559 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
10560 (build-system r-build-system)
10561 (home-page "https://cran.r-project.org/web/packages/pixmap")
10562 (synopsis "Tools for bitmap images")
10564 "This package provides functions for importing, exporting, plotting and
10565 other manipulations of bitmapped images.")
10566 (license license:gpl2)))
10568 (define-public r-rapidjsonr
10570 (name "r-rapidjsonr")
10575 (uri (cran-uri "rapidjsonr" version))
10578 "0h4phjjhykbb45rg5b1xn48vqxdcvcngbm0416ds8in7j469wbwd"))))
10579 (build-system r-build-system)
10580 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
10581 (synopsis "JSON parser")
10583 "This package provides JSON parsing capability through the Rapidjson
10585 (license license:expat)))
10587 (define-public r-ontologyindex
10589 (name "r-ontologyindex")
10594 (uri (cran-uri "ontologyIndex" version))
10597 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
10598 (properties `((upstream-name . "ontologyIndex")))
10599 (build-system r-build-system)
10600 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
10601 (synopsis "Functions for processing ontologies in R")
10603 "This package provides functions for reading ontologies into R as lists
10604 and manipulating sets of ontological terms.")
10605 (license license:gpl2+)))
10607 (define-public r-gargle
10614 (uri (cran-uri "gargle" version))
10617 "08zhfk2sl342w35i5n2c93ayypg3z0kbl0020l3y9adqka1vazgx"))))
10618 (build-system r-build-system)
10623 ("r-jsonlite" ,r-jsonlite)
10624 ("r-rlang" ,r-rlang)
10625 ("r-withr" ,r-withr)))
10626 (home-page "https://gargle.r-lib.org")
10627 (synopsis "Utilities for working with Google APIs")
10629 "This package provides utilities for working with Google APIs. This
10630 includes functions and classes for handling common credential types and for
10631 preparing, executing, and processing HTTP requests.")
10632 (license license:expat)))
10634 (define-public r-bigrquery
10636 (name "r-bigrquery")
10641 (uri (cran-uri "bigrquery" version))
10644 "1ggh2gngr5x0g6y7d55y6kvn94anf7qi1bkc28cjmw61hxjq38fb"))))
10645 (build-system r-build-system)
10647 `(("r-assertthat" ,r-assertthat)
10648 ("r-bit64" ,r-bit64)
10651 ("r-gargle" ,r-gargle)
10654 ("r-jsonlite" ,r-jsonlite)
10655 ("r-prettyunits" ,r-prettyunits)
10656 ("r-progress" ,r-progress)
10657 ("r-rapidjsonr" ,r-rapidjsonr)
10659 ("r-rlang" ,r-rlang)
10660 ("r-tibble" ,r-tibble)))
10661 (home-page "https://github.com/rstats-db/bigrquery")
10662 (synopsis "R interface to Google's BigQuery API")
10664 "This package provides an R interface to Google's BigQuery database.")
10665 (license license:gpl3)))
10667 (define-public r-gmp
10670 (version "0.5-13.5")
10674 (uri (cran-uri "gmp" version))
10677 "042mzsl6z6s61fy5m21yf9q83l08vnyqljn4iax7kqyiycpsp0gn"))))
10678 (build-system r-build-system)
10681 (modify-phases %standard-phases
10682 (add-after 'unpack 'set-CC
10683 (lambda _ (setenv "CC" "gcc") #t)))))
10684 (inputs `(("gmp" ,gmp)))
10685 (home-page "https://cran.r-project.org/web/packages/gmp")
10686 (synopsis "Multiple precision arithmetic")
10688 "This package supports multiple precision arithmetic (big integers and
10689 rationals, prime number tests, matrix computation), \"arithmetic without
10690 limitations\" using the GNU Multiple Precision library.")
10691 ;; Any version of the GPL.
10692 (license license:gpl3+)))
10694 (define-public r-rmpfr
10701 (uri (cran-uri "Rmpfr" version))
10704 "1zq3as34r27v2yc729731997wdhxb6cs5ilmak4nmsljabnac7gc"))))
10705 (properties `((upstream-name . "Rmpfr")))
10706 (build-system r-build-system)
10710 `(("r-gmp" ,r-gmp)))
10711 (home-page "http://rmpfr.r-forge.r-project.org/")
10712 (synopsis "R bindings to the MPFR library")
10714 "This package supports arithmetic (via S4 classes and methods) for
10715 arbitrary precision floating point numbers, including transcendental
10716 functions. To this end, the package interfaces with the @dfn{Multiple
10717 Precision Floating-Point Reliable} (MPFR) library.")
10718 (license license:gpl2+)))
10720 (define-public r-assertive-base
10722 (name "r-assertive-base")
10727 (uri (cran-uri "assertive.base" version))
10730 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
10732 `((upstream-name . "assertive.base")))
10733 (build-system r-build-system)
10734 (home-page "https://bitbucket.org/richierocks/assertive.base")
10735 (synopsis "Core of the assertive package")
10737 "This package provides a minimal set of predicates and assertions used by
10738 the assertive package. This is mainly for use by other package developers who
10739 want to include run-time testing features in their own packages.")
10740 (license license:gpl3+)))
10742 (define-public r-assertive-properties
10744 (name "r-assertive-properties")
10749 (uri (cran-uri "assertive.properties" version))
10752 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
10754 `((upstream-name . "assertive.properties")))
10755 (build-system r-build-system)
10757 `(("r-assertive-base" ,r-assertive-base)))
10758 (home-page "https://bitbucket.org/richierocks/assertive.properties")
10759 (synopsis "Assertions to check properties of variables")
10761 "This package provides a set of predicates and assertions for checking
10762 the properties of variables, such as length, names and attributes. This is
10763 mainly for use by other package developers who want to include run-time
10764 testing features in their own packages.")
10765 (license license:gpl3+)))
10767 (define-public r-assertive-numbers
10769 (name "r-assertive-numbers")
10774 (uri (cran-uri "assertive.numbers" version))
10777 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
10779 `((upstream-name . "assertive.numbers")))
10780 (build-system r-build-system)
10782 `(("r-assertive-base" ,r-assertive-base)))
10783 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
10784 (synopsis "Assertions to check properties of numbers")
10786 "This package provides a set of predicates and assertions for checking
10787 the properties of numbers. This is mainly for use by other package developers
10788 who want to include run-time testing features in their own packages.")
10789 (license license:gpl3+)))
10791 (define-public r-assertive-sets
10793 (name "r-assertive-sets")
10798 (uri (cran-uri "assertive.sets" version))
10801 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
10803 `((upstream-name . "assertive.sets")))
10804 (build-system r-build-system)
10806 `(("r-assertive-base" ,r-assertive-base)))
10807 (home-page "https://bitbucket.org/richierocks/assertive.sets")
10808 (synopsis "Assertions to check properties of sets")
10810 "This package provides a set of predicates and assertions for checking
10811 the properties of sets. This is mainly for use by other package developers
10812 who want to include run-time testing features in their own packages.")
10813 (license license:gpl3+)))
10815 (define-public r-assertive-matrices
10817 (name "r-assertive-matrices")
10822 (uri (cran-uri "assertive.matrices" version))
10825 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
10827 `((upstream-name . "assertive.matrices")))
10828 (build-system r-build-system)
10830 `(("r-assertive-base" ,r-assertive-base)))
10831 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
10832 (synopsis "Assertions to check properties of matrices")
10834 "This package provides a set of predicates and assertions for checking
10835 the properties of matrices. This is mainly for use by other package
10836 developers who want to include run-time testing features in their own
10838 (license license:gpl3+)))
10840 (define-public r-assertive-models
10842 (name "r-assertive-models")
10847 (uri (cran-uri "assertive.models" version))
10850 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
10852 `((upstream-name . "assertive.models")))
10853 (build-system r-build-system)
10855 `(("r-assertive-base" ,r-assertive-base)))
10856 (home-page "https://bitbucket.org/richierocks/assertive.models")
10857 (synopsis "Assertions to check properties of models")
10859 "This package provides a set of predicates and assertions for checking
10860 the properties of models. This is mainly for use by other package developers
10861 who want to include run-time testing features in their own packages.")
10862 (license license:gpl3+)))
10864 (define-public r-assertive-reflection
10866 (name "r-assertive-reflection")
10871 (uri (cran-uri "assertive.reflection" version))
10874 "19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj"))))
10876 `((upstream-name . "assertive.reflection")))
10877 (build-system r-build-system)
10879 `(("r-assertive-base" ,r-assertive-base)))
10880 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
10881 (synopsis "Assertions for checking the state of R")
10883 "This package provides a set of predicates and assertions for checking
10884 the state and capabilities of R, the operating system it is running on, and
10885 the IDE being used. This is mainly for use by other package developers who
10886 want to include run-time testing features in their own packages.")
10887 (license license:gpl3+)))
10889 (define-public r-assertive-types
10891 (name "r-assertive-types")
10896 (uri (cran-uri "assertive.types" version))
10899 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
10901 `((upstream-name . "assertive.types")))
10902 (build-system r-build-system)
10904 `(("r-assertive-base" ,r-assertive-base)
10905 ("r-assertive-properties" ,r-assertive-properties)
10906 ("r-codetools" ,r-codetools)))
10907 (home-page "https://bitbucket.org/richierocks/assertive.types")
10908 (synopsis "Assertions to check types of variables")
10910 "This package provides a set of predicates and assertions for checking
10911 the types of variables. This is mainly for use by other package developers
10912 who want to include run-time testing features in their own packages.")
10913 (license license:gpl3+)))
10915 (define-public r-assertive-files
10917 (name "r-assertive-files")
10922 (uri (cran-uri "assertive.files" version))
10925 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
10927 `((upstream-name . "assertive.files")))
10928 (build-system r-build-system)
10930 `(("r-assertive-base" ,r-assertive-base)
10931 ("r-assertive-numbers" ,r-assertive-numbers)))
10932 (home-page "https://bitbucket.org/richierocks/assertive.files")
10933 (synopsis "Assertions to check properties of files")
10935 "This package provides a set of predicates and assertions for checking
10936 the properties of files and connections. This is mainly for use by other
10937 package developers who want to include run-time testing features in their own
10939 (license license:gpl3+)))
10941 (define-public r-assertive-code
10943 (name "r-assertive-code")
10948 (uri (cran-uri "assertive.code" version))
10951 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
10953 `((upstream-name . "assertive.code")))
10954 (build-system r-build-system)
10956 `(("r-assertive-base" ,r-assertive-base)
10957 ("r-assertive-properties" ,r-assertive-properties)
10958 ("r-assertive-types" ,r-assertive-types)))
10959 (home-page "https://bitbucket.org/richierocks/assertive.code")
10960 (synopsis "Assertions to check properties of code")
10962 "This package provides a set of predicates and assertions for checking
10963 the properties of code. This is mainly for use by other package developers
10964 who want to include run-time testing features in their own packages.")
10965 (license license:gpl3+)))
10967 (define-public r-assertive-datetimes
10969 (name "r-assertive-datetimes")
10974 (uri (cran-uri "assertive.datetimes" version))
10977 "00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78"))))
10979 `((upstream-name . "assertive.datetimes")))
10980 (build-system r-build-system)
10982 `(("r-assertive-base" ,r-assertive-base)
10983 ("r-assertive-types" ,r-assertive-types)))
10984 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
10985 (synopsis "Assertions to check properties of dates and times")
10987 "This package provides a set of predicates and assertions for checking
10988 the properties of dates and times. This is mainly for use by other package
10989 developers who want to include run-time testing features in their own
10991 (license license:gpl3+)))
10993 (define-public r-assertive-strings
10995 (name "r-assertive-strings")
11000 (uri (cran-uri "assertive.strings" version))
11003 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
11005 `((upstream-name . "assertive.strings")))
11006 (build-system r-build-system)
11008 `(("r-assertive-base" ,r-assertive-base)
11009 ("r-assertive-types" ,r-assertive-types)
11010 ("r-stringi" ,r-stringi)))
11011 (home-page "https://bitbucket.org/richierocks/assertive.strings")
11012 (synopsis "Assertions to check properties of strings")
11014 "This package provides a set of predicates and assertions for checking
11015 the properties of strings. This is mainly for use by other package developers
11016 who want to include run-time testing features in their own packages.")
11017 (license license:gpl3+)))
11019 (define-public r-assertive-data-us
11021 (name "r-assertive-data-us")
11026 (uri (cran-uri "assertive.data.us" version))
11029 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
11031 `((upstream-name . "assertive.data.us")))
11032 (build-system r-build-system)
11034 `(("r-assertive-base" ,r-assertive-base)
11035 ("r-assertive-strings" ,r-assertive-strings)))
11036 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
11037 (synopsis "Assertions to check properties of strings")
11039 "This package provides a set of predicates and assertions for checking
11040 the properties of US-specific complex data types. This is mainly for use by
11041 other package developers who want to include run-time testing features in
11042 their own packages.")
11043 (license license:gpl3+)))
11045 (define-public r-assertive-data-uk
11047 (name "r-assertive-data-uk")
11052 (uri (cran-uri "assertive.data.uk" version))
11055 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
11057 `((upstream-name . "assertive.data.uk")))
11058 (build-system r-build-system)
11060 `(("r-assertive-base" ,r-assertive-base)
11061 ("r-assertive-strings" ,r-assertive-strings)))
11062 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
11063 (synopsis "Assertions to check properties of strings")
11065 "This package provides a set of predicates and assertions for checking
11066 the properties of UK-specific complex data types. This is mainly for use by
11067 other package developers who want to include run-time testing features in
11068 their own packages.")
11069 (license license:gpl3+)))
11071 (define-public r-assertive-data
11073 (name "r-assertive-data")
11078 (uri (cran-uri "assertive.data" version))
11081 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
11083 `((upstream-name . "assertive.data")))
11084 (build-system r-build-system)
11086 `(("r-assertive-base" ,r-assertive-base)
11087 ("r-assertive-strings" ,r-assertive-strings)))
11088 (home-page "https://bitbucket.org/richierocks/assertive.data")
11089 (synopsis "Assertions to check properties of data")
11091 "This package provides a set of predicates and assertions for checking
11092 the properties of (country independent) complex data types. This is mainly
11093 for use by other package developers who want to include run-time testing
11094 features in their own packages.")
11095 (license license:gpl3+)))
11097 (define-public r-assertive
11099 (name "r-assertive")
11104 (uri (cran-uri "assertive" version))
11107 "0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3"))))
11108 (build-system r-build-system)
11110 `(("r-assertive-base" ,r-assertive-base)
11111 ("r-assertive-code" ,r-assertive-code)
11112 ("r-assertive-data" ,r-assertive-data)
11113 ("r-assertive-data-uk" ,r-assertive-data-uk)
11114 ("r-assertive-data-us" ,r-assertive-data-us)
11115 ("r-assertive-datetimes" ,r-assertive-datetimes)
11116 ("r-assertive-files" ,r-assertive-files)
11117 ("r-assertive-matrices" ,r-assertive-matrices)
11118 ("r-assertive-models" ,r-assertive-models)
11119 ("r-assertive-numbers" ,r-assertive-numbers)
11120 ("r-assertive-properties" ,r-assertive-properties)
11121 ("r-assertive-reflection" ,r-assertive-reflection)
11122 ("r-assertive-sets" ,r-assertive-sets)
11123 ("r-assertive-strings" ,r-assertive-strings)
11124 ("r-assertive-types" ,r-assertive-types)
11125 ("r-knitr" ,r-knitr)))
11126 (home-page "https://bitbucket.org/richierocks/assertive")
11127 (synopsis "Readable check functions to ensure code integrity")
11129 "This package provides lots of predicates (@code{is_*} functions) to
11130 check the state of your variables, and assertions (@code{assert_*} functions)
11131 to throw errors if they aren't in the right form.")
11132 (license license:gpl3+)))
11134 (define-public r-dotcall64
11136 (name "r-dotcall64")
11141 (uri (cran-uri "dotCall64" version))
11144 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
11145 (properties `((upstream-name . "dotCall64")))
11146 (build-system r-build-system)
11147 (native-inputs `(("gfortran" ,gfortran)))
11148 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
11149 (synopsis "Enhanced foreign function interface supporting long vectors")
11151 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
11152 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
11153 supports long vectors, arguments of type 64-bit integer, and provides a
11154 mechanism to avoid unnecessary copies of read-only and write-only arguments.
11155 This makes it a convenient and fast interface to C/C++ and Fortran code.")
11156 (license license:gpl2+)))
11158 (define-public r-spam
11165 (uri (cran-uri "spam" version))
11167 (base32 "0ry0a76cljlmilrzcriiizcidxyhq1i7i9bqhvl1qda81ld8hifi"))))
11168 (build-system r-build-system)
11170 `(("r-dotcall64" ,r-dotcall64)))
11171 (native-inputs `(("gfortran" ,gfortran)))
11172 (home-page "https://www.math.uzh.ch/pages/spam/")
11173 (synopsis "Sparse matrix algebra")
11175 "This package provides a set of functions for sparse matrix algebra.
11176 Differences with other sparse matrix packages are:
11179 @item it only supports (essentially) one sparse matrix format;
11180 @item it is based on transparent and simple structure(s);
11181 @item it is tailored for MCMC calculations within G(M)RF;
11182 @item and it is fast and scalable (with the extension package @code{spam64}).
11184 ;; Either of these licenses
11185 (license (list license:bsd-3 license:lgpl2.0))))
11187 (define-public r-fields
11194 (uri (cran-uri "fields" version))
11196 (base32 "173zm5vr236ydiq0v27qy0l3x7h9fc7jly38iakg77j26i0a01il"))))
11197 (build-system r-build-system)
11199 `(("r-maps" ,r-maps)
11200 ("r-spam" ,r-spam)))
11202 `(("gfortran" ,gfortran)))
11203 (home-page "https://www.image.ucar.edu/fields")
11204 (synopsis "Tools for spatial data")
11206 "This is a package for curve, surface and function fitting with an
11207 emphasis on splines, spatial data and spatial statistics. The major methods
11208 include cubic, and thin plate splines, Kriging, and compactly supported
11209 covariance functions for large data sets.")
11210 (license license:gpl2+)))
11212 (define-public r-spatialextremes
11214 (name "r-spatialextremes")
11215 (version "2.0-7.2")
11219 (uri (cran-uri "SpatialExtremes" version))
11222 "0aqq9ryxi4xsdqjhc1lhb7ai8szs7m2vys6nn0ygps1w3pm4xwj8"))))
11224 `((upstream-name . "SpatialExtremes")))
11225 (build-system r-build-system)
11227 `(("r-fields" ,r-fields)
11228 ("r-maps" ,r-maps)))
11229 (home-page "http://spatialextremes.r-forge.r-project.org/")
11230 (synopsis "Modelling spatial extremes")
11232 "This package provides tools for the statistical modelling of spatial
11233 extremes using max-stable processes, copula or Bayesian hierarchical models.
11234 More precisely, this package allows (conditional) simulations from various
11235 parametric max-stable models, analysis of the extremal spatial dependence, the
11236 fitting of such processes using composite likelihoods or least square (simple
11237 max-stable processes only), model checking and selection and prediction.")
11238 (license license:gpl2+)))
11240 (define-public r-drc
11247 (uri (cran-uri "drc" version))
11250 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
11251 (build-system r-build-system)
11254 ("r-gtools" ,r-gtools)
11256 ("r-multcomp" ,r-multcomp)
11257 ("r-plotrix" ,r-plotrix)
11258 ("r-scales" ,r-scales)))
11259 (home-page "https://cran.r-project.org/web/packages/drc")
11260 (synopsis "Analysis of dose-response curves")
11262 "This package provides a suite of flexible and versatile model fitting
11263 and after-fitting functions for the analysis of dose-response data.")
11264 (license license:gpl2+)))
11266 (define-public r-rmeta
11273 (uri (cran-uri "rmeta" version))
11276 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
11277 (build-system r-build-system)
11278 (home-page "https://cran.r-project.org/web/packages/rmeta")
11279 (synopsis "Tools for meta-analysis")
11281 "This package provides functions for simple fixed and random effects
11282 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
11283 draws standard summary plots, funnel plots, and computes summaries and tests
11284 for association and heterogeneity.")
11285 (license license:gpl2)))
11287 (define-public r-bootstrap
11289 (name "r-bootstrap")
11294 (uri (cran-uri "bootstrap" version))
11297 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
11298 (build-system r-build-system)
11299 (native-inputs `(("gfortran" ,gfortran)))
11300 (home-page "https://cran.r-project.org/web/packages/bootstrap")
11301 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
11303 "This package provides software and data for the book \"An Introduction
11304 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
11305 This package is primarily provided for projects already based on it, and for
11306 support of the book. New projects should preferentially use the recommended
11307 package \"boot\".")
11308 (license license:bsd-3)))
11310 (define-public r-survivalroc
11312 (name "r-survivalroc")
11317 (uri (cran-uri "survivalROC" version))
11320 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
11321 (properties `((upstream-name . "survivalROC")))
11322 (build-system r-build-system)
11323 (home-page "https://cran.r-project.org/web/packages/survivalROC")
11324 (synopsis "Time-dependent ROC curve estimation from censored survival data")
11326 "Compute time-dependent ROC curve from censored survival data using
11327 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
11328 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
11329 (license license:gpl2+)))
11331 (define-public r-longitudinal
11333 (name "r-longitudinal")
11338 (uri (cran-uri "longitudinal" version))
11341 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
11342 (build-system r-build-system)
11343 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
11344 (home-page "http://strimmerlab.org/software/longitudinal/")
11345 (synopsis "Analysis of multiple time course data")
11347 "This package contains general data structures and functions for
11348 longitudinal data with multiple variables, repeated measurements, and
11349 irregularly spaced time points. It also implements a shrinkage estimator of
11350 dynamical correlation and dynamical covariance.")
11351 (license license:gpl3+)))
11353 (define-public r-genenet
11360 (uri (cran-uri "GeneNet" version))
11363 "0w52apk0nnr8nsskf26ff7ana8xiksr8wqmkjxzwhzgg7fncm61p"))))
11364 (properties `((upstream-name . "GeneNet")))
11365 (build-system r-build-system)
11367 `(("r-corpcor" ,r-corpcor)
11368 ("r-fdrtool" ,r-fdrtool)
11369 ("r-longitudinal" ,r-longitudinal)))
11370 (home-page "http://strimmerlab.org/software/genenet/")
11371 (synopsis "Modeling and inferring gene networks")
11373 "This package analyzes gene expression (time series) data with focus on
11374 the inference of gene networks. In particular, GeneNet implements the methods
11375 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
11376 for learning large-scale gene association networks (including assignment of
11377 putative directions).")
11378 (license license:gpl3+)))
11380 (define-public r-rbamtools
11382 (name "r-rbamtools")
11383 (version "2.16.17")
11387 (uri (cran-uri "rbamtools" version))
11390 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
11391 (build-system r-build-system)
11392 (inputs `(("zlib" ,zlib)))
11394 `(("r-refgenome" ,r-refgenome)))
11395 (home-page "https://cran.r-project.org/web/packages/rbamtools")
11396 (synopsis "Read and write BAM (binary alignment) files")
11398 "This package provides an R interface to functions of the SAMtools
11400 (license license:artistic2.0)))
11402 (define-public r-protviz
11409 (uri (cran-uri "protViz" version))
11412 "0cznzm1ijlq33yd5wsa61prav77y2vi698w0n2fx1xcv504c4bjv"))))
11413 (properties `((upstream-name . "protViz")))
11414 (build-system r-build-system)
11415 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11416 (home-page "https://github.com/protViz/protViz/")
11417 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
11419 "This package helps with quality checks, visualizations and analysis of
11420 mass spectrometry data, coming from proteomics experiments. The package is
11421 developed, tested and used at the Functional Genomics Center Zurich, where it
11422 is used mainly for prototyping, teaching, and having fun with proteomics data.
11423 But it can also be used to do data analysis for small scale data sets.")
11424 (license license:gpl3)))
11426 (define-public r-cmprsk
11433 (uri (cran-uri "cmprsk" version))
11435 (base32 "0xhgfg5b4i9skkaxp7gzkafgg5bqs5q1rp4hpw2jjmykg2nifn99"))))
11436 (build-system r-build-system)
11438 `(("r-survival" ,r-survival)))
11440 `(("gfortran" ,gfortran)))
11441 (home-page "https://cran.r-project.org/web/packages/cmprsk")
11442 (synopsis "Subdistribution analysis of competing risks")
11444 "This package provides tool for estimation, testing and regression
11445 modeling of subdistribution functions in competing risks, as described in
11446 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
11447 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
11448 A proportional hazards model for the subdistribution of a competing risk,
11449 JASA, 94:496-509.")
11450 (license license:gpl2+)))
11452 (define-public r-etm
11459 (uri (cran-uri "etm" version))
11462 "1yivbq8y0ijcl1m4nir4q9hp4pi6iphwxgjprygsdf7vp98wq677"))))
11463 (build-system r-build-system)
11465 `(("r-data-table" ,r-data-table)
11466 ("r-lattice" ,r-lattice)
11468 ("r-rcpparmadillo" ,r-rcpparmadillo)
11469 ("r-survival" ,r-survival)))
11470 (home-page "https://cran.r-project.org/web/packages/etm")
11471 (synopsis "Empirical transition matrix")
11473 "The @dfn{empirical transition matrix} (etm) package permits to estimate
11474 the matrix of transition probabilities for any time-inhomogeneous multistate
11475 model with finite state space using the Aalen-Johansen estimator.")
11476 (license license:expat)))
11478 (define-public r-epi
11485 (uri (cran-uri "Epi" version))
11488 "046y10vwks5y84pzccmrn6d4pd6qz70imvp1hw5ywp8fnwzfh4g5"))))
11489 (properties `((upstream-name . "Epi")))
11490 (build-system r-build-system)
11492 `(("r-cmprsk" ,r-cmprsk)
11493 ("r-data-table" ,r-data-table)
11496 ("r-matrix" ,r-matrix)
11498 ("r-numderiv" ,r-numderiv)
11500 ("r-survival" ,r-survival)
11502 (home-page "http://BendixCarstensen.com/Epi/")
11503 (synopsis "Statistical analysis in epidemiology")
11505 "This package provides functions for demographic and epidemiological
11506 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
11507 particular representation, manipulation and simulation of multistate data -
11508 the Lexis suite of functions, which includes interfaces to the @code{mstate},
11509 @code{etm} and @code{cmprsk} packages. It also contains functions for
11510 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
11511 data and some useful functions for tabulation and plotting, as well as a
11512 number of epidemiological data sets.")
11513 (license license:gpl2)))
11515 (define-public r-ppls
11518 (version "1.6-1.1")
11522 (uri (cran-uri "ppls" version))
11525 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
11526 (build-system r-build-system)
11527 (propagated-inputs `(("r-mass" ,r-mass)))
11528 (home-page "https://cran.r-project.org/web/packages/ppls")
11529 (synopsis "Penalized partial least squares")
11531 "This package contains linear and nonlinear regression methods based on
11532 partial least squares and penalization techniques. Model parameters are
11533 selected via cross-validation, and confidence intervals ans tests for the
11534 regression coefficients can be conducted via jackknifing.")
11535 (license license:gpl2+)))
11537 (define-public r-huge
11544 (uri (cran-uri "huge" version))
11546 (base32 "07n3j1va2z4v30rj22cww72khgzbz2xsp0yc0qswlrwyxi4my5i3"))))
11547 (build-system r-build-system)
11549 `(("r-igraph" ,r-igraph)
11551 ("r-matrix" ,r-matrix)
11553 ("r-rcppeigen" ,r-rcppeigen)))
11554 (home-page "https://cran.r-project.org/web/packages/huge")
11555 (synopsis "High-dimensional undirected graph estimation")
11557 "This package provides a general framework for high-dimensional
11558 undirected graph estimation. It integrates data preprocessing, neighborhood
11559 screening, graph estimation, and model selection techniques into a pipeline.")
11560 (license license:gpl2)))
11562 (define-public r-parcor
11569 (uri (cran-uri "parcor" version))
11572 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
11573 (build-system r-build-system)
11576 ("r-genenet" ,r-genenet)
11577 ("r-glmnet" ,r-glmnet)
11579 ("r-ppls" ,r-ppls)))
11580 (home-page "https://cran.r-project.org/web/packages/parcor")
11581 (synopsis "Regularized estimation of partial correlation matrices")
11583 "This package estimates the matrix of partial correlations based on
11584 different regularized regression methods: lasso, adaptive lasso, PLS, and
11585 Ridge Regression. In addition, the package provides model selection for
11586 lasso, adaptive lasso and Ridge regression based on cross-validation.")
11587 (license license:gpl2+)))
11589 (define-public r-mcmc
11596 (uri (cran-uri "mcmc" version))
11599 "1fc6a6asn53lx7x7pnlb5mb716nv4pcmbp99f1i30y4hzygihfj4"))))
11600 (build-system r-build-system)
11601 (home-page "http://www.stat.umn.edu/geyer/mcmc/")
11602 (synopsis "Markov chain Monte Carlo")
11604 "This package simulates continuous distributions of random vectors using
11605 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
11606 function that evaluates the log unnormalized density. Algorithms are random
11607 walk Metropolis algorithm (function @code{metrop}), simulated
11608 tempering (function @code{temper}), and morphometric random walk
11609 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
11610 by change of variable.")
11611 (license license:expat)))
11613 (define-public r-listenv
11620 (uri (cran-uri "listenv" version))
11623 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
11624 (build-system r-build-system)
11626 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11627 (home-page "https://github.com/HenrikBengtsson/listenv")
11628 (synopsis "Environments behaving (almost) as lists")
11630 "This package implements list environments. List environments are
11631 environments that have list-like properties. For instance, the elements of a
11632 list environment are ordered and can be accessed and iterated over using index
11634 (license license:lgpl2.1+)))
11636 (define-public r-globals
11643 (uri (cran-uri "globals" version))
11646 "1ha8iasgijp4q3v2b0b17y1wh7cd3nvzd9b03w49qm2bidkaf68m"))))
11647 (build-system r-build-system)
11649 `(("r-codetools" ,r-codetools)))
11650 (home-page "https://github.com/HenrikBengtsson/globals")
11651 (synopsis "Identify global objects in R expressions")
11653 "This package provides tools to identify global (\"unknown\" or \"free\")
11654 objects in R expressions by code inspection using various strategies, e.g.
11655 conservative or liberal. The objective of this package is to make it as
11656 simple as possible to identify global objects for the purpose of exporting
11657 them in distributed compute environments.")
11658 (license license:lgpl2.1+)))
11660 (define-public r-future
11667 (uri (cran-uri "future" version))
11670 "101hi8warqa0py9l6c5p98f7i9xjhx01w655z6a35jx1dhspykzd"))))
11671 (build-system r-build-system)
11673 `(("r-digest" ,r-digest)
11674 ("r-globals" ,r-globals)
11675 ("r-listenv" ,r-listenv)))
11677 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11678 (home-page "https://github.com/HenrikBengtsson/future")
11679 (synopsis "Unified parallel and distributed processing in R")
11681 "The purpose of this package is to provide a lightweight and unified
11682 Future API for sequential and parallel processing of R expression via futures.
11683 This package implements sequential, multicore, multisession, and cluster
11684 futures. With these, R expressions can be evaluated on the local machine, in
11685 parallel a set of local machines, or distributed on a mix of local and remote
11686 machines. Extensions to this package implement additional backends for
11687 processing futures via compute cluster schedulers etc. Because of its unified
11688 API, there is no need to modify any code in order to switch from sequential on
11689 the local machine to, say, distributed processing on a remote compute cluster.")
11690 (license license:lgpl2.1+)))
11692 (define-public r-future-apply
11694 (name "r-future-apply")
11699 (uri (cran-uri "future.apply" version))
11702 "0wd3bh114zkvrqlpn8gqz4ix1igr9hr8x72h2g00a7mqkfjfqx33"))))
11703 (properties `((upstream-name . "future.apply")))
11704 (build-system r-build-system)
11706 `(("r-future" ,r-future)
11707 ("r-globals" ,r-globals)))
11709 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11710 (home-page "https://github.com/HenrikBengtsson/future.apply")
11711 (synopsis "Apply function to elements in parallel using futures")
11713 "This package provides implementations of @code{apply()},
11714 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
11715 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
11716 can be resolved using any future-supported backend, e.g. parallel on the local
11717 machine or distributed on a compute cluster.")
11718 (license license:gpl2+)))
11720 (define-public r-rsvd
11727 (uri (cran-uri "rsvd" version))
11730 "0fia77y5fxnhwkcxlgp98ygb8fdfraky75x80hkf7kvvpwc5rzn8"))))
11731 (build-system r-build-system)
11733 `(("r-matrix" ,r-matrix)))
11734 (home-page "https://github.com/erichson/rSVD")
11735 (synopsis "Randomized singular value decomposition")
11737 "Low-rank matrix decompositions are fundamental tools and widely used for
11738 data analysis, dimension reduction, and data compression. Classically, highly
11739 accurate deterministic matrix algorithms are used for this task. However, the
11740 emergence of large-scale data has severely challenged our computational
11741 ability to analyze big data. The concept of randomness has been demonstrated
11742 as an effective strategy to quickly produce approximate answers to familiar
11743 problems such as the @dfn{singular value decomposition} (SVD). This package
11744 provides several randomized matrix algorithms such as the randomized singular
11745 value decomposition (@code{rsvd}), randomized principal component
11746 analysis (@code{rpca}), randomized robust principal component
11747 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
11748 and the randomized CUR decomposition (@code{rcur}). In addition several plot
11749 functions are provided.")
11750 (license license:gpl3+)))
11752 (define-public r-sloop
11759 (uri (cran-uri "sloop" version))
11762 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
11763 (build-system r-build-system)
11765 `(("r-codetools" ,r-codetools)
11766 ("r-crayon" ,r-crayon)
11767 ("r-purrr" ,r-purrr)
11768 ("r-rlang" ,r-rlang)
11769 ("r-tibble" ,r-tibble)))
11770 (home-page "https://github.com/r-lib/sloop")
11771 (synopsis "Helpers for object-oriented programming in R")
11773 "This package provides a collection of helper functions designed to
11774 help you to better understand object oriented programming in R, particularly
11776 (license license:gpl3)))
11778 (define-public r-capushe
11785 (uri (cran-uri "capushe" version))
11788 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
11789 (build-system r-build-system)
11790 (propagated-inputs `(("r-mass" ,r-mass)))
11791 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
11792 (synopsis "Calibrating penalties using slope heuristics")
11794 "This package provides tools for the calibration of penalized criteria
11795 for model selection. The calibration methods available are based on the slope
11797 (license license:gpl2+)))
11799 (define-public r-dorng
11806 (uri (cran-uri "doRNG" version))
11809 "1sb75aqkliprglfxc4x4wds6alqgzhvl2n812g1d32a88ra3slr7"))))
11810 (properties `((upstream-name . "doRNG")))
11811 (build-system r-build-system)
11813 `(("r-foreach" ,r-foreach)
11814 ("r-iterators" ,r-iterators)
11815 ("r-pkgmaker" ,r-pkgmaker)
11816 ("r-rngtools" ,r-rngtools)))
11817 (home-page "https://renozao.github.io/doRNG/")
11818 (synopsis "Generic reproducible parallel backend for foreach loops")
11820 "This package provides functions to perform reproducible parallel
11821 @code{foreach} loops, using independent random streams as generated by
11822 L'Ecuyer's combined multiple-recursive generator. It enables to easily
11823 convert standard @code{%dopar%} loops into fully reproducible loops,
11824 independently of the number of workers, the task scheduling strategy, or the
11825 chosen parallel environment and associated foreach backend.")
11826 (license license:gpl2+)))
11828 (define-public r-blockmodeling
11830 (name "r-blockmodeling")
11835 (uri (cran-uri "blockmodeling" version))
11838 "11v9903y9dwlzaqp8sx0fsibcg82phvappddy37r8lnxd4vchsd2"))))
11839 (build-system r-build-system)
11841 `(("r-doparallel" ,r-doparallel)
11842 ("r-dorng" ,r-dorng)
11843 ("r-foreach" ,r-foreach)
11844 ("r-matrix" ,r-matrix)))
11845 (native-inputs `(("gfortran" ,gfortran)))
11846 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
11847 (synopsis "Generalized and classical blockmodeling of valued networks")
11849 "This package is primarily meant as an implementation of generalized
11850 blockmodeling for valued networks. In addition, measures of similarity or
11851 dissimilarity based on structural equivalence and regular equivalence (REGE
11852 algorithms) can be computed and partitioned matrices can be plotted.")
11853 (license license:gpl2+)))
11855 (define-public r-upsetr
11862 (uri (cran-uri "UpSetR" version))
11865 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
11866 (properties `((upstream-name . "UpSetR")))
11867 (build-system r-build-system)
11869 `(("r-ggplot2" ,r-ggplot2)
11870 ("r-gridextra" ,r-gridextra)
11872 ("r-scales" ,r-scales)))
11873 (home-page "https://github.com/hms-dbmi/UpSetR")
11874 (synopsis "Visualize intersecting sets")
11876 "This package provides a more scalable alternative to Venn and Euler
11877 diagrams for visualizing intersecting sets. Create visualizations of
11878 intersecting sets using a novel matrix design, along with visualizations of
11879 several common set, element and attribute related tasks.")
11880 (license license:expat)))
11882 ;; This package includes a JavaScript file, which is not minified. When
11883 ;; upgrading please check that there are no new minified JavaScript files.
11884 (define-public r-shinybs
11891 (uri (cran-uri "shinyBS" version))
11894 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
11895 (properties `((upstream-name . "shinyBS")))
11896 (build-system r-build-system)
11897 ;; The tests spawn Shiny browser apps. They cannot be run
11898 ;; non-interactively.
11899 (arguments '(#:tests? #f))
11901 `(("r-htmltools" ,r-htmltools)
11902 ("r-shiny" ,r-shiny)))
11903 (home-page "https://ebailey78.github.io/shinyBS/")
11904 (synopsis "Twitter Bootstrap components for Shiny")
11906 "This package adds additional Twitter Bootstrap components to Shiny.")
11907 (license license:gpl3)))
11909 (define-public r-outliers
11911 (name "r-outliers")
11916 (uri (cran-uri "outliers" version))
11919 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
11920 (build-system r-build-system)
11921 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
11922 (synopsis "Tests for outliers")
11924 "This package provides a collection of some tests commonly used for
11925 identifying outliers.")
11926 (license license:gpl2+)))
11928 (define-public r-bayesm
11935 (uri (cran-uri "bayesm" version))
11937 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
11938 (build-system r-build-system)
11940 `(("r-rcpp" ,r-rcpp)
11941 ("r-rcpparmadillo" ,r-rcpparmadillo)))
11942 (home-page "http://www.perossi.org/home/bsm-1")
11943 (synopsis "Bayesian inference for marketing/micro-econometrics")
11945 "This package covers many important models used in marketing and
11946 micro-econometrics applications, including Bayes Regression (univariate or
11947 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
11948 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
11949 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
11950 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
11951 Estimation with normal base, Hierarchical Linear Models with normal prior and
11952 covariates, Hierarchical Linear Models with a mixture of normals prior and
11953 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
11954 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
11955 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
11956 analysis of choice-based conjoint data, Bayesian treatment of linear
11957 instrumental variables models, Analysis of Multivariate Ordinal survey data
11958 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
11959 Coefficient Logit Models.")
11960 (license license:gpl2+)))
11962 (define-public r-tensora
11969 (uri (cran-uri "tensorA" version))
11972 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
11973 (properties `((upstream-name . "tensorA")))
11974 (build-system r-build-system)
11975 (home-page "http://www.stat.boogaart.de/tensorA")
11976 (synopsis "Advanced tensor arithmetic with named indices")
11978 "This package provides convenience functions for advanced linear algebra
11979 with tensors and computation with datasets of tensors on a higher level
11980 abstraction. It includes Einstein and Riemann summing conventions, dragging,
11981 co- and contravariate indices, and parallel computations on sequences of
11983 (license license:gpl2+)))
11985 (define-public r-rarpack
11992 (uri (cran-uri "rARPACK" version))
11995 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
11996 (properties `((upstream-name . "rARPACK")))
11997 (build-system r-build-system)
11998 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
11999 (home-page "https://github.com/yixuan/rARPACK")
12000 (synopsis "Solvers for large scale eigenvalue and SVD problems")
12002 "This package was previously an R wrapper of the ARPACK library, and now
12003 a shell of the R package RSpectra, an R interface to the Spectra library for
12004 solving large scale eigenvalue/vector problems. The current version of
12005 rARPACK simply imports and exports the functions provided by RSpectra. New
12006 users of rARPACK are advised to switch to the RSpectra package.")
12007 (license license:bsd-3)))
12009 (define-public r-compositions
12011 (name "r-compositions")
12016 (uri (cran-uri "compositions" version))
12019 "103hbmibrf1n333pn4xpll1gqqsv4szms0n5gdq7zak31aar0bg4"))))
12020 (build-system r-build-system)
12022 `(("r-bayesm" ,r-bayesm)
12023 ("r-robustbase" ,r-robustbase)
12024 ("r-tensora" ,r-tensora)))
12025 (home-page "http://www.stat.boogaart.de/compositions")
12026 (synopsis "Compositional data analysis")
12028 "This package provides functions for the consistent analysis of
12029 compositional data (e.g. portions of substances) and positive
12030 numbers (e.g. concentrations).")
12031 (license license:gpl2+)))
12033 (define-public r-cobs
12040 (uri (cran-uri "cobs" version))
12043 "1pqvz7czcchri4x79g78hbwyagb3bqzdqb047zkbdinyz067c7kb"))))
12044 (build-system r-build-system)
12046 `(("r-quantreg" ,r-quantreg)
12047 ("r-sparsem" ,r-sparsem)))
12048 (home-page "https://cran.r-project.org/web/packages/cobs")
12049 (synopsis "Constrained B-Splines (sparse matrix based)")
12051 "This package provides qualitatively constrained (regression) smoothing
12052 splines via linear programming and sparse matrices.")
12053 (license license:gpl2+)))
12055 (define-public r-drimpute
12057 (name "r-drimpute")
12062 (uri (cran-uri "DrImpute" version))
12065 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
12066 (properties `((upstream-name . "DrImpute")))
12067 (build-system r-build-system)
12069 `(("r-rcpp" ,r-rcpp)
12070 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12071 (home-page "https://github.com/ikwak2/DrImpute")
12072 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
12074 "This is an R package for imputing dropout events. Many statistical
12075 methods in cell type identification, visualization and lineage reconstruction
12076 do not account for dropout events. DrImpute can improve the performance of
12077 such software by imputing dropout events.")
12078 (license license:gpl3)))
12080 (define-public r-gamlss-dist
12082 (name "r-gamlss-dist")
12087 (uri (cran-uri "gamlss.dist" version))
12089 (base32 "1rl7hzdg5xpvaq3yyzwxhsaqzzs0qidi3ibv454fisijgv8l4vqw"))))
12090 (properties `((upstream-name . "gamlss.dist")))
12091 (build-system r-build-system)
12092 (propagated-inputs `(("r-mass" ,r-mass)))
12093 (home-page "http://www.gamlss.org/")
12094 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
12096 "This package provides a set of distributions which can be used for
12097 modelling the response variables in Generalized Additive Models for Location
12098 Scale and Shape. The distributions can be continuous, discrete or mixed
12099 distributions. Extra distributions can be created, by transforming, any
12100 continuous distribution defined on the real line, to a distribution defined on
12101 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
12102 transformation, respectively.")
12103 ;; Either version of the GPL.
12104 (license (list license:gpl2 license:gpl3))))
12106 ;; This package includes JavaScript files, which are not minified. When
12107 ;; upgrading please check that there are no new minified JavaScript files.
12108 (define-public r-shinyjs
12115 (uri (cran-uri "shinyjs" version))
12118 "113zpijri0l80rlgrvqn6bxk0sdqgl79h7yhja2p76f9dc9i2sr8"))))
12119 (build-system r-build-system)
12121 `(("r-digest" ,r-digest)
12122 ("r-htmltools" ,r-htmltools)
12123 ("r-jsonlite" ,r-jsonlite)
12124 ("r-shiny" ,r-shiny)))
12125 (home-page "https://deanattali.com/shinyjs")
12126 (synopsis "Improve the user experience of your Shiny apps")
12128 "Perform common useful JavaScript operations in Shiny apps that will
12129 greatly improve your apps without having to know any JavaScript. Examples
12130 include: hiding an element, disabling an input, resetting an input back to its
12131 original value, delaying code execution by a few seconds, and many more useful
12132 functions for both the end user and the developer. Shinyjs can also be used
12133 to easily call your own custom JavaScript functions from R.")
12134 (license license:agpl3+)))
12136 ;; This package includes minified JavaScript files. When upgrading please
12137 ;; check that there are no new minified JavaScript files.
12138 (define-public r-colourpicker
12140 (name "r-colourpicker")
12145 (uri (cran-uri "colourpicker" version))
12148 "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
12149 (build-system r-build-system)
12151 `(#:modules ((guix build utils)
12152 (guix build r-build-system)
12156 (modify-phases %standard-phases
12157 (add-after 'unpack 'process-javascript
12158 (lambda* (#:key inputs #:allow-other-keys)
12159 (with-directory-excursion "inst"
12163 `((,(assoc-ref inputs "js-salvattore")
12164 "examples/colourInput/www/salvattore.min.js")
12165 (,(assoc-ref inputs "js-jquery")
12166 "htmlwidgets/lib/jquery/jquery.min.js")
12167 ("www/shared/colourpicker/js/colourpicker.js"
12168 "www/shared/colourpicker/js/colourpicker.min.js"))))
12169 (lambda (sources targets)
12170 (for-each (lambda (source target)
12171 (format #t "Processing ~a --> ~a~%"
12173 (delete-file target)
12174 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
12175 (call-with-output-file target
12177 (dump-port minified port)))))
12178 sources targets))))
12181 `(("r-ggplot2" ,r-ggplot2)
12182 ("r-htmltools" ,r-htmltools)
12183 ("r-htmlwidgets" ,r-htmlwidgets)
12184 ("r-jsonlite" ,r-jsonlite)
12185 ("r-miniui" ,r-miniui)
12186 ("r-shiny" ,r-shiny)
12187 ("r-shinyjs" ,r-shinyjs)))
12189 `(("uglify-js" ,uglify-js)
12193 (uri "https://code.jquery.com/jquery-3.3.1.js")
12196 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
12200 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
12203 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
12204 (home-page "https://github.com/daattali/colourpicker")
12205 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
12207 "This package provides a color picker that can be used as an input in
12208 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
12209 custom color palettes, and many more options. A plot color helper tool is
12210 available as an RStudio Addin, which helps you pick colors to use in your
12211 plots. A more generic color picker RStudio Addin is also provided to let you
12212 select colors to use in your R code.")
12213 (license license:expat)))
12215 (define-public r-ggextra
12222 (uri (cran-uri "ggExtra" version))
12225 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
12226 (properties `((upstream-name . "ggExtra")))
12227 (build-system r-build-system)
12229 `(("r-colourpicker" ,r-colourpicker)
12230 ("r-ggplot2" ,r-ggplot2)
12231 ("r-gtable" ,r-gtable)
12232 ("r-miniui" ,r-miniui)
12234 ("r-scales" ,r-scales)
12235 ("r-shiny" ,r-shiny)
12236 ("r-shinyjs" ,r-shinyjs)))
12237 (home-page "https://github.com/daattali/ggExtra")
12238 (synopsis "Marginal histograms for ggplot2 and other enhancements")
12240 "This package is a collection of functions and layers to enhance ggplot2.
12241 The flagship function is @code{ggMarginal()}, which can be used to add
12242 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
12243 (license license:expat)))
12245 (define-public r-minpack-lm
12247 (name "r-minpack-lm")
12252 (uri (cran-uri "minpack.lm" version))
12255 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
12256 (properties `((upstream-name . "minpack.lm")))
12257 (build-system r-build-system)
12258 (native-inputs `(("gfortran" ,gfortran)))
12259 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
12260 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
12262 "The @code{nls.lm} function provides an R interface to @code{lmder} and
12263 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
12264 problems by a modification of the Levenberg-Marquardt algorithm, with support
12265 for lower and upper parameter bounds. The implementation can be used via
12266 @code{nls}-like calls using the @code{nlsLM} function.")
12267 (license license:gpl3)))
12269 (define-public r-moments
12276 (uri (cran-uri "moments" version))
12279 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
12280 (build-system r-build-system)
12281 (home-page "https://cran.r-project.org/web/packages/moments")
12282 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
12284 "This package provides functions to calculate: moments, Pearson's
12285 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
12286 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
12287 (license license:gpl2+)))
12289 (define-public r-msir
12296 (uri (cran-uri "msir" version))
12299 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
12300 (build-system r-build-system)
12302 `(("r-mclust" ,r-mclust)))
12303 (home-page "https://cran.r-project.org/web/packages/msir")
12304 (synopsis "Model-based sliced inverse regression")
12306 "This is an R package for dimension reduction based on finite Gaussian
12307 mixture modeling of inverse regression.")
12308 (license license:gpl2+)))
12310 (define-public r-pbivnorm
12312 (name "r-pbivnorm")
12317 (uri (cran-uri "pbivnorm" version))
12320 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
12321 (build-system r-build-system)
12322 (native-inputs `(("gfortran" ,gfortran)))
12323 (home-page "https://github.com/brentonk/pbivnorm")
12324 (synopsis "Vectorized bivariate normal CDF")
12326 "This package provides a vectorized R function for calculating
12327 probabilities from a standard bivariate normal CDF.")
12328 (license license:gpl2+)))
12330 (define-public r-lavaan
12337 (uri (cran-uri "lavaan" version))
12340 "04kvsh2m6mnzlhv83phr3hjzy4sx1ck6f7dgsm7xb8cs84dnxszy"))))
12341 (build-system r-build-system)
12343 `(("r-mass" ,r-mass)
12344 ("r-mnormt" ,r-mnormt)
12345 ("r-numderiv" ,r-numderiv)
12346 ("r-pbivnorm" ,r-pbivnorm)))
12347 (home-page "http://lavaan.ugent.be")
12348 (synopsis "Latent variable analysis")
12350 "This package provides tools to fit a variety of latent variable models,
12351 including confirmatory factor analysis, structural equation modeling and
12352 latent growth curve models.")
12353 (license license:gpl2+)))
12355 (define-public r-nonnest2
12357 (name "r-nonnest2")
12362 (uri (cran-uri "nonnest2" version))
12365 "1bq44qqmm59j91m0sny4xnqmxqlga4cm48qdsw8xfs3x19xwmxk6"))))
12366 (build-system r-build-system)
12368 `(("r-compquadform" ,r-compquadform)
12369 ("r-lavaan" ,r-lavaan)
12370 ("r-mvtnorm" ,r-mvtnorm)
12371 ("r-sandwich" ,r-sandwich)))
12372 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
12373 (synopsis "Tests of non-nested models")
12375 "This package allows for testing of non-nested models. It includes tests
12376 of model distinguishability and of model fit that can be applied to both
12377 nested and non-nested models. The package also includes functionality to
12378 obtain confidence intervals associated with AIC and BIC.")
12379 ;; Either version of the GPL.
12380 (license (list license:gpl2 license:gpl3))))
12382 (define-public r-penalized
12384 (name "r-penalized")
12389 (uri (cran-uri "penalized" version))
12392 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
12393 (build-system r-build-system)
12395 `(("r-rcpp" ,r-rcpp)
12396 ("r-rcpparmadillo" ,r-rcpparmadillo)
12397 ("r-survival" ,r-survival)))
12398 (home-page "https://cran.r-project.org/web/packages/penalized/")
12399 (synopsis "Penalized estimation in GLMs and in the Cox model")
12401 "This package provides tools for fitting possibly high dimensional
12402 penalized regression models. The penalty structure can be any combination of
12403 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
12404 constraint on the regression coefficients. The supported regression models
12405 are linear, logistic and Poisson regression and the Cox Proportional Hazards
12406 model. Cross-validation routines allow optimization of the tuning
12408 (license license:gpl2+)))
12410 (define-public r-zim
12417 (uri (cran-uri "ZIM" version))
12420 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
12421 (properties `((upstream-name . "ZIM")))
12422 (build-system r-build-system)
12423 (propagated-inputs `(("r-mass" ,r-mass)))
12424 (home-page "https://github.com/biostatstudio/ZIM")
12425 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
12427 "Analyze count time series with excess zeros. Two types of statistical
12428 models are supported: Markov regression and state-space models. They are also
12429 known as observation-driven and parameter-driven models respectively in the
12430 time series literature. The functions used for Markov regression or
12431 observation-driven models can also be used to fit ordinary regression models
12432 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
12433 negative binomial (ZINB) assumption. The package also contains miscellaneous
12434 functions to compute density, distribution, quantile, and generate random
12435 numbers from ZIP and ZINB distributions.")
12436 (license license:gpl3)))
12438 (define-public r-nor1mix
12445 (uri (cran-uri "nor1mix" version))
12448 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
12449 (build-system r-build-system)
12450 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
12451 (synopsis "Normal (1-d) mixture models")
12453 "This package provides S3 classes and methods for one-dimensional normal
12454 mixture models, for, e.g., density estimation or clustering algorithms
12455 research and teaching; it provides the widely used Marron-Wand densities. It
12456 also provides tools for efficient random number generation and graphics.")
12457 (license license:gpl2+)))
12459 (define-public r-beanplot
12461 (name "r-beanplot")
12466 (uri (cran-uri "beanplot" version))
12469 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
12470 (build-system r-build-system)
12471 (home-page "https://cran.r-project.org/web/packages/beanplot/")
12472 (synopsis "Visualization via beanplots")
12474 "This package provides beanplots, an alternative to
12475 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
12477 (license license:gpl2)))
12479 (define-public r-pbdzmq
12486 (uri (cran-uri "pbdZMQ" version))
12489 "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
12490 (properties `((upstream-name . "pbdZMQ")))
12491 (build-system r-build-system)
12493 `(("zeromq" ,zeromq)
12496 `(("pkg-config" ,pkg-config)))
12497 (home-page "https://pbdr.org/")
12498 (synopsis "R interface to ZeroMQ")
12500 "ZeroMQ is a well-known library for high-performance asynchronous
12501 messaging in scalable, distributed applications. This package provides high
12502 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
12503 interactive client/server programming frameworks. A few wrapper functions
12504 compatible with @code{rzmq} are also provided.")
12505 (license license:gpl3)))
12507 (define-public r-repr
12514 (uri (cran-uri "repr" version))
12517 "0wn9fdddqjgn0bdfl75x89rcxahbgqs324bhg0pfq6va5q2mlbbw"))))
12518 (build-system r-build-system)
12520 `(("r-base64enc" ,r-base64enc)
12521 ("r-htmltools" ,r-htmltools)
12522 ("r-jsonlite" ,r-jsonlite)
12523 ("r-pillar" ,r-pillar)))
12524 (home-page "https://cran.r-project.org/web/packages/repr/")
12525 (synopsis "Serializable representations")
12527 "This package provides string and binary representations of objects for
12528 several formats and MIME types.")
12529 (license license:gpl3)))
12531 (define-public r-irdisplay
12533 (name "r-irdisplay")
12538 (uri (cran-uri "IRdisplay" version))
12541 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
12542 (properties `((upstream-name . "IRdisplay")))
12543 (build-system r-build-system)
12545 `(("r-repr" ,r-repr)))
12546 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
12547 (synopsis "Jupyter display machinery")
12549 "This package provides an interface to the rich display capabilities of
12550 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
12551 running IRkernel session.")
12552 (license license:expat)))
12554 (define-public r-irkernel
12556 (name "r-irkernel")
12561 (uri (cran-uri "IRkernel" version))
12564 "1viqxs91dys1z4cf7gb59rmqvzb8lc7jdp4azrpmhgwa8qf46s94"))))
12565 (properties `((upstream-name . "IRkernel")))
12566 (build-system r-build-system)
12569 (modify-phases %standard-phases
12570 (add-after 'install 'install-kernelspec
12571 (lambda* (#:key outputs #:allow-other-keys)
12572 (let ((out (assoc-ref outputs "out")))
12573 (setenv "HOME" "/tmp")
12574 (invoke "jupyter" "kernelspec" "install"
12577 (string-append out "/site-library/IRkernel/kernelspec"))
12578 ;; Record the absolute file name of the 'R' executable in
12580 (substitute* (string-append out "/share/jupyter"
12581 "/kernels/ir/kernel.json")
12583 (string-append "[\"" (which "R") "\",")))
12586 `(("jupyter" ,jupyter)))
12588 `(("r-crayon" ,r-crayon)
12589 ("r-digest" ,r-digest)
12590 ("r-evaluate" ,r-evaluate)
12591 ("r-irdisplay" ,r-irdisplay)
12592 ("r-jsonlite" ,r-jsonlite)
12593 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
12594 ("r-minimal" ,r-minimal)
12595 ("r-pbdzmq" ,r-pbdzmq)
12597 ("r-uuid" ,r-uuid)))
12598 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
12599 (synopsis "Native R kernel for Jupyter")
12601 "The R kernel for the Jupyter environment executes R code which the
12602 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
12604 (license license:expat)))
12606 (define-public r-gmodels
12613 (uri (cran-uri "gmodels" version))
12616 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
12617 (build-system r-build-system)
12619 `(("r-gdata" ,r-gdata)
12620 ("r-mass" ,r-mass)))
12621 (home-page "https://cran.r-project.org/web/packages/gmodels/")
12622 (synopsis "Various R programming tools for model fitting")
12624 "This package provides various R programming tools for model fitting.")
12625 (license license:gpl2)))
12627 (define-public r-apcluster
12629 (name "r-apcluster")
12634 (uri (cran-uri "apcluster" version))
12637 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
12638 (build-system r-build-system)
12640 `(("r-matrix" ,r-matrix)
12641 ("r-rcpp" ,r-rcpp)))
12642 (home-page "https://cran.r-project.org/web/packages/apcluster/")
12643 (synopsis "Affinity propagation clustering")
12645 "This package implements affinity propagation clustering introduced by
12646 Frey and Dueck (2007). The package further provides leveraged affinity
12647 propagation and an algorithm for exemplar-based agglomerative clustering that
12648 can also be used to join clusters obtained from affinity propagation. Various
12649 plotting functions are available for analyzing clustering results.")
12650 (license license:gpl2+)))
12652 (define-public r-valr
12659 (uri (cran-uri "valr" version))
12662 "14jhrwkiwmha3vlmm7b50n2xxyizj6ddmy89gb20mpzq7qhz1ika"))))
12663 (build-system r-build-system)
12665 `(("r-broom" ,r-broom)
12666 ("r-dplyr" ,r-dplyr)
12667 ("r-ggplot2" ,r-ggplot2)
12669 ("r-readr" ,r-readr)
12670 ("r-rlang" ,r-rlang)
12671 ("r-stringr" ,r-stringr)
12672 ("r-tibble" ,r-tibble)))
12673 (home-page "http://github.com/rnabioco/valr")
12674 (synopsis "Genome interval arithmetic in R")
12676 "This package enables you to read and manipulate genome intervals and
12677 signals. It provides functionality similar to command-line tool suites within
12678 R, enabling interactive analysis and visualization of genome-scale data.")
12679 (license license:expat)))
12681 (define-public r-rematch2
12683 (name "r-rematch2")
12688 (uri (cran-uri "rematch2" version))
12691 "00cznm6rk33b53w7zybkz7549bnydc66znpi5mb0xd24pmqp0rvq"))))
12692 (build-system r-build-system)
12694 `(("r-tibble" ,r-tibble)))
12695 (home-page "https://github.com/r-lib/rematch2")
12696 (synopsis "Tidy output from regular expression matching")
12698 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
12699 return the match results in tidy data frames.")
12700 (license license:expat)))
12702 (define-public r-picante
12709 (uri (cran-uri "picante" version))
12712 "1bcq2j7fs89c2jib68qq6la67rxyg9raryf162mwvjakpf6k19l1"))))
12713 (build-system r-build-system)
12717 ("r-vegan" ,r-vegan)))
12718 (home-page "https://cran.r-project.org/web/packages/picante/")
12719 (synopsis "Integrating phylogenies and ecology")
12721 "This package provides functions for phylocom integration, community
12722 analyses, null-models, traits and evolution. It implements numerous
12723 ecophylogenetic approaches including measures of community phylogenetic and
12724 trait diversity, phylogenetic signal, estimation of trait values for
12725 unobserved taxa, null models for community and phylogeny randomizations, and
12726 utility functions for data input/output and phylogeny plotting. A full
12727 description of package functionality and methods are provided by Kembel et
12729 (license license:gpl2)))
12731 (define-public r-reinforcelearn
12733 (name "r-reinforcelearn")
12738 (uri (cran-uri "reinforcelearn" version))
12741 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
12742 (build-system r-build-system)
12744 `(("r-checkmate" ,r-checkmate)
12746 ("r-purrr" ,r-purrr)
12748 (home-page "https://markusdumke.github.io/reinforcelearn")
12749 (synopsis "Reinforcement learning")
12751 "This package implements reinforcement learning environments and
12752 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
12753 can be used with function approximation, eligibility traces (Singh & Sutton,
12754 1996) and experience replay (Mnih et al., 2013).")
12755 (license license:expat)))
12757 (define-public r-lemon
12764 (uri (cran-uri "lemon" version))
12767 "0wsn5bfg10wq4dnrgpyraz2bzx9p19c7hf1pwj3h4zmpqfgsdbpw"))))
12768 (build-system r-build-system)
12770 `(("r-ggplot2" ,r-ggplot2)
12771 ("r-gridextra" ,r-gridextra)
12772 ("r-gtable" ,r-gtable)
12773 ("r-knitr" ,r-knitr)
12774 ("r-lattice" ,r-lattice)
12776 ("r-scales" ,r-scales)))
12777 (home-page "https://github.com/stefanedwards/lemon")
12778 (synopsis "Freshen up your ggplot2 plots")
12780 "This package provides functions for working with legends and axis lines
12781 of ggplot2, facets that repeat axis lines on all panels, and some knitr
12783 (license license:gpl3)))
12785 (define-public r-wgaim
12792 (uri (cran-uri "wgaim" version))
12794 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
12795 (build-system r-build-system)
12797 `(("r-ggplot2" ,r-ggplot2)
12799 (home-page "https://cran.r-project.org/web/packages/wgaim")
12800 (synopsis "Whole genome average interval mapping for QTL detection")
12802 "This package integrates sophisticated mixed modelling methods with a
12803 whole genome approach to detecting significant QTL in linkage maps.")
12804 (license license:gpl2+)))
12806 (define-public r-bedr
12813 (uri (cran-uri "bedr" version))
12816 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
12817 (build-system r-build-system)
12819 `(("r-data-table" ,r-data-table)
12820 ("r-r-utils" ,r-r-utils)
12821 ("r-testthat" ,r-testthat)
12822 ("r-venndiagram" ,r-venndiagram)
12825 ("bedtools" ,bedtools)
12826 ("htslib" ,htslib))) ; for tabix
12828 `(("r-knitr" ,r-knitr))) ; for vignettes
12829 (home-page "https://cran.r-project.org/web/packages/bedr")
12830 (synopsis "Genomic region processing")
12832 "This package is for genomic regions processing using command line tools
12833 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
12834 utilities to perform genome arithmetic e.g indexing, formatting and merging.
12835 The bedr package's API enhances access to these tools as well as offers
12836 additional utilities for genomic regions processing.")
12837 (license license:gpl2)))
12839 (define-public r-sets
12846 (uri (cran-uri "sets" version))
12849 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
12850 (properties `((upstream-name . "sets")))
12851 (build-system r-build-system)
12852 (home-page "https://cran.r-project.org/web/packages/sets")
12853 (synopsis "Sets, generalized sets, customizable sets and intervals")
12855 "This package provides data structures and basic operations for ordinary
12856 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
12857 customizable sets, and intervals.")
12858 (license license:gpl2)))
12860 (define-public r-partitions
12862 (name "r-partitions")
12867 (uri (cran-uri "partitions" version))
12870 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
12871 (build-system r-build-system)
12874 ("r-polynom" ,r-polynom)
12875 ("r-sets" ,r-sets)))
12876 (home-page "https://cran.r-project.org/web/packages/partitions")
12877 (synopsis "Additive partitions of integers")
12879 "This package provides tools to enumerates the partitions, unequal
12880 partitions, and restricted partitions of an integer; the three corresponding
12881 partition functions are also given.")
12882 ;; Any version of the GPL
12883 (license license:gpl2+)))
12885 (define-public r-brobdingnag
12887 (name "r-brobdingnag")
12892 (uri (cran-uri "Brobdingnag" version))
12895 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
12896 (properties `((upstream-name . "Brobdingnag")))
12897 (build-system r-build-system)
12898 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
12899 (synopsis "Very large numbers in R")
12901 "This package handles very large numbers in R. Real numbers are held
12902 using their natural logarithms, plus a logical flag indicating sign. The
12903 package includes a vignette that gives a step-by-step introduction to using S4
12905 ;; Any version of the GPL
12906 (license license:gpl2+)))
12908 (define-public r-untb
12915 (uri (cran-uri "untb" version))
12918 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
12919 (build-system r-build-system)
12921 `(("r-brobdingnag" ,r-brobdingnag)
12922 ("r-partitions" ,r-partitions)
12923 ("r-polynom" ,r-polynom)))
12924 (home-page "https://github.com/RobinHankin/untb.git")
12925 (synopsis "Ecological drift under the UNTB")
12927 "This package provides numerical simulations, and visualizations, of
12928 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
12929 (license license:gpl2+)))
12931 (define-public r-stepwise
12933 (name "r-stepwise")
12938 (uri (cran-uri "stepwise" version))
12941 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
12942 (build-system r-build-system)
12943 (home-page "http://stat.sfu.ca/statgen/research/stepwise.html")
12944 (synopsis "Stepwise detection of recombination breakpoints")
12946 "This package provides a stepwise approach to identifying recombination
12947 breakpoints in a genomic sequence alignment.")
12948 (license license:gpl2+)))
12950 (define-public r-snpmaxsel
12952 (name "r-snpmaxsel")
12957 (uri (cran-uri "SNPmaxsel" version))
12960 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
12961 (properties `((upstream-name . "SNPmaxsel")))
12962 (build-system r-build-system)
12964 `(("r-combinat" ,r-combinat)
12965 ("r-mvtnorm" ,r-mvtnorm)))
12966 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
12967 (synopsis "Maximally selected statistics for SNP data")
12969 "This package implements asymptotic methods related to maximally selected
12970 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
12972 (license license:gpl2+)))
12974 (define-public r-acsnminer
12976 (name "r-acsnminer")
12977 (version "0.16.8.25")
12980 (uri (cran-uri "ACSNMineR" version))
12983 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
12984 (properties `((upstream-name . "ACSNMineR")))
12985 (build-system r-build-system)
12987 `(("r-ggplot2" ,r-ggplot2)
12988 ("r-gridextra" ,r-gridextra)))
12989 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
12990 (synopsis "Gene enrichment analysis")
12992 "This package provides tools to compute and represent gene set enrichment
12993 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
12994 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
12995 enrichment can be run with hypergeometric test or Fisher exact test, and can
12996 use multiple corrections. Visualization of data can be done either by
12997 barplots or heatmaps.")
12998 (license license:gpl2+)))
13000 (define-public r-seqinr
13007 (uri (cran-uri "seqinr" version))
13010 "0j30za6kji6y3v09cvcydiacnp65pv6ig8aw7cydl47l5s9chky4"))))
13011 (build-system r-build-system)
13013 `(("r-ade4" ,r-ade4)
13014 ("r-segmented" ,r-segmented)))
13017 (home-page "http://seqinr.r-forge.r-project.org/")
13018 (synopsis "Biological sequences retrieval and analysis")
13020 "This package provides tools for exploratory data analysis and data
13021 visualization of biological sequence (DNA and protein) data. It also includes
13022 utilities for sequence data management under the ACNUC system.")
13023 (license license:gpl2+)))
13025 (define-public r-units
13032 (uri (cran-uri "units" version))
13035 "02nls8m0r1r7kljs4x35naz3szq62hyqyd5vracf1xwi1kz5kdsh"))))
13036 (build-system r-build-system)
13038 `(("udunits" ,udunits)))
13040 `(("r-rcpp" ,r-rcpp)))
13041 (home-page "https://github.com/r-quantities/units/")
13042 (synopsis "Measurement Units for R Vectors")
13044 "This package provides support for measurement units in R vectors,
13045 matrices and arrays: automatic propagation, conversion, derivation and
13046 simplification of units; raising errors in case of unit incompatibility. It
13047 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
13049 (license license:gpl2)))
13051 (define-public r-classint
13053 (name "r-classint")
13058 (uri (cran-uri "classInt" version))
13061 "0w980hrw8sgfdfyd5dsimalq7gwhvqm7507abk7k363pvgks23dv"))))
13062 (properties `((upstream-name . "classInt")))
13063 (build-system r-build-system)
13065 `(("r-class" ,r-class)
13066 ("r-e1071" ,r-e1071)
13067 ("r-kernsmooth" ,r-kernsmooth)))
13068 (native-inputs `(("gfortran" ,gfortran)))
13069 (home-page "https://github.com/r-spatial/classInt/")
13070 (synopsis "Choose univariate class intervals")
13072 "This package provides selected commonly used methods for choosing
13073 univariate class intervals for mapping or other graphics purposes.")
13074 (license license:gpl2+)))
13076 (define-public r-spdata
13083 (uri (cran-uri "spData" version))
13086 "190msrrpn226x27pcnck4ac34f9k4xcn26cyz2apdri2nzkr6zbw"))))
13087 (properties `((upstream-name . "spData")))
13088 (build-system r-build-system)
13089 (home-page "https://github.com/Nowosad/spData")
13090 (synopsis "Datasets for spatial analysis")
13092 "This a package containing diverse spatial datasets for demonstrating,
13093 benchmarking and teaching spatial data analysis. It includes R data of class
13094 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
13095 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
13096 of the datasets are designed to illustrate specific analysis techniques.
13097 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
13098 illustrate point pattern analysis techniques.")
13099 (license license:cc0)))
13101 (define-public r-learnbayes
13103 (name "r-learnbayes")
13108 (uri (cran-uri "LearnBayes" version))
13111 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
13112 (properties `((upstream-name . "LearnBayes")))
13113 (build-system r-build-system)
13114 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
13115 (synopsis "Functions for learning Bayesian inference")
13117 "This package provides a collection of functions helpful in learning the
13118 basic tenets of Bayesian statistical inference. It contains functions for
13119 summarizing basic one and two parameter posterior distributions and predictive
13120 distributions. It contains MCMC algorithms for summarizing posterior
13121 distributions defined by the user. It also contains functions for regression
13122 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
13124 (license license:gpl2+)))
13126 (define-public r-deldir
13133 (uri (cran-uri "deldir" version))
13136 "0790dwxb2mz1ffz8gd5vwdr0if2q76dzy3vab5rsykf9kz72n4g0"))))
13137 (build-system r-build-system)
13138 (native-inputs `(("gfortran" ,gfortran)))
13139 (home-page "https://cran.r-project.org/web/packages/deldir")
13140 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
13142 "This package provides tools for calculating the Delaunay triangulation
13143 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
13144 of a planar point set. It plots triangulations and tessellations in various
13145 ways, clips tessellations to sub-windows, calculates perimeters of
13146 tessellations, and summarizes information about the tiles of the
13148 (license license:gpl2+)))
13150 (define-public r-sf
13157 (uri (cran-uri "sf" version))
13160 "05dyq0vcz2f1fl03hk3v1a4nz4s84yyqw4rc9w9cwfq71gvm9qwf"))))
13161 (build-system r-build-system)
13168 `(("r-classint" ,r-classint)
13170 ("r-magrittr" ,r-magrittr)
13172 ("r-units" ,r-units)))
13173 (native-inputs `(("pkg-config" ,pkg-config)))
13174 (home-page "https://github.com/r-spatial/sf/")
13175 (synopsis "Simple features for R")
13177 "This package provides support for simple features, a standardized way to
13178 encode spatial vector data. It binds to GDAL for reading and writing data, to
13179 GEOS for geometrical operations, and to PROJ for projection conversions and
13180 datum transformations.")
13181 ;; Either of these licenses
13182 (license (list license:gpl2 license:expat))))
13184 (define-public r-spdep
13191 (uri (cran-uri "spdep" version))
13194 "1f8cjffqqc6rnb3n4qym70ca6nz2kvrsd3g587wrqdr79nnbwnrk"))))
13195 (build-system r-build-system)
13197 `(("r-boot" ,r-boot)
13199 ("r-deldir" ,r-deldir)
13201 ("r-gmodels" ,r-gmodels)
13202 ("r-learnbayes" ,r-learnbayes)
13204 ("r-matrix" ,r-matrix)
13208 ("r-spdata" ,r-spdata)))
13209 (home-page "https://github.com/r-spatial/spdep/")
13210 (synopsis "Spatial dependence: weighting schemes, statistics and models")
13212 "This package provides a collection of functions to create spatial
13213 weights matrix objects from polygon contiguities, from point patterns by
13214 distance and tessellations, for summarizing these objects, and for permitting
13215 their use in spatial data analysis, including regional aggregation by minimum
13217 (license license:gpl2+)))
13219 (define-public r-adegenet
13221 (name "r-adegenet")
13226 (uri (cran-uri "adegenet" version))
13229 "0ynfblp0hbd3dp3k86fn1wyhqr28lk6hs2bg4q7gyf0sfdfzwhrh"))))
13230 (build-system r-build-system)
13232 `(("r-ade4" ,r-ade4)
13235 ("r-dplyr" ,r-dplyr)
13236 ("r-ggplot2" ,r-ggplot2)
13237 ("r-igraph" ,r-igraph)
13239 ("r-reshape2" ,r-reshape2)
13240 ("r-seqinr" ,r-seqinr)
13241 ("r-shiny" ,r-shiny)
13242 ("r-spdep" ,r-spdep)
13243 ("r-vegan" ,r-vegan)))
13244 (home-page "https://github.com/thibautjombart/adegenet")
13245 (synopsis "Exploratory analysis of genetic and genomic data")
13247 "This package provides a toolset for the exploration of genetic and
13248 genomic data. Adegenet provides formal (S4) classes for storing and handling
13249 various genetic data, including genetic markers with varying ploidy and
13250 hierarchical population structure (@code{genind} class), alleles counts by
13251 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
13252 also implements original multivariate methods (DAPC, sPCA), graphics,
13253 statistical tests, simulation tools, distance and similarity measures, and
13254 several spatial methods. A range of both empirical and simulated datasets is
13255 also provided to illustrate various methods.")
13256 (license license:gpl2+)))
13258 (define-public r-pegas
13265 (uri (cran-uri "pegas" version))
13267 (base32 "0sb8cmz4d238mcb56hv9fa0cagm00k82r7aj4cj4lxa1flxlpy8p"))))
13268 (build-system r-build-system)
13270 `(("r-adegenet" ,r-adegenet)
13272 (home-page "http://ape-package.ird.fr/pegas.html")
13273 (synopsis "Population and evolutionary genetics analysis system")
13275 "This package provides functions for reading, writing, plotting,
13276 analysing, and manipulating allelic and haplotypic data, including from VCF
13277 files, and for the analysis of population nucleotide sequences and
13278 micro-satellites including coalescent analyses, linkage disequilibrium,
13279 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
13280 minimum spanning tree and network, and median-joining networks.")
13281 (license license:gpl2+)))
13283 (define-public r-rmetasim
13285 (name "r-rmetasim")
13290 (uri (cran-uri "rmetasim" version))
13293 "0sz4mdprdi6sgkfwfdvh2hr9nxiwq17sw0vggq3cvs7lzb0i6m9r"))))
13294 (build-system r-build-system)
13296 `(("r-ade4" ,r-ade4)
13297 ("r-adegenet" ,r-adegenet)
13298 ("r-gtools" ,r-gtools)
13299 ("r-pegas" ,r-pegas)))
13300 (home-page "https://cran.r-project.org/web/packages/rmetasim")
13301 (synopsis "Individual-based population genetic simulation environment")
13303 "This package provides an interface between R and the metasim simulation
13304 engine. The simulation environment is documented in: Strand, A.(2002),
13305 Metasim 1.0: an individual-based environment for simulating population
13306 genetics of complex population dynamics.")
13308 (license license:gpl2+)))
13310 (define-public r-genetics
13312 (name "r-genetics")
13313 (version "1.3.8.1.2")
13317 (uri (cran-uri "genetics" version))
13320 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
13321 (build-system r-build-system)
13323 `(("r-combinat" ,r-combinat)
13324 ("r-gdata" ,r-gdata)
13325 ("r-gtools" ,r-gtools)
13327 ("r-mvtnorm" ,r-mvtnorm)))
13328 (home-page "https://cran.r-project.org/web/packages/genetics/")
13329 (synopsis "Population genetics")
13331 "This package provides classes and methods for handling genetic data.
13332 It includes classes to represent genotypes and haplotypes at single markers up
13333 to multiple markers on multiple chromosomes. Function include allele
13334 frequencies, flagging homo/heterozygotes, flagging carriers of certain
13335 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
13336 and testing for linkage disequilibrium, ...")
13337 ;; Any GPL version.
13338 (license license:gpl2+)))
13340 (define-public r-snp-plotter
13342 (name "r-snp-plotter")
13347 (uri (cran-uri "snp.plotter" version))
13350 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
13351 (properties `((upstream-name . "snp.plotter")))
13352 (build-system r-build-system)
13353 (propagated-inputs `(("r-genetics" ,r-genetics)))
13354 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
13355 (synopsis "Plot p-values using single SNP and/or haplotype data")
13357 "This package helps you create plots of p-values using single SNP and/or
13358 haplotype data. Main features of the package include options to display a
13359 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
13360 datasets simultaneously. Plots can be created using global and/or individual
13361 haplotype p-values along with single SNP p-values. Images are created as
13362 either PDF/EPS files.")
13363 (license license:gpl2+)))
13365 (define-public r-polspline
13367 (name "r-polspline")
13372 (uri (cran-uri "polspline" version))
13374 (base32 "0c7fnxpqpy3hibiim4yib6l6bq363s97wwvllxp4lp8h06fjcyyn"))))
13375 (build-system r-build-system)
13376 (native-inputs `(("gfortran" ,gfortran)))
13377 (home-page "https://cran.r-project.org/web/packages/polspline/")
13378 (synopsis "Polynomial spline routines")
13380 "This package provides routines for the polynomial spline fitting
13381 routines hazard regression, hazard estimation with flexible tails, logspline,
13382 lspec, polyclass, and polymars.")
13383 (license license:gpl2+)))
13385 (define-public r-rms
13392 (uri (cran-uri "rms" version))
13394 (base32 "19knh1sw0icw6jh9wfb2hq5jf49i2qfvp9myvqm5paa495689x9q"))))
13395 (build-system r-build-system)
13397 `(("r-ggplot2" ,r-ggplot2)
13398 ("r-hmisc" ,r-hmisc)
13399 ("r-htmltable" ,r-htmltable)
13400 ("r-htmltools" ,r-htmltools)
13401 ("r-lattice" ,r-lattice)
13402 ("r-multcomp" ,r-multcomp)
13404 ("r-polspline" ,r-polspline)
13405 ("r-quantreg" ,r-quantreg)
13406 ("r-rpart" ,r-rpart)
13407 ("r-sparsem" ,r-sparsem)
13408 ("r-survival" ,r-survival)))
13409 (native-inputs `(("gfortran" ,gfortran)))
13410 (home-page "http://biostat.mc.vanderbilt.edu/rms")
13411 (synopsis "Regression modeling strategies")
13413 "This is a package for regression modeling, testing, estimation,
13414 validation, graphics, prediction, and typesetting by storing enhanced model
13415 design attributes in the fit. The rms package is a collection of functions
13416 that assist with and streamline modeling. It also contains functions for
13417 binary and ordinal logistic regression models, ordinal models for continuous Y
13418 with a variety of distribution families, and the Buckley-James multiple
13419 regression model for right-censored responses, and implements penalized
13420 maximum likelihood estimation for logistic and ordinary linear models. The
13421 package works with almost any regression model, but it was especially written
13422 to work with binary or ordinal regression models, Cox regression, accelerated
13423 failure time models, ordinary linear models, the Buckley-James model,
13424 generalized least squares for serially or spatially correlated observations,
13425 generalized linear models, and quantile regression.")
13426 (license license:gpl2+)))
13428 (define-public r-haplo-stats
13430 (name "r-haplo-stats")
13435 (uri (cran-uri "haplo.stats" version))
13438 "19kxascqq5qz0zdxx0w837ji207y1z2ggxkl4vmlbay03k2dw2mx"))))
13439 (properties `((upstream-name . "haplo.stats")))
13440 (build-system r-build-system)
13442 `(("r-rms" ,r-rms)))
13444 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
13445 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
13446 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
13448 "This package provides routines for the analysis of indirectly measured
13449 haplotypes. The statistical methods assume that all subjects are unrelated
13450 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
13451 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
13452 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
13453 examples in the vignette.")
13454 (license license:gpl2+)))
13456 (define-public r-bqtl
13463 (uri (cran-uri "bqtl" version))
13466 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
13467 (build-system r-build-system)
13468 (native-inputs `(("gfortran" ,gfortran)))
13469 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
13470 (synopsis "Bayesian QTL mapping toolkit")
13472 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
13473 lines. It includes maximum likelihood and Bayesian tools.")
13474 (license license:gpl2+)))
13476 (define-public r-ibdreg
13483 (uri (cran-uri "ibdreg" version))
13486 "1kaa5q1byi30wzr0mw4w2cv1ssxprzcwf91wrpqwkgcsdy7dkh2g"))))
13487 (build-system r-build-system)
13488 (home-page "https://www.mayo.edu/research/labs/\
13489 statistical-genetics-genetic-epidemiology/software")
13490 (synopsis "Regression methods for IBD linkage with covariates")
13492 "This package provides a method to test genetic linkage with covariates
13493 by regression methods with response IBD sharing for relative pairs. Account
13494 for correlations of IBD statistics and covariates for relative pairs within
13495 the same pedigree.")
13496 (license license:gpl2+)))
13498 (define-public r-dlmap
13505 (uri (cran-uri "dlmap" version))
13508 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
13509 (build-system r-build-system)
13511 `(("r-ibdreg" ,r-ibdreg)
13515 ("r-wgaim" ,r-wgaim)))
13516 (home-page "https://cran.r-project.org/web/packages/dlmap/")
13517 (synopsis "Detection localization mapping for QTL")
13519 "This is package for QTL mapping in a mixed model framework with separate
13520 detection and localization stages. The first stage detects the number of QTL
13521 on each chromosome based on the genetic variation due to grouped markers on
13522 the chromosome; the second stage uses this information to determine the most
13523 likely QTL positions. The mixed model can accommodate general fixed and
13524 random effects, including spatial effects in field trials and pedigree
13525 effects. It is applicable to backcrosses, doubled haploids, recombinant
13526 inbred lines, F2 intercrosses, and association mapping populations.")
13527 (license license:gpl2)))
13529 (define-public r-ldheatmap
13531 (name "r-ldheatmap")
13536 (uri (cran-uri "LDheatmap" version))
13539 "1r0j8bihi5z1x0sgaf7dwzpsw9i0nc1vylvipvc0cia2ka1lr9dc"))))
13540 (properties `((upstream-name . "LDheatmap")))
13541 (build-system r-build-system)
13543 `(("r-genetics" ,r-genetics)
13545 ("r-snpstats" ,r-snpstats)))
13546 (home-page "http://stat.sfu.ca/statgen/research/ldheatmap.html")
13547 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
13549 "This package provides tools to produce a graphical display, as a heat
13550 map, of measures of pairwise linkage disequilibria between SNPs. Users may
13551 optionally include the physical locations or genetic map distances of each SNP
13553 (license license:gpl3)))
13555 (define-public r-hwde
13562 (uri (cran-uri "hwde" version))
13565 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
13566 (build-system r-build-system)
13567 (home-page "https://cran.r-project.org/web/packages/hwde/")
13568 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
13570 "This package fits models for genotypic disequilibria, as described in
13571 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
13572 terms are available that account for first order interactions between loci.
13573 It also implements, for a single locus in a single population, a conditional
13574 exact test for Hardy-Weinberg equilibrium.")
13575 (license license:gpl2+)))
13577 (define-public r-tdthap
13584 (uri (cran-uri "tdthap" version))
13587 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
13588 (build-system r-build-system)
13589 (home-page "https://cran.r-project.org/web/packages/tdthap/")
13590 (synopsis "TDT tests for extended haplotypes")
13592 "Functions and examples are provided for transmission/disequilibrium
13593 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
13594 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
13595 (license license:artistic2.0)))
13597 (define-public r-sparql
13603 (uri (cran-uri "SPARQL" version))
13606 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
13607 (properties `((upstream-name . "SPARQL")))
13608 (build-system r-build-system)
13610 `(("r-rcurl" ,r-rcurl)
13612 (home-page "https://cran.r-project.org/web/packages/SPARQL")
13613 (synopsis "SPARQL client for R")
13614 (description "This package provides an interface to use SPARQL to pose
13615 SELECT or UPDATE queries to an end-point.")
13616 ;; The only license indication is found in the DESCRIPTION file,
13617 ;; which states GPL-3. So we cannot assume GPLv3+.
13618 (license license:gpl3)))
13620 (define-public r-bookdown
13622 (name "r-bookdown")
13626 (uri (cran-uri "bookdown" version))
13629 "1gwgvx1yg6q3wccnhidr3gshdvlgr42i4pvlg4h29kpsa7smjiv1"))))
13630 (build-system r-build-system)
13632 `(("r-htmltools" ,r-htmltools)
13633 ("r-knitr" ,r-knitr)
13634 ("r-rmarkdown" ,r-rmarkdown)
13635 ("r-tinytex" ,r-tinytex)
13637 ("pandoc" ,ghc-pandoc)))
13638 (home-page "https://github.com/rstudio/bookdown")
13639 (synopsis "Authoring books and technical documents with R markdown")
13640 (description "This package provides output formats and utilities for
13641 authoring books and technical documents with R Markdown.")
13642 (license license:gpl3)))
13644 (define-public r-optparse
13646 (name "r-optparse")
13651 (uri (cran-uri "optparse" version))
13654 "0wyrc42ja3ab5szx46zmz8lm7vzfqxkjca0m0sms8g9hqbmmay6d"))))
13655 (build-system r-build-system)
13657 `(("r-getopt" ,r-getopt)))
13658 (home-page "https://github.com/trevorld/optparse")
13659 (synopsis "Command line option parser")
13661 "This package provides a command line parser inspired by Python's
13662 @code{optparse} library to be used with Rscript to write shebang scripts
13663 that accept short and long options.")
13664 (license license:gpl2+)))
13666 (define-public r-wgcna
13673 (uri (cran-uri "WGCNA" version))
13676 "1s7gy5vd7x67hpgli8r7ba2z99w3psiyv5hqmrh94zw141dg210a"))))
13677 (properties `((upstream-name . "WGCNA")))
13678 (build-system r-build-system)
13680 `(("r-annotationdbi" ,r-annotationdbi)
13681 ("r-doparallel" ,r-doparallel)
13682 ("r-dynamictreecut" ,r-dynamictreecut)
13683 ("r-fastcluster" ,r-fastcluster)
13684 ("r-foreach" ,r-foreach)
13685 ("r-go-db" ,r-go-db)
13686 ("r-hmisc" ,r-hmisc)
13687 ("r-impute" ,r-impute)
13689 ("r-robust" ,r-robust)
13690 ("r-survival" ,r-survival)
13691 ("r-matrixstats" ,r-matrixstats)
13692 ("r-preprocesscore" ,r-preprocesscore)))
13694 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
13695 (synopsis "Weighted correlation network analysis")
13697 "This package provides functions necessary to perform Weighted
13698 Correlation Network Analysis on high-dimensional data. It includes functions
13699 for rudimentary data cleaning, construction and summarization of correlation
13700 networks, module identification and functions for relating both variables and
13701 modules to sample traits. It also includes a number of utility functions for
13702 data manipulation and visualization.")
13703 (license license:gpl2+)))
13705 (define-public r-kernlab
13712 (uri (cran-uri "kernlab" version))
13714 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
13715 (build-system r-build-system)
13716 (home-page "https://cran.r-project.org/web/packages/kernlab")
13717 (synopsis "Kernel-based machine learning tools")
13719 "This package provides kernel-based machine learning methods for
13720 classification, regression, clustering, novelty detection, quantile regression
13721 and dimensionality reduction. Among other methods @code{kernlab} includes
13722 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
13724 (license license:gpl2)))
13726 (define-public r-hierfstat
13728 (name "r-hierfstat")
13729 (version "0.04-22")
13733 (uri (cran-uri "hierfstat" version))
13736 "1fav2v2996v5kb1ffa6v5wxfm921syxg6as034vd3j4jfhdibyfx"))))
13737 (build-system r-build-system)
13739 `(("r-ade4" ,r-ade4)
13740 ("r-adegenet" ,r-adegenet)
13741 ("r-gtools" ,r-gtools)))
13742 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
13743 (synopsis "Estimation and tests of hierarchical F-statistics")
13745 "This package allows the estimation of hierarchical F-statistics from
13746 haploid or diploid genetic data with any numbers of levels in the hierarchy,
13747 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
13748 are also given to test via randomisations the significance of each F and
13749 variance components, using the likelihood-ratio statistics G.")
13750 (license license:gpl2+)))
13752 (define-public r-hapassoc
13754 (name "r-hapassoc")
13759 (uri (cran-uri "hapassoc" version))
13762 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
13763 (build-system r-build-system)
13764 (home-page "http://stat.sfu.ca/statgen/research/hapassoc.html")
13765 (synopsis "Inference of trait associations with SNP haplotypes")
13767 "Hapassoc performs likelihood inference of trait associations with
13768 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
13769 functions are developed primarily for data collected in cohort or
13770 cross-sectional studies. They can accommodate uncertain haplotype phase and
13771 handle missing genotypes at some SNPs.")
13772 (license license:gpl2)))
13774 (define-public r-sampling
13776 (name "r-sampling")
13781 (uri (cran-uri "sampling" version))
13784 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
13785 (build-system r-build-system)
13787 `(("r-lpsolve" ,r-lpsolve)
13788 ("r-mass" ,r-mass)))
13789 (home-page "https://cran.r-project.org/web/packages/sampling/")
13790 (synopsis "Survey sampling")
13792 "This package provides functions for drawing and calibrating samples.")
13793 (license license:gpl2+)))
13795 (define-public r-r2html
13802 (uri (cran-uri "R2HTML" version))
13805 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
13806 (properties `((upstream-name . "R2HTML")))
13807 (build-system r-build-system)
13808 (home-page "https://github.com/nalimilan/R2HTML")
13809 (synopsis "HTML export for R objects")
13811 "This package includes HTML functions and methods to write in an HTML
13812 file. Thus, making HTML reports is easy. It includes a function that allows
13813 redirection on the fly, which appears to be very useful for teaching purposes,
13814 as the student can keep a copy of the produced output to keep all that they
13815 did during the course. The package comes with a vignette describing how to
13816 write HTML reports for statistical analysis. Finally, a driver for Sweave
13817 allows to parse HTML flat files containing R code and to automatically write
13818 the corresponding outputs (tables and graphs).")
13819 (license license:gpl2+)))
13821 (define-public r-rjava
13828 (uri (cran-uri "rJava" version))
13831 "0s9cjy1wh7snmbqwznh8f1r4ipylr7mgda4a979z963a8lqy32n2"))))
13832 (properties `((upstream-name . "rJava")))
13833 (build-system r-build-system)
13835 `(#:modules ((guix build utils)
13836 (guix build r-build-system)
13839 (modify-phases %standard-phases
13840 (add-after 'unpack 'set-JAVA_HOME
13841 (lambda* (#:key inputs #:allow-other-keys)
13842 (let ((jdk (assoc-ref inputs "jdk")))
13843 (setenv "JAVA_HOME" jdk)
13844 (setenv "JAVA" (which "java"))
13845 (setenv "JAR" (which "jar"))
13846 (setenv "JAVAC" (which "javac"))
13847 (setenv "JAVAH" (which "javah"))
13848 (setenv "JAVA_CPPFLAGS"
13849 (string-append "-I" jdk "/include "
13850 "-I" jdk "/include/linux"))
13851 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
13852 ((lib) (setenv "JAVA_LIBS" lib))
13853 (_ (error "Could not find libjvm.so"))))
13857 ("jdk" ,icedtea-8 "jdk")
13860 (home-page "http://www.rforge.net/rJava/")
13861 (synopsis "Low-Level R to Java interface")
13863 "This package provides a low-level interface to the Java VM very much
13864 like .C/.Call and friends. It allows the creation of objects, calling methods
13865 and accessing fields.")
13866 (license license:gpl2)))
13868 (define-public r-svmisc
13875 (uri (cran-uri "svMisc" version))
13878 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
13879 (properties `((upstream-name . "svMisc")))
13880 (build-system r-build-system)
13881 (home-page "https://github.com/SciViews/svMisc")
13882 (synopsis "Miscellaneous functions for SciViews")
13884 "This package provides miscellaneous functions for SciViews or general
13885 use, including tools to manage a temporary environment attached to the search
13886 path for temporary variables you do not want to @code{save()} or
13887 @code{load()}; test the current platform; showing progress bars, etc.")
13888 (license license:gpl2)))
13890 (define-public r-xyz
13897 (uri (cran-uri "xyz" version))
13900 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
13901 (build-system r-build-system)
13903 `(("r-rcpp" ,r-rcpp)))
13904 (home-page "https://cran.r-project.org/web/packages/xyz/")
13905 (synopsis "Algorithm for fast interaction search in high-dimensional data")
13907 "High dimensional interaction search by brute force requires a quadratic
13908 computational cost in the number of variables. The xyz algorithm provably
13909 finds strong interactions in almost linear time. For details of the algorithm
13910 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
13911 interaction search in high-dimensional data.")
13912 ;; Any version of the GPL.
13913 (license license:gpl2+)))
13915 (define-public r-rttf2pt1
13917 (name "r-rttf2pt1")
13922 (uri (cran-uri "Rttf2pt1" version))
13925 "12hf9r3mhjr9sawdvf7qhjf1zph2q64f77i81jwvy7awidbm0kja"))))
13926 (properties `((upstream-name . "Rttf2pt1")))
13927 (build-system r-build-system)
13928 (home-page "https://github.com/wch/Rttf2pt1")
13929 (synopsis "Font conversion utility")
13931 "This package contains the program @code{ttf2pt1}, for use with the
13932 @code{extrafont} package.")
13933 ;; Most of the files are covered under the Expat license. Some files are
13934 ;; covered under BSD-3. Deviations for individual files are recorded in
13935 ;; the LICENSE file.
13936 (license (list license:bsd-3 license:expat
13937 (license:non-copyleft "file://LICENSE")))))
13939 (define-public r-extrafontdb
13941 (name "r-extrafontdb")
13946 (uri (cran-uri "extrafontdb" version))
13949 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
13950 (build-system r-build-system)
13951 (home-page "https://github.com/wch/extrafontdb")
13952 (synopsis "Database for the extrafont package")
13954 "This package holds the database for the @code{extrafont} package.")
13955 (license license:gpl2)))
13957 (define-public r-extrafont
13959 (name "r-extrafont")
13964 (uri (cran-uri "extrafont" version))
13967 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
13968 (build-system r-build-system)
13970 `(("r-extrafontdb" ,r-extrafontdb)
13971 ("r-rttf2pt1" ,r-rttf2pt1)))
13972 (home-page "https://github.com/wch/extrafont")
13973 (synopsis "Tools for using fonts in R")
13975 "The extrafont package makes it easier to use fonts other than the basic
13976 PostScript fonts that R uses. Fonts that are imported into extrafont can be
13977 used with PDF or PostScript output files. There are two hurdles for using
13978 fonts in PDF (or Postscript) output files:
13981 @item Making R aware of the font and the dimensions of the characters.
13982 @item Embedding the fonts in the PDF file so that the PDF can be displayed
13983 properly on a device that doesn't have the font. This is usually needed if
13984 you want to print the PDF file or share it with others.
13987 The extrafont package makes both of these things easier.")
13988 (license license:gpl2)))
13990 (define-public r-xkcd
13997 (uri (cran-uri "xkcd" version))
14000 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
14001 (build-system r-build-system)
14003 `(("r-extrafont" ,r-extrafont)
14004 ("r-ggplot2" ,r-ggplot2)
14005 ("r-hmisc" ,r-hmisc)))
14006 (home-page "https://cran.r-project.org/web/packages/xkcd/")
14007 (synopsis "Plot ggplot2 graphics in the XKCD style")
14009 "This package provides the means to plot ggplot2 graphs in the style of
14010 the XKCD web comic.")
14011 (license license:gpl3)))
14013 (define-public r-msigdbr
14020 (uri (cran-uri "msigdbr" version))
14023 "19p8z617m3my8la7n1qgb1s2msf940r372im3q30qkbcx3qxg3sd"))))
14024 (build-system r-build-system)
14026 `(("r-dplyr" ,r-dplyr)
14027 ("r-magrittr" ,r-magrittr)
14028 ("r-rlang" ,r-rlang)
14029 ("r-tibble" ,r-tibble)))
14030 (home-page "https://github.com/igordot/msigdbr")
14031 (synopsis "MSigDB gene sets for multiple organisms")
14033 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
14034 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
14035 software in a standard R data frame with key-value pairs. Included are the
14036 original human gene symbols and Entrez IDs as well as the equivalents for
14037 various frequently studied model organisms such as mouse, rat, pig, fly, and
14039 ;; The package is covered under the Expat license, but the upstream MSigDB
14040 ;; files are made available under the Creative Commons Attribution 4.0
14041 ;; International license.
14042 (license (list license:expat license:cc-by4.0))))
14044 (define-public r-gridgraphics
14046 (name "r-gridgraphics")
14051 (uri (cran-uri "gridGraphics" version))
14054 "1kr3p54bkv2q7agxrva30y9bkwkiq1k2cfl5z1kvyjv6f5xi4w5p"))))
14055 (properties `((upstream-name . "gridGraphics")))
14056 (build-system r-build-system)
14057 (home-page "https://github.com/pmur002/gridgraphics")
14058 (synopsis "Redraw base graphics using @code{grid} graphics")
14060 "This package provides functions to convert a page of plots drawn with
14061 the @code{graphics} package into identical output drawn with the @code{grid}
14062 package. The result looks like the original @code{graphics}-based plot, but
14063 consists of @code{grid} grobs and viewports that can then be manipulated with
14064 @code{grid} functions (e.g., edit grobs and revisit viewports).")
14065 (license license:gpl2+)))
14067 (define-public r-farver
14074 (uri (cran-uri "farver" version))
14077 "0aq1hk561pz3s3lpay1adwsihha6mxp7zbj4n1m6307g34awlhhn"))))
14078 (build-system r-build-system)
14079 (home-page "https://github.com/thomasp85/farver")
14080 (synopsis "Vectorized color conversion and comparison")
14082 "The encoding of color can be handled in many different ways, using
14083 different color spaces. As different color spaces have different uses,
14084 efficient conversion between these representations are important. This
14085 package provides a set of functions that gives access to very fast color space
14086 conversion and comparisons implemented in C++, and offers 100-fold speed
14087 improvements over the @code{convertColor} function in the @code{grDevices}
14089 (license license:expat)))
14091 (define-public r-ggplotify
14093 (name "r-ggplotify")
14098 (uri (cran-uri "ggplotify" version))
14101 "0nv3wdmxnc5ww9m3xlgnb0jp30j45dg33nqc6gg3y36svg8anjcg"))))
14102 (build-system r-build-system)
14104 `(("r-ggplot2" ,r-ggplot2)
14105 ("r-gridgraphics" ,r-gridgraphics)
14106 ("r-rvcheck" ,r-rvcheck)))
14107 (home-page "https://github.com/GuangchuangYu/ggplotify")
14108 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
14110 "This package provides tools to convert plot function calls (using
14111 expression or formula) to @code{grob} or @code{ggplot} objects that are
14112 compatible with the @code{grid} and @code{ggplot2} environment. With this
14113 package, we are able to e.g. use @code{cowplot} to align plots produced by
14114 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
14115 converting them to @code{ggplot} objects.")
14116 (license license:artistic2.0)))
14118 (define-public r-triebeard
14120 (name "r-triebeard")
14125 (uri (cran-uri "triebeard" version))
14128 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
14129 (build-system r-build-system)
14130 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
14131 (home-page "https://github.com/Ironholds/triebeard/")
14132 (synopsis "Radix trees in Rcpp")
14134 "Radix trees, or tries, are key-value data structures optimized for
14135 efficient lookups, similar in purpose to hash tables. This package provides
14136 an implementation of radix trees for use in R programming and in developing
14137 packages with Rcpp.")
14138 (license license:expat)))
14140 (define-public r-tweenr
14147 (uri (cran-uri "tweenr" version))
14150 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
14151 (build-system r-build-system)
14153 `(("r-farver" ,r-farver)
14154 ("r-magrittr" ,r-magrittr)
14156 ("r-rlang" ,r-rlang)))
14157 (home-page "https://github.com/thomasp85/tweenr")
14158 (synopsis "Interpolate data for smooth animations")
14160 "In order to create smooth animation between states of data, tweening is
14161 necessary. This package provides a range of functions for creating tweened
14162 data that can be used as basis for animation. Furthermore it adds a number of
14163 vectorized interpolaters for common R data types such as numeric, date and
14165 (license license:expat)))
14167 (define-public r-polyclip
14169 (name "r-polyclip")
14174 (uri (cran-uri "polyclip" version))
14177 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
14178 (build-system r-build-system)
14179 (native-inputs `(("pkg-config" ,pkg-config)))
14180 (home-page "http://www.angusj.com/delphi/clipper.php")
14181 (synopsis "Polygon clipping")
14183 "This package provides an R port of the library Clipper. It performs
14184 polygon clipping operations (intersection, union, set minus, set difference)
14185 for polygonal regions of arbitrary complexity, including holes. It computes
14186 offset polygons (spatial buffer zones, morphological dilations, Minkowski
14187 dilations) for polygonal regions and polygonal lines. It computes the
14188 Minkowski Sum of general polygons. There is a function for removing
14189 self-intersections from polygon data.")
14190 (license license:boost1.0)))
14192 (define-public r-urltools
14194 (name "r-urltools")
14199 (uri (cran-uri "urltools" version))
14202 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
14203 (build-system r-build-system)
14205 `(("r-rcpp" ,r-rcpp)
14206 ("r-triebeard" ,r-triebeard)))
14207 (home-page "https://github.com/Ironholds/urltools/")
14208 (synopsis "Vectorized tools for URL handling and parsing")
14210 "This package provides a toolkit for all URL-handling needs, including
14211 encoding and decoding, parsing, parameter extraction and modification. All
14212 functions are designed to be both fast and entirely vectorized. It is
14213 intended to be useful for people dealing with web-related datasets, such as
14214 server-side logs, although may be useful for other situations involving large
14216 (license license:expat)))
14218 (define-public r-ggforce
14225 (uri (cran-uri "ggforce" version))
14228 "04926cqrda6psvy2nzkkw4czwyxdp7fnxg76byp14v12kgd72lm0"))))
14229 (build-system r-build-system)
14231 `(("r-ggplot2" ,r-ggplot2)
14232 ("r-gtable" ,r-gtable)
14234 ("r-polyclip" ,r-polyclip)
14236 ("r-rcppeigen" ,r-rcppeigen)
14237 ("r-rlang" ,r-rlang)
14238 ("r-scales" ,r-scales)
14239 ("r-tidyselect" ,r-tidyselect)
14240 ("r-tweenr" ,r-tweenr)
14241 ("r-withr" ,r-withr)))
14242 (home-page "https://ggforce.data-imaginist.com")
14243 (synopsis "Accelerating ggplot2")
14245 "The aim of the ggplot2 package is to aid in visual data investigations.
14246 This focus has led to a lack of facilities for composing specialized plots.
14247 Thi package aims to be a collection of mainly new statistics and geometries
14248 that fills this gap.")
14249 (license license:expat)))
14251 (define-public r-europepmc
14253 (name "r-europepmc")
14258 (uri (cran-uri "europepmc" version))
14261 "1ngqs1sqzkbwv98dd5z4cxj8bnz41wyd0g060a2vpqi3s99s4i2h"))))
14262 (build-system r-build-system)
14264 `(("r-dplyr" ,r-dplyr)
14266 ("r-jsonlite" ,r-jsonlite)
14268 ("r-progress" ,r-progress)
14269 ("r-purrr" ,r-purrr)
14270 ("r-urltools" ,r-urltools)
14271 ("r-xml2" ,r-xml2)))
14272 (home-page "https://github.com/ropensci/europepmc/")
14273 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
14275 "This package provides an R Client for the
14276 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
14277 Service}. It gives access to both metadata on life science literature and
14278 open access full texts. Europe PMC indexes all PubMed content and other
14279 literature sources including Agricola, a bibliographic database of citations
14280 to the agricultural literature, or Biological Patents. In addition to
14281 bibliographic metadata, the client allows users to fetch citations and
14282 reference lists. Links between life-science literature and other EBI
14283 databases, including ENA, PDB or ChEMBL are also accessible.")
14284 (license license:gpl3)))
14286 (define-public r-ggraph
14293 (uri (cran-uri "ggraph" version))
14296 "0qj7w3af0pgmd9mil6y571jikfkln7b8csvzg6b08spwbglfy1s3"))))
14297 (build-system r-build-system)
14299 `(("r-digest" ,r-digest)
14300 ("r-dplyr" ,r-dplyr)
14301 ("r-ggforce" ,r-ggforce)
14302 ("r-ggplot2" ,r-ggplot2)
14303 ("r-ggrepel" ,r-ggrepel)
14304 ("r-graphlayouts" ,r-graphlayouts)
14305 ("r-gtable" ,r-gtable)
14306 ("r-igraph" ,r-igraph)
14309 ("r-rlang" ,r-rlang)
14310 ("r-scales" ,r-scales)
14311 ("r-tidygraph" ,r-tidygraph)
14312 ("r-viridis" ,r-viridis)))
14313 (home-page "https://cran.r-project.org/web/packages/ggraph/")
14314 (synopsis "Implementation of grammar of graphics for graphs and networks")
14316 "The grammar of graphics as implemented in ggplot2 is a poor fit for
14317 graph and network visualizations due to its reliance on tabular data input.
14318 The ggraph package is an extension of the ggplot2 API tailored to graph
14319 visualizations and provides the same flexible approach to building up plots
14321 (license license:gpl3)))
14323 (define-public r-varselrf
14325 (name "r-varselrf")
14330 (uri (cran-uri "varSelRF" version))
14333 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
14334 (properties `((upstream-name . "varSelRF")))
14335 (build-system r-build-system)
14337 `(("r-randomforest" ,r-randomforest)))
14338 (home-page "http://ligarto.org/rdiaz/Software/Software.html")
14339 (synopsis "Variable selection using random forests")
14341 "This package provides tools for the variable selection from random
14342 forests using both backwards variable elimination (for the selection of small
14343 sets of non-redundant variables) and selection based on the importance
14344 spectrum (somewhat similar to scree plots; for the selection of large,
14345 potentially highly-correlated variables). The main applications are in
14346 high-dimensional data (e.g., microarray data, and other genomics and
14347 proteomics applications).")
14348 (license license:gpl2+)))
14350 (define-public r-pamr
14357 (uri (cran-uri "pamr" version))
14360 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
14361 (build-system r-build-system)
14363 `(("r-cluster" ,r-cluster)
14364 ("r-survival" ,r-survival)))
14365 (native-inputs `(("gfortran" ,gfortran)))
14366 (home-page "https://cran.r-project.org/web/packages/pamr/")
14367 (synopsis "Prediction Analysis for Microarrays")
14369 "This package provides some functions for sample classification in
14371 (license license:gpl2)))
14373 (define-public r-rda
14376 (version "1.0.2-2.1")
14380 (uri (cran-uri "rda" version))
14383 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
14384 (build-system r-build-system)
14385 (home-page "https://cran.r-project.org/web/packages/rda/")
14386 (synopsis "Shrunken centroids regularized discriminant analysis")
14388 "This package provides tools for shrunken centroids regularized
14389 discriminant analysis for the purpose of classifying high dimensional data.")
14390 (license license:gpl2+)))
14392 (define-public r-ggvis
14399 (uri (cran-uri "ggvis" version))
14402 "091i9f17912j8qcyxppjgwzjnyqj7769ixs9d2gjg6f2clskqdw2"))))
14403 (build-system r-build-system)
14405 `(("r-assertthat" ,r-assertthat)
14406 ("r-dplyr" ,r-dplyr)
14407 ("r-htmltools" ,r-htmltools)
14408 ("r-jsonlite" ,r-jsonlite)
14409 ("r-lazyeval" ,r-lazyeval)
14410 ("r-magrittr" ,r-magrittr)
14411 ("r-shiny" ,r-shiny)))
14412 (home-page "https://ggvis.rstudio.com/")
14413 (synopsis "Interactive grammar of graphics")
14415 "This package is a data visualization package for R providing an
14416 implementation of an interactive grammar of graphics, taking the best parts of
14417 ggplot2, combining them with the reactive framework of Shiny and drawing web
14418 graphics using Vega.")
14419 (license license:gpl2)))
14421 (define-public r-gbm
14428 (uri (cran-uri "gbm" version))
14431 "0vs6ljaqhwwpgr8wlbhmm4v147rd82kl16rpaijqiylxcc8dxyq6"))))
14432 (build-system r-build-system)
14434 `(("r-gridextra" ,r-gridextra)
14435 ("r-lattice" ,r-lattice)
14436 ("r-survival" ,r-survival)))
14437 (home-page "https://github.com/gbm-developers/gbm")
14438 (synopsis "Generalized boosted regression models")
14440 "This package is an implementation of extensions to Freund and Schapire's
14441 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
14442 regression methods for least squares, absolute loss, t-distribution loss,
14443 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
14444 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
14445 and Learning to Rank measures (LambdaMart).")
14446 (license license:gpl2+)))
14448 (define-public r-threejs
14455 (uri (cran-uri "threejs" version))
14458 "1s3rdlzy7man6177ycayg6xsh6k8y1r9rdj9yzn3b93j2rs0nxbi"))))
14459 (build-system r-build-system)
14461 `(#:modules ((guix build utils)
14462 (guix build r-build-system)
14466 (modify-phases %standard-phases
14467 (add-after 'unpack 'process-javascript
14468 (lambda* (#:key inputs #:allow-other-keys)
14469 (with-directory-excursion "inst"
14473 `((,(assoc-ref inputs "js-jquery")
14474 "htmlwidgets/lib/jquery/jquery.min.js")
14475 (,(assoc-ref inputs "js-threejs-85")
14476 "htmlwidgets/lib/threejs-85/three.min.js"))))
14477 (lambda (sources targets)
14478 (for-each (lambda (source target)
14479 (format #t "Processing ~a --> ~a~%"
14481 (delete-file target)
14482 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14483 (call-with-output-file target
14485 (dump-port minified port)))))
14486 sources targets))))
14489 `(("r-base64enc" ,r-base64enc)
14490 ("r-crosstalk" ,r-crosstalk)
14491 ("r-htmlwidgets" ,r-htmlwidgets)
14492 ("r-igraph" ,r-igraph)))
14494 `(("uglify-js" ,uglify-js)
14498 (uri "https://code.jquery.com/jquery-3.3.1.js")
14501 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
14505 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r85/build/three.js")
14508 "17khh3dmijdjw4qb9qih1rqhxgrmm3pc6w8lzdx6rf6a3mrc9xnl"))))))
14509 (home-page "https://bwlewis.github.io/rthreejs")
14510 (synopsis "Interactive 3D scatter plots, networks and globes")
14512 "Create interactive 3D scatter plots, network plots, and globes in R
14513 using the three.js visualization library.")
14514 (license license:expat)))
14516 (define-public r-mlbench
14523 (uri (cran-uri "mlbench" version))
14526 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
14527 (build-system r-build-system)
14528 (home-page "https://cran.r-project.org/web/packages/mlbench/")
14529 (synopsis "Machine learning benchmark problems")
14531 "This package provides a collection of artificial and real-world machine
14532 learning benchmark problems, including, e.g., several data sets from the UCI
14534 (license license:gpl2)))
14536 (define-public r-mpm
14543 (uri (cran-uri "mpm" version))
14546 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
14547 (build-system r-build-system)
14549 `(("r-kernsmooth" ,r-kernsmooth)
14550 ("r-mass" ,r-mass)))
14551 (home-page "http://mpm.r-forge.r-project.org")
14552 (synopsis "Multivariate projection methods")
14554 "This is a package for exploratory graphical analysis of multivariate
14555 data, specifically gene expression data with different projection methods:
14556 principal component analysis, correspondence analysis, spectral map
14558 (license license:gpl2+)))
14560 (define-public r-png
14566 (uri (cran-uri "png" version))
14569 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
14570 (build-system r-build-system)
14572 `(("libpng" ,libpng)
14574 (home-page "http://www.rforge.net/png/")
14575 (synopsis "Read and write PNG images")
14577 "This package provides an easy and simple way to read, write and display
14578 bitmap images stored in the PNG format. It can read and write both files and
14579 in-memory raw vectors.")
14580 ;; Any of these GPL versions.
14581 (license (list license:gpl2 license:gpl3))))
14583 (define-public r-ggcorrplot
14585 (name "r-ggcorrplot")
14590 (uri (cran-uri "ggcorrplot" version))
14593 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
14594 (build-system r-build-system)
14596 `(("r-ggplot2" ,r-ggplot2)
14597 ("r-reshape2" ,r-reshape2)))
14598 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
14599 (synopsis "Visualization of a correlation matrix using ggplot2")
14601 "The ggcorrplot package can be used to visualize easily a correlation
14602 matrix using ggplot2. It provides a solution for reordering the correlation
14603 matrix and displays the significance level on the plot. It also includes a
14604 function for computing a matrix of correlation p-values.")
14605 (license license:gpl2)))
14607 (define-public r-flexdashboard
14609 (name "r-flexdashboard")
14610 (version "0.5.1.1")
14614 (uri (cran-uri "flexdashboard" version))
14617 "0fy3nbrr67zqgd44r2mc850s5sp0hzfcw3zqs15m8kxzj1aw067x"))))
14618 (build-system r-build-system)
14620 `(#:modules ((guix build utils)
14621 (guix build r-build-system)
14625 (ice-9 textual-ports))
14627 (modify-phases %standard-phases
14628 (add-after 'unpack 'process-javascript
14629 (lambda* (#:key inputs #:allow-other-keys)
14630 (with-directory-excursion "inst"
14631 ;; Concatenate all components of prism.js
14632 (let ((contents (string-join
14633 (map (lambda (name)
14634 (call-with-input-file
14635 (assoc-ref inputs name)
14639 "js-prism-line-numbers"))
14641 (call-with-output-file "prism-src.js"
14642 (cut display contents <>)))
14646 `(("www/stickytableheaders/jquery.stickytableheaders.js"
14647 "www/stickytableheaders/jquery.stickytableheaders.min.js")
14649 "www/sly/sly.min.js")
14651 "www/prism/prism.js")
14652 (,(assoc-ref inputs "js-raphael")
14653 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
14654 (,(assoc-ref inputs "js-featherlight")
14655 "www/featherlight/featherlight.min.js"))))
14656 (lambda (sources targets)
14657 (for-each (lambda (source target)
14658 (format #t "Processing ~a --> ~a~%"
14660 (delete-file target)
14661 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14662 (call-with-output-file target
14664 (dump-port minified port)))))
14665 sources targets))))
14668 `(("r-htmltools" ,r-htmltools)
14669 ("r-htmlwidgets" ,r-htmlwidgets)
14670 ("r-jsonlite" ,r-jsonlite)
14671 ("r-knitr" ,r-knitr)
14672 ("r-rmarkdown" ,r-rmarkdown)
14673 ("r-shiny" ,r-shiny)))
14675 `(("uglify-js" ,uglify-js)
14679 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
14682 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
14686 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
14689 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
14693 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
14696 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
14697 ("js-prism-line-numbers"
14700 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
14703 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
14707 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
14710 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
14711 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
14712 (synopsis "R Markdown format for flexible dashboards")
14714 "This package provides an R Markdown format for converting an R Markdown
14715 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
14716 of its components to the containing web page.")
14717 (license license:expat)))
14719 (define-public r-preseqr
14726 (uri (cran-uri "preseqR" version))
14729 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
14730 (properties `((upstream-name . "preseqR")))
14731 (build-system r-build-system)
14733 `(("r-polynom" ,r-polynom)))
14734 (home-page "https://cran.r-project.org/web/packages/preseqR/")
14735 (synopsis "Predicting species accumulation curves")
14737 "This package can be used to predict the r-species accumulation
14738 curve (r-SAC), which is the number of species represented at least r times as
14739 a function of the sampling effort. When r = 1, the curve is known as the
14740 species accumulation curve, or the library complexity curve in high-throughput
14741 genomic sequencing. The package includes both parametric and nonparametric
14742 methods, as described by Deng C, et al. (2018).")
14743 (license license:gpl3)))
14745 (define-public r-mapplots
14747 (name "r-mapplots")
14752 (uri (cran-uri "mapplots" version))
14755 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
14756 (build-system r-build-system)
14757 (home-page "https://cran.r-project.org/web/packages/mapplots/")
14758 (synopsis "Data visualization on maps")
14760 "This package helps you create simple maps; add sub-plots like pie plots
14761 to a map or any other plot; format, plot and export gridded data. The package
14762 was developed for displaying fisheries data but most functions can be used for
14763 more generic data visualisation.")
14764 (license license:gpl2+)))
14766 (define-public r-pmcmr
14773 (uri (cran-uri "PMCMR" version))
14776 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
14777 (properties `((upstream-name . "PMCMR")))
14778 (build-system r-build-system)
14779 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
14780 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
14782 "This is a deprecated package for calculating pairwise multiple
14783 comparisons of mean rank sums. This package is superseded by the novel
14784 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
14785 compatibility of dependent packages for some time.")
14786 (license license:gpl3+)))
14788 (define-public r-downloader
14790 (name "r-downloader")
14795 (uri (cran-uri "downloader" version))
14798 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
14799 (build-system r-build-system)
14801 `(("r-digest" ,r-digest)))
14802 (home-page "https://github.com/wch/downloader")
14803 (synopsis "Download files over HTTP and HTTPS")
14805 "This package provides a wrapper for the @code{download.file} function,
14806 making it possible to download files over HTTPS across platforms. The
14807 @code{RCurl} package provides this functionality (and much more) but has
14808 external dependencies. This package has is implemented purely in R.")
14809 (license license:gpl2)))
14811 (define-public r-rex
14818 (uri (cran-uri "rex" version))
14821 "0alsadgjgass3wr8y5d247j12qqzg454sc84vpskclrkmz778g5x"))))
14822 (build-system r-build-system)
14824 `(("r-lazyeval" ,r-lazyeval)
14825 ("r-magrittr" ,r-magrittr)))
14826 (home-page "https://github.com/kevinushey/rex")
14827 (synopsis "Friendly regular expressions")
14829 "This package provides a friendly interface for the construction of
14830 regular expressions. Regular expressions are a very powerful feature, however
14831 they are often difficult to interpret. Rex allows you to build complex
14832 regular expressions from human readable expressions")
14833 (license license:expat)))
14835 (define-public r-xmlparsedata
14837 (name "r-xmlparsedata")
14842 (uri (cran-uri "xmlparsedata" version))
14845 "0gjr3l5z5dp276lchr2649as1rkj56d2mlvbr66yg393zzw50lsh"))))
14846 (properties `((upstream-name . "xmlparsedata")))
14847 (build-system r-build-system)
14848 (home-page "https://github.com/r-lib/xmlparsedata#readme")
14849 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
14851 "This package provides tools to convert the output of
14852 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
14853 @code{XPath}, and is easier to manipulate in general.")
14854 (license license:expat)))
14856 (define-public r-cyclocomp
14858 (name "r-cyclocomp")
14863 (uri (cran-uri "cyclocomp" version))
14866 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
14867 (properties `((upstream-name . "cyclocomp")))
14868 (build-system r-build-system)
14870 `(("r-callr" ,r-callr)
14871 ("r-crayon" ,r-crayon)
14873 ("r-remotes" ,r-remotes)
14874 ("r-withr" ,r-withr)))
14875 (home-page "https://github.com/MangoTheCat/cyclocomp")
14876 (synopsis "Cyclomatic complexity of R code")
14878 "Cyclomatic complexity is a software metric, used to indicate the
14879 complexity of a program. It is a quantitative measure of the number of
14880 linearly independent paths through a program's source code. This package
14881 provides tools to compute this metric.")
14882 (license license:expat)))
14884 (define-public r-lintr
14891 (uri (cran-uri "lintr" version))
14894 "09gbci4v5n4gsfzminly8332fw7faxdi1kkyvpa10dydx02sjcwb"))))
14895 (properties `((upstream-name . "lintr")))
14896 (build-system r-build-system)
14898 `(("r-codetools" ,r-codetools)
14899 ("r-crayon" ,r-crayon)
14900 ("r-cyclocomp" ,r-cyclocomp)
14901 ("r-digest" ,r-digest)
14903 ("r-jsonlite" ,r-jsonlite)
14904 ("r-knitr" ,r-knitr)
14906 ("r-rstudioapi" ,r-rstudioapi)
14907 ("r-stringdist" ,r-stringdist)
14908 ("r-testthat" ,r-testthat)
14910 ("r-xmlparsedata" ,r-xmlparsedata)))
14911 (home-page "https://github.com/jimhester/lintr")
14912 (synopsis "Linter for R code")
14913 (description "This package checks adherence to a given style, syntax
14914 errors and possible semantic issues. It supports on the fly checking of R
14915 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
14916 (license license:expat)))
14918 (define-public r-sctransform
14920 (name "r-sctransform")
14925 (uri (cran-uri "sctransform" version))
14928 "07v3lzccsrkh1glfxd1q20r8f8gl9ls5az0s1dvxm4vcls0hlhyn"))))
14929 (build-system r-build-system)
14931 `(("r-future-apply" ,r-future-apply)
14932 ("r-ggplot2" ,r-ggplot2)
14933 ("r-gridextra" ,r-gridextra)
14935 ("r-matrix" ,r-matrix)
14937 ("r-rcppeigen" ,r-rcppeigen)
14938 ("r-reshape2" ,r-reshape2)))
14939 (home-page "https://github.com/ChristophH/sctransform")
14940 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
14942 "This package provides a normalization method for single-cell UMI count
14943 data using a variance stabilizing transformation. The transformation is based
14944 on a negative binomial regression model with regularized parameters. As part
14945 of the same regression framework, this package also provides functions for
14946 batch correction, and data correction.")
14947 (license license:gpl3)))
14949 (define-public r-styler
14956 (uri (cran-uri "styler" version))
14959 "0rdbz60x8bymis6r6188ia1y0ip3nhf5y363i4cmakr618irjab9"))))
14960 (build-system r-build-system)
14962 `(("r-backports" ,r-backports)
14964 ("r-magrittr" ,r-magrittr)
14965 ("r-purrr" ,r-purrr)
14966 ("r-rematch2" ,r-rematch2)
14967 ("r-rlang" ,r-rlang)
14968 ("r-rprojroot" ,r-rprojroot)
14969 ("r-tibble" ,r-tibble)
14970 ("r-withr" ,r-withr)
14971 ("r-xfun" ,r-xfun)))
14972 (home-page "https://github.com/r-lib/styler")
14973 (synopsis "Non-invasive pretty printing of R code")
14975 "This is a package for pretty-printing R code without changing the user's
14976 formatting intent.")
14977 (license license:gpl3)))
14979 (define-public r-scrime
14986 (uri (cran-uri "scrime" version))
14989 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
14990 (build-system r-build-system)
14991 (home-page "https://cran.r-project.org/web/packages/scrime/")
14992 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
14994 "This package provides tools for the analysis of high-dimensional data
14995 developed/implemented at the group \"Statistical Complexity Reduction In
14996 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
14997 the functions can also be applied to other types of categorical data.")
14998 (license license:gpl2)))
15000 (define-public r-pbmcapply
15002 (name "r-pbmcapply")
15007 (uri (cran-uri "pbmcapply" version))
15010 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
15011 (build-system r-build-system)
15012 (home-page "https://github.com/kvnkuang/pbmcapply")
15013 (synopsis "Track the progress of apply procedures with a progress bar")
15015 "This light-weight package helps you track and visualize the progress of
15016 parallel versions of vectorized R functions of the @code{mc*apply} family.")
15017 (license license:expat)))
15019 (define-public r-blme
15026 (uri (cran-uri "blme" version))
15029 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
15030 (build-system r-build-system)
15031 (propagated-inputs `(("r-lme4" ,r-lme4)))
15032 (home-page "https://github.com/vdorie/blme")
15033 (synopsis "Bayesian linear mixed-effects models")
15035 "This package provides tools for maximum a posteriori estimation for
15036 linear and generalized linear mixed-effects models in a Bayesian setting. It
15037 extends the lme4 package.")
15038 (license license:gpl2+)))
15040 (define-public r-batchtools
15042 (name "r-batchtools")
15047 (uri (cran-uri "batchtools" version))
15050 "02mj21ypcjv5fs7ajf63p6bq0cyvihdl55hlpqx6kmsfjin1cr0v"))))
15051 (build-system r-build-system)
15053 `(("r-backports" ,r-backports)
15054 ("r-base64url" ,r-base64url)
15056 ("r-checkmate" ,r-checkmate)
15057 ("r-data-table" ,r-data-table)
15058 ("r-digest" ,r-digest)
15060 ("r-progress" ,r-progress)
15062 ("r-rappdirs" ,r-rappdirs)
15063 ("r-stringi" ,r-stringi)
15064 ("r-withr" ,r-withr)))
15065 (home-page "https://github.com/mllg/batchtools")
15066 (synopsis "Tools for computation on batch systems")
15068 "As a successor of the packages BatchJobs and BatchExperiments, this
15069 package provides a parallel implementation of the Map function for high
15070 performance computing systems managed by various schedulers. A multicore and
15071 socket mode allow the parallelization on a local machines, and multiple
15072 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
15073 the package provides an abstraction mechanism to define large-scale computer
15074 experiments in a well-organized and reproducible way.")
15075 (license license:lgpl3)))
15077 (define-public r-clue
15084 (uri (cran-uri "clue" version))
15087 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
15088 (build-system r-build-system)
15089 (propagated-inputs `(("r-cluster" ,r-cluster)))
15090 (home-page "https://cran.r-project.org/web/packages/clue/")
15091 (synopsis "Tools for analyzing cluster ensembles")
15092 (description "Cluster ensembles are collections of individual solutions to
15093 a given clustering problem which are useful or necessary to consider in a wide
15094 range of applications. This R package provides an extensible computational
15095 environment for creating and analyzing cluster ensembles, with basic data
15096 structures for representing partitions and hierarchies, and facilities for
15097 computing on them, including methods for measuring proximity and obtaining
15098 consensus and secondary clusterings.")
15099 (license license:gpl2)))
15101 (define-public r-sitmo
15108 (uri (cran-uri "sitmo" version))
15111 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
15112 (build-system r-build-system)
15113 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
15114 (home-page "https://github.com/coatless/sitmo/")
15115 (synopsis "Parallel pseudo random number generator header files")
15117 "This package provides two high quality and fast PPRNGs that may be used
15118 in an OpenMP parallel environment. In addition, there is a generator for one
15119 dimensional low-discrepancy sequence.")
15120 (license license:expat)))
15122 (define-public r-dqrng
15129 (uri (cran-uri "dqrng" version))
15132 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
15133 (build-system r-build-system)
15137 ("r-sitmo" ,r-sitmo)))
15138 (home-page "https://www.daqana.org/dqrng")
15139 (synopsis "Fast pseudo random number generators")
15141 "Several fast random number generators are provided as C++ header-only
15142 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
15143 Additionally, fast functions for generating random numbers according to a
15144 uniform, normal and exponential distribution are included. The latter two use
15145 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
15146 functions are exported to R and as a C++ interface and are enabled for use
15147 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
15148 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
15149 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
15150 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
15151 ;; whole is distributed under the terms of the AGPL 3.
15152 (license license:agpl3)))
15154 (define-public r-dalex
15161 (uri (cran-uri "DALEX" version))
15164 "1zviaf7530v8w996lbma0vplabrapgwldi7h70pr0439sxaqd421"))))
15165 (properties `((upstream-name . "DALEX")))
15166 (build-system r-build-system)
15167 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
15168 (home-page "https://pbiecek.github.io/DALEX/")
15169 (synopsis "Descriptive machine learning explanations")
15171 "Machine Learning models are widely used and have various applications in
15172 classification or regression. Models created with boosting, bagging, stacking
15173 or similar techniques are often used due to their high performance, but such
15174 black-box models usually lack interpretability. The DALEX package contains
15175 various explainers that help to understand the link between input variables
15176 and model output.")
15177 ;; Any version of the GPL
15178 (license license:gpl3+)))
15180 (define-public r-enrichr
15187 (uri (cran-uri "enrichR" version))
15190 "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
15191 (properties `((upstream-name . "enrichR")))
15192 (build-system r-build-system)
15194 `(("r-httr" ,r-httr)
15195 ("r-rjson" ,r-rjson)))
15196 (home-page "https://cran.r-project.org/web/packages/enrichR/")
15197 (synopsis "R Interface to Enrichr database for analyzing gene sets")
15199 "This package provides an R interface to all Enrichr databases, a
15200 web-based tool for analyzing gene sets and returns any enrichment of common
15201 annotated biological functions.")
15202 (license license:gpl2+)))
15204 (define-public r-plot3d
15211 (uri (cran-uri "plot3D" version))
15214 "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
15215 (properties `((upstream-name . "plot3D")))
15216 (build-system r-build-system)
15217 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
15218 (home-page "https://cran.r-project.org/web/packages/plot3D")
15219 (synopsis "Plot multi-dimensional data")
15221 "This package provides functions for viewing 2D and 3D data, including
15222 perspective plots, slice plots, surface plots, scatter plots, etc. It
15223 includes data sets from oceanography.")
15224 (license license:gpl3+)))
15226 (define-public r-ggfortify
15228 (name "r-ggfortify")
15233 (uri (cran-uri "ggfortify" version))
15236 "191q2z7w0l4v7swjlxs2hjgbjngw2838688s7ygnj0kigsm310f3"))))
15237 (build-system r-build-system)
15239 `(("r-dplyr" ,r-dplyr)
15240 ("r-ggplot2" ,r-ggplot2)
15241 ("r-gridextra" ,r-gridextra)
15242 ("r-scales" ,r-scales)
15243 ("r-stringr" ,r-stringr)
15244 ("r-tibble" ,r-tibble)
15245 ("r-tidyr" ,r-tidyr)))
15246 (home-page "https://github.com/sinhrks/ggfortify")
15247 (synopsis "Data visualization tools for statistical analysis results")
15249 "This package provides unified plotting tools for statistics commonly
15250 used, such as GLM, time series, PCA families, clustering and survival
15251 analysis. The package offers a single plotting interface for these analysis
15252 results and plots in a unified style using the @code{ggplot2} package.")
15253 (license license:gpl2)))
15255 (define-public r-refmanager
15257 (name "r-refmanager")
15262 (uri (cran-uri "RefManageR" version))
15265 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
15266 (properties `((upstream-name . "RefManageR")))
15267 (build-system r-build-system)
15269 `(("r-bibtex" ,r-bibtex)
15271 ("r-jsonlite" ,r-jsonlite)
15272 ("r-lubridate" ,r-lubridate)
15274 ("r-stringr" ,r-stringr)
15275 ("r-xml2" ,r-xml2)))
15276 (home-page "https://github.com/ropensci/RefManageR/")
15277 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
15279 "This package provides tools for importing and working with bibliographic
15280 references. It greatly enhances the @code{bibentry} class by providing a
15281 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
15282 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
15283 by various formats for name lists (author by last names, translator by full
15284 names, etc.). Entries can be updated, combined, sorted, printed in a number
15285 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
15286 into R and converted to @code{BibEntry} objects.")
15287 ;; Any of these licenses may be picked.
15288 (license (list license:gpl2 license:gpl3 license:bsd-3))))
15290 (define-public r-citr
15297 (uri (cran-uri "citr" version))
15300 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
15301 (build-system r-build-system)
15303 `(("r-assertthat" ,r-assertthat)
15306 ("r-miniui" ,r-miniui)
15307 ("r-refmanager" ,r-refmanager)
15308 ("r-rstudioapi" ,r-rstudioapi)
15309 ("r-shiny" ,r-shiny)
15310 ("r-shinyjs" ,r-shinyjs)
15311 ("r-yaml" ,r-yaml)))
15312 (home-page "https://github.com/crsh/citr")
15313 (synopsis "RStudio add-in to insert Markdown citations")
15315 "This package provides functions and an RStudio add-in that search a
15316 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
15317 the current document.")
15318 (license license:expat)))
15320 (define-public r-xgboost
15323 (version "0.90.0.2")
15327 (uri (cran-uri "xgboost" version))
15330 "1gy9rzg43mjpfis893vf15drmbigfn0481zrzss9ajnmnk0q8194"))))
15331 (build-system r-build-system)
15333 `(("r-data-table" ,r-data-table)
15334 ("r-magrittr" ,r-magrittr)
15335 ("r-matrix" ,r-matrix)
15336 ("r-stringi" ,r-stringi)))
15337 (home-page "https://github.com/dmlc/xgboost")
15338 (synopsis "Extreme gradient boosting")
15340 "This package provides an R interface to Extreme Gradient Boosting, which
15341 is an efficient implementation of the gradient boosting framework from Chen
15342 and Guestrin (2016). The package includes efficient linear model solver and
15343 tree learning algorithms. The package can automatically do parallel
15344 computation on a single machine. It supports various objective functions,
15345 including regression, classification and ranking. The package is made to be
15346 extensible, so that users are also allowed to define their own objectives
15348 (license license:asl2.0)))
15350 (define-public r-umap
15353 (version "0.2.4.0")
15357 (uri (cran-uri "umap" version))
15360 "1dzbwq96k5vqr64wk6s26ks4311h570xg6gf0prr4vnn033pqnch"))))
15361 (build-system r-build-system)
15363 `(("r-openssl" ,r-openssl)
15365 ("r-reticulate" ,r-reticulate)
15366 ("r-rspectra" ,r-rspectra)))
15367 (home-page "https://github.com/tkonopka/umap")
15368 (synopsis "Uniform manifold approximation and projection")
15370 "Uniform manifold approximation and projection is a technique for
15371 dimension reduction. This package provides an interface to the UMAP algorithm
15372 in R, including a translation of the original algorithm into R.")
15373 (license license:expat)))
15375 (define-public r-uwot
15382 (uri (cran-uri "uwot" version))
15385 "0pz9wa89xq4d119q86lskrznf979m0r1db8iaprcz7kxbi6b8lrj"))))
15386 (build-system r-build-system)
15388 `(("r-dqrng" ,r-dqrng)
15390 ("r-irlba" ,r-irlba)
15391 ("r-matrix" ,r-matrix)
15393 ("r-rcppannoy" ,r-rcppannoy)
15394 ("r-rcppparallel" ,r-rcppparallel)
15395 ("r-rcppprogress" ,r-rcppprogress)
15396 ("r-rspectra" ,r-rspectra)))
15397 (home-page "https://github.com/jlmelville/uwot")
15398 (synopsis "Uniform manifold approximation and projection")
15400 "This package provides an implementation of the Uniform Manifold
15401 Approximation and Projection dimensionality reduction by McInnes et
15402 al. (2018). It also provides means to transform new data and to carry out
15403 supervised dimensionality reduction. An implementation of the related
15404 LargeVis method of Tang et al. (2016) is also provided.")
15405 (license license:gpl3)))
15407 (define-public r-kableextra
15409 (name "r-kableextra")
15414 (uri (cran-uri "kableExtra" version))
15417 "1nicvw06xsf3a1f5c10mih07b76m2v5s5h165vmz0qx6n1a3492i"))))
15418 (properties `((upstream-name . "kableExtra")))
15419 (build-system r-build-system)
15421 `(("r-digest" ,r-digest)
15423 ("r-htmltools" ,r-htmltools)
15424 ("r-knitr" ,r-knitr)
15425 ("r-magrittr" ,r-magrittr)
15426 ("r-readr" ,r-readr)
15427 ("r-rmarkdown" ,r-rmarkdown)
15428 ("r-rstudioapi" ,r-rstudioapi)
15429 ("r-rvest" ,r-rvest)
15430 ("r-scales" ,r-scales)
15431 ("r-stringr" ,r-stringr)
15432 ("r-viridislite" ,r-viridislite)
15433 ("r-webshot" ,r-webshot)
15434 ("r-xml2" ,r-xml2)))
15435 (home-page "https://haozhu233.github.io/kableExtra/")
15436 (synopsis "Construct complex tables with pipe syntax")
15438 "Build complex HTML or LaTeX tables using @code{kable()} from
15439 @code{knitr} and the piping syntax from @code{magrittr}. The function
15440 @code{kable()} is a light weight table generator coming from @code{knitr}.
15441 This package simplifies the way to manipulate the HTML or LaTeX codes
15442 generated by @code{kable()} and allows users to construct complex tables and
15443 customize styles using a readable syntax.")
15444 (license license:expat)))
15446 (define-public r-glasso
15453 (uri (cran-uri "glasso" version))
15455 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
15456 (build-system r-build-system)
15457 (native-inputs `(("gfortran" ,gfortran)))
15458 (home-page "http://www-stat.stanford.edu/~tibs/glasso")
15459 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
15461 "This is a package for estimation of a sparse inverse covariance matrix
15462 using a lasso (L1) penalty. Facilities are provided for estimates along a
15463 path of values for the regularization parameter.")
15464 (license license:gpl2)))
15466 (define-public r-rhpcblasctl
15468 (name "r-rhpcblasctl")
15469 (version "0.18-205")
15473 (uri (cran-uri "RhpcBLASctl" version))
15476 "1ls2286fvrp1g7p8v4l6axznychh3qndranfpzqz806cm9ml1cdp"))))
15477 (properties `((upstream-name . "RhpcBLASctl")))
15478 (build-system r-build-system)
15479 (home-page "http://prs.ism.ac.jp/~nakama/Rhpc/")
15480 (synopsis "Control the number of threads on BLAS")
15482 "This package allows you to control the number of threads the BLAS
15483 library uses. It is also possible to control the number of threads in
15485 (license license:agpl3+)))
15487 (define-public r-lda
15494 (uri (cran-uri "lda" version))
15497 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
15498 (build-system r-build-system)
15499 (home-page "https://cran.r-project.org/web/packages/lda/")
15500 (synopsis "Collapsed Gibbs sampling methods for topic models")
15502 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
15503 related models. This includes (but is not limited to) sLDA, corrLDA, and the
15504 mixed-membership stochastic blockmodel. Inference for all of these models is
15505 implemented via a fast collapsed Gibbs sampler written in C. Utility
15506 functions for reading/writing data typically used in topic models, as well as
15507 tools for examining posterior distributions are also included.")
15508 ;; Any version of the LGPL
15509 (license license:lgpl3+)))
15511 (define-public r-rann-l1
15518 (uri (cran-uri "RANN.L1" version))
15521 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
15522 (properties `((upstream-name . "RANN.L1")))
15523 (build-system r-build-system)
15524 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
15525 (synopsis "Fast nearest neighbour search using L1 metric")
15527 "This package provides tools to find the k nearest neighbours for every
15528 point in a given dataset in O(N log N) time using Arya and Mount's ANN
15529 library. There is support for approximate as well as exact searches, fixed
15530 radius searches and @code{bd} as well as @code{kd} trees. The distance is
15531 computed using the L1 (Manhattan, taxicab) metric.")
15532 (license license:gpl3+)))
15534 (define-public r-leiden
15541 (uri (cran-uri "leiden" version))
15544 "19gq27zin4gf4sh7h24gyq3f8jjir20n2l36a7pk1pbzcr4ixyhp"))))
15545 (properties `((upstream-name . "leiden")))
15546 (build-system r-build-system)
15548 `(("r-igraph" ,r-igraph)
15549 ("r-matrix" ,r-matrix)
15550 ("r-reticulate" ,r-reticulate)))
15551 (home-page "https://github.com/TomKellyGenetics/leiden")
15552 (synopsis "R implementation of Leiden clustering algorithm")
15554 "This package implements the Python @code{leidenalg} module to be called
15555 in R. It enables clustering using the Leiden algorithm for partitioning a
15556 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
15557 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
15558 (license license:gpl3)))
15560 (define-public r-patchwork
15561 ;; There has been no public release yet.
15562 (let ((commit "fd7958bae3e7a1e30237c751952e412a0a1d1242")
15565 (name "r-patchwork")
15566 (version (git-version "0.0.1" revision commit))
15570 (uri (git-reference
15571 (url "https://github.com/thomasp85/patchwork.git")
15573 (file-name (git-file-name name version))
15576 "00fq520xwy1ysg4k8x48x9b0yy9wyi8y8zj6dvxjg4bwx0yyp6s4"))))
15577 (build-system r-build-system)
15579 `(("r-ggplot2" ,r-ggplot2)
15580 ("r-gtable" ,r-gtable)))
15581 (home-page "https://github.com/thomasp85/patchwork")
15582 (synopsis "Compose ggplot2 plots")
15584 "The @code{ggplot2} package provides a strong API for sequentially
15585 building up a plot, but does not concern itself with composition of multiple
15586 plots. Patchwork is a package that expands the API to allow for arbitrarily
15587 complex composition of plots by providing mathmatical operators for combining
15589 (license license:expat))))
15591 (define-public r-liger
15598 (uri (git-reference
15599 (url "https://github.com/MacoskoLab/liger.git")
15600 (commit (string-append "v" version))))
15601 (file-name (git-file-name name version))
15604 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
15605 (modules '((guix build utils)))
15608 (delete-file "inst/java/ModularityOptimizer.jar")
15610 (build-system r-build-system)
15613 (modify-phases %standard-phases
15614 (add-after 'unpack 'build-java-part
15615 (lambda* (#:key inputs #:allow-other-keys)
15616 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
15617 (for-each (lambda (file) (invoke "javac" file))
15618 (find-files "." "\\.java$"))
15619 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
15620 (find-files "." "\\.class$"))
15623 `(("r-cowplot" ,r-cowplot)
15624 ("r-dosnow" ,r-dosnow)
15625 ("r-dplyr" ,r-dplyr)
15627 ("r-foreach" ,r-foreach)
15628 ("r-ggplot2" ,r-ggplot2)
15629 ("r-ggrepel" ,r-ggrepel)
15630 ("r-hmisc" ,r-hmisc)
15632 ("r-irlba" ,r-irlba)
15633 ("r-matrix" ,r-matrix)
15634 ("r-mclust" ,r-mclust)
15635 ("r-patchwork" ,r-patchwork)
15637 ("r-rann-l1" ,r-rann-l1)
15639 ("r-rcpparmadillo" ,r-rcpparmadillo)
15640 ("r-riverplot" ,r-riverplot)
15641 ("r-rtsne" ,r-rtsne)
15642 ("r-snow" ,r-snow)))
15644 `(("jdk" ,icedtea "jdk")
15645 ;; See https://github.com/MacoskoLab/liger/issues/96
15646 ;; The optimizer is released under the Expat license.
15650 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
15653 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
15655 ("r-knitr" ,r-knitr))) ; for vignettes
15656 (home-page "https://github.com/MacoskoLab/liger")
15657 (synopsis "Integrate and analyze multiple single-cell datasets")
15659 "LIGER is a package for integrating and analyzing multiple single-cell
15660 datasets, developed and maintained by the Macosko lab. It relies on
15661 integrative non-negative matrix factorization to identify shared and
15662 dataset-specific factors.")
15663 (license license:gpl3)))
15665 (define-public r-harmony
15666 ;; There are no tagged commits
15667 (let ((commit "4d1653870d4dd70fff1807c182882db1fbf9af5a")
15671 (version (git-version "1.0" revision commit))
15675 (uri (git-reference
15676 (url "https://github.com/immunogenomics/harmony")
15678 (file-name (git-file-name name version))
15681 "1gasdldr4aalr9h2q9kmm3y4i7azkgnhdn4bmvsszs7lg9xacw85"))))
15682 (build-system r-build-system)
15684 `(("r-cowplot" ,r-cowplot)
15685 ("r-dplyr" ,r-dplyr)
15686 ("r-ggplot2" ,r-ggplot2)
15687 ("r-irlba" ,r-irlba)
15688 ("r-matrix" ,r-matrix)
15690 ("r-rcpparmadillo" ,r-rcpparmadillo)
15691 ("r-rcppprogress" ,r-rcppprogress)
15692 ("r-rlang" ,r-rlang)
15693 ("r-tibble" ,r-tibble)
15694 ("r-tidyr" ,r-tidyr)))
15695 (home-page "https://github.com/immunogenomics/harmony")
15696 (synopsis "Integration of single cell sequencing data")
15698 "This package provides an implementation of the Harmony algorithm for
15699 single cell integration, described in Korsunsky et al
15700 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
15701 function and interfaces to external frameworks.")
15702 (license license:gpl3))))
15704 (define-public r-covr
15711 (uri (cran-uri "covr" version))
15713 (base32 "0p44kr6yz5sqza5zvq6divqglzkpv0if9pjpjmzhmdaaddjrqzg5"))))
15714 (properties `((upstream-name . "covr")))
15715 (build-system r-build-system)
15717 `(("r-crayon" ,r-crayon)
15718 ("r-digest" ,r-digest)
15720 ("r-jsonlite" ,r-jsonlite)
15722 ("r-withr" ,r-withr)
15723 ("r-yaml" ,r-yaml)))
15724 (home-page "https://github.com/r-lib/covr")
15725 (synopsis "Test coverage for R packages")
15727 "Thisp package enables you to track and report code coverage for your
15728 package and (optionally) upload the results to a coverage service. Code
15729 coverage is a measure of the amount of code being exercised by a set of tests.
15730 It is an indirect measure of test quality and completeness. This package is
15731 compatible with any testing methodology or framework and tracks coverage of
15732 both R code and compiled C/C++/FORTRAN code.")
15733 (license license:gpl3)))
15735 (define-public r-systemfonts
15737 (name "r-systemfonts")
15742 (uri (cran-uri "systemfonts" version))
15745 "0m0ljid683xcam2f14x7k2zv1yx4npac38a3gfv11vhxfbnpgp0z"))))
15746 (properties `((upstream-name . "systemfonts")))
15747 (build-system r-build-system)
15749 `(("fontconfig" ,fontconfig)
15750 ("freetype" ,freetype)
15753 `(("pkg-config" ,pkg-config)))
15754 (home-page "https://github.com/r-lib/systemfonts")
15755 (synopsis "System native font finding")
15757 "This package provides system native access to the font catalogue. As
15758 font handling varies between systems it is difficult to correctly locate
15759 installed fonts across different operating systems. The 'systemfonts' package
15760 provides bindings to the native libraries for finding font files that can then
15761 be used further by e.g. graphic devices.")
15762 (license license:expat)))
15764 (define-public r-graphlayouts
15766 (name "r-graphlayouts")
15771 (uri (cran-uri "graphlayouts" version))
15774 "03dizbhhdhnzbj2i5zvqgs617kwcv4h2pha4f16adic0fph1rxl3"))))
15775 (properties `((upstream-name . "graphlayouts")))
15776 (build-system r-build-system)
15778 `(("r-igraph" ,r-igraph)
15780 ("r-rcpparmadillo" ,r-rcpparmadillo)))
15781 (home-page "https://github.com/schochastics/graphlayouts")
15782 (synopsis "Additional layout algorithms for network visualizations")
15784 "This package provides several layout algorithms to visualize networks
15785 which are not part of the igraph library. Most are based on the concept of
15786 stress majorization by Gansner et al. (2004)
15787 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms allow to
15788 emphasize hidden group structures in networks or focus on specific nodes.")
15789 (license license:expat)))
15791 (define-public r-tidygraph
15793 (name "r-tidygraph")
15798 (uri (cran-uri "tidygraph" version))
15801 "1zpsarm74afbc7p5dlyb0whc09670qdcddw1ckb25cfc9hfh0hjn"))))
15802 (properties `((upstream-name . "tidygraph")))
15803 (build-system r-build-system)
15805 `(("r-dplyr" ,r-dplyr)
15806 ("r-igraph" ,r-igraph)
15807 ("r-magrittr" ,r-magrittr)
15808 ("r-pillar" ,r-pillar)
15811 ("r-rlang" ,r-rlang)
15812 ("r-tibble" ,r-tibble)
15813 ("r-tidyr" ,r-tidyr)))
15814 (home-page "https://github.com/thomasp85/tidygraph")
15815 (synopsis "Tidy API for graph manipulation")
15817 "This package provides a graph implementation that can be thought of as
15818 two tidy data frames describing node and edge data respectively. It provides
15819 an approach to manipulate these two virtual data frames using the API defined
15820 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
15821 common graph algorithms.")
15822 (license license:expat)))
15824 (define-public r-soupx
15825 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
15829 (version (git-version "0.3.1" revision commit))
15833 (uri (git-reference
15834 (url "https://github.com/constantAmateur/SoupX")
15836 (file-name (git-file-name name version))
15839 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
15840 (properties `((upstream-name . "SoupX")))
15841 (build-system r-build-system)
15843 `(("r-ggplot2" ,r-ggplot2)
15844 ("r-matrix" ,r-matrix)
15845 ("r-seurat" ,r-seurat)))
15846 (home-page "https://github.com/constantAmateur/SoupX")
15847 (synopsis "Single cell mRNA Soup eXterminator")
15849 "This package provides a package for quantifying, profiling and
15850 removing cell free mRNA contamination (the \"soup\") from droplet based single
15851 cell RNA-seq experiments.")
15852 (license license:gpl2))))
15854 (define-public r-assertr
15861 (uri (cran-uri "assertr" version))
15864 "0g4ii6vhp0155a29ljhs64a09x0nzy5ybvwwchhk4mkcgsvnvfkj"))))
15865 (build-system r-build-system)
15867 `(("r-dplyr" ,r-dplyr)
15869 ("r-rlang" ,r-rlang)))
15871 `(("r-knitr" ,r-knitr))) ; needed for vignette
15872 (home-page "https://github.com/ropensci/assertr")
15873 (synopsis "Assertive programming for R analysis pipelines")
15875 "This package provides functionality to assert conditions that have to be
15876 met so that errors in data used in analysis pipelines can fail quickly. It is
15877 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
15879 (license license:expat)))
15881 (define-public r-parameters
15883 (name "r-parameters")
15888 (uri (cran-uri "parameters" version))
15891 "0ifb9g1h8sn661q7jf9d8glk58gxdcym5ywbmx7phwn0y3is5wdv"))))
15892 (properties `((upstream-name . "parameters")))
15893 (build-system r-build-system)
15895 `(("r-bayestestr" ,r-bayestestr)
15896 ("r-insight" ,r-insight)))
15897 (home-page "https://cran.r-project.org/web/packages/parameters")
15898 (synopsis "Processing of model parameters")
15900 "This package provides utilities for processing the parameters of various
15901 statistical models. Beyond computing p values, CIs, and other indices for a
15902 wide variety of models, this package implements features like standardization
15903 or bootstrapping of parameters and models, feature reduction (feature
15904 extraction and variable selection) as well as conversion between indices of
15906 (license license:gpl3)))
15908 (define-public r-rgdal
15915 (uri (cran-uri "rgdal" version))
15917 (base32 "1jd691amf3ghznq5im15gvhl6v6k25klpl75m4ngrqf9xlxaa3as"))))
15918 (properties `((upstream-name . "rgdal")))
15919 (build-system r-build-system)
15927 `(("pkg-config" ,pkg-config)))
15928 (home-page "http://rgdal.r-forge.r-project.org")
15929 (synopsis "Bindings for the Geospatial Data Abstraction Library")
15931 "This package provides bindings to the Geospatial Data Abstraction
15932 Library (GDAL) and access to projection/transformation operations from the
15934 (license license:gpl2+)))
15936 (define-public r-insol
15943 (uri (cran-uri "insol" version))
15946 "1d2vqmbp94ff80mfkmq4a8y12r6ryym8hh1568ip9qbn7snc64v1"))))
15947 (properties `((upstream-name . "insol")))
15948 (build-system r-build-system)
15950 `(("r-raster" ,r-raster)))
15952 `(("gfortran" ,gfortran)))
15953 (home-page "https://meteoexploration.com/R/insol/index.html")
15954 (synopsis "Tools for calculating solar radiation")
15956 "This package provides functions to compute insolation on tilted
15957 surfaces, computes atmospheric transmittance and related parameters such as:
15958 Earth radius vector, declination, sunset and sunrise, daylength, equation of
15959 time, vector in the direction of the sun, vector normal to surface, and some
15960 atmospheric physics.")
15961 (license license:gpl2+)))
15963 (define-public r-lifecycle
15965 (name "r-lifecycle")
15970 (uri (cran-uri "lifecycle" version))
15973 "11rk7hkw63rfrf4aqmb4xrb88kg95xh8hajpjvjfwjym2v02h74n"))))
15974 (properties `((upstream-name . "lifecycle")))
15975 (build-system r-build-system)
15977 `(("r-glue" ,r-glue)
15978 ("r-rlang" ,r-rlang)))
15979 (home-page "https://github.com/r-lib/lifecycle")
15980 (synopsis "Manage the life cycle of your package functions")
15982 "Manage the life cycle of your exported functions with shared
15983 conventions, documentation badges, and non-invasive deprecation warnings. The
15984 lifecycle package defines four development stages (experimental, maturing,
15985 stable, and questioning) and three deprecation stages (soft-deprecated,
15986 deprecated, and defunct). It makes it easy to insert badges corresponding to
15987 these stages in your documentation. Usage of deprecated functions are
15988 signalled with increasing levels of non-invasive verbosity.")
15989 (license license:gpl3)))
15991 (define-public r-assertable
15993 (name "r-assertable")
15998 (uri (cran-uri "assertable" version))
16001 "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
16002 (build-system r-build-system)
16004 `(("r-data-table" ,r-data-table)))
16005 (home-page "https://cran.r-project.org/web/packages/assertable/")
16006 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
16007 (description "This package provides simple, flexible assertions on
16008 data.frame or data.table objects with verbose output for vetting. While other
16009 assertion packages apply towards more general use-cases, @code{assertable} is
16010 tailored towards tabular data. It includes functions to check variable names
16011 and values, whether the dataset contains all combinations of a given set of
16012 unique identifiers, and whether it is a certain length. In addition,
16013 @code{assertable} includes utility functions to check the existence of target
16014 files and to efficiently import multiple tabular data files into one
16016 (license license:gpl3)))
16018 (define-public r-quadprog
16020 (name "r-quadprog")
16025 (uri (cran-uri "quadprog" version))
16027 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
16028 (build-system r-build-system)
16030 `(("gfortran" ,gfortran)))
16031 (home-page "https://cran.r-project.org/web/packages/quadprog")
16032 (synopsis "Functions to solve quadratic programming problems")
16034 "This package contains routines and documentation for solving quadratic
16035 programming problems.")
16036 (license license:gpl3+)))
16038 (define-public r-desolve
16045 (uri (cran-uri "deSolve" version))
16047 (base32 "1qhjq4vxlxd9qmhf6i26x1k7bzhldlxzbby1zgcplicdvlqk951d"))))
16048 (properties `((upstream-name . "deSolve")))
16049 (build-system r-build-system)
16051 `(("gfortran" ,gfortran)))
16052 (home-page "https://desolve.r-forge.r-project.org/")
16053 (synopsis "Solvers for initial value problems of differential equations")
16054 (description "This package provides functions that solve initial value
16055 problems of a system of first-order @dfn{ordinary differential
16056 equations} (ODE), of @dfn{partial differential equations} (PDE), of
16057 @dfn{differential algebraic equations} (DAE), and of delay differential
16058 equations. The functions provide an interface to the FORTRAN functions
16059 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
16060 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
16061 C-implementation of solvers of the Runge-Kutta family with fixed or variable
16062 time steps. The package contains routines designed for solving ODEs resulting
16063 from 1-D, 2-D and 3-D partial differential equations that have been converted
16064 to ODEs by numerical differencing.")
16065 (license license:gpl2+)))
16067 (define-public r-pracma
16073 (uri (cran-uri "pracma" version))
16075 (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc"))))
16076 (build-system r-build-system)
16077 (home-page "https://cran.r-project.org/web/packages/pracma/")
16078 (synopsis "Practical numerical math functions")
16079 (description "This package provides functions for numerical analysis and
16080 linear algebra, numerical optimization, differential equations, plus some
16081 special functions. It uses Matlab function names where appropriate to simplify
16083 (license license:gpl3+)))
16085 (define-public r-subplex
16092 (uri (cran-uri "subplex" version))
16095 "10cbgbx1bgsax5z7gz6716g360xpq4mvq19cf4qqrxv02mmwz57z"))))
16096 (build-system r-build-system)
16098 `(("gfortran" ,gfortran)))
16099 (home-page "https://cran.r-project.org/web/packages/subplex")
16100 (synopsis "Unconstrained optimization using the subplex algorithm")
16102 "This package implements the Subplex optimization algorithm.
16103 It solves unconstrained optimization problems using a simplex method on
16104 subspaces. The method is well suited for optimizing objective functions that
16105 are noisy or are discontinuous at the solution.")
16106 (license license:gpl3+)))
16108 (define-public r-txtplot
16115 (uri (cran-uri "txtplot" version))
16118 "1949ab1bzvysdb79g8x1gaknj0ih3d6g63pv9512h5m5l3a6c31h"))))
16119 (build-system r-build-system)
16120 (home-page "https://cran.r-project.org/web/packages/txtplot/")
16121 (synopsis "Text-based plotting")
16122 (description "This package provides functions to produce rudimentary ASCII
16123 graphics directly in the terminal window. This package provides a basic
16124 plotting function (and equivalents of curve, density, acf and barplot) as well
16125 as a boxplot function.")
16126 (license license:lgpl3+)))
16128 (define-public r-bio3d
16135 (uri (cran-uri "bio3d" version))
16138 "0ikpk1ppdp50m9kd289z616i382j9i7ji1zchyd4xqfyk8lnxf4s"))))
16139 (properties `((upstream-name . "bio3d")))
16140 (build-system r-build-system)
16141 (inputs `(("zlib" ,zlib)))
16142 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
16143 (home-page "http://thegrantlab.org/bio3d/")
16144 (synopsis "Biological structure analysis")
16146 "This package provides utilities to process, organize and explore protein
16147 structure, sequence and dynamics data. Features include the ability to read
16148 and write structure, sequence and dynamic trajectory data, perform sequence
16149 and structure database searches, data summaries, atom selection, alignment,
16150 superposition, rigid core identification, clustering, torsion analysis,
16151 distance matrix analysis, structure and sequence conservation analysis, normal
16152 mode analysis, principal component analysis of heterogeneous structure data,
16153 and correlation network analysis from normal mode and molecular dynamics data.
16154 In addition, various utility functions are provided to enable the statistical
16155 and graphical power of the R environment to work with biological sequence and
16157 (license license:gpl2+)))
16159 (define-public r-bios2cor
16161 (name "r-bios2cor")
16166 (uri (cran-uri "Bios2cor" version))
16169 "1rrz0vs6wbkwys3l5jv1rdnlhyb4r1q9pv7jlnmsx6c1b4f4vz5n"))))
16170 (properties `((upstream-name . "Bios2cor")))
16171 (build-system r-build-system)
16173 `(("r-bigmemory" ,r-bigmemory)
16174 ("r-bio3d" ,r-bio3d)
16175 ("r-circular" ,r-circular)
16176 ("r-igraph" ,r-igraph)))
16177 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
16178 (synopsis "From biological sequences and simulations to correlation analysis")
16180 "This package provides utilities for computation and analysis of
16181 correlation/covariation in multiple sequence alignments and in side chain
16182 motions during molecular dynamics simulations. Features include the
16183 computation of correlation/covariation scores using a variety of scoring
16184 functions between either sequence positions in alignments or side chain
16185 dihedral angles in molecular dynamics simulations and utilities to analyze the
16186 correlation/covariation matrix through a variety of tools including network
16187 representation and principal components analysis. In addition, several
16188 utility functions are based on the R graphical environment to provide friendly
16189 tools for help in data interpretation.")
16190 (license license:gpl2+)))
16192 ;; This package includes minified JavaScript files. When upgrading please
16193 ;; check that there are no new minified JavaScript files.
16194 (define-public r-networkd3
16196 (name "r-networkd3")
16201 (uri (cran-uri "networkD3" version))
16204 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
16207 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
16209 (properties `((upstream-name . "networkD3")))
16210 (build-system r-build-system)
16212 `(#:modules ((guix build utils)
16213 (guix build r-build-system)
16217 (modify-phases %standard-phases
16218 (add-after 'unpack 'process-javascript
16219 (lambda* (#:key inputs #:allow-other-keys)
16220 (with-directory-excursion "inst/htmlwidgets/lib/"
16224 `((,(assoc-ref inputs "d3.v4.js")
16225 "d3-4.5.0/d3.min.js"))))
16226 (lambda (sources targets)
16227 (for-each (lambda (source target)
16228 (format #t "Processing ~a --> ~a~%"
16230 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16231 (call-with-output-file target
16233 (dump-port minified port)))))
16234 sources targets))))
16237 `(("uglify-js" ,uglify-js)
16238 ;; NOTE: Make sure that this version of d3 is still valid when
16239 ;; upgrading the package.
16243 (uri "https://d3js.org/d3.v4.js")
16246 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
16248 `(("r-htmlwidgets" ,r-htmlwidgets)
16249 ("r-igraph" ,r-igraph)
16250 ("r-magrittr" ,r-magrittr)))
16251 (home-page "https://cran.r-project.org/package=networkD3")
16252 (synopsis "D3 JavaScript network graphs from R")
16254 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
16256 (license license:gpl3+)))
16258 (define-public r-aasea
16265 (uri (cran-uri "aaSEA" version))
16268 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
16269 (properties `((upstream-name . "aaSEA")))
16270 (build-system r-build-system)
16272 `(("r-bios2cor" ,r-bios2cor)
16274 ("r-hmisc" ,r-hmisc)
16275 ("r-magrittr" ,r-magrittr)
16276 ("r-networkd3" ,r-networkd3)
16277 ("r-plotly" ,r-plotly)
16278 ("r-seqinr" ,r-seqinr)
16279 ("r-shiny" ,r-shiny)
16280 ("r-shinydashboard" ,r-shinydashboard)))
16281 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
16282 (synopsis "Amino acid substitution effect analyzer")
16284 "Given a protein multiple sequence alignment, it is a daunting task to
16285 assess the effects of substitutions along sequence length. The aaSEA package
16286 is intended to help researchers to rapidly analyze property changes caused by
16287 single, multiple and correlated amino acid substitutions in proteins.")
16288 (license license:gpl3)))
16290 (define-public r-abacus
16297 (uri (cran-uri "ABACUS" version))
16300 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
16301 (properties `((upstream-name . "ABACUS")))
16302 (build-system r-build-system)
16304 `(("r-ggplot2" ,r-ggplot2)
16305 ("r-shiny" ,r-shiny)))
16306 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
16307 (synopsis "Apps-based activities for communicating and understanding statistics")
16309 "This package provides a set of Shiny apps for effective communication
16310 and understanding in statistics. The current version includes properties of
16311 normal distribution, properties of sampling distribution, one-sample z and t
16312 tests, two samples independent (unpaired) t test and analysis of variance.")
16313 (license license:gpl3)))
16315 (define-public r-abc-rap
16322 (uri (cran-uri "ABC.RAP" version))
16325 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
16326 (properties `((upstream-name . "ABC.RAP")))
16327 (build-system r-build-system)
16328 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
16329 (synopsis "Array-based CpG region analysis pipeline")
16331 "This package aims to identify candidate genes that are differentially
16332 methylated between cases and controls. It applies Student's t-test and delta
16333 beta analysis to identify candidate genes containing multiple CpG sites.")
16334 (license license:gpl3)))
16336 (define-public r-abcadm
16343 (uri (cran-uri "abcADM" version))
16346 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
16347 (properties `((upstream-name . "abcADM")))
16348 (build-system r-build-system)
16351 ("r-rcpp" ,r-rcpp)))
16352 (home-page "https://cran.r-project.org/web/packages/abcADM/")
16353 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
16355 "This package provides tools to estimate parameters of accumulated
16356 damage (load duration) models based on failure time data under a Bayesian
16357 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
16358 long-term reliability under stochastic load profiles.")
16359 (license license:gpl3)))
16361 (define-public r-rglpk
16368 (uri (cran-uri "Rglpk" version))
16371 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
16372 (properties `((upstream-name . "Rglpk")))
16373 (build-system r-build-system)
16375 `(("r-slam" ,r-slam)))
16378 (home-page "http://R-Forge.R-project.org/projects/rglp/")
16379 (synopsis "R interface to the GNU Linear Programming Kit")
16381 "This package provides an R interface to the GNU Linear Programming Kit,
16382 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
16383 integer linear programming} (MILP) and other related problems.")
16385 (license (list license:gpl2 license:gpl3))))
16387 (define-public r-abcdefba
16389 (name "r-abcdefba")
16394 (uri (cran-uri "abcdeFBA" version))
16397 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
16398 (properties `((upstream-name . "abcdeFBA")))
16399 (build-system r-build-system)
16401 `(("r-corrplot" ,r-corrplot)
16402 ("r-lattice" ,r-lattice)
16404 ("r-rglpk" ,r-rglpk)))
16405 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
16406 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
16408 "This package provides functions for Constraint Based Simulation using
16409 Flux Balance Analysis and informative analysis of the data generated during
16411 (license license:gpl2)))
16413 (define-public r-abcrlda
16420 (uri (cran-uri "abcrlda" version))
16423 "0j29ifsvmxfx2g6v4bpbb4s6miwfpf4vlkpbgj6f2q078s4clc85"))))
16424 (properties `((upstream-name . "abcrlda")))
16425 (build-system r-build-system)
16426 (home-page "https://ieeexplore.ieee.org/document/8720003/")
16427 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
16429 "This package offers methods to perform @dfn{asymptotically
16430 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
16431 cost-sensitive binary classification. The bias-correction is an estimate of
16432 the bias term added to regularized discriminant analysis that minimizes the
16434 (license license:gpl3)))
16436 (define-public r-abemus
16443 (uri (cran-uri "abemus" version))
16446 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
16447 (properties `((upstream-name . "abemus")))
16448 (build-system r-build-system)
16450 `(("r-data-table" ,r-data-table)))
16451 (home-page "https://cran.r-project.org/web/packages/abemus/")
16452 (synopsis "Adaptive base error model in ultra-deep sequencing data")
16454 "This package provides an implementation of @dfn{Adaptive Base Error
16455 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
16456 platform-specific genetic knowledge and empirical signal to readily detect and
16457 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
16458 cell free DNA} (cfDNA).")
16459 (license license:gpl3)))
16461 ;; This package includes minified JavaScript files. When upgrading please
16462 ;; check that there are no new minified JavaScript files.
16463 (define-public r-rintrojs
16465 (name "r-rintrojs")
16470 (uri (cran-uri "rintrojs" version))
16473 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
16474 (properties `((upstream-name . "rintrojs")))
16475 (build-system r-build-system)
16477 `(#:modules ((guix build utils)
16478 (guix build r-build-system)
16482 (modify-phases %standard-phases
16483 (add-after 'unpack 'process-javascript
16484 (lambda* (#:key inputs #:allow-other-keys)
16485 (with-directory-excursion "inst/javascript/introjs/"
16489 `((,(assoc-ref inputs "intro.js")
16491 (lambda (sources targets)
16492 (for-each (lambda (source target)
16493 (format #t "Processing ~a --> ~a~%"
16495 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16496 (call-with-output-file target
16498 (dump-port minified port)))))
16499 sources targets))))
16502 `(("uglify-js" ,uglify-js)
16506 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
16509 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
16511 `(("r-jsonlite" ,r-jsonlite)
16512 ("r-shiny" ,r-shiny)))
16513 (home-page "https://github.com/carlganz/rintrojs")
16514 (synopsis "Wrapper for the Intro.js library")
16516 "This package provides a wrapper for the @url{http://www.introjs.com,
16517 Intro.js} library. This package makes it easy to include step-by-step
16518 introductions, and clickable hints in a Shiny application. It supports both
16519 static introductions in the UI, and programmatic introductions from the
16521 (license license:agpl3+)))
16523 (define-public r-sysfonts
16525 (name "r-sysfonts")
16530 (uri (cran-uri "sysfonts" version))
16533 "0wng902plryf2d8fc7k7m3jx11acz51kb2d91cqbyhq7xpk06z43"))))
16534 (properties `((upstream-name . "sysfonts")))
16535 (build-system r-build-system)
16537 `(("freetype" ,freetype)
16541 `(("pkg-config" ,pkg-config)))
16542 (home-page "https://github.com/yixuan/sysfonts")
16543 (synopsis "Loading fonts into R")
16545 "This is a package to simplify loading of system fonts and Google Fonts
16546 into R, in order to support other packages.")
16547 (license license:gpl2)))
16549 (define-public r-showtextdb
16551 (name "r-showtextdb")
16556 (uri (cran-uri "showtextdb" version))
16559 "1qwwj9x2jvadvwn60h75k99c9xi7yhqjsgaakahz5paxgj583bsh"))))
16560 (properties `((upstream-name . "showtextdb")))
16561 (build-system r-build-system)
16563 `(("r-sysfonts" ,r-sysfonts)))
16564 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
16565 (synopsis "Font files for the 'showtext' package")
16567 "This package provides font files that can be used by the @code{showtext}
16569 (license license:asl2.0)))
16571 (define-public r-showtext
16573 (name "r-showtext")
16578 (uri (cran-uri "showtext" version))
16581 "1ihgqzfia36b0n9aa41p1w98wxxvs1lxh1zz0570hbfqmph1sk73"))))
16582 (properties `((upstream-name . "showtext")))
16583 (build-system r-build-system)
16585 `(("freetype" ,freetype)
16589 `(("r-showtextdb" ,r-showtextdb)
16590 ("r-sysfonts" ,r-sysfonts)))
16591 (native-inputs `(("pkg-config" ,pkg-config)))
16592 (home-page "https://github.com/yixuan/showtext")
16593 (synopsis "Using fonts more easily in R graphs")
16595 "This package aims to make it easy to use various types of
16596 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
16597 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
16598 will be converted into polygons or raster images, hence after the plot has
16599 been created, it no longer relies on the font files. No external software
16600 such as Ghostscript is needed to use this package.")
16601 (license license:asl2.0)))
16603 (define-public r-emojifont
16605 (name "r-emojifont")
16610 (uri (cran-uri "emojifont" version))
16613 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
16614 (properties `((upstream-name . "emojifont")))
16615 (build-system r-build-system)
16617 `(("r-ggplot2" ,r-ggplot2)
16618 ("r-proto" ,r-proto)
16619 ("r-showtext" ,r-showtext)
16620 ("r-sysfonts" ,r-sysfonts)))
16621 (home-page "https://guangchuangyu.github.io/emojifont")
16622 (synopsis "Emoji and Font Awesome in R graphics")
16624 "This package enables the use of emoji and the Font Awesome glyphs in
16625 both base and ggplot2 graphics.")
16626 (license license:artistic2.0)))
16628 (define-public r-abstractr
16630 (name "r-abstractr")
16635 (uri (cran-uri "abstractr" version))
16638 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
16639 (properties `((upstream-name . "abstractr")))
16640 (build-system r-build-system)
16642 `(("r-colourpicker" ,r-colourpicker)
16643 ("r-emojifont" ,r-emojifont)
16644 ("r-ggplot2" ,r-ggplot2)
16645 ("r-gridextra" ,r-gridextra)
16646 ("r-rintrojs" ,r-rintrojs)
16647 ("r-shiny" ,r-shiny)
16648 ("r-shinythemes" ,r-shinythemes)))
16649 (home-page "https://matt-kumar.shinyapps.io/portfolio")
16650 (synopsis "R-Shiny application for creating visual abstracts")
16652 "This package provides an R Shiny application to create visual abstracts
16653 for original research. A variety of user defined options and formatting are
16655 (license license:gpl3)))
16657 (define-public r-abtest
16664 (uri (cran-uri "abtest" version))
16667 "1ky3cf827kj24bhcpk00v5zl5jdkii1gca0x81ay1cjkzfispgws"))))
16668 (properties `((upstream-name . "abtest")))
16669 (build-system r-build-system)
16671 `(("r-matrix" ,r-matrix)
16672 ("r-mvtnorm" ,r-mvtnorm)
16673 ("r-plotrix" ,r-plotrix)
16674 ("r-rcolorbrewer" ,r-rcolorbrewer)
16677 ("r-truncnorm" ,r-truncnorm)
16678 ("r-vgam" ,r-vgam)))
16679 (home-page "https://cran.r-project.org/web/packages/abtest/")
16680 (synopsis "Bayesian A/B testing")
16682 "This package provides functions for Bayesian A/B testing including prior
16683 elicitation options based on Kass and Vaidyanathan (1992)
16684 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
16685 (license license:gpl2+)))
16687 (define-public r-accept
16694 (uri (cran-uri "accept" version))
16697 "1r4mhy9g4wjcjgdd0gwdarmr09292il3vdkmx0hz7vh9mffyr9kx"))))
16698 (properties `((upstream-name . "accept")))
16699 (build-system r-build-system)
16701 `(("r-dplyr" ,r-dplyr)
16702 ("r-extrafont" ,r-extrafont)
16704 ("r-plotly" ,r-plotly)
16705 ("r-stringr" ,r-stringr)
16706 ("r-viridis" ,r-viridis)))
16707 (home-page "https://cran.r-project.org/web/packages/accept/")
16708 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
16710 "This package allows clinicians to predict the rate and severity of
16711 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
16712 Disease} (COPD) patients, based on the clinical prediction model published in
16713 Adibi et al. (2019) @url{doi:10.1101/651901}.")
16714 (license license:gpl3)))
16716 (define-public r-smpracticals
16718 (name "r-smpracticals")
16723 (uri (cran-uri "SMPracticals" version))
16726 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
16727 (properties `((upstream-name . "SMPracticals")))
16728 (build-system r-build-system)
16730 `(("r-ellipse" ,r-ellipse)
16733 ("r-survival" ,r-survival)))
16734 (home-page "http://statwww.epfl.ch/davison/SM/")
16735 (synopsis "Practicals for use with Davison (2003) Statistical Models")
16737 "This package contains the datasets and a few functions for use with the
16738 practicals outlined in Appendix A of the book Statistical Models (Davison,
16739 2003, Cambridge University Press). The practicals themselves can be found at
16740 @url{http://statwww.epfl.ch/davison/SM/}.")
16741 (license license:gpl2+)))
16743 (define-public r-fgui
16750 (uri (cran-uri "fgui" version))
16753 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
16754 (properties `((upstream-name . "fgui")))
16755 (build-system r-build-system)
16757 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
16758 (synopsis "Create GUI for R functions")
16760 "Rapidly create a GUI for a function you created by automatically
16761 creating widgets for arguments of the function. This package automatically
16762 parses help routines for context-sensitive help to these arguments. The
16763 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
16764 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
16765 incorporated into the interface for greater customization for the more
16767 ;; Any version of the GPL.
16768 (license (list license:gpl2+ license:gpl3+))))
16770 (define-public r-tcltk2
16777 (uri (cran-uri "tcltk2" version))
16780 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
16781 (properties `((upstream-name . "tcltk2")))
16782 (build-system r-build-system)
16786 (home-page "http://www.sciviews.org/SciViews-R")
16787 (synopsis "Tcl/Tk additions")
16789 "This package provides a series of additional Tcl commands and Tk widgets
16790 with style and various functions to supplement the tcltk package")
16791 (license license:lgpl3)))
16793 (define-public r-accrual
16800 (uri (cran-uri "accrual" version))
16803 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
16804 (properties `((upstream-name . "accrual")))
16805 (build-system r-build-system)
16807 `(("r-fgui" ,r-fgui)
16808 ("r-smpracticals" ,r-smpracticals)
16809 ("r-tcltk2" ,r-tcltk2)))
16810 (home-page "https://cran.r-project.org/web/packages/accrual/")
16811 (synopsis "Bayesian accrual prediction")
16813 "Subject recruitment for medical research is challenging. Slow patient
16814 accrual leads to delay in research. Accrual monitoring during the process of
16815 recruitment is critical. Researchers need reliable tools to manage the
16816 accrual rate. This package provides an implementation of a Bayesian method
16817 that integrates researcher's experience on previous trials and data from the
16818 current study, providing reliable prediction on accrual rate for clinical
16819 studies. It provides functions for Bayesian accrual prediction which can be
16820 easily used by statisticians and clinical researchers.")
16821 (license license:gpl2)))
16823 (define-public r-accrued
16830 (uri (cran-uri "accrued" version))
16833 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
16834 (properties `((upstream-name . "accrued")))
16835 (build-system r-build-system)
16836 (home-page "https://cran.r-project.org/web/packages/accrued/")
16837 (synopsis "Data quality visualization tools for partially accruing data")
16839 "This is a package for visualizing data quality of partially accruing
16841 (license license:gpl3)))
16843 (define-public r-mda
16850 (uri (cran-uri "mda" version))
16853 "19g6kn6g0shidrjfffklbmzc5w7mcimrxhagx4nmpslg59ibqdkh"))))
16854 (properties `((upstream-name . "mda")))
16855 (build-system r-build-system)
16856 (propagated-inputs `(("r-class" ,r-class)))
16857 (native-inputs `(("gfortran" ,gfortran)))
16858 (home-page "https://cran.r-project.org/web/packages/mda/")
16859 (synopsis "Mixture and flexible discriminant analysis")
16861 "This is a package for mixture and flexible discriminant analysis,
16862 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
16863 (license license:gpl2)))
16865 (define-public r-elasticnet
16867 (name "r-elasticnet")
16872 (uri (cran-uri "elasticnet" version))
16875 "0p9dplnsp28z4s2fl6afbwrgd0aj339fak8mmndicmrh7bb7rpmb"))))
16876 (properties `((upstream-name . "elasticnet")))
16877 (build-system r-build-system)
16879 `(("r-lars" ,r-lars)))
16880 (home-page "http://www.stat.umn.edu/~hzou")
16881 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
16883 "This package provides functions for fitting the entire solution path of
16884 the Elastic-Net and also provides functions for estimating sparse Principal
16885 Components. The Lasso solution paths can be computed by the same function.")
16886 (license license:gpl2+)))
16888 (define-public r-sparselda
16890 (name "r-sparselda")
16895 (uri (cran-uri "sparseLDA" version))
16898 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
16899 (properties `((upstream-name . "sparseLDA")))
16900 (build-system r-build-system)
16902 `(("r-elasticnet" ,r-elasticnet)
16905 (home-page "http://www.imm.dtu.dk/~lhc")
16906 (synopsis "Sparse discriminant analysis")
16908 "This package performs sparse linear discriminant analysis for Gaussians
16909 and mixture of Gaussian models.")
16910 (license license:gpl2+)))
16912 (define-public r-accsda
16919 (uri (cran-uri "accSDA" version))
16922 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
16923 (properties `((upstream-name . "accSDA")))
16924 (build-system r-build-system)
16926 `(("r-ggplot2" ,r-ggplot2)
16927 ("r-ggthemes" ,r-ggthemes)
16928 ("r-gridextra" ,r-gridextra)
16930 ("r-rarpack" ,r-rarpack)
16931 ("r-sparselda" ,r-sparselda)))
16932 (home-page "https://github.com/gumeo/accSDA/wiki")
16933 (synopsis "Accelerated sparse discriminant analysis")
16935 "This package provides an implementation of sparse linear discriminant
16936 analysis, which is a supervised classification method for multiple classes.
16937 Various novel optimization approaches to this problem are implemented
16938 including @dfn{alternating direction method of multipliers} (ADMM),
16939 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
16940 Functions for performing cross validation are also supplied along with basic
16941 prediction and plotting functions. @dfn{Sparse zero variance
16942 discriminant} (SZVD) analysis is also included in the package.")
16943 (license license:gpl2+)))
16945 (define-public r-ace2fastq
16947 (name "r-ace2fastq")
16952 (uri (cran-uri "ace2fastq" version))
16955 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
16956 (properties `((upstream-name . "ace2fastq")))
16957 (build-system r-build-system)
16959 `(("r-stringr" ,r-stringr)))
16960 (home-page "https://github.com/c5sire/ace2fastq")
16961 (synopsis "ACE file to FASTQ converter")
16963 "The ACE file format is used in genomics to store contigs from sequencing
16964 machines. This tools converts it into FASTQ format. Both formats contain the
16965 sequence characters and their corresponding quality information. Unlike the
16966 FASTQ file, the ACE file stores the quality values numerically. The
16967 conversion algorithm uses the standard Sanger formula. The package
16968 facilitates insertion into pipelines, and content inspection.")
16969 (license license:gpl3)))
16971 (define-public r-rngwell
16978 (uri (cran-uri "rngWELL" version))
16981 "0b4ys525gksgqwqx9id4bdgyi9mwj6n3r87xdzf4fc9hp3cc16jb"))))
16982 (properties `((upstream-name . "rngWELL")))
16983 (build-system r-build-system)
16984 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
16985 (synopsis "Toolbox for WELL random number generators")
16987 "This is a dedicated package to WELL pseudo random generators, which were
16988 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
16989 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
16990 (license license:bsd-3)))
16992 (define-public r-randtoolbox
16994 (name "r-randtoolbox")
16999 (uri (cran-uri "randtoolbox" version))
17002 "141p13ajgzmb2s89rlac7zrra92mi1izvpfrngb4kqzlf3igdsqd"))))
17003 (properties `((upstream-name . "randtoolbox")))
17004 (build-system r-build-system)
17006 `(("r-rngwell" ,r-rngwell)))
17008 `(("gfortran" ,gfortran)))
17009 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
17010 (synopsis "Toolbox for pseudo and quasi random number generation")
17012 "This package provides
17015 @item pseudo random generators, such as general linear
17016 congruential generators, multiple recursive generators and generalized
17017 feedback shift register (SF-Mersenne Twister algorithm and WELL
17020 @item quasi random generators, such as the Torus algorithm, the Sobol
17021 sequence, the Halton sequence (including the Van der Corput sequence), and
17023 @item some generator tests: the gap test, the serial test, the poker test.
17026 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
17027 (license license:bsd-3)))
17029 (define-public r-lhs
17036 (uri (cran-uri "lhs" version))
17039 "0lzaqr7xi3ckln5nglv5xf5njm359slpz1jc6s02hpsqdw6armd4"))))
17040 (properties `((upstream-name . "lhs")))
17041 (build-system r-build-system)
17042 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
17043 (home-page "https://github.com/bertcarnell/lhs")
17044 (synopsis "Latin Hypercube Samples")
17046 "This package provides a number of methods for creating and augmenting
17047 Latin Hypercube Samples.")
17048 (license license:gpl3)))
17050 (define-public r-acebayes
17052 (name "r-acebayes")
17057 (uri (cran-uri "acebayes" version))
17060 "1xm6bw0qm2vlcrk274x0bawzb2lnacb1wsmzba5mg3i75a55pqln"))))
17061 (properties `((upstream-name . "acebayes")))
17062 (build-system r-build-system)
17064 `(("r-compare" ,r-compare)
17066 ("r-randtoolbox" ,r-randtoolbox)
17068 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17069 (home-page "https://cran.r-project.org/web/packages/acebayes/")
17070 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
17072 "Finding an optimal Bayesian experimental design involves maximizing an
17073 objective function given by the expectation of some appropriately chosen
17074 utility function with respect to the joint distribution of unknown
17075 quantities (including responses). This objective function is usually not
17076 available in closed form and the design space can be continuous and of high
17077 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
17078 to maximise an approximation to the expectation of the utility function.")
17079 (license license:gpl2)))
17081 (define-public r-acet
17088 (uri (cran-uri "ACEt" version))
17091 "0626d6kg485xjya164wagrr5z223jvi93ywbwpdns7fkm03c0dlq"))))
17092 (properties `((upstream-name . "ACEt")))
17093 (build-system r-build-system)
17098 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17099 (home-page "https://cran.r-project.org/web/packages/ACEt/")
17100 (synopsis "Estimating dynamic heritability and twin model comparison")
17102 "This package supports twin models that are able to estimate the dynamic
17103 behaviour of the variance components in the classical twin models with respect
17104 to age using B-splines and P-splines.")
17105 (license license:gpl2+)))
17107 (define-public r-acfmperiod
17109 (name "r-acfmperiod")
17114 (uri (cran-uri "acfMPeriod" version))
17117 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
17118 (properties `((upstream-name . "acfMPeriod")))
17119 (build-system r-build-system)
17121 `(("r-mass" ,r-mass)))
17122 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
17123 (synopsis "Estimation of the ACF from the M-periodogram")
17125 "This package support non-robust and robust computations of the sample
17126 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
17127 univariate and multivariate processes. The methodology consists in reversing
17128 the diagonalization procedure involving the periodogram or the
17129 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
17130 ACOVF or the ACF as discussed in Fuller (1995)
17131 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
17132 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
17133 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
17134 (license license:gpl2+)))
17136 (define-public r-gamlss-data
17138 (name "r-gamlss-data")
17143 (uri (cran-uri "gamlss.data" version))
17146 "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
17147 (properties `((upstream-name . "gamlss.data")))
17148 (build-system r-build-system)
17149 (home-page "http://www.gamlss.org/")
17150 (synopsis "GAMLSS data")
17152 "This package provides data used as examples to demonstrate GAMLSS
17154 ;; Either version of the license
17155 (license (list license:gpl2 license:gpl3))))
17157 (define-public r-gamlss
17164 (uri (cran-uri "gamlss" version))
17167 "0gcngfck0dk2rhjg0z1fnc61dqs0s049jy2rkywaf57531s2k8bc"))))
17168 (properties `((upstream-name . "gamlss")))
17169 (build-system r-build-system)
17171 `(("r-gamlss-data" ,r-gamlss-data)
17172 ("r-gamlss-dist" ,r-gamlss-dist)
17175 ("r-survival" ,r-survival)))
17176 (home-page "http://www.gamlss.org/")
17177 (synopsis "Generalized additive models for location scale and shape")
17179 "This package provides functions for fitting the generalized additive
17180 models for location scale and shape introduced by Rigby and
17181 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
17182 use a distributional regression approach where all the parameters of the
17183 conditional distribution of the response variable are modelled using
17184 explanatory variables.")
17185 ;; Either version of the license
17186 (license (list license:gpl2 license:gpl3))))
17188 (define-public r-acid
17195 (uri (cran-uri "acid" version))
17198 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
17199 (properties `((upstream-name . "acid")))
17200 (build-system r-build-system)
17202 `(("r-gamlss" ,r-gamlss)
17203 ("r-gamlss-dist" ,r-gamlss-dist)
17204 ("r-hmisc" ,r-hmisc)))
17205 (home-page "https://cran.r-project.org/web/packages/acid/")
17206 (synopsis "Analysing conditional income distributions")
17208 "This package provides functions for the analysis of income distributions
17209 for subgroups of the population as defined by a set of variables like age,
17210 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
17211 distribution as well as functions for moments, inequality measures, entropy
17212 measures and polarisation measures of income distributions. This package thus
17213 aides the analysis of income inequality by offering tools for the exploratory
17214 analysis of income distributions at the disaggregated level.")
17215 (license license:gpl3)))
17217 (define-public r-acm4r
17224 (uri (cran-uri "acm4r" version))
17227 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
17228 (properties `((upstream-name . "acm4r")))
17229 (build-system r-build-system)
17230 (propagated-inputs `(("r-mass" ,r-mass)))
17231 (home-page "https://cran.r-project.org/web/packages/acm4r/")
17232 (synopsis "Align-and-count method comparisons of RFLP data")
17234 "This is a package to compare sequence fragment lengths or molecular
17235 weights from pairs of lanes. The number of matching bands in the
17236 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
17237 the align-and-count method.")
17238 ;; Any version of the GPL
17239 (license (list license:gpl2+ license:gpl3+))))
17241 (define-public r-filematrix
17243 (name "r-filematrix")
17248 (uri (cran-uri "filematrix" version))
17251 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
17252 (properties `((upstream-name . "filematrix")))
17253 (build-system r-build-system)
17254 ;; These inputs are needed for vignettes
17256 `(("r-knitr" ,r-knitr)
17257 ("r-rmarkdown" ,r-rmarkdown)
17258 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
17259 (home-page "https://github.com/andreyshabalin/filematrix")
17260 (synopsis "File-backed matrix class with convenient read and write access")
17262 "This package provides an interface for working with large matrices
17263 stored in files, not in computer memory. It supports multiple non-character
17264 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
17265 byte real values). Access to parts of the matrix is done by indexing, exactly
17266 as with usual R matrices. It supports very large matrices; the package has
17267 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
17268 columns, ad allows for quick addition of extra columns to a filematrix.")
17269 (license license:lgpl3)))
17271 (define-public r-acmeeqtl
17273 (name "r-acmeeqtl")
17278 (uri (cran-uri "ACMEeqtl" version))
17281 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
17282 (properties `((upstream-name . "ACMEeqtl")))
17283 (build-system r-build-system)
17285 `(("r-filematrix" ,r-filematrix)))
17286 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
17287 (synopsis "Estimation of interpretable eQTL effect sizes")
17289 "This package provides a non-linear model, termed ACME, that reflects a
17290 parsimonious biological model for allelic contributions of cis-acting eQTLs.
17291 With non-linear least-squares algorithm the maximum likelihood parameters can
17292 be estimated. The ACME model provides interpretable effect size estimates and
17293 p-values with well controlled Type-I error.")
17294 (license license:lgpl3)))
17296 (define-public r-acmer
17303 (uri (cran-uri "acmeR" version))
17306 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
17307 (properties `((upstream-name . "acmeR")))
17308 (build-system r-build-system)
17309 (propagated-inputs `(("r-foreign" ,r-foreign)))
17310 (home-page "https://cran.r-project.org/web/packages/acmeR/")
17311 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
17313 "This package provides an implementation of the ACME estimator, described
17314 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
17315 Mortality at Wind Turbines. Unlike most other models, this estimator supports
17316 decreasing-hazard Weibull model for persistence; decreasing search proficiency
17317 as carcasses age; variable bleed-through at successive searches; and interval
17318 mortality estimates. The package provides, based on search data, functions
17319 for estimating the mortality inflation factor in Frequentist and Bayesian
17321 (license license:expat)))
17323 (define-public r-r-huge
17330 (uri (cran-uri "R.huge" version))
17333 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
17334 (properties `((upstream-name . "R.huge")))
17335 (build-system r-build-system)
17337 `(("r-r-methodss3" ,r-r-methodss3)
17339 ("r-r-utils" ,r-r-utils)))
17340 (home-page "https://github.com/HenrikBengtsson/R.huge")
17341 (synopsis "Methods for accessing huge amounts of data")
17343 "This is a deprecated package for accessing huge amounts of data.
17344 Cross-platform alternatives are the following packages: bigmemory (CRAN),
17345 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
17346 the @code{aroma.affymetrix} package.")
17347 (license license:lgpl2.1+)))
17349 (define-public r-r-filesets
17351 (name "r-r-filesets")
17356 (uri (cran-uri "R.filesets" version))
17359 "124rygq0bl9n4akxcm868nl30cyk3rz0iprb98zlpk62gci9f5fg"))))
17360 (properties `((upstream-name . "R.filesets")))
17361 (build-system r-build-system)
17363 `(("r-digest" ,r-digest)
17364 ("r-r-cache" ,r-r-cache)
17365 ("r-r-methodss3" ,r-r-methodss3)
17367 ("r-r-utils" ,r-r-utils)))
17368 (home-page "https://github.com/HenrikBengtsson/R.filesets")
17369 (synopsis "Easy handling of and access to files")
17371 "This package provides classes and methods to locate, setup, subset,
17372 navigate and iterate file sets, i.e. sets of files located in one or more
17373 directories on the file system. The API is designed such that these classes
17374 can be extended via inheritance to provide a richer API for special file
17375 formats. Moreover, a specific name format is defined such that filenames and
17376 directories can be considered to have full names which consists of a name
17377 followed by comma-separated tags. This adds additional flexibility to
17378 identify file sets and individual files.")
17379 (license license:lgpl2.1+)))
17381 (define-public r-r-devices
17383 (name "r-r-devices")
17388 (uri (cran-uri "R.devices" version))
17391 "15zlnq3g27whq26fbcy5zfl5hiddm256h4rga4frblg6wqlbkvdd"))))
17392 (properties `((upstream-name . "R.devices")))
17393 (build-system r-build-system)
17395 `(("r-base64enc" ,r-base64enc)
17396 ("r-r-methodss3" ,r-r-methodss3)
17398 ("r-r-utils" ,r-r-utils)))
17399 (home-page "https://github.com/HenrikBengtsson/R.devices")
17400 (synopsis "Unified handling of graphics devices")
17402 "This package provides functions for creating plots and image files in a
17403 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
17404 Default device options as well as scales and aspect ratios are controlled in a
17405 uniform way across all device types. Switching output format requires minimal
17406 changes in code. This package is ideal for large-scale batch processing,
17407 because it will never leave open graphics devices or incomplete image files
17408 behind, even on errors or user interrupts.")
17409 (license license:lgpl2.1+)))
17411 (define-public r-acnr
17418 (uri (cran-uri "acnr" version))
17421 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
17422 (properties `((upstream-name . "acnr")))
17423 (build-system r-build-system)
17424 (home-page "https://github.com/mpierrejean/acnr")
17425 (synopsis "Annotated copy-number regions")
17427 "This package provides SNP array data from different types of copy-number
17428 regions. These regions were identified manually by the authors of the package
17429 and may be used to generate realistic data sets with known truth.")
17430 (license license:lgpl2.1+)))
17432 (define-public r-acopula
17439 (uri (cran-uri "acopula" version))
17442 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
17443 (properties `((upstream-name . "acopula")))
17444 (build-system r-build-system)
17445 (home-page "https://cran.r-project.org/web/packages/acopula/")
17446 (synopsis "Modelling dependence with multivariate Archimax copulas")
17448 "Archimax copulas are a mixture of Archimedean and EV copulas. This
17449 package provides definitions of several parametric families of generator and
17450 dependence function, computes CDF and PDF, estimates parameters, tests for
17451 goodness of fit, generates random sample and checks copula properties for
17452 custom constructs. In the 2-dimensional case explicit formulas for density
17453 are used, contrary to higher dimensions when all derivatives are linearly
17454 approximated. Several non-archimax families (normal, FGM, Plackett) are
17455 provided as well.")
17456 (license license:gpl2)))
17458 (define-public r-tuner
17465 (uri (cran-uri "tuneR" version))
17468 "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
17469 (properties `((upstream-name . "tuneR")))
17470 (build-system r-build-system)
17471 (propagated-inputs `(("r-signal" ,r-signal)))
17472 (home-page "https://cran.r-project.org/web/packages/tuneR/")
17473 (synopsis "Analysis of music and speech")
17475 "This is a package for the analysis of music and speech. Analyze music
17476 and speech, extract features like MFCCs, handle wave files and their
17477 representation in various ways, read MP3, read MIDI, perform steps of a
17478 transcription, ...")
17479 ;; Either of these versions.
17480 (license (list license:gpl2 license:gpl3))))
17482 (define-public r-seewave
17489 (uri (cran-uri "seewave" version))
17492 "1qg8f5gik9pw6f9mcxqmrc9x3003s8vdm6g01pjjpyc9qaqiz2vi"))))
17493 (properties `((upstream-name . "seewave")))
17494 (build-system r-build-system)
17496 `(("r-tuner" ,r-tuner)))
17497 (home-page "http://rug.mnhn.fr/seewave")
17498 (synopsis "Sound analysis and synthesis")
17500 "This package provides functions for analysing, manipulating, displaying,
17501 editing and synthesizing time waves (particularly sound). This package
17502 processes time analysis (oscillograms and envelopes), spectral content,
17503 resonance quality factor, entropy, cross correlation and autocorrelation,
17504 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
17505 and 3D spectrograms and many other analyses.")
17506 (license license:gpl2+)))
17508 (define-public r-acousticndlcoder
17510 (name "r-acousticndlcoder")
17515 (uri (cran-uri "AcousticNDLCodeR" version))
17518 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
17520 `((upstream-name . "AcousticNDLCodeR")))
17521 (build-system r-build-system)
17523 `(("r-seewave" ,r-seewave)
17524 ("r-tuner" ,r-tuner)
17526 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
17527 (synopsis "Coding sound files for use with NDL")
17529 "Make acoustic cues to use with the R package @code{ndl}.
17530 The package implements functions used in the PLoS ONE paper \"Words from
17531 spontaneous conversational speech can be recognized with human-like accuracy
17532 by an error-driven learning algorithm that discriminates between meanings
17533 straight from smart acoustic features, bypassing the phoneme as recognition
17534 unit.\" @url{doi:10.1371/journal.pone.0174623}")
17535 (license license:gpl2+)))
17537 (define-public r-acp
17544 (uri (cran-uri "acp" version))
17547 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
17548 (properties `((upstream-name . "acp")))
17549 (build-system r-build-system)
17551 `(("r-quantmod" ,r-quantmod)
17552 ("r-tseries" ,r-tseries)))
17553 (home-page "https://cran.r-project.org/web/packages/acp/")
17554 (synopsis "Autoregressive conditional Poisson")
17556 "This package supports the analysis of count data exhibiting
17557 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
17558 model (ACP(p,q)) proposed by Heinen (2003).")
17559 (license license:gpl2)))
17561 (define-public r-ada
17568 (uri (cran-uri "ada" version))
17571 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
17572 (properties `((upstream-name . "ada")))
17573 (build-system r-build-system)
17574 (propagated-inputs `(("r-rpart" ,r-rpart)))
17575 (home-page "https://cran.r-project.org/web/packages/ada/")
17576 (synopsis "Stochastic boosting")
17578 "This package provides a straightforward, well-documented, and broad
17579 boosting routine for classification, ideally suited for small to
17580 moderate-sized data sets. It performs discrete, real, and gentle boost under
17581 both exponential and logistic loss on a given data set.")
17582 ;; Any version of the GPL.
17583 (license (list license:gpl2+ license:gpl3+))))
17585 (define-public r-genalg
17592 (uri (cran-uri "genalg" version))
17595 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
17596 (properties `((upstream-name . "genalg")))
17597 (build-system r-build-system)
17598 (home-page "https://github.com/egonw/genalg")
17599 (synopsis "R based genetic algorithm")
17601 "This package provides an R based genetic algorithm for binary and
17602 floating point chromosomes.")
17603 (license license:gpl2)))
17605 (define-public r-kernelfactory
17607 (name "r-kernelfactory")
17612 (uri (cran-uri "kernelFactory" version))
17615 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
17616 (properties `((upstream-name . "kernelFactory")))
17617 (build-system r-build-system)
17620 ("r-genalg" ,r-genalg)
17621 ("r-kernlab" ,r-kernlab)
17622 ("r-randomforest" ,r-randomforest)))
17623 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
17624 (synopsis "Ensemble of kernel machines")
17626 "Kernel factory is an ensemble method where each base classifier (random
17627 forest) is fit on the kernel matrix of a subset of the training data.")
17628 (license license:gpl2+)))
17630 (define-public r-dummies
17637 (uri (cran-uri "dummies" version))
17640 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
17641 (properties `((upstream-name . "dummies")))
17642 (build-system r-build-system)
17643 (home-page "http://www.decisionpatterns.com")
17644 (synopsis "Create dummy/indicator variables flexibly and efficiently")
17646 "This package lets you expand factors, characters and other eligible
17647 classes into dummy/indicator variables.")
17648 (license license:gpl2+)))
17650 (define-public r-acrm
17657 (uri (cran-uri "aCRM" version))
17660 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
17661 (properties `((upstream-name . "aCRM")))
17662 (build-system r-build-system)
17665 ("r-dummies" ,r-dummies)
17666 ("r-kernelfactory" ,r-kernelfactory)
17667 ("r-randomforest" ,r-randomforest)))
17668 (home-page "https://cran.r-project.org/web/packages/aCRM/")
17669 (synopsis "Convenience functions for analytical customer relationship management")
17671 "This package provides convenience functions for data preparation and
17672 modeling often used in @dfn{analytical customer relationship
17673 management} (aCRM).")
17674 (license license:gpl2+)))
17676 (define-public r-treeclust
17678 (name "r-treeclust")
17683 (uri (cran-uri "treeClust" version))
17686 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
17687 (properties `((upstream-name . "treeClust")))
17688 (build-system r-build-system)
17690 `(("r-cluster" ,r-cluster)
17691 ("r-rpart" ,r-rpart)))
17692 (home-page "https://cran.r-project.org/web/packages/treeClust/")
17693 (synopsis "Cluster distances through trees")
17695 "This package provides tools to create a measure of inter-point
17696 dissimilarity useful for clustering mixed data, and, optionally, perform the
17698 (license license:gpl2+)))
17700 (define-public r-acrosstic
17702 (name "r-acrosstic")
17707 (uri (cran-uri "AcrossTic" version))
17710 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
17711 (properties `((upstream-name . "AcrossTic")))
17712 (build-system r-build-system)
17714 `(("r-lpsolve" ,r-lpsolve)
17715 ("r-treeclust" ,r-treeclust)))
17716 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
17717 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
17719 "This is a package for constructing minimum-cost regular spanning
17720 subgraph as part of a non-parametric two-sample test for equality of
17722 (license license:gpl2+)))
17724 (define-public r-acrt
17731 (uri (cran-uri "acrt" version))
17734 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
17735 (properties `((upstream-name . "acrt")))
17736 (build-system r-build-system)
17738 `(("r-rcpp" ,r-rcpp)
17739 ("r-rcppeigen" ,r-rcppeigen)
17740 ("r-sandwich" ,r-sandwich)))
17741 (home-page "https://cran.r-project.org/web/packages/acrt/")
17742 (synopsis "Autocorrelation robust testing")
17744 "This package provides functions for testing affine hypotheses on the
17745 regression coefficient vector in regression models with autocorrelated
17747 (license license:gpl2)))
17749 (define-public r-acs
17756 (uri (cran-uri "acs" version))
17759 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
17760 (properties `((upstream-name . "acs")))
17761 (build-system r-build-system)
17763 `(("r-httr" ,r-httr)
17766 ("r-stringr" ,r-stringr)
17768 (home-page "http://dusp.mit.edu/faculty/ezra-glenn")
17769 (synopsis "Work with data from the US Census")
17771 "This package provides a general toolkit for downloading, managing,
17772 analyzing, and presenting data from the
17773 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
17774 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
17775 American Community Survey (ACS). Confidence intervals provided with ACS data
17776 are converted to standard errors to be bundled with estimates in complex
17777 @code{acs} objects. The package provides new methods to conduct standard
17778 operations on @code{acs} objects and present/plot data in statistically
17779 appropriate ways.")
17780 (license license:gpl3)))
17782 (define-public r-acss-data
17784 (name "r-acss-data")
17789 (uri (cran-uri "acss.data" version))
17792 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
17793 (properties `((upstream-name . "acss.data")))
17794 (build-system r-build-system)
17795 (home-page "http://complexitycalculator.com/methodology.html")
17796 (synopsis "Data for algorithmic complexity of short strings")
17798 "This is a data only package providing the algorithmic complexity of
17799 short strings, computed using the coding theorem method. For a given set of
17800 symbols in a string, all possible or a large number of random samples of
17801 Turing machines with a given number of states (e.g., 5) and number of symbols
17802 corresponding to the number of symbols in the strings were simulated until
17803 they reached a halting state or failed to end. This package contains data on
17804 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
17805 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
17806 distribution of the halting states.")
17807 (license license:gpl2+)))
17809 (define-public r-acss
17816 (uri (cran-uri "acss" version))
17819 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
17820 (properties `((upstream-name . "acss")))
17821 (build-system r-build-system)
17823 `(("r-acss-data" ,r-acss-data)
17825 (home-page "http://complexitycalculator.com/methodology.html")
17826 (synopsis "Algorithmic complexity for short strings")
17828 "The main purpose of this package is to provide the algorithmic
17829 complexity for short strings, an approximation of the Kolmogorov Complexity of
17830 a short string using the coding theorem method. While the database containing
17831 the complexity is provided in the data only package @code{acss.data}, this
17832 package provides functions accessing the data such as @code{prob_random}
17833 returning the posterior probability that a given string was produced by a
17834 random process. In addition, two traditional (but problematic) measures of
17835 complexity are also provided: entropy and change complexity.")
17836 (license license:gpl2+)))
17838 (define-public r-acswr
17845 (uri (cran-uri "ACSWR" version))
17848 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
17849 (properties `((upstream-name . "ACSWR")))
17850 (build-system r-build-system)
17852 `(("r-mass" ,r-mass)))
17853 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
17854 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
17856 "This is a companion package for the book \"A Course in Statistics with
17857 R\" (ISBN 978-1-119-15272-9.)")
17858 (license license:gpl2)))
17860 (define-public r-alabama
17863 (version "2015.3-1")
17867 (uri (cran-uri "alabama" version))
17870 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
17871 (properties `((upstream-name . "alabama")))
17872 (build-system r-build-system)
17873 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
17874 (home-page "https://cran.r-project.org/web/packages/alabama/")
17875 (synopsis "Constrained nonlinear optimization")
17877 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
17878 Algorithm; it is used for optimizing smooth nonlinear objective functions with
17879 constraints. Linear or nonlinear equality and inequality constraints are
17881 (license license:gpl2+)))
17883 (define-public r-gdina
17890 (uri (cran-uri "GDINA" version))
17893 "0875xfbm36gqzr0116xzlbm8rlff85rybr4s4hjzfflfvjdhgvfx"))))
17894 (properties `((upstream-name . "GDINA")))
17895 (build-system r-build-system)
17897 `(("r-alabama" ,r-alabama)
17898 ("r-ggplot2" ,r-ggplot2)
17900 ("r-nloptr" ,r-nloptr)
17901 ("r-numderiv" ,r-numderiv)
17903 ("r-rcpparmadillo" ,r-rcpparmadillo)
17904 ("r-rsolnp" ,r-rsolnp)
17905 ("r-shiny" ,r-shiny)
17906 ("r-shinydashboard" ,r-shinydashboard)))
17907 (home-page "https://github.com/Wenchao-Ma/GDINA")
17908 (synopsis "Generalized DINA model framework")
17910 "This package provides a set of psychometric tools for cognitive
17911 diagnosis modeling based on the generalized deterministic inputs, noisy and
17912 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
17913 and its extensions, including the sequential G-DINA model by Ma and de la
17914 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
17915 polytomous G-DINA model by Chen and de la Torre
17916 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
17917 distribution can be independent, saturated, higher-order, loglinear smoothed
17918 or structured. Q-matrix validation, item and model fit statistics, model
17919 comparison at test and item level and differential item functioning can also
17920 be conducted. A graphical user interface is also provided.")
17921 (license license:gpl3)))
17923 (define-public r-actcd
17930 (uri (cran-uri "ACTCD" version))
17933 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
17934 (properties `((upstream-name . "ACTCD")))
17935 (build-system r-build-system)
17937 `(("r-gdina" ,r-gdina)
17938 ("r-r-methodss3" ,r-r-methodss3)))
17940 `(("gfortran" ,gfortran)))
17941 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
17942 (synopsis "Asymptotic classification theory for cognitive diagnosis")
17944 "This is a package supporting cluster analysis for cognitive diagnosis
17945 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
17946 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
17947 sum-scores, cluster analysis techniques can be used to classify examinees into
17948 latent classes based on their attribute patterns. In addition to the
17949 algorithms used to classify data, three labeling approaches are proposed to
17950 label clusters so that examinees' attribute profiles can be obtained.")
17951 (license license:gpl2+)))
17953 (define-public r-ineq
17960 (uri (cran-uri "ineq" version))
17963 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
17964 (properties `((upstream-name . "ineq")))
17965 (build-system r-build-system)
17966 (home-page "https://cran.r-project.org/web/packages/ineq/")
17967 (synopsis "Measuring inequality, concentration, and poverty")
17969 "This package provides tools for measuring inequality, concentration, and
17970 poverty measures. It provides both empirical and theoretical Lorenz curves.")
17971 ;; Either of these two versions.
17972 (license (list license:gpl2 license:gpl3))))
17974 (define-public r-actfrag
17981 (uri (cran-uri "ActFrag" version))
17984 "06l5a679j6289008ls57v420mnzpq9a4ln7svi5bh0vpvws7sr9d"))))
17985 (properties `((upstream-name . "ActFrag")))
17986 (build-system r-build-system)
17988 `(("r-accelerometry" ,r-accelerometry)
17989 ("r-dplyr" ,r-dplyr)
17991 ("r-survival" ,r-survival)
17992 ("r-tidyr" ,r-tidyr)))
17993 (home-page "https://github.com/junruidi/ActFrag")
17994 (synopsis "Activity fragmentation metrics extraction")
17996 "This package provides functions to extract commonly used fragmentation
17997 metrics to quantify time accumulation strategies based on minute level
17998 actigraphy-measured activity counts data.")
17999 (license license:gpl3)))
18001 (define-public r-fda
18008 (uri (cran-uri "fda" version))
18011 "0n39rzbhg1hipzn51rzmbchn2358qgapg08iv7lmiqj5y7i9qns2"))))
18012 (properties `((upstream-name . "fda")))
18013 (build-system r-build-system)
18015 `(("r-matrix" ,r-matrix)))
18016 (home-page "http://www.functionaldata.org")
18017 (synopsis "Functional data analysis")
18019 "These functions were developed to support functional data analysis as
18020 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
18021 Analysis. The package includes data sets and script files working many
18023 (license license:gpl2+)))
18025 (define-public r-actigraphy
18027 (name "r-actigraphy")
18032 (uri (cran-uri "Actigraphy" version))
18035 "0y0ccmxhdfhdmi4k6pbfvnqknkqbgvfsf2qf7z7rc4xpfgym6574"))))
18036 (properties `((upstream-name . "Actigraphy")))
18037 (build-system r-build-system)
18040 ("r-sdmtools" ,r-sdmtools)))
18041 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
18042 (synopsis "Actigraphy data analysis")
18044 "This package provides tools for functional linear modeling and analysis
18045 of actigraphy data.")
18046 (license license:asl2.0)))
18048 (define-public r-activedriver
18050 (name "r-activedriver")
18055 (uri (cran-uri "ActiveDriver" version))
18058 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
18059 (properties `((upstream-name . "ActiveDriver")))
18060 (build-system r-build-system)
18062 `(("r-mass" ,r-mass)))
18063 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
18064 (synopsis "Tools for finding cancer driver proteins")
18066 "This package provides a mutation analysis tool that discovers cancer
18067 driver genes with frequent mutations in protein signalling sites such as
18068 post-translational modifications (phosphorylation, ubiquitination, etc). The
18069 Poisson generalized linear regression model identifies genes where cancer
18070 mutations in signalling sites are more frequent than expected from the
18071 sequence of the entire gene. Integration of mutations with signalling
18072 information helps find new driver genes and propose candidate mechanisms to
18074 (license license:gpl2+)))
18076 (define-public r-activitycounts
18078 (name "r-activitycounts")
18083 (uri (cran-uri "activityCounts" version))
18086 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
18088 `((upstream-name . "activityCounts")))
18089 (build-system r-build-system)
18091 `(("r-lubridate" ,r-lubridate)
18092 ("r-magrittr" ,r-magrittr)
18093 ("r-seewave" ,r-seewave)
18094 ("r-signal" ,r-signal)
18095 ("r-tibble" ,r-tibble)))
18096 (home-page "https://github.com/walkabillylab/activityCounts")
18097 (synopsis "Generate ActiLife counts")
18099 "ActiLife generates activity counts from data collected by Actigraph
18100 accelerometers. Actigraph is one of the most common research-grade
18101 accelerometers. There is considerable research validating and developing
18102 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
18103 counts are proprietary and difficult to implement if researchers use different
18104 accelerometer brands. The code creates ActiLife counts from raw acceleration
18105 data for different accelerometer brands.")
18106 (license license:gpl3)))
18108 (define-public r-activityindex
18110 (name "r-activityindex")
18115 (uri (cran-uri "ActivityIndex" version))
18118 "14k6d78s15j7kb7jhixf4msrdjdl28d0r264cbvy41p8dkq7ysvk"))))
18119 (properties `((upstream-name . "ActivityIndex")))
18120 (build-system r-build-system)
18122 `(("r-data-table" ,r-data-table)
18123 ("r-matrixstats" ,r-matrixstats)
18124 ("r-r-utils" ,r-r-utils)))
18125 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
18126 (synopsis "Activity Index calculation using raw accelerometry data")
18128 "This is a package to read raw accelerometry from GT3X+ accelerometry
18129 data and plain table data to calculate the Activity Index from Bai et
18130 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
18131 (license license:gpl3)))
18133 (define-public r-activpal
18135 (name "r-activpal")
18140 (uri (cran-uri "activPAL" version))
18143 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
18144 (properties `((upstream-name . "activPAL")))
18145 (build-system r-build-system)
18147 `(("r-devtools" ,r-devtools)
18148 ("r-dplyr" ,r-dplyr)
18149 ("r-ggplot2" ,r-ggplot2)
18150 ("r-lubridate" ,r-lubridate)
18151 ("r-magrittr" ,r-magrittr)
18152 ("r-tidyr" ,r-tidyr)))
18153 (home-page "https://cran.r-project.org/web/packages/activPAL")
18154 (synopsis "Processing and chart generation from activPAL events files")
18156 "This package contains functions to generate pre-defined summary
18157 statistics from activPAL events files. The package also contains functions to
18158 produce informative graphics that visualize physical activity behaviour and
18159 trends. This includes generating graphs that align physical activity
18160 behaviour with additional time based observations described by other data
18161 sets, such as sleep diaries and continuous glucose monitoring data.")
18162 (license license:gpl3)))
18164 (define-public r-activpalprocessing
18166 (name "r-activpalprocessing")
18171 (uri (cran-uri "activpalProcessing" version))
18174 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
18176 `((upstream-name . "activpalProcessing")))
18177 (build-system r-build-system)
18179 `(("r-chron" ,r-chron)))
18180 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
18181 (synopsis "Process activPAL events files")
18183 "This package performs estimation of physical activity and sedentary
18184 behavior variables from activPAL events files.")
18185 ;; Either version of the GPL.
18186 (license (list license:gpl2 license:gpl3))))
18188 (define-public r-actogrammr
18190 (name "r-actogrammr")
18195 (uri (cran-uri "actogrammr" version))
18198 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
18199 (properties `((upstream-name . "actogrammr")))
18200 (build-system r-build-system)
18202 `(("r-dplyr" ,r-dplyr)
18203 ("r-ggplot2" ,r-ggplot2)
18204 ("r-lubridate" ,r-lubridate)
18205 ("r-readr" ,r-readr)
18206 ("r-tidyr" ,r-tidyr)))
18207 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
18208 (synopsis "Read in activity data and plot actograms")
18210 "Read in activity measurements from standard file formats used by
18211 circadian rhythm researchers, currently only ClockLab format, and process and
18212 plot the data. The central type of plot is the actogram, as first described
18213 in \"Activity and distribution of certain wild mice in relation to biotic
18214 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
18215 (license license:gpl3)))
18217 (define-public r-expint
18224 (uri (cran-uri "expint" version))
18227 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
18228 (properties `((upstream-name . "expint")))
18229 (build-system r-build-system)
18230 (home-page "https://gitlab.com/vigou3/expint")
18231 (synopsis "Exponential integral and incomplete Gamma function")
18233 "This package provides the exponential integrals @code{E_1(x)},
18234 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
18235 function @code{G(a, x)} defined for negative values of its first argument.
18236 The package also gives easy access to the underlying C routines through an
18237 API; see the package vignette for details.")
18238 (license license:gpl2+)))
18240 (define-public r-actuar
18247 (uri (cran-uri "actuar" version))
18250 "0aw3hlan5y22mdqk1wvnw9ksqhwp4yy5hi0dpv21p7s0hyxhphih"))))
18251 (properties `((upstream-name . "actuar")))
18252 (build-system r-build-system)
18253 (propagated-inputs `(("r-expint" ,r-expint)))
18254 (home-page "https://gitlab.com/vigou3/actuar")
18255 (synopsis "Actuarial functions and heavy tailed distributions")
18257 "This package provides functions and data sets for actuarial science:
18258 modeling of loss distributions; risk theory and ruin theory; simulation of
18259 compound models, discrete mixtures and compound hierarchical models;
18260 credibility theory. It boasts support for many additional probability
18261 distributions to model insurance loss amounts and loss frequency: 19
18262 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
18263 distribution; zero-truncated and zero-modified extensions of the standard
18264 discrete distributions. It also supports phase-type distributions commonly
18265 used to compute ruin probabilities.")
18266 (license license:gpl2+)))
18268 (define-public r-bmp
18275 (uri (cran-uri "bmp" version))
18278 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
18279 (properties `((upstream-name . "bmp")))
18280 (build-system r-build-system)
18281 (home-page "https://cran.r-project.org/web/packages/bmp/")
18282 (synopsis "Read Bitmap (BMP) images")
18284 "This package provides pure R tools to read BMP format images. It is
18285 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
18286 (license license:gpl2+)))
18288 (define-public r-readbitmap
18290 (name "r-readbitmap")
18295 (uri (cran-uri "readbitmap" version))
18298 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
18299 (properties `((upstream-name . "readbitmap")))
18300 (build-system r-build-system)
18302 `(("libjpeg" ,libjpeg)
18303 ("libpng" ,libpng)))
18308 ("r-tiff" ,r-tiff)))
18309 (home-page "https://github.com/jefferis/readbitmap")
18310 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
18312 "This package provides tools to identify and read BMP, JPEG, PNG, and
18313 TIFF format bitmap images. Identification defaults to the use of the magic
18314 number embedded in the file rather than the file extension.")
18315 (license license:gpl2+)))
18317 (define-public r-imager
18324 (uri (cran-uri "imager" version))
18327 "19fqgjhg04garbipx20g72h9dd6k0jj4ac48nby6km4h665vrs4v"))))
18328 (properties `((upstream-name . "imager")))
18329 (build-system r-build-system)
18332 ("libtiff" ,libtiff)
18336 `(("r-cairo" ,r-cairo)
18337 ("r-downloader" ,r-downloader)
18338 ("r-igraph" ,r-igraph)
18340 ("r-magrittr" ,r-magrittr)
18343 ("r-purrr" ,r-purrr)
18345 ("r-readbitmap" ,r-readbitmap)
18346 ("r-stringr" ,r-stringr)))
18347 (native-inputs `(("pkg-config" ,pkg-config)))
18348 (home-page "http://dahtah.github.io/imager")
18349 (synopsis "Image processing library")
18351 "This is a package for fast image processing for images in up to 4
18352 dimensions (two spatial dimensions, one time/depth dimension, one color
18353 dimension). It provides most traditional image processing tools (filtering,
18354 morphology, transformations, etc.) as well as various functions for easily
18355 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
18356 simple, modern C++ library for image processing.")
18357 (license license:lgpl3)))
18359 (define-public r-acuityview
18361 (name "r-acuityview")
18366 (uri (cran-uri "AcuityView" version))
18369 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
18370 (properties `((upstream-name . "AcuityView")))
18371 (build-system r-build-system)
18373 `(("r-fftwtools" ,r-fftwtools)
18374 ("r-imager" ,r-imager)
18375 ("r-plotrix" ,r-plotrix)))
18376 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
18377 (synopsis "Display scenes as seen by an animal with less acute vision")
18379 "This package provides a simple method for representing a visual scene as
18380 it may be seen by an animal with less acute vision.")
18381 (license license:gpl2+)))
18383 (define-public r-adabag
18390 (uri (cran-uri "adabag" version))
18393 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
18394 (properties `((upstream-name . "adabag")))
18395 (build-system r-build-system)
18397 `(("r-caret" ,r-caret)
18398 ("r-doparallel" ,r-doparallel)
18399 ("r-foreach" ,r-foreach)
18400 ("r-rpart" ,r-rpart)))
18401 (home-page "https://cran.r-project.org/web/packages/adabag/")
18402 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
18404 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
18405 Breiman's Bagging algorithm using classification trees as individual
18406 classifiers. Once these classifiers have been trained, they can be used to
18407 predict on new data. Also, cross validation estimation of the error can be
18409 (license license:gpl2+)))
18411 (define-public r-adagio
18418 (uri (cran-uri "adagio" version))
18421 "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
18422 (properties `((upstream-name . "adagio")))
18423 (build-system r-build-system)
18424 (native-inputs `(("gfortran" ,gfortran)))
18425 (home-page "https://cran.r-project.org/web/packages/adagio/")
18426 (synopsis "Discrete and global optimization routines")
18428 "This package provides methods and algorithms for discrete optimization,
18429 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
18430 Hooke-Jeeves minimization, and some (evolutionary) global optimization
18432 (license license:gpl3+)))
18434 (define-public r-univoutl
18436 (name "r-univoutl")
18441 (uri (cran-uri "univOutl" version))
18444 "193wrpkvgmlrx43nag8w3ivrlqm37nm6g86wcvd3bgw3hchs70gi"))))
18445 (properties `((upstream-name . "univOutl")))
18446 (build-system r-build-system)
18448 `(("r-hmisc" ,r-hmisc)
18449 ("r-robustbase" ,r-robustbase)))
18450 (home-page "https://github.com/marcellodo/univOutl")
18451 (synopsis "Detection of univariate outliers")
18453 "This package provides well-known outlier detection techniques in the
18454 univariate case. Methods to deal with skewed distribution are included too.
18455 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
18456 historical data is implemented as well. When available, survey weights can be
18457 used in outliers detection.")
18458 (license license:gpl2+)))
18460 (define-public r-tolerance
18462 (name "r-tolerance")
18467 (uri (cran-uri "tolerance" version))
18470 "17qh4ad1f3fbcpwlxxqh8qr9bnwjcl4yxk0l3fkbr6b2l4rc5p86"))))
18471 (properties `((upstream-name . "tolerance")))
18472 (build-system r-build-system)
18474 `(("r-rgl" ,r-rgl)))
18475 (home-page "https://cran.r-project.org/web/packages/tolerance/")
18476 (synopsis "Statistical tolerance intervals and regions")
18478 "This package provides functions for estimating tolerance
18479 limits (intervals) for various univariate distributions (binomial, Cauchy,
18480 discrete Pareto, exponential, two-parameter exponential, extreme value,
18481 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
18482 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
18483 Bayesian normal tolerance limits, multivariate normal tolerance regions,
18484 nonparametric tolerance intervals, tolerance bands for regression
18485 settings (linear regression, nonlinear regression, nonparametric regression,
18486 and multivariate regression), and analysis of variance tolerance intervals.
18487 Visualizations are also available for most of these settings.")
18488 (license license:gpl2+)))
18490 (define-public r-additivitytests
18492 (name "r-additivitytests")
18497 (uri (cran-uri "additivityTests" version))
18500 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
18502 `((upstream-name . "additivityTests")))
18503 (build-system r-build-system)
18504 (home-page "https://github.com/simecek/additivityTests")
18505 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
18507 "This package provides an implementation of the Tukey, Mandel,
18508 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
18509 (license license:gpl3)))
18511 (define-public r-flexclust
18513 (name "r-flexclust")
18518 (uri (cran-uri "flexclust" version))
18521 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
18522 (properties `((upstream-name . "flexclust")))
18523 (build-system r-build-system)
18525 `(("r-class" ,r-class)
18526 ("r-lattice" ,r-lattice)
18527 ("r-modeltools" ,r-modeltools)))
18528 (home-page "https://cran.r-project.org/web/packages/flexclust/")
18529 (synopsis "Flexible cluster algorithms")
18531 "The main function @code{kcca} implements a general framework for
18532 k-centroids cluster analysis supporting arbitrary distance measures and
18533 centroid computation. Further cluster methods include hard competitive
18534 learning, neural gas, and QT clustering. There are numerous visualization
18535 methods for cluster results (neighborhood graphs, convex cluster hulls,
18536 barcharts of centroids, ...), and bootstrap methods for the analysis of
18537 cluster stability.")
18538 (license license:gpl2)))
18540 (define-public r-biclust
18547 (uri (cran-uri "biclust" version))
18550 "1y5n6wfa1lx88ck3x09rcg0dh3pw89225h85hmq2la1s1fpa48i0"))))
18551 (properties `((upstream-name . "biclust")))
18552 (build-system r-build-system)
18554 `(("r-additivitytests" ,r-additivitytests)
18555 ("r-colorspace" ,r-colorspace)
18556 ("r-flexclust" ,r-flexclust)
18557 ("r-ggplot2" ,r-ggplot2)
18558 ("r-lattice" ,r-lattice)
18560 ("r-tidyr" ,r-tidyr)))
18561 (home-page "https://cran.r-project.org/web/packages/biclust/")
18562 (synopsis "BiCluster algorithms")
18564 "The main function @code{biclust()} provides several algorithms to find
18565 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
18566 In addition, the package provides methods for data
18567 preprocessing (normalization and discretization), visualization, and
18568 validation of bicluster solutions.")
18569 (license license:gpl3)))
18571 (define-public r-icge
18578 (uri (cran-uri "ICGE" version))
18581 "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
18582 (properties `((upstream-name . "ICGE")))
18583 (build-system r-build-system)
18585 `(("r-cluster" ,r-cluster)
18586 ("r-mass" ,r-mass)))
18587 (home-page "https://cran.r-project.org/web/packages/ICGE/")
18588 (synopsis "Cluster estimation and identification of atypical units")
18590 "ICGE is a package that helps to estimate the number of real clusters in
18591 data as well as to identify atypical units. The underlying methods are based
18592 on distances rather than on unit x variables.")
18593 (license license:gpl2+)))
18595 (define-public r-depth
18598 (version "2.1-1.1")
18602 (uri (cran-uri "depth" version))
18605 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
18606 (properties `((upstream-name . "depth")))
18607 (build-system r-build-system)
18609 `(("r-abind" ,r-abind)
18610 ("r-circular" ,r-circular)
18613 `(("gfortran" ,gfortran)))
18614 (home-page "https://cran.r-project.org/web/packages/depth/")
18615 (synopsis "Nonparametric depth functions for multivariate analysis")
18617 "This package provides tools for depth functions methodology applied to
18618 multivariate analysis. Besides allowing calculation of depth values and
18619 depth-based location estimators, the package includes functions or drawing
18620 contour plots and perspective plots of depth functions. Euclidian and
18621 spherical depths are supported.")
18622 (license license:gpl2)))
18624 (define-public r-archetypes
18626 (name "r-archetypes")
18627 (version "2.2-0.1")
18631 (uri (cran-uri "archetypes" version))
18634 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
18635 (properties `((upstream-name . "archetypes")))
18636 (build-system r-build-system)
18638 `(("r-modeltools" ,r-modeltools)
18639 ("r-nnls" ,r-nnls)))
18640 (home-page "https://cran.r-project.org/web/packages/archetypes")
18641 (synopsis "Archetypal analysis")
18643 "The main function @code{archetypes} implements a framework for
18644 archetypal analysis supporting arbitrary problem solving mechanisms for the
18645 different conceptual parts of the algorithm.")
18646 (license license:gpl2+)))
18648 (define-public r-shapes
18655 (uri (cran-uri "shapes" version))
18658 "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s"))))
18659 (properties `((upstream-name . "shapes")))
18660 (build-system r-build-system)
18662 `(("r-mass" ,r-mass)
18663 ("r-minpack-lm" ,r-minpack-lm)
18665 ("r-scatterplot3d" ,r-scatterplot3d)))
18666 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
18667 (synopsis "Statistical shape analysis")
18669 "This package provides routines for the statistical analysis of landmark
18670 shapes, including Procrustes analysis, graphical displays, principal
18671 components analysis, permutation and bootstrap tests, thin-plate spline
18672 transformation grids and comparing covariance matrices. See Dryden, I.L. and
18673 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
18674 Edition), John Wiley and Sons.")
18675 (license license:gpl2)))
18677 (define-public r-anthropometry
18679 (name "r-anthropometry")
18684 (uri (cran-uri "Anthropometry" version))
18687 "1f568ri1s6psaby8y737vrkarbjg64v89d4jyw23hy17apdmszr8"))))
18688 (properties `((upstream-name . "Anthropometry")))
18689 (build-system r-build-system)
18691 `(("r-archetypes" ,r-archetypes)
18692 ("r-biclust" ,r-biclust)
18693 ("r-cluster" ,r-cluster)
18694 ("r-depth" ,r-depth)
18699 ("r-shapes" ,r-shapes)))
18700 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
18701 (synopsis "Statistical methods for anthropometric data")
18703 "This package provides statistical methods especially developed to
18704 analyze anthropometric data. These methods are aimed at providing effective
18705 solutions to some commons problems related to Ergonomics and Anthropometry.
18706 They are based on clustering, the statistical concept of data depth,
18707 statistical shape analysis and archetypal analysis.")
18708 (license license:gpl2+)))
18710 (define-public r-adamethods
18712 (name "r-adamethods")
18717 (uri (cran-uri "adamethods" version))
18720 "0mp73zh5x6h18gv29v981kb9n632kb58lvlcxwr6vcvrx393nrxh"))))
18721 (properties `((upstream-name . "adamethods")))
18722 (build-system r-build-system)
18724 `(("r-anthropometry" ,r-anthropometry)
18725 ("r-archetypes" ,r-archetypes)
18727 ("r-foreach" ,r-foreach)
18729 ("r-tolerance" ,r-tolerance)
18730 ("r-univoutl" ,r-univoutl)))
18731 (home-page "https://cran.r-project.org/web/packages/adamethods/")
18732 (synopsis "Archetypoid algorithms and anomaly detection")
18734 "This package is a collection of several algorithms to obtain
18735 archetypoids with small and large databases and with both classical
18736 multivariate data and functional data (univariate and multivariate). Some of
18737 these algorithms also allow to detect anomalies (outliers).")
18738 (license license:gpl2+)))
18740 (define-public r-idpmisc
18747 (uri (cran-uri "IDPmisc" version))
18750 "13qcvfm703frs367paddz1wq9k3p17f9p5347m56bhky5hjkaphd"))))
18751 (properties `((upstream-name . "IDPmisc")))
18752 (build-system r-build-system)
18754 `(("r-lattice" ,r-lattice)))
18755 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
18756 (synopsis "Functions for data analyses and visualization")
18758 "This package provides different high-level graphics functions for
18759 displaying large datasets, displaying circular data in a very flexible way,
18760 finding local maxima, brewing color ramps, drawing nice arrows, zooming
18761 2D-plots, creating figures with differently colored margin and plot region.
18762 In addition, the package contains auxiliary functions for data manipulation
18763 like omitting observations with irregular values or selecting data by logical
18764 vectors, which include NAs. Other functions are especially useful in
18765 spectroscopy and analyses of environmental data: robust baseline fitting,
18766 finding peaks in spectra, converting humidity measures.")
18767 (license license:gpl3+)))
18769 (define-public r-qqman
18776 (uri (cran-uri "qqman" version))
18779 "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
18780 (properties `((upstream-name . "qqman")))
18781 (build-system r-build-system)
18783 `(("r-calibrate" ,r-calibrate)))
18784 (home-page "https://cran.r-project.org/web/packages/qqman/")
18785 (synopsis "Q-Q and Manhattan plots for GWAS data")
18787 "This package allows you to create Q-Q and Manhattan plots for GWAS data
18788 from PLINK results.")
18789 (license license:gpl3)))
18791 (define-public r-ggplot-multistats
18793 (name "r-ggplot-multistats")
18798 (uri (cran-uri "ggplot.multistats" version))
18801 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
18803 `((upstream-name . "ggplot.multistats")))
18804 (build-system r-build-system)
18806 `(("r-ggplot2" ,r-ggplot2)
18807 ("r-hexbin" ,r-hexbin)
18808 ("r-rlang" ,r-rlang)
18809 ("r-scales" ,r-scales)))
18810 (home-page "https://github.com/flying-sheep/ggplot.multistats")
18811 (synopsis "Multiple summary statistics for binned stats/geometries")
18813 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
18814 which functions similar to its singular form, but allows the use of multiple
18815 statistics per bin. Those statistics can be mapped to multiple bin
18817 (license license:gpl3)))
18819 (define-public r-knn-covertree
18821 (name "r-knn-covertree")
18826 (uri (cran-uri "knn.covertree" version))
18829 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
18830 (properties `((upstream-name . "knn.covertree")))
18831 (build-system r-build-system)
18833 `(("r-matrix" ,r-matrix)
18835 ("r-rcppeigen" ,r-rcppeigen)))
18836 (home-page "https://github.com/flying-sheep/knn.covertree")
18837 (synopsis "Accurate kNN Implementation with multiple distance measures")
18839 "Similarly to the FNN package, this package allows calculation of the k
18840 nearest neighbors (kNN) of a data matrix. The implementation is based on
18841 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
18842 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
18843 (license license:agpl3+)))
18845 (define-public r-poibin
18852 (uri (cran-uri "poibin" version))
18855 "1rllgmk7yanb5amysl33kmi11lx86q5kqblyb8qqb3ckj2w4jhm2"))))
18856 (properties `((upstream-name . "poibin")))
18857 (build-system r-build-system)
18858 (home-page "https://cran.r-project.org/web/packages/poibin/")
18859 (synopsis "Poisson binomial distribution")
18861 "This package provides an implementation of both the exact and
18862 approximation methods for computing the @dfn{cumulative distribution
18863 function} (CDF) of the Poisson binomial distribution. It also provides the
18864 @dfn{probability mass function} (PMF), quantile function, and random number
18865 generation for the Poisson binomial distribution.")
18866 (license license:gpl2)))
18868 (define-public r-diagram
18875 (uri (cran-uri "diagram" version))
18878 "0f6ffprn5k0ir1s7m9s7izc64aa17r3gnygagz5bihrlsvawaavw"))))
18879 (properties `((upstream-name . "diagram")))
18880 (build-system r-build-system)
18882 `(("r-shape" ,r-shape)))
18883 (home-page "https://cran.r-project.org/web/packages/diagram/")
18884 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
18886 "This package provides tools to visualize simple graphs (networks) based
18887 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
18888 electrical networks, etc. It also includes supporting material for the book
18889 \"A practical guide to ecological modelling - using R as a simulation
18890 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
18891 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
18892 Francesca Mazzia (2012).")
18893 (license license:gpl2+)))
18895 (define-public r-lim
18902 (uri (cran-uri "LIM" version))
18905 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
18906 (properties `((upstream-name . "LIM")))
18907 (build-system r-build-system)
18909 `(("r-diagram" ,r-diagram)
18910 ("r-limsolve" ,r-limsolve)))
18911 (home-page "https://cran.r-project.org/web/packages/LIM/")
18912 (synopsis "Linear inverse model examples and solution methods")
18914 "This package provides functions that read and solve linear inverse
18915 problems (food web problems, linear programming problems).")
18916 (license license:gpl2+)))
18918 (define-public r-shinycssloaders
18920 (name "r-shinycssloaders")
18925 (uri (cran-uri "shinycssloaders" version))
18928 "1bpzsm7m7c366sjl1qndp4m5dg2vlm68rjgdy9n1ija9xbp0r2g4"))))
18930 `((upstream-name . "shinycssloaders")))
18931 (build-system r-build-system)
18933 `(("r-digest" ,r-digest)
18935 ("r-shiny" ,r-shiny)))
18936 (home-page "https://github.com/andrewsali/shinycssloaders")
18937 (synopsis "Add CSS loading animations to Shiny outputs")
18939 "This package provides tools to create a lightweight Shiny wrapper for
18940 the css-loaders created by Luke Hass
18941 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
18942 automatically show a loader when the output is (re)calculating.")
18943 (license license:gpl3)))
18945 (define-public r-rsvg
18952 (uri (cran-uri "rsvg" version))
18955 "11mccgf6hfskg45wqc114sx3qy2r494y6axdf73z6xwhs1wpm97g"))))
18956 (properties `((upstream-name . "rsvg")))
18957 (build-system r-build-system)
18959 `(("librsvg" ,librsvg)
18962 `(("pkg-config" ,pkg-config)))
18963 (home-page "https://github.com/jeroen/rsvg#readme")
18964 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
18966 "This package allows you to render vector-based SVG images into
18967 high-quality custom-size bitmap arrays using the librsvg2 library. The
18968 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
18969 addition, the package can convert images directly to various formats such as
18970 PDF or PostScript.")
18971 (license license:expat)))
18973 (define-public r-influencer
18975 (name "r-influencer")
18980 (uri (cran-uri "influenceR" version))
18983 "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
18984 (properties `((upstream-name . "influenceR")))
18985 (build-system r-build-system)
18987 `(("r-igraph" ,r-igraph)
18988 ("r-matrix" ,r-matrix)))
18989 (home-page "https://github.com/rcc-uchicago/influenceR")
18990 (synopsis "Tools to quantify structural importance of nodes in a network")
18992 "This package provides functionality to compute various node centrality
18993 measures on networks. Included are functions to compute betweenness
18994 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
18995 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
18996 algorithm to identify key players, and Valente's bridging metric. The
18997 betweenness, Key Players, and bridging implementations are parallelized with
18999 (license license:gpl2)))
19001 (define-public r-emplik
19004 (version "1.0-4.3")
19008 (uri (cran-uri "emplik" version))
19011 "1g4hz85bvw29c77zs0ig487z92jjl682vv457x81l077h0psvk7c"))))
19012 (properties `((upstream-name . "emplik")))
19013 (build-system r-build-system)
19015 `(("r-quantreg" ,r-quantreg)))
19016 (home-page "http://www.ms.uky.edu/~mai/EmpLik.html")
19017 (synopsis "Empirical likelihood ratio for censored/truncated data")
19019 "This package provides empirical likelihood ratio tests for
19020 means/quantiles/hazards from possibly censored and/or truncated data. It also
19022 (license license:gpl2+)))
19024 (define-public r-imputeyn
19026 (name "r-imputeyn")
19031 (uri (cran-uri "imputeYn" version))
19034 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
19035 (properties `((upstream-name . "imputeYn")))
19036 (build-system r-build-system)
19038 `(("r-boot" ,r-boot)
19039 ("r-emplik" ,r-emplik)
19040 ("r-mvtnorm" ,r-mvtnorm)
19041 ("r-quadprog" ,r-quadprog)
19042 ("r-survival" ,r-survival)))
19043 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
19044 (synopsis "Impute last largest censored observation under weighted least squares")
19046 "This package allows for the imputation of the last largest censored
19047 observantions. This method brings less bias and more efficient estimates for
19049 (license license:gpl2)))
19051 (define-public r-adapenetclass
19053 (name "r-adapenetclass")
19058 (uri (cran-uri "AdapEnetClass" version))
19061 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
19062 (properties `((upstream-name . "AdapEnetClass")))
19063 (build-system r-build-system)
19065 `(("r-glmnet" ,r-glmnet)
19066 ("r-imputeyn" ,r-imputeyn)
19068 ("r-quadprog" ,r-quadprog)))
19069 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
19070 (synopsis "Class of adaptive elastic net methods for censored data")
19072 "This package provides methods for variable selection for AFT models.")
19073 (license license:gpl2)))
19075 (define-public r-flock
19082 (uri (cran-uri "flock" version))
19085 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
19086 (properties `((upstream-name . "flock")))
19087 (build-system r-build-system)
19088 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
19089 (home-page "https://cran.r-project.org/web/packages/flock/")
19090 (synopsis "Process synchronization using file locks")
19092 "This package implements synchronization between R processes (spawned by
19093 using the @code{parallel} package for instance) using file locks. It supports
19094 both exclusive and shared locking.")
19095 (license license:asl2.0)))
19097 (define-public r-archivist
19099 (name "r-archivist")
19104 (uri (cran-uri "archivist" version))
19107 "1i11hrcq1910jgd6diw6h3sxx624v57zjianm49pqvb2dvd0b8y7"))))
19108 (properties `((upstream-name . "archivist")))
19109 (build-system r-build-system)
19112 ("r-digest" ,r-digest)
19113 ("r-flock" ,r-flock)
19115 ("r-lubridate" ,r-lubridate)
19116 ("r-magrittr" ,r-magrittr)
19117 ("r-rcurl" ,r-rcurl)
19118 ("r-rsqlite" ,r-rsqlite)))
19119 (home-page "https://pbiecek.github.io/archivist/")
19120 (synopsis "Tools for storing, restoring and searching for R objects")
19122 "Data exploration and modelling is a process in which a lot of data
19123 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
19124 statistical models, different versions of data sets and different versions of
19125 results. Archivist helps to store and manage artifacts created in R. It
19126 allows you to store selected artifacts as binary files together with their
19127 metadata and relations. Archivist allows sharing artifacts with others. It
19128 can look for already created artifacts by using its class, name, date of the
19129 creation or other properties. It also makes it easy to restore such
19131 (license license:gpl2)))
19133 (define-public r-versions
19135 (name "r-versions")
19140 (uri (cran-uri "versions" version))
19143 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
19144 (properties `((upstream-name . "versions")))
19145 (build-system r-build-system)
19146 (home-page "https://cran.r-project.org/web/packages/versions/")
19147 (synopsis "Query and install specific versions of CRAN packages")
19149 "This package allows you to install specified versions of R packages
19150 hosted on CRAN and provides functions to list available versions and the
19151 versions of currently installed packages.")
19152 (license license:bsd-3)))
19154 (define-public r-adapr
19161 (uri (cran-uri "adapr" version))
19164 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
19165 (properties `((upstream-name . "adapr")))
19166 (build-system r-build-system)
19168 `(("r-archivist" ,r-archivist)
19169 ("r-devtools" ,r-devtools)
19170 ("r-digest" ,r-digest)
19171 ("r-doparallel" ,r-doparallel)
19172 ("r-gdata" ,r-gdata)
19173 ("r-ggplot2" ,r-ggplot2)
19174 ("r-git2r" ,r-git2r)
19175 ("r-igraph" ,r-igraph)
19176 ("r-knitr" ,r-knitr)
19177 ("r-plotly" ,r-plotly)
19179 ("r-rmarkdown" ,r-rmarkdown)
19180 ("r-shiny" ,r-shiny)
19181 ("r-shinydashboard" ,r-shinydashboard)
19182 ("r-versions" ,r-versions)))
19183 (home-page "https://cran.r-project.org/web/packages/adapr/")
19184 (synopsis "Implementation of an accountable data analysis process")
19186 "This package tracks reading and writing within R scripts that are
19187 organized into a directed acyclic graph. It contains an interactive Shiny
19188 application @code{adaprApp()}. It uses Git and file hashes to track version
19189 histories of inputs and outputs.")
19190 (license license:lgpl2.0)))
19192 (define-public r-adapsamp
19194 (name "r-adapsamp")
19199 (uri (cran-uri "AdapSamp" version))
19202 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
19203 (properties `((upstream-name . "AdapSamp")))
19204 (build-system r-build-system)
19205 (propagated-inputs `(("r-pracma" ,r-pracma)))
19206 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
19207 (synopsis "Adaptive sampling algorithms")
19209 "For distributions whose probability density functions are log-concave,
19210 the adaptive rejection sampling algorithm can be used to build envelope
19211 functions for sampling. For others, the modified adaptive rejection sampling
19212 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
19213 adaptive slice sampling algorithm can be used. This R package mainly includes
19214 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
19215 @code{rASS()}. These functions can realize sampling based on the algorithms
19217 (license license:gpl2)))
19219 (define-public r-adaptalint
19221 (name "r-adaptalint")
19226 (uri (cran-uri "adaptalint" version))
19229 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
19230 (properties `((upstream-name . "adaptalint")))
19231 (build-system r-build-system)
19233 `(("r-dplyr" ,r-dplyr)
19234 ("r-lintr" ,r-lintr)
19235 ("r-purrr" ,r-purrr)))
19236 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
19237 (synopsis "Check R code style")
19239 "This package provides tools to infer the code style (which style rules
19240 are followed and which ones are not) from one package and use it to check
19241 another. This makes it easier to find and correct the most important problems
19243 (license license:gpl3)))