1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
4 ;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
5 ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
6 ;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen <roel@gnu.org>
7 ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
8 ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
9 ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
10 ;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net>
11 ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
12 ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
13 ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
14 ;;; Copyright © 2018, 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
15 ;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com>
16 ;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
17 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
18 ;;; Copyright © 2018, 2019 Brett Gilio <brettg@gnu.org>
19 ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
20 ;;; Copyright © 2019, 2020, 2021 Wiktor Żelazny <wzelazny@vurv.cz>
21 ;;; Copyright © 2019 Arne Babenhauserheide <arne_bab@web.de>
22 ;;; Copyright © 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
23 ;;; Copyright © 2020 Todor Kondić <tk.code@protonmail.com>
24 ;;; Copyright © 2020 Danjela Lura <danielaluraa@gmail.com>
25 ;;; Copyright © 2020 Naga Malleswari <nagamalli@riseup.net>
26 ;;; Copyright © 2020 Eric Brown <ecbrown@ericcbrown.com>
27 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
28 ;;; Copyright © 2020 Rafael Luque Leiva <rafael.luque@osoco.es>
29 ;;; Copyright © 2020, 2021 Lars-Dominik Braun <ldb@leibniz-psychology.org>
30 ;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
31 ;;; Copyright © 2020 Antoine Côté <antoine.cote@posteo.net>
32 ;;; Copyright © 2020 Arun Isaac <arunisaac@systemreboot.net>
33 ;;; Copyright © 2020 Magali Lemes <magalilemes00@gmail.com>
34 ;;; Copyright © 2020, 2021 Simon Tournier <zimon.toutoune@gmail.com>
35 ;;; Copyright © 2020 Aniket Patil <aniket112.patil@gmail.com>
36 ;;; Copyright © 2021 Marcel Schilling <marcel.schilling@uni-luebeck.de>
37 ;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net>
39 ;;; This file is part of GNU Guix.
41 ;;; GNU Guix is free software; you can redistribute it and/or modify it
42 ;;; under the terms of the GNU General Public License as published by
43 ;;; the Free Software Foundation; either version 3 of the License, or (at
44 ;;; your option) any later version.
46 ;;; GNU Guix is distributed in the hope that it will be useful, but
47 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
48 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
49 ;;; GNU General Public License for more details.
51 ;;; You should have received a copy of the GNU General Public License
52 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
54 (define-module (gnu packages cran)
55 #:use-module ((guix licenses) #:prefix license:)
56 #:use-module (guix packages)
57 #:use-module (guix download)
58 #:use-module (guix git-download)
59 #:use-module (guix utils)
60 #:use-module (guix build-system gnu)
61 #:use-module (guix build-system r)
62 #:use-module (gnu packages)
63 #:use-module (gnu packages algebra)
64 #:use-module (gnu packages autotools)
65 #:use-module (gnu packages base)
66 #:use-module (gnu packages bioinformatics)
67 #:use-module (gnu packages c)
68 #:use-module (gnu packages compression)
69 #:use-module (gnu packages crypto)
70 #:use-module (gnu packages curl)
71 #:use-module (gnu packages databases)
72 #:use-module (gnu packages fontutils)
73 #:use-module (gnu packages fribidi)
74 #:use-module (gnu packages gcc)
75 #:use-module (gnu packages geo)
76 #:use-module (gnu packages ghostscript)
77 #:use-module (gnu packages gl)
78 #:use-module (gnu packages gnome)
79 #:use-module (gnu packages graph)
80 #:use-module (gnu packages gtk)
81 #:use-module (gnu packages haskell-xyz)
82 #:use-module (gnu packages icu4c)
83 #:use-module (gnu packages image)
84 #:use-module (gnu packages imagemagick)
85 #:use-module (gnu packages java)
86 #:use-module (gnu packages javascript)
87 #:use-module (gnu packages libevent)
88 #:use-module (gnu packages machine-learning)
89 #:use-module (gnu packages maths)
90 #:use-module (gnu packages mpi)
91 #:use-module (gnu packages multiprecision)
92 #:use-module (gnu packages networking)
93 #:use-module (gnu packages node)
94 #:use-module (gnu packages pcre)
95 #:use-module (gnu packages pdf)
96 #:use-module (gnu packages perl)
97 #:use-module (gnu packages pkg-config)
98 #:use-module (gnu packages pulseaudio) ;libsndfile
99 #:use-module (gnu packages protobuf)
100 #:use-module (gnu packages python)
101 #:use-module (gnu packages python-xyz)
102 #:use-module (gnu packages sqlite)
103 #:use-module (gnu packages statistics)
104 #:use-module (gnu packages tcl)
105 #:use-module (gnu packages textutils)
106 #:use-module (gnu packages tls)
107 #:use-module (gnu packages uglifyjs)
108 #:use-module (gnu packages version-control)
109 #:use-module (gnu packages video)
110 #:use-module (gnu packages web)
111 #:use-module (gnu packages xml)
112 #:use-module (gnu packages xorg))
114 (define-public r-brio
121 (uri (cran-uri "brio" version))
124 "1vviykwx1z71yhk1xl87riaygj8sq0sj7ixyig1irqsi66aydpa2"))))
125 (properties `((upstream-name . "brio")))
126 (build-system r-build-system)
127 (home-page "https://github.com/r-lib/brio")
128 (synopsis "Basic R input output")
130 "This package provides functions to handle basic input output. These
131 functions always read and write UTF-8 (8-bit Unicode Transformation Format)
132 files and provide more explicit control over line endings.")
133 (license license:expat)))
135 (define-public r-cachem
142 (uri (cran-uri "cachem" version))
145 "0r0q5w8lsxak46crnkbi739qzys90hlw7cqqqhv99xzkpkvm554s"))))
146 (properties `((upstream-name . "cachem")))
147 (build-system r-build-system)
149 (list r-fastmap r-rlang))
150 (home-page "https://cachem.r-lib.org/")
151 (synopsis "Cache R objects with automatic pruning")
153 "This package provides key-value stores with automatic pruning. Caches
154 can limit either their total size or the age of the oldest object (or both),
155 automatically pruning objects to maintain the constraints.")
156 (license license:expat)))
158 (define-public r-curry
165 (uri (cran-uri "curry" version))
168 "1ps9hvbnb02m0b8hlw4admwbziyjvswj08ldi2dk3ymnrpawcc29"))))
169 (properties `((upstream-name . "curry")))
170 (build-system r-build-system)
171 (home-page "https://github.com/thomasp85/curry")
172 (synopsis "Partial function application")
174 "Partial application is the process of reducing the arity of a function
175 by fixing one or more arguments, thus creating a new function lacking the
176 fixed arguments. The @code{curry} package provides three different ways of
177 performing partial function application by fixing arguments from either end of
178 the argument list (currying and tail currying) or by fixing multiple named
179 arguments (partial application). This package provides this functionality
180 through the @code{%<%}, @code{%-<%}, and @code{%><%} operators which allows
181 for a programming style comparable to modern functional languages. Compared
182 to other implementations such a @code{purrr::partial()} the operators in
183 @code{curry} composes functions with named arguments, aiding in autocomplete
185 (license license:gpl2+)))
187 (define-public r-datawizard
189 (name "r-datawizard")
194 (uri (cran-uri "datawizard" version))
197 "062phzfcvn79npn4s58gz1m5ignyvr4q2zlqnyxla4p7l760djl9"))))
198 (properties `((upstream-name . "datawizard")))
199 (build-system r-build-system)
204 (home-page "https://easystats.github.io/datawizard/")
205 (synopsis "Easy data wrangling")
207 "This package provides a lightweight package to easily manipulate,
208 clean, transform, and prepare your data for analysis. It also forms the data
209 wrangling backend for the packages in the @code{easystats} ecosystem.")
210 (license license:gpl3)))
212 (define-public r-diffobj
219 (uri (cran-uri "diffobj" version))
222 "0q6gwd9pqh41f6j5p9jl92aji4p8kx9inffpha93d7jc3ndsfq6q"))))
223 (properties `((upstream-name . "diffobj")))
224 (build-system r-build-system)
225 (propagated-inputs (list r-crayon))
226 (native-inputs (list r-knitr))
227 (home-page "https://github.com/brodieG/diffobj")
228 (synopsis "Diffs for R objects")
230 "Generate a colorized diff of two R objects for an intuitive
231 visualization of their differences.")
232 (license license:gpl2+)))
234 (define-public r-emdist
241 (uri (cran-uri "emdist" version))
244 "1z14pb9z9nkd0f2c8pln4hzkfqa9dk9n3vg8czc8jiv0ndnqi7rq"))))
245 (properties `((upstream-name . "emdist")))
246 (build-system r-build-system)
247 (home-page "http://www.rforge.net/emd")
248 (synopsis "Earth mover's distance")
250 "This package provides tools to calculate the Earth Mover's
252 (license license:expat)))
254 (define-public r-googledrive
256 (name "r-googledrive")
261 (uri (cran-uri "googledrive" version))
264 "09jsiknzyfgxd0nzdr3wrrjw24allch2x74h96qg8vh8dad4cp30"))))
265 (properties `((upstream-name . "googledrive")))
266 (build-system r-build-system)
284 (home-page "https://googledrive.tidyverse.org")
285 (synopsis "Interface to Google Drive")
286 (description "This package lets you manage Google Drive files from R.")
287 (license license:expat)))
296 (uri (cran-uri "ids" version))
299 "1s6ga94gds5ydr9f8qbjfgfpg2dvbnkcrlybqlb33hk3c0c2l8dn"))))
300 (properties `((upstream-name . "ids")))
301 (build-system r-build-system)
303 (list r-openssl r-uuid))
304 (native-inputs (list r-knitr))
305 (home-page "https://github.com/richfitz/ids")
306 (synopsis "Generate random identifiers")
308 "This package lets you generate random or human readable and
309 pronounceable identifiers.")
310 (license license:expat)))
312 (define-public r-googlesheets4
314 (name "r-googlesheets4")
319 (uri (cran-uri "googlesheets4" version))
322 "0yncqwv9l5knyrv88ys5gwcv44hl1j0mbklpins6v7f9m9v7s40a"))))
323 (properties `((upstream-name . "googlesheets4")))
324 (build-system r-build-system)
340 (home-page "https://github.com/tidyverse/googlesheets4")
341 (synopsis "Access Google Sheets using the Sheets API V4")
343 "This package lets you interact with Google Sheets through the
344 @url{https://developers.google.com/sheets/api,Sheets API v4}. This package
345 can read and write both the metadata and the cell data in a Sheet.")
346 (license license:expat)))
348 (define-public r-waldo
355 (uri (cran-uri "waldo" version))
358 "16q1xjbl9g04l1r1x3nid9hmz1sa35q6j33bigdzh4y4zcd8qb7c"))))
359 (properties `((upstream-name . "waldo")))
360 (build-system r-build-system)
369 (home-page "https://github.com/r-lib/waldo")
370 (synopsis "Find differences between R objects")
372 "Compare complex R objects and reveal the key differences. This package
373 was designed particularly for use in testing packages where being able to
374 quickly isolate key differences makes understanding test failures much
376 (license license:expat)))
378 (define-public r-rticles
385 (uri (cran-uri "rticles" version))
388 "0xk0xz97k8r8srmniihn3y4dkxddxf97yjbsljcxlgcq8f0zcc2s"))))
389 (properties `((upstream-name . "rticles")))
390 (build-system r-build-system)
392 (list r-knitr r-rmarkdown r-tinytex r-xfun r-yaml))
393 (home-page "https://github.com/rstudio/rticles")
394 (synopsis "Article formats for R Markdown")
396 "This package provides a suite of custom R Markdown formats and templates
397 for authoring journal articles and conference submissions.")
398 (license license:gpl3)))
400 (define-public r-benchmarkmedata
402 (name "r-benchmarkmedata")
406 (uri (cran-uri "benchmarkmeData" version))
409 "1n4vjkagqlm6kw2hilf4gjfcdjad0bcg652j9nl2ygbq3kdnh1vf"))))
410 (build-system r-build-system)
412 (list r-dplyr r-tibble))
413 (home-page "https://github.com/csgillespie/benchmarkme-data")
414 (synopsis "Data set for the @code{benchmarkme} package")
415 (description "This package contains the data set for the crowd-sourced
416 benchmarks from running the @code{benchmarkme} package.")
417 (license license:gpl2+)))
419 (define-public r-benchmarkme
421 (name "r-benchmarkme")
425 (uri (cran-uri "benchmarkme" version))
428 "0ymgsxzrvnpyvs0cff09d3lrkl12qyqx5bwammsc4vgl5ng9p69p"))))
429 (build-system r-build-system)
433 (list r-benchmarkmedata
440 (home-page "https://csgillespie.github.io/benchmarkme/")
441 (synopsis "Crowd-sourced system benchmarks")
442 (description "This package provides functionality to benchmark your CPU
443 and compare against other CPUs. Also provides functions for obtaining system
444 specifications, such as RAM, CPU type, and R version.")
445 (license license:gpl2+)))
447 (define-public r-bezier
453 (uri (cran-uri "bezier" version))
456 "1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"))))
457 (build-system r-build-system)
458 (home-page "https://cran.r-project.org/web/packages/bezier/")
459 (synopsis "Bezier curve and spline toolkit")
461 "This package is a toolkit for working with Bezier curves and splines.
462 The package provides functions for point generation, arc length estimation,
463 degree elevation and curve fitting.")
464 (license license:gpl2+)))
473 (uri (cran-uri "V8" version))
476 "0xqk4rcv255r2wll2jpzf9ix8j6hbhw0vbhg2g9i6z2apyc9i5m3"))))
477 (properties `((upstream-name . "V8")))
478 (build-system r-build-system)
481 (modify-phases %standard-phases
482 (add-after 'unpack 'find-v8
483 (lambda* (#:key inputs #:allow-other-keys)
484 (substitute* "configure"
486 (string-append "PKG_LIBS="
487 (assoc-ref inputs "node")
488 "/lib/libnode.so.64\n")))
489 (setenv "INCLUDE_DIR"
491 (assoc-ref inputs "node")
495 (assoc-ref inputs "node") "/lib"))
501 (list r-curl r-jsonlite r-rcpp))
504 (home-page "https://jeroen.cran.dev/V8")
505 (synopsis "Embedded JavaScript and WebAssembly engine for R")
507 "This package provides an R interface to V8: Google's JavaScript and
508 WebAssembly engine.")
509 (license license:expat)))
518 (uri (cran-uri "DOT" version))
521 "0qh5n57cp9c2n5yn59q4wggz82943pwfanp3kx869aba2x3sj30i"))))
522 (properties `((upstream-name . "DOT")))
523 (build-system r-build-system)
526 (home-page "http://haghish.com/dot")
527 (synopsis "Render and Export DOT Graphs in R")
529 "This package provides tools to render DOT diagram markup language in R
530 and also provides the possibility to export the graphs in PostScript and
531 SVG (Scalable Vector Graphics) formats. In addition, it supports literate
532 programming packages such as @code{knitr} and @code{rmarkdown}.")
533 (license license:expat)))
535 (define-public r-clipr
542 (uri (cran-uri "clipr" version))
545 "1ywa4kipwc2d7na6iiz3wzdah99h6aynnh74yxl3nzl40xxlgbgz"))))
546 (build-system r-build-system)
549 (home-page "https://github.com/mdlincoln/clipr")
550 (synopsis "Read and write from the system clipboard")
552 "This package provides simple utility functions to read from and write to
553 the system clipboards.")
554 (license license:gpl3)))
562 (uri (cran-uri "zoo" version))
565 "18vjywalpgzqyk66gajb8x1yp8avdaaf11ykynld9fd8cy82bgmp"))))
566 (build-system r-build-system)
569 (home-page "http://zoo.R-Forge.R-project.org/")
570 (synopsis "S3 infrastructure for regular and irregular time series")
571 (description "This package contains an S3 class with methods for totally
572 ordered indexed observations. It is particularly aimed at irregular time
573 series of numeric vectors/matrices and factors.")
574 (license license:gpl2+)))
576 (define-public r-fontawesome
578 (name "r-fontawesome")
583 (uri (cran-uri "fontawesome" version))
585 (base32 "0r6zb5175cr4ybqj6bl0mbhadwv9xjxaf32yjc0y76rw3d6vcbap"))))
586 (properties `((upstream-name . "fontawesome")))
587 (build-system r-build-system)
589 (list r-htmltools r-rlang))
590 (home-page "https://github.com/rstudio/fontawesome")
591 (synopsis "Easily work with Font Awesome icons")
593 "Easily and flexibly insert Font Awesome icons into R Markdown documents
594 and Shiny apps. These icons can be inserted into HTML content through inline
595 SVG tags or @code{i} tags. There is also a utility function for exporting
596 Font Awesome icons as PNG images for those situations where raster graphics
598 (license license:expat)))
600 (define-public r-fingerprint
602 (name "r-fingerprint")
607 (uri (cran-uri "fingerprint" version))
609 (base32 "04jcwkydjrs31pia6kq8z2n9s54im950q08hs2ay15xjxxkmb8ic"))))
610 (properties `((upstream-name . "fingerprint")))
611 (build-system r-build-system)
612 (home-page "https://cran.r-project.org/package=fingerprint")
613 (synopsis "Functions to Operate on Binary Fingerprint Data")
615 "This package provides functions to manipulate binary fingerprints of
616 arbitrary length. A fingerprint is represented by an object of S4 class
617 @code{fingerprint}. The bitwise logical functions in R are overridden so that
618 they can be used directly with @code{fingerprint} objects. A number of
619 distance metrics are also available. Fingerprints can be converted to
620 Euclidean vectors (i.e., points on the unit hypersphere) and can also be
621 folded. Arbitrary fingerprint formats can be handled via line handlers.
622 Currently handlers are provided for CDK, MOE and BCI fingerprint data.")
623 ;; Any version of the GPL
624 (license (list license:gpl2+ license:gpl3+))))
626 (define-public r-fpeek
633 (uri (cran-uri "fpeek" version))
635 (base32 "0kv46g21ndxchg3q8ynq7hjjkh6i2zlc21axn5y1jjzigrw047ii"))))
636 (properties `((upstream-name . "fpeek")))
637 (build-system r-build-system)
638 (propagated-inputs (list r-rcpp))
639 (home-page "https://github.com/davidgohel/fpeek")
640 (synopsis "Check text files content at a glance")
642 "This package provides tools to help working with text files. It can
643 return the number of lines; print the first and last lines; convert encoding.
644 Operations are made without reading the entire file before starting, resulting
645 in good performances with large files.")
646 (license license:expat)))
648 (define-public r-ggalluvial
650 (name "r-ggalluvial")
654 (uri (cran-uri "ggalluvial" version))
657 "0mkan9gxg3yxjism22yxbhvlh2lh7wpbrqpb355za790prcmjbh3"))))
658 (properties `((upstream-name . "ggalluvial")))
659 (build-system r-build-system)
669 (home-page "http://corybrunson.github.io/ggalluvial/")
670 (synopsis "Alluvial plots for ggplot2")
671 (description "This package provides alluvial plots for @code{ggplot2}.
672 Alluvial plots use variable-width ribbons and stacked bar plots to represent
673 multi-dimensional or repeated-measures data with categorical or ordinal
675 (license license:gpl3)))
677 (define-public r-ggpp
684 (uri (cran-uri "ggpp" version))
687 "0m2wq9kqlxqxlzyx9fd0c4iw6qb7kpjrq7fqqa2kvwyj79vx6ahj"))))
688 (properties `((upstream-name . "ggpp")))
689 (build-system r-build-system)
707 (home-page "https://docs.r4photobiology.info/ggpp/")
708 (synopsis "Grammar extensions to ggplot2")
710 "This package contains extensions to ggplot2.
713 @item Geomas: @code{geom_table}, @code{geom_plot} and @code{geom_grob} add
714 insets to plots using native data coordinates, while @code{geom_table_npc},
715 @code{geom_plot_npc} and @code{geom_grob_npc} do the same using @code{npc}
716 coordinates through new aesthetics @code{npcx} and @code{npcy}.
717 @item Statistics: select observations based on 2D density.
718 @item Positions: radial nudging away from a center point and nudging away from
722 (license license:gpl2+)))
724 (define-public r-lmodel2
731 (uri (cran-uri "lmodel2" version))
733 (base32 "1fiin2nkffbihz1s8ixmw9lgf8mn3j9krr8iiflizk10mdv54hnb"))))
734 (properties `((upstream-name . "lmodel2")))
735 (build-system r-build-system)
736 (home-page "https://cran.r-project.org/package=lmodel2")
737 (synopsis "Model II regression")
739 "This package computes model II simple linear regression using
740 @dfn{ordinary least squares} (OLS), @dfn{major axis} (MA), @dfn{standard major
741 axis} (SMA), and @dfn{ranged major axis} (RMA).")
742 (license license:gpl2)))
744 (define-public r-ggpmisc
750 (uri (cran-uri "ggpmisc" version))
753 "01dnr2a33zmgi0gjsxlcz4hp68b18xsi8z1lkhgcla5im59qf9xi"))))
754 (build-system r-build-system)
772 (home-page "https://www.r4photobiology.info/")
773 (synopsis "Miscellaneous Extensions to @code{ggplot2}")
774 (description "This package provides extensions to @code{ggplot2},
775 respecting the grammar of its graphics paradigm.")
776 (license license:gpl2+)))
778 (define-public r-gprofiler
785 (uri (cran-uri "gProfileR" version))
788 "1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k"))))
789 (properties `((upstream-name . "gProfileR")))
790 (build-system r-build-system)
792 (list r-plyr r-rcurl))
793 (home-page "https://cran.r-project.org/web/packages/gProfileR/")
794 (synopsis "Interface to the g:Profiler toolkit")
796 "This package provides tools for functional enrichment analysis,
797 gene identifier conversion and mapping homologous genes across related
798 organisms via the @code{g:Profiler} toolkit.")
799 (license license:gpl2+)))
801 (define-public r-gprofiler2
803 (name "r-gprofiler2")
808 (uri (cran-uri "gprofiler2" version))
811 "0r0h34b35xzgd9rh55yndn0anxy0z45zdlqa6qfmpn91b6v1bb1g"))))
812 (properties `((upstream-name . "gprofiler2")))
813 (build-system r-build-system)
824 (native-inputs (list r-knitr))
825 (home-page "https://cran.r-project.org/web/packages/gprofiler2/")
826 (synopsis "Interface to the g:Profiler toolset")
828 "This package provides a toolset for functional enrichment analysis and
829 visualization, gene/protein/SNP identifier conversion and mapping orthologous
830 genes across species via @url{https://biit.cs.ut.ee/gprofiler,g:Profiler}.
834 @item @code{g:GOSt}, functional enrichment analysis and visualization of gene
836 @item @code{g:Convert}, gene/protein/transcript identifier conversion across
838 @item @code{g:Orth}, orthology search across species;
839 @item @code{g:SNPense}, mapping SNP rs identifiers to chromosome positions,
840 genes and variant effects.
843 This package is an R interface corresponding to the 2019 update of
844 @code{g:Profiler} and provides access to versions @code{e94_eg41_p11} and
846 (license license:gpl2+)))
848 (define-public r-oenb
855 (uri (cran-uri "oenb" version))
858 "1jgxw7ycx2lcdzglg9nix8k08fs4r6i5jdsjzrd6w1dg6smsinl5"))))
859 (properties `((upstream-name . "oenb")))
860 (build-system r-build-system)
862 (list r-dplyr r-xml))
863 (native-inputs (list r-knitr))
864 (home-page "https://github.com/franzmohr/oenb")
865 (synopsis "Tools for the OeNB Data Web Service")
867 "Tools to access data from the data web service of the
868 @acronym{OeNB, Oesterreichische Nationalbank},
869 @url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.")
870 (license license:gpl2+)))
872 (define-public r-scales
879 (uri (cran-uri "scales" version))
881 (base32 "019ps0njjc0rzrjygqiyn8b9vp0c3c0jd56h1yi19wzi49jvdcj0"))))
882 (build-system r-build-system)
891 (home-page "https://github.com/hadley/scales")
892 (synopsis "Scale functions for visualization")
894 "This package provides graphical scales that map data to aesthetics, and
895 provides methods for automatically determining breaks and labels for axes and
897 (license license:expat)))
899 (define-public r-pacman
905 (uri (cran-uri "pacman" version))
908 "0z7gngd6h83cpjhq1vg75wvzhdjbgjh7gj5d4zvvi9gd2lmagjcy"))))
909 (build-system r-build-system)
912 (home-page "https://github.com/trinker/pacman")
913 (synopsis "Package Management Tool")
914 (description "This package provides tools to more conveniently perform
915 tasks associated with add-on packages. @code{pacman} conveniently wraps
916 library and package related functions and names them in an intuitive and
917 consistent fashion. It seeks to combine functionality from lower level
918 functions which can speed up workflow.")
919 (license license:gpl2)))
921 (define-public r-pheatmap
928 (uri (cran-uri "pheatmap" version))
931 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
932 (build-system r-build-system)
934 (list r-gtable r-rcolorbrewer r-scales))
935 (home-page "https://cran.r-project.org/web/packages/pheatmap")
936 (synopsis "Pretty heatmaps")
938 "This package provides an implementation of heatmaps that offers more
939 control over dimensions and appearance.")
940 (license license:gpl2+)))
942 (define-public r-pnwcolors
949 (uri (cran-uri "PNWColors" version))
952 "1phplnclkficfv8s6wsyrckk4ixzbayiy5iix6dddg40485l9nyj"))))
953 (properties `((upstream-name . "PNWColors")))
954 (build-system r-build-system)
955 (home-page "https://github.com/jakelawlor/PNWColors")
956 (synopsis "Color palettes for data visualizations")
958 "This package provides color palettes. They are checked for colorblind
959 accessibility from hue, saturation, and lightness value scaling using the
960 Chroma.js Color Palette Helper. See @url{https://gka.github.io/palettes}.")
961 (license license:cc0)))
969 (uri (cran-uri "ecp" version))
972 "0n602jssl6rf596nwm6hbl7s9vdlqi20w8mrhxicj373mw5v22m8"))))
973 (build-system r-build-system)
976 (home-page "https://cran.r-project.org/web/packages/ecp/")
977 (synopsis "Multiple change-point analysis of multivariate data")
979 "This package implements various procedures for finding multiple
980 change-points. Two methods make use of dynamic programming and pruning, with
981 no distributional assumptions other than the existence of certain absolute
982 moments in one method. Hierarchical and exact search methods are included.
983 All methods return the set of estimated change-points as well as other summary
985 (license license:gpl2+)))
987 (define-public r-ellipsis
994 (uri (cran-uri "ellipsis" version))
997 "0n0mm9jngklv7j9wa64jdji035z0smmnsp2dfwcz9isrxgjnc0m9"))))
998 (build-system r-build-system)
1001 (home-page "https://github.com/hadley/ellipsis")
1002 (synopsis "Tools for working with additional arguments")
1004 "In S3 generics, it's useful to take @code{...} so that methods can have
1005 additional arguments. But this flexibility comes at a cost: misspelled
1006 arguments will be silently ignored. The @code{ellipsis} package is an
1007 experiment that allows a generic to warn if any arguments passed in @code{...}
1009 (license license:gpl3)))
1011 (define-public r-grr
1018 (uri (cran-uri "grr" version))
1021 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
1022 (build-system r-build-system)
1023 (home-page "https://cran.r-project.org/web/packages/grr")
1024 (synopsis "Alternative implementations of base R functions")
1026 "This package provides alternative implementations of some base R
1027 functions, including @code{sort}, @code{order}, and @code{match}. The
1028 functions are simplified but can be faster or have other advantages.")
1029 (license license:gpl3)))
1031 (define-public r-matrix-utils
1033 (name "r-matrix-utils")
1038 (uri (cran-uri "Matrix.utils" version))
1041 "0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb"))))
1042 (properties `((upstream-name . "Matrix.utils")))
1043 (build-system r-build-system)
1045 (list r-grr r-matrix))
1046 (home-page "https://github.com/cvarrichio/Matrix.utils")
1048 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
1050 "This package implements data manipulation methods such as @code{cast},
1051 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
1053 (license license:gpl3)))
1055 (define-public r-mboost
1061 (uri (cran-uri "mboost" version))
1064 "0yg07fdd1sbjfhhxn1dqgph2vzqyq7l52cdk5iq2a2zy1vh176yg"))))
1065 (build-system r-build-system)
1074 (home-page "https://github.com/boost-R/mboost")
1075 (synopsis "Model-based boosting")
1077 "This package provides a functional gradient descent algorithm (boosting)
1078 for optimizing general risk functions utilizing component-wise (penalised)
1079 least squares estimates or regression trees as base-learners for fitting
1080 generalized linear, additive and interaction models to potentially
1081 high-dimensional data.")
1082 (license license:gpl2)))
1084 (define-public r-shadowtext
1086 (name "r-shadowtext")
1090 (uri (cran-uri "shadowtext" version))
1093 "1g6mgnfnzf2c17yzqk3zybfc5y62p5ndrbikxb3xcm2hiljiiqna"))))
1094 (properties `((upstream-name . "shadowtext")))
1095 (build-system r-build-system)
1097 (list r-ggplot2 r-scales))
1100 (home-page "https://github.com/GuangchuangYu/shadowtext/")
1101 (synopsis "Shadow text grob and layer")
1102 (description "This package implements @code{shadowtextGrob()} for
1103 @code{grid} and @code{geom_shadowtext()} layer for @code{ggplot2}.
1104 These functions draw text grob with background shadow.")
1105 (license license:artistic2.0)))
1107 (define-public r-sys
1114 (uri (cran-uri "sys" version))
1117 "11q4zmx62w44p1j34frwmrsp23mc7l4n354i0zyziw92yax8zy0p"))))
1118 (build-system r-build-system)
1119 (home-page "https://github.com/jeroen/sys")
1120 (synopsis "Powerful and reliable tools for running system commands in R")
1122 "This package provides drop-in replacements for the base @code{system2()}
1123 function with fine control and consistent behavior across platforms. It
1124 supports clean interruption, timeout, background tasks, and streaming STDIN /
1125 STDOUT / STDERR over binary or text connections. The package also provides
1126 functions for evaluating expressions inside a temporary fork. Such
1127 evaluations have no side effects on the main R process, and support reliable
1128 interrupts and timeouts. This provides the basis for a sandboxing
1130 (license license:expat)))
1132 (define-public r-ashr
1138 (uri (cran-uri "ashr" version))
1141 "1rqb5j30ylaf1h4l66x4jxyn5inrvhc42d90qd5mgkxsq0ghdlr4"))))
1142 (properties `((upstream-name . "ashr")))
1143 (build-system r-build-system)
1154 (home-page "https://github.com/stephens999/ashr")
1155 (synopsis "Methods for adaptive shrinkage, using empirical bayes")
1156 (description "This package implements an empirical Bayes approach for
1157 large-scale hypothesis testing and false discovery rate estimation.")
1158 (license license:gpl3+)))
1160 (define-public r-askpass
1167 (uri (cran-uri "askpass" version))
1170 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
1171 (build-system r-build-system)
1172 (propagated-inputs (list r-sys))
1173 (home-page "https://github.com/jeroen/askpass")
1174 (synopsis "Safe password entry for R")
1176 "This package provides cross-platform utilities for prompting the user
1177 for credentials or a passphrase, for example to authenticate with a server or
1178 read a protected key.")
1179 (license license:expat)))
1181 (define-public r-astsa
1188 (uri (cran-uri "astsa" version))
1190 (base32 "09zx2q419p0b1c336ybh4i62v5dvn3sp39dxn5kwlrqchjj7f5z6"))))
1191 (properties `((upstream-name . "astsa")))
1192 (build-system r-build-system)
1193 (home-page "https://github.com/nickpoison/astsa/")
1194 (synopsis "Applied statistical time series analysis")
1196 "This package provides data sets and scripts to accompany Time Series
1197 Analysis and Its Applications: With R Examples (4th ed), by R.H. Shumway and
1198 D.S. Stoffer. Springer Texts in Statistics, 2017,
1199 @url{https://doi.org/10.1007/978-3-319-52452-8}, and Time Series: A Data
1200 Analysis Approach Using R. Chapman-Hall, 2019,
1201 @url{https://doi.org/10.1201/9780429273285}.")
1202 (license license:gpl3)))
1204 (define-public r-vegan
1211 (uri (cran-uri "vegan" version))
1214 "0aj6m9l1vkh32sar6fyvq4p8j4h2f2f347w1300qnzgaa5lmhfz6"))))
1215 (build-system r-build-system)
1217 (list r-knitr ; needed for vignettes
1220 (list r-cluster r-lattice r-mass r-mgcv r-permute))
1221 (home-page "https://cran.r-project.org/web/packages/vegan")
1222 (synopsis "Functions for community ecology")
1224 "The vegan package provides tools for descriptive community ecology. It
1225 has most basic functions of diversity analysis, community ordination and
1226 dissimilarity analysis. Most of its multivariate tools can be used for other
1227 data types as well.")
1228 (license license:gpl2+)))
1230 (define-public r-tidyverse
1232 (name "r-tidyverse")
1237 (uri (cran-uri "tidyverse" version))
1240 "0ck6xmsw5p168jmw2fqv79fzfnw5jckfra7mfii261j6kl89bkw3"))))
1241 (build-system r-build-system)
1274 (home-page "https://tidyverse.tidyverse.org")
1275 (synopsis "Install and load packages from the \"Tidyverse\"")
1277 "The @code{tidyverse} is a set of packages that work in harmony because
1278 they share common data representations and API design. This package is
1279 designed to make it easy to install and load multiple tidyverse packages in a
1281 (license license:gpl3)))
1283 (define-public r-rvest
1290 (uri (cran-uri "rvest" version))
1292 (base32 "1905vxgnj3q09l1wf6rwxpbpydznp06nbkrclnc05j2415z4gfw9"))))
1293 (build-system r-build-system)
1304 (home-page "https://github.com/hadley/rvest")
1305 (synopsis "Simple web scraping for R")
1307 "@code{r-rvest} helps you scrape information from web pages. It is
1308 designed to work with @code{magrittr} to make it easy to express common web
1309 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
1310 (license license:gpl3)))
1312 (define-public r-selectr
1319 (uri (cran-uri "selectr" version))
1321 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
1322 (build-system r-build-system)
1324 (list r-stringr r-r6))
1325 (home-page "https://sjp.co.nz/projects/selectr/")
1326 (synopsis "Translate CSS selectors to XPath expressions")
1328 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
1329 expression. This allows you to use CSS selectors when working with the XML
1330 package as it can only evaluate XPath expressions. Also provided are
1331 convenience functions useful for using CSS selectors on XML nodes. This
1332 package is a port of the Python package @code{cssselect}.")
1333 (license license:bsd-3)))
1335 (define-public r-reprex
1342 (uri (cran-uri "reprex" version))
1345 "09k4rasp7mz6n796dsklcbc5l7prljiznrm7fra16qybr9kqcv8f"))))
1346 (build-system r-build-system)
1360 (home-page "https://github.com/tidyverse/reprex")
1361 (synopsis "Prepare reproducible R code examples for sharing")
1363 "This package provides a convenience wrapper that uses the
1364 @code{rmarkdown} package to render small snippets of code to target formats
1365 that include both code and output. The goal is to encourage the sharing of
1366 small, reproducible, and runnable examples on code-oriented websites or email.
1367 @code{reprex} also extracts clean, runnable R code from various common formats,
1368 such as copy/paste from an R session.")
1369 (license license:expat)))
1371 (define-public r-reordercluster
1373 (name "r-reordercluster")
1377 (uri (cran-uri "ReorderCluster" version))
1380 "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58"))))
1381 (build-system r-build-system)
1383 (list r-gplots r-rcpp))
1384 (home-page "https://cran.r-project.org/web/packages/ReorderCluster")
1385 (synopsis "Reordering the dendrogram according to the class labels")
1386 (description "This package provides tools for performing the leaf reordering
1387 for the dendrogram that preserves the hierarchical clustering result and at the
1388 same time tries to group instances from the same class together.")
1389 (license license:gpl3+)))
1391 (define-public r-callr
1398 (uri (cran-uri "callr" version))
1401 "02inaf3c7b0hikii7p2zwaphrq5myv4in92d9jxd1ilmhla5awnn"))))
1402 (build-system r-build-system)
1404 (list r-r6 r-processx))
1405 (home-page "https://github.com/r-lib/callr#readme")
1406 (synopsis "Call R from R")
1408 "It is sometimes useful to perform a computation in a separate R process,
1409 without affecting the current R process at all. This package does exactly
1411 (license license:expat)))
1413 (define-public r-depmixs4
1419 (uri (cran-uri "depmixS4" version))
1422 "1pacvhw5m4fsk3ysbal50fdqbvlaz8ywyqp6bn1wh42wipqbb2i8"))))
1424 (list r-nnet r-nlme r-mass r-rsolnp))
1425 (build-system r-build-system)
1426 (home-page "https://cran.r-project.org/web/packages/depmixS4/")
1427 (synopsis "Dependent Mixture Models")
1428 (description "This package fits latent (hidden) Markov models on mixed
1429 categorical and continuous (time series) data, otherwise known as dependent
1431 (license license:gpl2+)))
1433 (define-public r-readxl
1440 (uri (cran-uri "readxl" version))
1443 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
1444 (build-system r-build-system)
1446 (list r-cellranger r-progress r-rcpp r-tibble))
1447 (home-page "https://readxl.tidyverse.org")
1448 (synopsis "Read Excel files")
1450 "This package lets you import Excel files into R. It supports
1451 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
1452 the embedded @code{RapidXML} C++ library.")
1453 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
1454 ;; 'rapidxml' which is Boost.
1455 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
1457 (define-public r-model4you
1459 (name "r-model4you")
1463 (uri (cran-uri "model4you" version))
1466 "0pni9v3nradvy8sp2m07903vc7z610xrh426lf19dxss12kgrfi8"))))
1467 (build-system r-build-system)
1475 (home-page "https://cran.r-project.org/web/packages/model4you/")
1476 (synopsis "Stratified and personalised models based on trees and forests")
1478 "This package provides procedures for model-based trees for subgroup
1479 analyses in clinical trials and model-based forests for the estimation and
1480 prediction of personalised treatment effects. Currently partitioning of linear
1481 models, @code{lm()}, generalised linear models, @code{glm()}, and
1482 Weibull models, @code{survreg()}, are supported. Advanced plotting functionality is
1483 supported for the trees and a test for parameter heterogeneity is provided for
1484 the personalised models.")
1485 (license license:gpl2+)))
1487 (define-public r-modelr
1494 (uri (cran-uri "modelr" version))
1497 "1i31nff7bqibk6r4hhd4j1vzwbyaf8493v0bjaagn36njmysfnw2"))))
1498 (build-system r-build-system)
1508 (home-page "https://github.com/tidyverse/modelr")
1509 (synopsis "Helper functions for modelling in pipelines")
1511 "Functions for modelling that help you seamlessly integrate modelling
1512 into a pipeline of data manipulation and visualisation.")
1513 (license license:gpl3)))
1515 (define-public r-hmm
1521 (uri (cran-uri "HMM" version))
1524 "0z0hcqfixx1l2a6d3lpy5hmh0n4gjgs0jnck441akpp3vh37glzw"))))
1525 (properties `((upstream-name . "HMM")))
1526 (build-system r-build-system)
1527 (home-page "https://cran.r-project.org/web/packages/HMM/")
1528 (synopsis "Hidden Markov Models")
1529 (description "This package provides an easy to use library to setup, apply
1530 and make inference with discrete time and discrete space hidden Markov
1532 (license license:gpl2+)))
1534 (define-public r-hiddenmarkov
1536 (name "r-hiddenmarkov")
1540 (uri (cran-uri "HiddenMarkov" version))
1543 "05dm3nl0ffsz2ziw3bz5bivyxk7r5bxs8xhky3hz660qaqzd51ki"))))
1544 (build-system r-build-system)
1547 (home-page "https://cran.r-project.org/web/packages/HiddenMarkov/")
1548 (synopsis "Hidden markov models for R")
1549 (description "This package contains functions for the analysis of Discrete
1550 Time Hidden Markov Models, Markov Modulated GLMs and the Markov Modulated
1551 Poisson Process. It includes functions for simulation, parameter estimation,
1552 and the Viterbi algorithm. The algorithms are based of those of Walter
1554 (license license:gpl2+)))
1556 (define-public r-httpuv
1562 (uri (cran-uri "httpuv" version))
1565 "0xh8y05k4jxdwp9xh4x478y3scnv80q05l9gxk2ni6f0dk43iqxz"))
1566 ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv
1567 ;; only contains fixes for building on Solaris.
1568 (patches (search-patches "r-httpuv-1.5.5-unvendor-libuv.patch"))
1569 (modules '((guix build utils)))
1570 ;; Cannot unbundle http-parser, because it contains local
1573 '(delete-file-recursively "src/libuv"))))
1574 (build-system r-build-system)
1577 (modify-phases %standard-phases
1578 (add-after 'unpack 'unbundle-libuv
1579 (lambda* (#:key outputs #:allow-other-keys)
1580 (substitute* (find-files "src" "\\.cpp$|\\.h$")
1581 (("\"libuv/include/uv\\.h\"")
1583 ;; Fix https://github.com/rstudio/httpuv/issues/282
1584 (substitute* "src/http.cpp"
1585 (("uv_pipe_init\\(pLoop, &pSocket->handle\\.pipe, true\\);")
1586 "uv_pipe_init(pLoop, &pSocket->handle.pipe, 0);")))))))
1590 (list r-later r-promises r-r6 r-rcpp))
1591 (home-page "https://github.com/rstudio/httpuv")
1592 (synopsis "HTTP and WebSocket server library for R")
1594 "The httpuv package provides low-level socket and protocol support for
1595 handling HTTP and WebSocket requests directly from within R. It is primarily
1596 intended as a building block for other packages, rather than making it
1597 particularly easy to create complete web applications using httpuv alone.")
1598 ;; This package includes third-party code that was originally released
1599 ;; under various non-copyleft licenses. Full licensing information can be
1600 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
1601 (license license:gpl3+)))
1603 (define-public r-jsonlite
1609 (uri (cran-uri "jsonlite" version))
1612 "1lhzcpz9clwq04i5m6jzkvw9x03pwlqrixv4l9xzchjr8d84nd86"))))
1613 (build-system r-build-system)
1616 (home-page "https://arxiv.org/abs/1403.2805")
1617 (synopsis "Robust, high performance JSON parser and generator for R")
1619 "The jsonlite package provides a fast JSON parser and generator optimized
1620 for statistical data and the web. It offers flexible, robust, high
1621 performance tools for working with JSON in R and is particularly powerful for
1622 building pipelines and interacting with a web API. In addition to converting
1623 JSON data from/to R objects, jsonlite contains functions to stream, validate,
1624 and prettify JSON data. The unit tests included with the package verify that
1625 all edge cases are encoded and decoded consistently for use with dynamic data
1626 in systems and applications.")
1627 (license license:expat)))
1629 (define-public r-servr
1635 (uri (cran-uri "servr" version))
1638 "11x0857m3xzdbzr4z0vx4fcdk36arfagyf2qgamvprich0qisknr"))))
1639 (build-system r-build-system)
1641 (list r-httpuv r-jsonlite r-mime r-xfun))
1642 (home-page "https://github.com/yihui/servr")
1643 (synopsis "Simple HTTP server to serve static files or dynamic documents")
1645 "Servr provides an HTTP server in R to serve static files, or dynamic
1646 documents that can be converted to HTML files (e.g., R Markdown) under a given
1648 (license license:expat)))
1650 (define-public r-howmany
1656 (uri (cran-uri "howmany" version))
1659 "045ck8qahfg2swbgyf7dpl32ryq1m4sbalhr7m5qdgpm62vz8h7f"))))
1660 (build-system r-build-system)
1661 (home-page "https://cran.r-project.org/web/packages/howmany/")
1662 (synopsis "Lower bound for the number of correct rejections")
1663 (description "When testing multiple hypotheses simultaneously, this package
1664 provides functionality to calculate a lower bound for the number of correct
1665 rejections (as a function of the number of rejected hypotheses), which holds
1666 simultaneously -with high probability- for all possible number of rejections.
1667 As a special case, a lower bound for the total number of false null hypotheses
1668 can be inferred. Dependent test statistics can be handled for multiple tests
1669 of associations. For independent test statistics, it is sufficient to provide
1670 a list of p-values.")
1671 (license license:gpl2+)))
1673 (define-public r-htmltools
1675 (name "r-htmltools")
1679 (uri (cran-uri "htmltools" version))
1682 "1yv74ydyqm28gfhimmr7825sj1iaawpwsnzq05c2ma756q2dbivx"))))
1683 (build-system r-build-system)
1685 (list r-base64enc r-digest r-fastmap r-rlang))
1686 (home-page "https://cran.r-project.org/web/packages/htmltools")
1687 (synopsis "R tools for HTML")
1689 "This package provides tools for HTML generation and output in R.")
1690 (license license:expat)))
1692 (define-public r-htmlwidgets
1694 (name "r-htmlwidgets")
1698 (uri (cran-uri "htmlwidgets" version))
1701 "1hgz8sx8xrvfcdwa4q15k942w4qsqg8lyxbbf7qyfzbi807wcgqs"))))
1702 (build-system r-build-system)
1704 (list r-htmltools r-jsonlite r-yaml))
1707 (home-page "https://github.com/ramnathv/htmlwidgets")
1708 (synopsis "HTML Widgets for R")
1710 "HTML widgets is a framework for creating HTML widgets that render in
1711 various contexts including the R console, R Markdown documents, and Shiny web
1713 (license license:expat)))
1715 (define-public r-htmltable
1717 (name "r-htmltable")
1722 (uri (cran-uri "htmlTable" version))
1724 (base32 "0xx5fza40six81mkfjsja6a8j6cg1mlzg0cxfgv084riyq79l387"))))
1725 (properties `((upstream-name . "htmlTable")))
1726 (build-system r-build-system)
1737 (home-page "http://gforge.se/packages/")
1738 (synopsis "Advanced tables for Markdown/HTML")
1740 "This package provides functions to build tables with advanced layout
1741 elements such as row spanners, column spanners, table spanners, zebra
1742 striping, and more. While allowing advanced layout, the underlying
1743 CSS-structure is simple in order to maximize compatibility with word
1744 processors such as LibreOffice. The package also contains a few text
1745 formatting functions that help outputting text compatible with HTML or
1747 (license license:gpl3+)))
1749 (define-public r-curl
1755 (uri (cran-uri "curl" version))
1758 "0s55022hy8shjm1pzax1dqzrg20bv4nvlwnjnddk3dp89g5zmcch"))))
1759 (build-system r-build-system)
1762 (modify-phases %standard-phases
1763 ;; The environment variable CURL_CA_BUNDLE is only respected when
1764 ;; running Windows, so we disable the platform checks.
1765 ;; This can be removed once the libcurl has been patched.
1766 (add-after 'unpack 'allow-CURL_CA_BUNDLE
1768 (substitute* "R/onload.R"
1769 (("if \\(!grepl\\(\"mingw\".*")
1771 (substitute* "src/handle.c"
1772 (("/\\* Only set" m)
1774 const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
1775 if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
1781 (list pkg-config r-knitr))
1782 (home-page "https://github.com/jeroenooms/curl")
1783 (synopsis "HTTP client for R")
1785 "The @code{curl()} and @code{curl_download()} functions provide highly
1786 configurable drop-in replacements for base @code{url()} and
1787 @code{download.file()} with better performance, support for encryption, gzip
1788 compression, authentication, and other @code{libcurl} goodies. The core of
1789 the package implements a framework for performing fully customized requests
1790 where data can be processed either in memory, on disk, or streaming via the
1791 callback or connection interfaces.")
1792 (license license:expat)))
1794 (define-public r-hwriter
1801 (uri (cran-uri "hwriter" version))
1804 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
1805 (build-system r-build-system)
1806 (home-page "https://cran.r-project.org/web/packages/hwriter")
1807 (synopsis "Output R objects in HTML format")
1809 "This package provides easy-to-use and versatile functions to output R
1810 objects in HTML format.")
1811 (license license:lgpl2.1+)))
1813 (define-public r-rjson
1820 (uri (cran-uri "rjson" version))
1823 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
1824 (build-system r-build-system)
1825 (home-page "https://cran.r-project.org/web/packages/rjson")
1826 (synopsis "JSON library for R")
1828 "This package provides functions to convert R objects into JSON objects
1830 (license license:gpl2+)))
1832 (define-public r-fastmap
1839 (uri (cran-uri "fastmap" version))
1842 "0aw29hnq3ppn7bsnwg9d9sp84k1cvq30lrmfzqn315n0nhkfa4wi"))))
1843 (properties `((upstream-name . "fastmap")))
1844 (build-system r-build-system)
1845 (home-page "https://r-lib.github.io/fastmap/")
1846 (synopsis "Fast implementation of a key-value store")
1848 "This package provides a fast implementation of a key-value store.
1849 Environments are commonly used as key-value stores, but every time a new key
1850 is used, it is added to R's global symbol table, causing a small amount of
1851 memory leakage. This can be problematic in cases where many different keys
1852 are used. Fastmap avoids this memory leak issue by implementing the map using
1853 data structures in C++.")
1854 (license license:expat)))
1856 (define-public r-fastghquad
1858 (name "r-fastghquad")
1863 (uri (cran-uri "fastGHQuad" version))
1866 "1rjia8wggadr9xwxcmzmal0rc4g6pa3dr5888fbbnb6abl8b2lrj"))))
1867 (properties `((upstream-name . "fastGHQuad")))
1868 (build-system r-build-system)
1871 (home-page "https://github.com/awblocker/fastGHQuad")
1872 (synopsis "Fast Rcpp implementation of Gauss-Hermite Quadrature")
1874 "This package implements numerically-stable Gauss-Hermite quadrature
1875 rules and utility functions for adaptive GH quadrature.")
1876 (license license:expat)))
1878 (define-public r-rstpm2
1885 (uri (cran-uri "rstpm2" version))
1888 "0c6l3z250b2kn6mh2xyb0bd2y5nsbj11n9xfi51dac9s8xq3v7m4"))))
1889 (properties `((upstream-name . "rstpm2")))
1890 (build-system r-build-system)
1902 (home-page "https://github.com/mclements/rstpm2")
1903 (synopsis "Link-based survival models")
1905 "This package provides R implementations of @dfn{generalized survival
1906 models} (GSMs), smooth @dfn{accelerated failure time} (AFT) models and Markov
1907 multi-state models.")
1908 ;; One of these licenses
1909 (license (list license:gpl2 license:gpl3))))
1911 ;; This package includes minified JavaScript files. When upgrading please
1912 ;; check that there are no new minified JavaScript files.
1913 (define-public r-jquerylib
1915 (name "r-jquerylib")
1920 (uri (cran-uri "jquerylib" version))
1923 "04a40v4znpj98j7y6009d74a6g9dchj5rr3p08cgz9p3rlfw3g7h"))
1925 '(for-each delete-file
1926 '("inst/lib/1.12.4/jquery-1.12.4.min.js"
1927 "inst/lib/2.2.4/jquery-2.2.4.min.js"
1928 "inst/lib/3.6.0/jquery-3.6.0.min.js")))))
1929 (properties `((upstream-name . "jquerylib")))
1930 (build-system r-build-system)
1932 `(#:modules ((guix build utils)
1933 (guix build r-build-system)
1936 (modify-phases %standard-phases
1937 (add-after 'unpack 'process-javascript
1938 (lambda* (#:key inputs #:allow-other-keys)
1939 (with-directory-excursion "inst/lib/"
1943 `(("1.12.4/jquery-1.12.4.js"
1944 "1.12.4/jquery-1.12.4.min.js")
1945 ("2.2.4/jquery-2.2.4.js"
1946 "2.2.4/jquery-2.2.4.min.js")
1947 ("3.6.0/jquery-3.6.0.js"
1948 "3.6.0/jquery-3.6.0.min.js"))))
1949 (lambda (sources targets)
1950 (for-each (lambda (source target)
1951 (format #t "Processing ~a --> ~a~%"
1953 (invoke "esbuild" source "--minify"
1954 (string-append "--outfile=" target)))
1955 sources targets)))))))))
1960 (home-page "https://cran.r-project.org/package=jquerylib")
1961 (synopsis "Obtain jQuery as an HTML dependency object")
1963 "Obtain any major version of jQuery and use it in any webpage generated
1964 by htmltools (e.g. shiny, htmlwidgets, and rmarkdown). Most R users don't
1965 need to use this package directly, but other R packages (e.g. shiny,
1966 rmarkdown, etc.) depend on this package to avoid bundling redundant copies of
1968 (license license:expat)))
1970 (define-public r-sass
1977 (uri (cran-uri "sass" version))
1980 "0axw358bbk3vxsqg3wq0bz3xigasa6af8fxvi2ga8hli4cawl1kx"))))
1981 (properties `((upstream-name . "sass")))
1982 (build-system r-build-system)
1984 (list r-fs r-htmltools r-r6 r-rappdirs r-rlang))
1985 (native-inputs (list r-knitr))
1986 (home-page "https://github.com/rstudio/sass")
1987 (synopsis "Syntactically Awesome Style Sheets (SASS)")
1989 "This package provides an SCSS compiler, powered by the libsass library.
1990 With this, R developers can use variables, inheritance, and functions to
1991 generate dynamic style sheets. The package uses the Sass CSS extension
1992 language, which is stable, powerful, and CSS compatible.")
1993 (license license:expat)))
1995 ;; This package includes minified JavaScript files. When upgrading please
1996 ;; check that there are no new minified JavaScript files.
1997 (define-public r-bslib
2004 (uri (cran-uri "bslib" version))
2007 "0jcqklry1nkibz0sydsz5xdsnb4wnrrhvmyr9ji3k45bbipbap2z"))
2009 '(for-each delete-file
2010 '("inst/lib/bs-a11y-p/plugins/js/bootstrap-accessibility.min.js"
2011 "inst/lib/bs-colorpicker/js/bootstrap-colorpicker.min.js"
2012 "inst/lib/bs3/assets/javascripts/bootstrap.min.js"
2013 "inst/lib/bs4/dist/js/bootstrap.bundle.min.js"
2014 "inst/lib/bs5/dist/js/bootstrap.bundle.min.js")))))
2015 (properties `((upstream-name . "bslib")))
2016 (build-system r-build-system)
2018 `(#:modules ((guix build utils)
2019 (guix build r-build-system)
2022 (modify-phases %standard-phases
2023 (add-after 'unpack 'process-javascript
2024 (lambda* (#:key inputs #:allow-other-keys)
2025 (with-directory-excursion "inst/lib/"
2029 `(("bs-a11y-p/plugins/js/bootstrap-accessibility.js"
2030 "bs-a11y-p/plugins/js/bootstrap-accessibility.min.js")
2031 ("bs-colorpicker/js/bootstrap-colorpicker.js"
2032 "bs-colorpicker/js/bootstrap-colorpicker.min.js")
2033 ("bs3/assets/javascripts/bootstrap.js"
2034 "bs3/assets/javascripts/bootstrap.min.js")
2035 (,(assoc-ref inputs "js-bootstrap4-bundle")
2036 "bs4/dist/js/bootstrap.bundle.min.js")
2037 (,(assoc-ref inputs "js-bootstrap5-bundle")
2038 "bs5/dist/js/bootstrap.bundle.min.js"))))
2039 (lambda (sources targets)
2040 (for-each (lambda (source target)
2041 (format #t "Processing ~a --> ~a~%"
2043 (invoke "esbuild" source "--minify"
2044 (string-append "--outfile=" target)))
2045 sources targets)))))))))
2047 (list r-htmltools r-jquerylib r-jsonlite r-rlang r-sass))
2049 `(("esbuild" ,esbuild)
2050 ("js-bootstrap4-bundle"
2053 (uri "https://raw.githubusercontent.com/twbs/bootstrap/v4.6.0/dist/js/bootstrap.bundle.js")
2056 "04abvgp923w36qfqkkl2syim3bl119nwxbgials90z1jyb8jgss1"))))
2057 ("js-bootstrap5-bundle"
2060 (uri "https://raw.githubusercontent.com/twbs/bootstrap/v5.0.2/dist/js/bootstrap.bundle.js")
2063 "06vin94nqw1vzs4zrqcms8z9js9fckbj8gwyx07awm8jkjhnqfhl"))))))
2064 (home-page "https://rstudio.github.io/bslib/")
2065 (synopsis "Custom Bootstrap Sass themes for shiny and rmarkdown")
2067 "This package simplifies custom CSS styling of both shiny and rmarkdown
2068 via Bootstrap Sass. It supports both Bootstrap 3 and 4 as well as their
2069 various Bootswatch themes. An interactive widget is also provided for
2070 previewing themes in real time.")
2071 (license license:expat)))
2073 ;; This package includes minified JavaScript files. When upgrading please
2074 ;; check that there are no new minified JavaScript files.
2075 (define-public r-shiny
2083 (url "https://github.com/rstudio/shiny")
2084 (commit (string-append "v" version))))
2085 (file-name (git-file-name name version))
2088 "0wvc6jlgs41p05wbk8gahnl7sfnc4hpliyh9dbi5w52ngsg6wcr7"))
2090 '(for-each delete-file
2091 '("inst/www/shared/bootstrap/js/bootstrap.min.js"
2092 "inst/www/shared/bootstrap/accessibility/js/bootstrap-accessibility.min.js" ; TODO
2093 "inst/www/shared/datatables/js/jquery.dataTables.min.js"
2094 "inst/www/shared/datepicker/js/bootstrap-datepicker.min.js"
2095 "inst/www/shared/highlight/highlight.pack.js"
2096 "inst/www/shared/ionrangeslider/js/ion.rangeSlider.min.js"
2097 "inst/www/shared/jquery.min.js"
2098 "inst/www/shared/jqueryui/jquery-ui.min.js"
2099 "inst/www/shared/legacy/jquery.min.js"
2100 "inst/www/shared/selectize/accessibility/js/selectize-plugin-a11y.min.js"
2101 "inst/www/shared/selectize/js/selectize.min.js"
2102 "inst/www/shared/shiny.min.js"
2103 "inst/www/shared/showdown/compressed/showdown.js"
2104 "inst/www/shared/strftime/strftime-min.js")))))
2105 (build-system r-build-system)
2107 `(#:modules ((guix build r-build-system)
2108 (guix build minify-build-system)
2111 #:imported-modules (,@%r-build-system-modules
2112 (guix build minify-build-system))
2114 (modify-phases (@ (guix build r-build-system) %standard-phases)
2115 (add-after 'unpack 'replace-bundled-minified-JavaScript
2116 (lambda* (#:key inputs #:allow-other-keys)
2117 (let ((replace-file (lambda (old new)
2118 (format #t "replacing ~a with ~a\n" old new)
2119 (symlink new old))))
2120 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
2121 ;; contain just data. They are not minified code, so we don't
2123 (with-directory-excursion "inst/www/shared"
2124 (replace-file "strftime/strftime-min.js"
2125 (search-input-file inputs
2126 "/share/javascript/strftime.min.js"))
2127 (replace-file "highlight/highlight.pack.js"
2128 (search-input-file inputs
2129 "/share/javascript/highlight.min.js"))
2130 (replace-file "datatables/js/jquery.dataTables.min.js"
2131 (search-input-file inputs
2132 "/share/javascript/jquery.dataTables.min.js"))
2133 (replace-file "selectize/js/selectize.min.js"
2134 (search-input-file inputs
2135 "/share/javascript/selectize.min.js"))
2136 (for-each (match-lambda
2138 (minify source #:target target)))
2139 `(("jqueryui/jquery-ui.js" .
2140 "jqueryui/jquery-ui.min.js")
2141 ("datepicker/js/bootstrap-datepicker.js" .
2142 "datepicker/js/bootstrap-datepicker.min.js")
2143 ("ionrangeslider/js/ion.rangeSlider.js" .
2144 "ionrangeslider/js/ion.rangeSlider.min.js")
2145 ("bootstrap/js/bootstrap.js" .
2146 "bootstrap/js/bootstrap.min.js")
2147 (,(assoc-ref inputs "js-bootstrap-accessibility") .
2148 "bootstrap/accessibility/js/bootstrap-accessibility.min.js")
2153 ("legacy/jquery.js" .
2154 "legacy/jquery.min.js")
2155 ("selectize/accessibility/js/selectize-plugin-a11y.js" .
2156 "selectize/accessibility/js/selectize-plugin-a11y.min.js")
2157 ("showdown/src/showdown.js" .
2158 "showdown/compressed/showdown.js"))))))))))
2181 (list js-datatables js-selectize js-strftime js-highlight))
2183 `(("uglifyjs" ,node-uglify-js)
2184 ("gfortran" ,gfortran)
2185 ("js-bootstrap-accessibility"
2188 (uri "https://raw.githubusercontent.com/paypal/bootstrap-accessibility-plugin/\
2189 v1.0.7/_site/plugins/js/bootstrap-accessibility.js")
2192 "1489wyzwrpf86y7vhc13n4v3mszmsfybhd3f75jkpnbvyp5sncm8"))))))
2193 (home-page "https://shiny.rstudio.com")
2194 (synopsis "Easy interactive web applications with R")
2196 "Makes it incredibly easy to build interactive web applications
2197 with R. Automatic \"reactive\" binding between inputs and outputs and
2198 extensive prebuilt widgets make it possible to build beautiful,
2199 responsive, and powerful applications with minimal effort.")
2200 (license license:artistic2.0)))
2202 ;; This package includes minified JavaScript files. When upgrading please
2203 ;; check that there are no new minified JavaScript files.
2204 (define-public r-shinytree
2206 (name "r-shinytree")
2211 (uri (cran-uri "shinyTree" version))
2214 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
2215 (modules '((guix build utils)))
2218 ;; Delete minified JavaScript
2219 (for-each delete-file
2220 '("inst/www/jsTree-3.3.7/libs/require.js"
2221 "inst/www/jsTree-3.3.7/libs/jquery.js"
2222 "inst/www/jsTree-3.3.7/jstree.min.js"))
2224 (properties `((upstream-name . "shinyTree")))
2225 (build-system r-build-system)
2227 `(#:modules ((guix build utils)
2228 (guix build r-build-system)
2232 (modify-phases %standard-phases
2233 (add-after 'unpack 'replace-minified-javascript
2234 (lambda* (#:key inputs #:allow-other-keys)
2235 (with-directory-excursion "inst/www/jsTree-3.3.7/"
2236 (symlink (search-input-file inputs
2237 "/share/javascript/require.min.js")
2242 `((,(assoc-ref inputs "js-jquery")
2246 (lambda (sources targets)
2247 (for-each (lambda (source target)
2248 (format #t "Processing ~a --> ~a~%"
2250 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
2251 (call-with-output-file target
2253 (dump-port minified port)))))
2257 (list r-htmlwidgets r-jsonlite r-promises r-shiny r-stringr))
2259 (list js-requirejs))
2261 `(("uglifyjs" ,node-uglify-js)
2265 (uri "https://code.jquery.com/jquery-3.3.1.js")
2268 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
2269 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
2270 (synopsis "jsTree bindings for Shiny")
2272 "This package exposes R bindings to jsTree, a JavaScript library that
2273 supports interactive trees, to enable rich, editable trees in Shiny.")
2274 (license license:expat)))
2276 (define-public r-shinydashboard
2278 (name "r-shinydashboard")
2282 (uri (cran-uri "shinydashboard" version))
2285 "0hrqkwlpb8rnmp5j74p134g4c4cl16icmwc2ip6k1634fa2y8vm5"))))
2286 (build-system r-build-system)
2287 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
2288 ;; Regenerate it from the included sources.
2291 (modify-phases %standard-phases
2292 (add-after 'unpack 'generate-minified-javascript
2294 (with-directory-excursion "inst/AdminLTE"
2295 (let ((target "app.min.js")
2297 (format #t "Processing ~a --> ~a~%"
2299 (delete-file target)
2300 (invoke "esbuild" source "--minify"
2301 (string-append "--outfile=" target)))))))))
2303 (list r-htmltools r-promises r-shiny))
2306 (home-page "https://rstudio.github.io/shinydashboard/")
2307 (synopsis "Create dashboards with shiny")
2308 (description "This package provides an extension to the Shiny web
2309 application framework for R, making it easy to create attractive dashboards.")
2310 ;; This package includes software that was released under the Expat
2311 ;; license, but the whole package is released under GPL version 2 or
2313 (license license:gpl2+)))
2315 (define-public r-shinyfiles
2317 (name "r-shinyfiles")
2322 (uri (cran-uri "shinyFiles" version))
2324 (base32 "0f8dfdiar376lx0979ccyghgx5rhr08v5z3z60asrrjsxlq4cs85"))))
2325 (properties `((upstream-name . "shinyFiles")))
2326 (build-system r-build-system)
2328 (list r-fs r-htmltools r-jsonlite r-shiny r-tibble))
2329 (home-page "https://github.com/thomasp85/shinyFiles")
2330 (synopsis "Server-side file system viewer for Shiny")
2332 "This package provides functionality for client-side navigation of the
2333 server side file system in shiny apps. In case the app is running locally
2334 this gives the user direct access to the file system without the need to
2335 \"download\" files to a temporary location. Both file and folder selection as
2336 well as file saving is available.")
2337 (license license:gpl2+)))
2339 (define-public r-shinythemes
2341 (name "r-shinythemes")
2346 (uri (cran-uri "shinythemes" version))
2349 "0qr9bfxw8afxns44i2j4msignf6g5qb2nzpay2lpv343rrlqbmip"))))
2350 (properties `((upstream-name . "shinythemes")))
2351 (build-system r-build-system)
2352 (propagated-inputs (list r-shiny))
2353 (home-page "https://rstudio.github.io/shinythemes/")
2354 (synopsis "Themes for Shiny")
2356 "This package provides themes for use with Shiny. It includes several
2357 Bootstrap themes, which are packaged for use with Shiny applications.")
2358 ;; The package is released under version 3 of the GPL, but it includes
2359 ;; source files that are covered by the Expat license. It also includes
2360 ;; fonts under SIL or the ASL.
2361 (license (list license:gpl3 license:expat
2362 license:silofl1.1 license:asl2.0))))
2364 ;; The package sources include minified variants of d3.js and non-minified
2365 ;; source code of d3-jetpack.
2366 (define-public r-d3r
2373 (uri (cran-uri "d3r" version))
2376 "1qijkllfaaw0lb29j8mappm8jz9kg8gkihxq5wqhb4gabsazdwva"))))
2377 (build-system r-build-system)
2379 `(#:modules ((guix build utils)
2380 (guix build r-build-system)
2383 (modify-phases %standard-phases
2384 (add-after 'unpack 'process-javascript
2385 (lambda* (#:key inputs #:allow-other-keys)
2386 (with-directory-excursion "inst/www/d3/"
2390 `((,(assoc-ref inputs "d3.v3.js")
2391 "v3/dist/d3.min.js")
2392 (,(assoc-ref inputs "d3.v4.js")
2393 "v4/dist/d3.min.js")
2394 (,(assoc-ref inputs "d3.v5.js")
2395 "v5/dist/d3.min.js")
2396 (,(assoc-ref inputs "d3.v6.js")
2397 "v6/dist/d3.min.js")
2398 (,(assoc-ref inputs "d3.v7.js")
2399 "v7/dist/d3.min.js"))))
2400 (lambda (sources targets)
2401 (for-each (lambda (source target)
2402 (format #t "Processing ~a --> ~a~%"
2404 (delete-file target)
2405 (invoke "esbuild" source "--minify"
2406 (string-append "--outfile=" target)))
2407 sources targets)))))))))
2409 (list r-dplyr r-htmltools r-rlang r-tidyr))
2411 `(("esbuild" ,esbuild)
2415 (uri "https://d3js.org/d3.v3.js")
2418 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
2422 (uri "https://d3js.org/d3.v4.js")
2425 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
2429 (uri "https://d3js.org/d3.v5.js")
2432 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))
2436 (uri "https://d3js.org/d3.v6.js")
2439 "1x6432ca7p1pfxhz3airzw943fincn9izzxkclc1wmphcvv2n2p9"))))
2443 (uri "https://d3js.org/d3.v7.js")
2446 "0sd6vavxs8mx5xyb8xahlqghdiczqd284a7d5wravhqnrj0bw097"))))))
2447 (home-page "https://github.com/timelyportfolio/d3r")
2448 (synopsis "d3.js utilities for R")
2450 "This package provides a suite of functions to help ease the use of the
2451 d3.js visualization library in R. These helpers include
2452 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
2453 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
2454 R objects into the JSON format that the d3.js library expects.")
2455 (license license:bsd-3)))
2457 ;; We use the latest commit here because the last release was in 2016 while
2458 ;; the latest commit was in 2018.
2459 (define-public r-sankeyd3
2460 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
2464 (version (git-version "0.3.2" revision commit))
2469 (url "https://github.com/fbreitwieser/sankeyD3")
2471 (file-name (git-file-name name version))
2474 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
2475 (build-system r-build-system)
2477 (list r-d3r r-htmlwidgets r-shiny r-magrittr))
2478 (home-page "https://github.com/fbreitwieser/sankeyD3")
2479 (synopsis "Sankey network graphs from R")
2481 "This package provides an R library to generate Sankey network graphs
2482 in R and Shiny via the D3 visualization library.")
2483 ;; The R code is licensed under GPLv3+. It includes the non-minified
2484 ;; JavaScript source code of d3-sankey, which is released under the
2485 ;; 3-clause BSD license.
2486 (license (list license:gpl3+ license:bsd-3)))))
2488 (define-public r-wesanderson
2490 (name "r-wesanderson")
2495 (uri (cran-uri "wesanderson" version))
2498 "09mr6p2jmqdjq27cz974w5hyxgn929zp9z3inhxqmmh1582fmdi2"))))
2499 (properties `((upstream-name . "wesanderson")))
2500 (build-system r-build-system)
2501 (home-page "https://github.com/karthik/wesanderson")
2502 (synopsis "Wes Anderson color palette generator")
2504 "This package provides color palettes that have been generated mostly
2505 from Wes Anderson movies.")
2506 (license license:expat)))
2508 (define-public r-gg-gap
2515 (uri (cran-uri "gg.gap" version))
2518 "0m66050ryn31xmsmmikjsssllasvjdmp9yjbwfdwfpwdv106zn9h"))))
2519 (properties `((upstream-name . "gg.gap")))
2520 (build-system r-build-system)
2522 (list r-cowplot r-ggplot2))
2523 (home-page "https://github.com/ChrisLou-bioinfo/gg.gap")
2524 (synopsis "Define segments on the y-axis for ggplot2")
2526 "The @code{gg.gap} function enables you to define segments for the y-axis
2527 in a ggplot2 plot.")
2528 (license license:gpl3)))
2530 (define-public r-tablerdash
2532 (name "r-tablerdash")
2537 (uri (cran-uri "tablerDash" version))
2540 "1mnp6lxa7d669r325aynq1n3f35r9sy4v1fvdh4cymbf33s8mkmm"))
2543 ;; Delete minified JavaScript
2544 (for-each delete-file
2545 '("inst/tablerDash-0.1.0/require.min.js"
2546 "inst/bootstrap-4.0.0/bootstrap.bundle.min.js"))
2548 (properties `((upstream-name . "tablerDash")))
2549 (build-system r-build-system)
2551 `(#:modules ((guix build utils)
2552 (guix build r-build-system)
2555 (modify-phases %standard-phases
2556 (add-after 'unpack 'process-javascript
2557 (lambda* (#:key inputs #:allow-other-keys)
2558 (with-directory-excursion "inst"
2562 `((,(assoc-ref inputs "js-requirejs")
2563 "tablerDash-0.1.0/require.min.js")
2564 (,(assoc-ref inputs "js-bootstrap")
2565 "bootstrap-4.0.0/bootstrap.bundle.min.js"))))
2566 (lambda (sources targets)
2567 (for-each (lambda (source target)
2568 (format #t "Processing ~a --> ~a~%"
2570 (invoke "esbuild" source "--minify"
2571 (string-append "--outfile=" target)))
2575 (list r-htmltools r-knitr r-shiny))
2577 `(("esbuild" ,esbuild)
2581 (uri "https://raw.githubusercontent.com/requirejs/requirejs/2.3.5/require.js")
2584 "06w32mwqii9cx409ivda88z58qbkcdb4p6hf6jawchsgagaziyds"))))
2588 (uri "https://raw.githubusercontent.com/twbs/bootstrap/\
2589 v4.0.0/dist/js/bootstrap.bundle.js")
2592 "0cvfqffn45vfbj3fk6wmrhkyndhk4id89vgydssbbzxjkfwprfrj"))))))
2593 (home-page "https://rinterface.github.io/tablerDash/")
2594 (synopsis "Tabler API for Shiny")
2596 "This package provides an R interface to the
2597 @url{https://tabler.io,Tabler} HTML template. tablerDash is a light Bootstrap
2598 4 dashboard template. There are different layouts available such as a one
2599 page dashboard or a multi-page template, where the navigation menu is
2600 contained in the navigation bar.")
2601 (license license:gpl2+)))
2603 (define-public r-spelling
2610 (uri (cran-uri "spelling" version))
2613 "179nj9w1v27qq9q5240ddvggp0795998sxyqjvbqjvq9dmach3bl"))))
2614 (properties `((upstream-name . "spelling")))
2615 (build-system r-build-system)
2617 (list r-commonmark r-hunspell r-knitr r-xml2))
2618 (home-page "https://docs.ropensci.org/spelling/")
2619 (synopsis "Tools for spell checking in R")
2621 "This is an R package for spell checking common document formats
2622 including LaTeX, markdown, manual pages, and DESCRIPTION files. It includes
2623 utilities to automate checking of documentation and vignettes as a unit test
2624 during @code{R CMD check}. Both British and American English are supported
2625 out of the box and other languages can be added. In addition, packages may
2626 define a wordlist to allow custom terminology without having to abuse
2628 (license license:expat)))
2630 (define-public r-crosstalk
2632 (name "r-crosstalk")
2637 (uri (cran-uri "crosstalk" version))
2640 "180y7mhpj17axpadwhh7s0qvrpdnag7g977vk256l96d6nmvlds2"))))
2641 (build-system r-build-system)
2643 (list r-htmltools r-jsonlite r-lazyeval r-r6))
2644 (home-page "https://rstudio.github.io/crosstalk/")
2645 (synopsis "Inter-widget interactivity for HTML widgets")
2647 "This package provides building blocks for allowing HTML widgets to
2648 communicate with each other, with Shiny or without (i.e. static @code{.html}
2649 files). It currently supports linked brushing and filtering.")
2650 (license license:expat)))
2652 (define-public r-rook
2659 (uri (cran-uri "Rook" version))
2662 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
2663 (properties `((upstream-name . "Rook")))
2664 (build-system r-build-system)
2665 (propagated-inputs (list r-brew))
2666 (home-page "https://cran.r-project.org/web/packages/Rook")
2667 (synopsis "Web server interface for R")
2669 "This package contains the Rook specification and convenience software
2670 for building and running Rook applications. A Rook application is an R
2671 reference class object that implements a @code{call} method or an R closure
2672 that takes exactly one argument, an environment, and returns a list with three
2673 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
2674 (license license:gpl2)))
2676 (define-public r-miniui
2683 (uri (cran-uri "miniUI" version))
2686 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
2687 (properties `((upstream-name . "miniUI")))
2688 (build-system r-build-system)
2690 (list r-htmltools r-shiny))
2691 (home-page "https://cran.r-project.org/web/packages/miniUI/")
2692 (synopsis "Shiny UI widgets for small screens")
2694 "This package provides UI widget and layout functions for writing Shiny apps that
2695 work well on small screens.")
2696 (license license:gpl3)))
2698 (define-public r-feather
2705 (uri (cran-uri "feather" version))
2708 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
2709 (build-system r-build-system)
2711 (list r-hms r-rcpp r-tibble))
2712 (home-page "https://github.com/wesm/feather")
2713 (synopsis "R Bindings to the Feather API")
2714 (description "Read and write feather files, a lightweight binary columnar
2715 data store designed for maximum speed.")
2716 (license license:asl2.0)))
2718 (define-public r-maps
2725 (uri (cran-uri "maps" version))
2728 "0ispkx1szgwxhr0zzhdzgqqwcgc6psg7vry4sj4rb89w76rcq63r"))))
2729 (build-system r-build-system)
2730 (home-page "https://cran.r-project.org/web/packages/maps")
2731 (synopsis "Draw geographical maps")
2732 (description "This package provides an R module for display of maps.
2733 Projection code and larger maps are in separate packages (@code{mapproj} and
2735 (license license:gpl2)))
2737 (define-public r-mapproj
2744 (uri (cran-uri "mapproj" version))
2747 "0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h"))))
2748 (build-system r-build-system)
2749 (propagated-inputs (list r-maps))
2750 (home-page "https://cran.r-project.org/web/packages/mapproj")
2751 (synopsis "Map projection in R")
2752 (description "This package converts latitude/longitude into projected
2754 (license (list license:gpl2 ; The R interface
2755 (license:non-copyleft ; The C code
2756 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
2757 "Lucent Public License Version 1.02")))))
2759 (define-public r-rgooglemaps
2761 (name "r-rgooglemaps")
2766 (uri (cran-uri "RgoogleMaps" version))
2769 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
2770 (properties `((upstream-name . "RgoogleMaps")))
2771 (build-system r-build-system)
2774 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
2775 (synopsis "Use Google Maps in R")
2776 (description "This package serves two purposes:
2778 @item Provide a comfortable R interface to query the Google server for static
2780 @item Use the map as a background image to overlay plots within R. This
2781 requires proper coordinate scaling.
2783 (license license:gpl2+)))
2785 (define-public r-geosphere
2787 (name "r-geosphere")
2792 (uri (cran-uri "geosphere" version))
2795 "0bg4vfmrw140j2ax0p6bflvb77w03ir39wa87l96rj473jpa9hzj"))))
2796 (build-system r-build-system)
2797 (propagated-inputs (list r-sp))
2798 (home-page "https://cran.r-project.org/web/packages/geosphere")
2799 (synopsis "Spherical trigonometry")
2800 (description "This package computes spherical trigonometry for geographic
2801 applications. That is, compute distances and related measures for angular
2802 (longitude/latitude) locations.")
2803 (license license:gpl3+)))
2805 (define-public r-jpeg
2812 (uri (cran-uri "jpeg" version))
2815 "0wihj538wdnr71wdldym83qadb4kh68a6rkallwbh2f25r27b881"))))
2816 (build-system r-build-system)
2817 (inputs `(("libjpeg" ,libjpeg-turbo)))
2818 (home-page "https://www.rforge.net/jpeg/")
2819 (synopsis "Read and write JPEG images with R")
2820 (description "This package provides a way to read, write and display
2821 bitmap images stored in the JPEG format with R. It can read and write both
2822 files and in-memory raw vectors.")
2823 (license license:gpl2+)))
2825 (define-public r-ggmap
2832 (uri (cran-uri "ggmap" version))
2835 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
2836 (build-system r-build-system)
2855 (home-page "https://github.com/dkahle/ggmap")
2856 (synopsis "Spatial visualization with ggplot2")
2857 (description "This package provides a collection of functions to visualize
2858 spatial data and models on top of static maps from various online sources (e.g
2859 Google Maps and Stamen Maps). It includes tools common to those tasks,
2860 including functions for geolocation and routing.")
2861 (license license:gpl2)))
2863 (define-public r-haven
2870 (uri (cran-uri "haven" version))
2873 "0pr9jcdk1r9pi9iz0xm1g5yy5qyjk5r7hh9467abx4kpwx3hzdwm"))
2874 (modules '((guix build utils)))
2876 ;; unvendor readstat
2877 '(delete-file-recursively "src/readstat"))))
2878 (build-system r-build-system)
2881 (modify-phases %standard-phases
2882 (add-after 'unpack 'unbundle-readstat
2884 ;; Not required, since we’re not building readstat.
2885 (substitute* "src/Makevars"
2886 (("-lz") "-lreadstat")))))))
2900 (home-page "https://haven.tidyverse.org")
2901 (synopsis "Import and export SPSS, Stata and SAS files")
2903 "This package lets you import foreign statistical formats into R via the
2904 @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
2905 (license license:expat)))
2907 (define-public r-amap
2913 (uri (cran-uri "amap" version))
2916 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
2917 (build-system r-build-system)
2920 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
2921 (synopsis "Another multidimensional analysis package")
2922 (description "This package provides tools for clustering and principal
2923 component analysis (with robust methods, and parallelized functions).")
2924 (license license:gpl2+)))
2926 (define-public r-ape
2933 (uri (cran-uri "ape" version))
2936 "16i9sny7j90zi0k3znfff5lpnj5naxcy1142v73zxslr9g3h3am3"))))
2937 (build-system r-build-system)
2939 (list r-lattice r-nlme r-rcpp))
2940 (home-page "http://ape-package.ird.fr/")
2941 (synopsis "Analyses of phylogenetics and evolution")
2943 "This package provides functions for reading, writing, plotting, and
2944 manipulating phylogenetic trees, analyses of comparative data in a
2945 phylogenetic framework, ancestral character analyses, analyses of
2946 diversification and macroevolution, computing distances from DNA sequences,
2947 and several other tools.")
2948 (license license:gpl2+)))
2950 (define-public r-abbyyr
2957 (uri (cran-uri "abbyyR" version))
2960 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
2961 (properties `((upstream-name . "abbyyR")))
2962 (build-system r-build-system)
2970 (home-page "https://github.com/soodoku/abbyyR")
2971 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
2973 "This package provides tools to get text from images of text using Abbyy
2974 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
2975 OCR images, barcodes, forms, documents with machine readable zones, e.g.
2976 passports and get the results in a variety of formats including plain text and
2977 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
2978 (license license:expat)))
2980 (define-public r-colorspace
2982 (name "r-colorspace")
2987 (uri (cran-uri "colorspace" version))
2989 (base32 "0fhq2aykdkxh3r90i8aqjyb37p5api3mjd19ch8mzv99q4pcv4dq"))))
2990 (build-system r-build-system)
2993 (home-page "https://cran.r-project.org/web/packages/colorspace")
2994 (synopsis "Color space manipulation")
2996 "This package carries out a mapping between assorted color spaces
2997 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
2998 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
2999 colors are provided.")
3000 (license license:bsd-3)))
3002 (define-public r-glue
3009 (uri (cran-uri "glue" version))
3012 "1wjar579m46j1jnch34h7976sc1qbj6hzdyz5jm16nz1iw6z47jv"))))
3013 (build-system r-build-system)
3014 ;; knitr depends on glue, so we can't add knitr here to build the
3018 `(("r-knitr" ,r-knitr)))
3019 (home-page "https://github.com/tidyverse/glue")
3020 (synopsis "Interpreted string literals")
3022 "This package provides an implementation of interpreted string literals,
3023 inspired by Python's Literal String Interpolation (PEP-0498) and
3024 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
3025 (license license:expat)))
3027 (define-public r-palmerpenguins
3029 (name "r-palmerpenguins")
3034 (uri (cran-uri "palmerpenguins" version))
3037 "0q1k3cdkliq7kwrg1n0vs9b6cjwyfarhlgdijhp9c6riy6y5ik7x"))))
3039 `((upstream-name . "palmerpenguins")))
3040 (build-system r-build-system)
3041 (home-page "https://allisonhorst.github.io/palmerpenguins/")
3042 (synopsis "Palmer Archipelago (Antarctica) penguin data")
3044 "This package includes size measurements, clutch observations, and blood
3045 isotope ratios for adult foraging Adélie, Chinstrap, and Gentoo penguins
3046 observed on islands in the Palmer Archipelago near Palmer Station, Antarctica.
3047 Data were collected and made available by Dr. Kristen Gorman and the Palmer
3048 Station Long Term Ecological Research (LTER) Program.")
3049 (license license:cc0)))
3051 (define-public r-pastecs
3057 (uri (cran-uri "pastecs" version))
3060 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
3061 (build-system r-build-system)
3064 (home-page "https://github.com/phgrosjean/pastecs")
3065 (synopsis "Analysis of space-time ecological series")
3067 "This package provides functions for regulation, decomposition and analysis
3068 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
3069 initiative to bring PASSTEC 2000 functionalities to R.")
3070 (license license:gpl2+)))
3072 (define-public r-partykit
3078 (uri (cran-uri "partykit" version))
3081 "1b73s5l19yicwginqsg5xr7fzb005x372n0wb34kk6jb5x5lbsdj"))))
3082 (build-system r-build-system)
3090 (home-page "http://partykit.R-Forge.R-project.org/partykit")
3091 (synopsis "Toolkit for recursive partytioning")
3093 "This package provides a toolkit with infrastructure for representing,
3094 summarizing, and visualizing tree-structured regression and classification
3096 (license license:gpl2+)))
3098 (define-public r-plogr
3105 (uri (cran-uri "plogr" version))
3108 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
3109 (build-system r-build-system)
3110 (home-page "https://github.com/krlmlr/plogr")
3111 (synopsis "R bindings for the plog C++ logging library")
3113 "This package provides the header files for a stripped-down version of
3114 the plog header-only C++ logging library, and a method to log to R's standard
3116 (license license:expat)))
3118 (define-public r-pls
3125 (uri (cran-uri "pls" version))
3127 (base32 "1gqq8rcq6p0hs2gfzwfj690rz3pwywmnv8qzcv0wsd6aaqkskwzg"))))
3128 (build-system r-build-system)
3129 (home-page "https://mevik.net/work/software/pls.html")
3130 (synopsis "Partial Least Squares and Principal Component Regression")
3132 "The pls package implements multivariate regression methods: Partial Least
3133 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
3134 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
3137 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
3138 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
3139 @item multi-response models (or @dfn{PLS2})
3140 @item flexible cross-validation
3141 @item Jackknife variance estimates of regression coefficients
3142 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
3143 (R)MSEP, R², and correlation loadings
3144 @item formula interface, modelled after @code{lm()}, with methods for predict,
3145 print, summary, plot, update, etc.
3146 @item extraction functions for coefficients, scores, and loadings
3147 @item MSEP, RMSEP, and R² estimates
3148 @item multiplicative scatter correction (@dfn{MSC})
3150 (license license:gpl2)))
3159 (uri (cran-uri "ps" version))
3161 (base32 "0cdzjqgap108whhsilxllg12m2d05pgksryhrz5bq608bvf7vbc9"))))
3162 (build-system r-build-system)
3163 (home-page "https://ps.r-lib.org")
3164 (synopsis "List, query, and manipulate system processes")
3166 "The ps package implements an API to list, query, and manipulate system
3167 processes. Most of its code is based on the @code{psutil} Python package.")
3168 (license license:bsd-3)))
3170 (define-public r-pkgbuild
3177 (uri (cran-uri "pkgbuild" version))
3179 (base32 "0qx920h2viwjg10va81nj0xja495d8ni6vcc25ggvzki6a6k069f"))))
3180 (build-system r-build-system)
3190 (home-page "https://github.com/r-pkgs/pkgbuild")
3191 (synopsis "Find tools needed to build R packages")
3193 "This package provides functions used to build R packages. It locates
3194 compilers needed to build R packages on various platforms and ensures the PATH
3195 is configured appropriately so R can use them.")
3196 (license license:gpl3)))
3198 (define-public r-pkgload
3205 (uri (cran-uri "pkgload" version))
3208 "0jdkaj5cl0viy0i0hkcm4n2wlg1mfv3camr7f385njfararfanhh"))))
3209 (build-system r-build-system)
3218 (home-page "https://github.com/r-lib/pkgload")
3219 (synopsis "Simulate package installation and attach")
3221 "This package simulates the process of installing a package and then
3222 attaching it. This is a key part of the @code{devtools} package as it allows
3223 you to rapidly iterate while developing a package.")
3224 (license license:gpl3)))
3226 (define-public r-pvclust
3232 (uri (cran-uri "pvclust" version))
3235 "0082icm54k2yq60k06qpr92a626k39j2jr0046lva4ylmhxqb4kq"))))
3236 (build-system r-build-system)
3237 (home-page "https://github.com/shimo-lab/pvclust")
3239 "Hierarchical clustering with P-values via multiscale bootstrap resampling")
3240 (description "This package provides an implementation of multiscale bootstrap
3241 resampling for assessing the uncertainty in hierarchical cluster analysis. It
3242 provides an AU (approximately unbiased) P-value as well as a BP (bootstrap probability)
3243 value for each cluster in a dendrogram.")
3244 (license license:gpl2+)))
3246 (define-public r-rcpp
3253 (uri (cran-uri "Rcpp" version))
3255 (base32 "07fwlgmx0ib4nziqbrylla2dlakw04vzny9w4qbfvnhn49rs9r8m"))))
3256 (build-system r-build-system)
3257 (home-page "http://www.rcpp.org")
3258 (synopsis "Seamless R and C++ integration")
3260 "The Rcpp package provides R functions as well as C++ classes which offer
3261 a seamless integration of R and C++. Many R data types and objects can be
3262 mapped back and forth to C++ equivalents which facilitates both writing of new
3263 code as well as easier integration of third-party libraries. Documentation
3264 about Rcpp is provided by several vignettes included in this package, via the
3265 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
3266 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
3267 @code{citation(\"Rcpp\")} for details on these last two.")
3268 (license license:gpl2+)))
3270 (define-public r-rcppthread
3272 (name "r-rcppthread")
3277 (uri (cran-uri "RcppThread" version))
3280 "1xfcxrny779kgknlvnc4j02ifprnakndnkhx8bhy50d39vp4hjjl"))))
3281 (properties `((upstream-name . "RcppThread")))
3282 (build-system r-build-system)
3284 "https://github.com/tnagler/RcppThread")
3285 (synopsis "R threading in C++")
3287 "This package provides a C++11-style thread class and thread pool that can
3288 safely be interrupted from R.")
3289 (license license:expat)))
3291 (define-public r-rcppnumerical
3293 (name "r-rcppnumerical")
3297 (uri (cran-uri "RcppNumerical" version))
3300 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
3301 (build-system r-build-system)
3303 (list r-rcpp r-rcppeigen))
3304 (home-page "https://github.com/yixuan/RcppNumerical")
3305 (synopsis"Numerical computing libraries integration with @code{Rcpp}")
3306 (description "This package provides a collection of libraries for numerical
3307 computing (numerical integration, optimization, etc.) and their integration
3309 (license license:gpl2+)))
3311 (define-public r-bindr
3318 (uri (cran-uri "bindr" version))
3321 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
3322 (build-system r-build-system)
3323 (home-page "https://github.com/krlmlr/bindr")
3324 (synopsis "Parametrized active bindings")
3326 "This package provides a simple interface for creating active bindings
3327 where the bound function accepts additional arguments.")
3328 (license license:expat)))
3330 (define-public r-bindrcpp
3337 (uri (cran-uri "bindrcpp" version))
3340 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
3341 (build-system r-build-system)
3343 (list r-bindr r-plogr r-rcpp))
3344 (home-page "https://github.com/krlmlr/bindrcpp")
3345 (synopsis "Rcpp interface to active bindings")
3347 "This package provides an easy way to fill an environment with active
3348 bindings that call a C++ function.")
3349 (license license:expat)))
3351 (define-public r-auc
3358 (uri (cran-uri "AUC" version))
3361 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
3362 (properties `((upstream-name . "AUC")))
3363 (build-system r-build-system)
3364 (home-page "https://cran.r-project.org/web/packages/AUC")
3365 (synopsis "Compute the area under the curve of selected measures")
3367 "This package includes functions to compute the area under the curve of
3368 selected measures: the area under the sensitivity curve (AUSEC), the area
3369 under the specificity curve (AUSPC), the area under the accuracy
3370 curve (AUACC), and the area under the receiver operating characteristic
3371 curve (AUROC). The curves can also be visualized. Support for partial areas
3373 (license license:gpl2+)))
3375 (define-public r-calibrate
3377 (name "r-calibrate")
3382 (uri (cran-uri "calibrate" version))
3384 (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi"))))
3385 (build-system r-build-system)
3388 (home-page "https://cran.r-project.org/web/packages/calibrate")
3389 (synopsis "Calibration of scatterplot and biplot axes")
3391 "This is a package for drawing calibrated scales with tick marks
3392 on (non-orthogonal) variable vectors in scatterplots and biplots.")
3393 (license license:gpl2)))
3395 (define-public r-shape
3402 (uri (cran-uri "shape" version))
3405 "0yqbrrx2ywmfl99s6d1n6jblc63k1mxbiqyv8y0kq8jws1g3w45r"))))
3406 (build-system r-build-system)
3407 (home-page "https://cran.r-project.org/web/packages/shape")
3408 (synopsis "Functions for plotting graphical shapes")
3410 "This package provides functions for plotting graphical shapes such as
3411 ellipses, circles, cylinders, arrows, ...")
3412 (license license:gpl3+)))
3414 (define-public r-globaloptions
3416 (name "r-globaloptions")
3421 (uri (cran-uri "GlobalOptions" version))
3423 (base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7"))))
3424 (properties `((upstream-name . "GlobalOptions")))
3425 (build-system r-build-system)
3428 (home-page "https://github.com/jokergoo/GlobalOptions")
3429 (synopsis "Generate functions to get or set global options")
3431 "This package provides more controls on the option values such as
3432 validation and filtering on the values, making options invisible or private.")
3433 (license license:gpl2+)))
3435 (define-public r-circlize
3442 (uri (cran-uri "circlize" version))
3445 "16rnqlkgzhnm69y70k9fiz8vvwlm5dyng04hlxqvvaxix3wdpfkc"))))
3446 (build-system r-build-system)
3448 (list r-colorspace r-globaloptions r-shape))
3451 (home-page "https://github.com/jokergoo/circlize")
3452 (synopsis "Circular visualization")
3454 "Circular layout is an efficient way to visualise huge amounts of
3455 information. This package provides an implementation of circular layout
3456 generation in R as well as an enhancement of available software. Its
3457 flexibility is based on the usage of low-level graphics functions such that
3458 self-defined high-level graphics can be easily implemented by users for
3459 specific purposes. Together with the seamless connection between the powerful
3460 computational and visual environment in R, it gives users more convenience and
3461 freedom to design figures for better understanding complex patterns behind
3462 multi-dimensional data.")
3463 (license license:gpl2+)))
3465 (define-public r-powerlaw
3472 (uri (cran-uri "poweRlaw" version))
3474 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
3475 (properties `((upstream-name . "poweRlaw")))
3476 (build-system r-build-system)
3481 (home-page "https://github.com/csgillespie/poweRlaw")
3482 (synopsis "Tools for the analysis of heavy tailed distributions")
3484 "This package provides an implementation of maximum likelihood estimators
3485 for a variety of heavy tailed distributions, including both the discrete and
3486 continuous power law distributions. Additionally, a goodness-of-fit based
3487 approach is used to estimate the lower cut-off for the scaling region.")
3488 ;; Any of these GPL versions.
3489 (license (list license:gpl2 license:gpl3))))
3491 (define-public r-compare
3498 (uri (cran-uri "compare" version))
3501 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
3502 (build-system r-build-system)
3503 (home-page "https://cran.r-project.org/web/packages/compare")
3504 (synopsis "Comparing objects for differences")
3506 "This package provides functions to compare a model object to a
3507 comparison object. If the objects are not identical, the functions can be
3508 instructed to explore various modifications of the objects (e.g., sorting
3509 rows, dropping names) to see if the modified versions are identical.")
3510 (license license:gpl2+)))
3512 (define-public r-dendextend
3514 (name "r-dendextend")
3519 (uri (cran-uri "dendextend" version))
3522 "06wjs8451hmnimzgngpzbai3yrgy33133vzzapa8jib9crdqi8sb"))))
3523 (build-system r-build-system)
3525 (list r-ggplot2 r-magrittr r-viridis))
3528 (home-page "https://cran.r-project.org/web/packages/dendextend")
3529 (synopsis "Extending 'dendrogram' functionality in R")
3531 "This package offers a set of functions for extending @code{dendrogram}
3532 objects in R, letting you visualize and compare trees of hierarchical
3533 clusterings. You can adjust a tree's graphical parameters (the color, size,
3534 type, etc of its branches, nodes and labels) and visually and statistically
3535 compare different dendrograms to one another.")
3536 ;; Any of these versions
3537 (license (list license:gpl2 license:gpl3))))
3539 (define-public r-getoptlong
3541 (name "r-getoptlong")
3546 (uri (cran-uri "GetoptLong" version))
3549 "00fpm6nd3kqa2ikasxa62jzywi46fvvmx1mdavcp5yrxxn37j8wc"))))
3550 (properties `((upstream-name . "GetoptLong")))
3551 (build-system r-build-system)
3555 (list r-crayon r-globaloptions r-rjson))
3558 (home-page "https://github.com/jokergoo/GetoptLong")
3559 (synopsis "Parsing command-line arguments and variable interpolation")
3561 "This is yet another command-line argument parser which wraps the
3562 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
3563 use in R. It also provides a simple way for variable interpolation in R.")
3564 (license license:gpl2+)))
3566 (define-public r-fastmatch
3568 (name "r-fastmatch")
3573 (uri (cran-uri "fastmatch" version))
3576 "0qcq1gwl9pijgp34giyq5y9rk0ly3d7xza2b7r68xx63ifqa1vqx"))))
3577 (build-system r-build-system)
3578 (home-page "https://www.rforge.net/fastmatch")
3579 (synopsis "Fast match function")
3581 "This package provides a fast @code{match} replacement for cases that
3582 require repeated look-ups. It is slightly faster that R's built-in
3583 @code{match} function on first match against a table, but extremely fast on
3584 any subsequent lookup as it keeps the hash table in memory.")
3585 (license license:gpl2)))
3594 (uri (cran-uri "ff" version))
3597 "0dsh6llfdz04w94xr3yl2b4vkk9g3rwhvfnxcd025v2424krxfls"))))
3598 (build-system r-build-system)
3599 (propagated-inputs (list r-bit))
3600 (home-page "http://ff.r-forge.r-project.org/")
3601 (synopsis "Memory-efficient storage of large data on disk and access functions")
3603 "This package provides data structures that are stored on disk but
3604 behave (almost) as if they were in RAM by transparently mapping only a section
3606 ;; error Architecture not supported.
3607 (supported-systems (delete "aarch64-linux" %supported-systems))
3608 (license license:gpl2)))
3610 (define-public r-ffbase
3617 (uri (cran-uri "ffbase" version))
3620 "1dp6lblfq2j7r1b4b8ls47jlx8j27n88d5vp8w116lb8pa01zxmk"))))
3621 (build-system r-build-system)
3623 (list r-bit r-fastmatch r-ff))
3624 (home-page "https://github.com/edwindj/ffbase")
3625 (synopsis "Basic statistical functions for package 'ff'")
3627 "This package extends the out of memory vectors of @code{ff} with
3628 statistical functions and other utilities to ease their usage.")
3629 (license license:gpl3)))
3631 (define-public r-prettyunits
3633 (name "r-prettyunits")
3638 (uri (cran-uri "prettyunits" version))
3641 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
3642 (build-system r-build-system)
3643 (home-page "https://github.com/gaborcsardi/prettyunits")
3644 (synopsis "Pretty, human readable formatting of quantities")
3646 "This package provides tools for pretty, human readable formatting of
3648 (license license:expat)))
3650 (define-public r-princurve
3652 (name "r-princurve")
3656 (uri (cran-uri "princurve" version))
3659 "0wzk329bxljkzz57y220lsfckpsn45w348m6dcxh29zbj0ik65h2"))))
3660 (build-system r-build-system)
3663 (home-page "https://github.com/rcannood/princurve")
3664 (synopsis "Fit a principal curve in arbitrary dimension")
3665 (description "This package provides procedures for fitting a principal
3666 curve to a data matrix in arbitrary dimensions.")
3667 (license license:gpl2)))
3669 (define-public r-reshape
3676 (uri (cran-uri "reshape" version))
3679 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
3680 (build-system r-build-system)
3682 (list r-plyr r-rcpp))
3683 (home-page "http://had.co.nz/reshape")
3684 (synopsis "Flexibly reshape data")
3686 "Flexibly restructure and aggregate data using just two functions:
3687 @code{melt} and @code{cast}. This package provides them.")
3688 (license license:expat)))
3690 (define-public r-restrserve
3692 (name "r-restrserve")
3697 (uri (cran-uri "RestRserve" version))
3699 (base32 "1486hrzj5q5w4nbrsbqlv7vv20ly01y90qc2vygl5syzwvyjd422"))))
3700 (build-system r-build-system)
3711 (home-page "https://restrserve.org")
3712 (synopsis "R web API framework")
3714 "RestRserve is an R web API framework for building high-performance AND
3715 robust microservices and app backends. With Rserve backend on UNIX-like
3716 systems it is parallel by design. It will handle incoming requests in
3717 parallel - each request in a separate fork.")
3718 (license license:gpl2+)))
3720 (define-public r-progress
3727 (uri (cran-uri "progress" version))
3730 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
3731 (build-system r-build-system)
3733 (list r-crayon r-hms r-prettyunits r-r6))
3734 (home-page "https://github.com/gaborcsardi/progress")
3735 (synopsis "Terminal progress bars")
3737 "This package provides configurable progress bars. They may include
3738 percentage, elapsed time, and/or the estimated completion time. They work in
3739 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
3740 package also provides a C++ API, that works with or without Rcpp.")
3741 (license license:expat)))
3743 (define-public r-ggally
3750 (uri (cran-uri "GGally" version))
3753 "1r98zgh2grn8330cf26r1c20gl131zm778szvn5wj6q6pwv2yd9h"))))
3754 (properties `((upstream-name . "GGally")))
3755 (build-system r-build-system)
3771 (home-page "https://ggobi.github.io/ggally")
3772 (synopsis "Extension to ggplot2")
3774 "The R package ggplot2 is a plotting system based on the grammar of
3775 graphics. GGally extends ggplot2 by adding several functions to reduce the
3776 complexity of combining geometric objects with transformed data. Some of
3777 these functions include a pairwise plot matrix, a two group pairwise plot
3778 matrix, a parallel coordinates plot, a survival plot, and several functions to
3780 (license license:gpl2+)))
3782 (define-public r-proxy
3789 (uri (cran-uri "proxy" version))
3792 "0k8sr24mjfvxp12sf1j9228ah3ngy15nqmm0jw14x5s32f1assv7"))))
3793 (build-system r-build-system)
3794 (home-page "https://cran.r-project.org/web/packages/proxy")
3795 (synopsis "Distance and similarity measures")
3797 "This package provides an extensible framework for the efficient
3798 calculation of auto- and cross-proximities, along with implementations of the
3799 most popular ones.")
3800 (license license:gpl2)))
3809 (uri (cran-uri "sp" version))
3811 (base32 "09m2ddbrbs2aqnq5si42ipa0g1vbd0pxg4zbcx59is2047pv7sws"))))
3812 (build-system r-build-system)
3817 (home-page "https://cran.r-project.org/web/packages/sp")
3818 (synopsis "Classes and methods for spatial data")
3820 "This package provides classes and methods for spatial data; the classes
3821 document where the spatial location information resides, for 2D or 3D data.
3822 Utility functions are provided, e.g. for plotting data as maps, spatial
3823 selection, as well as methods for retrieving coordinates, for subsetting,
3824 print, summary, etc.")
3825 (license license:gpl2+)))
3827 (define-public r-laplacesdemon
3829 (name "r-laplacesdemon")
3834 (uri (cran-uri "LaplacesDemon" version))
3836 (base32 "1dsfp65cg06f25zjzd5ib4qyn1alfhbhpgyvpcw5n6bszn13idap"))))
3837 (properties `((upstream-name . "LaplacesDemon")))
3838 (build-system r-build-system)
3839 (home-page "https://github.com/LaplacesDemonR/LaplacesDemon")
3840 (synopsis "Complete environment for Bayesian inference")
3842 "This package provides a complete environment for Bayesian inference using
3843 a variety of different samplers.")
3844 (license license:expat)))
3846 (define-public r-rmtstat
3853 (uri (cran-uri "RMTstat" version))
3856 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
3857 (properties `((upstream-name . "RMTstat")))
3858 (build-system r-build-system)
3859 (home-page "https://cran.r-project.org/web/packages/RMTstat")
3860 (synopsis "Distributions, statistics and tests derived from random matrix theory")
3862 "This package provides functions for working with the Tracy-Widom laws
3863 and other distributions related to the eigenvalues of large Wishart
3865 (license license:bsd-3)))
3867 (define-public r-rmpi
3873 (uri (cran-uri "Rmpi" version))
3876 "06mxqgrimhfsag5giv810c7ycdbaycqs4qcj41pnfbj0jypw32im"))))
3877 (properties `((upstream-name . "Rmpi")))
3878 (build-system r-build-system)
3880 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
3881 #:phases (modify-phases %standard-phases
3882 (add-before 'install 'mpi-setup
3888 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
3889 (synopsis "R interface to message-passing interface (MPI)")
3891 "This package provides an interface (wrapper) to MPI APIs. It also
3892 provides an interactive R manager and worker environment.")
3893 (license license:gpl2+)))
3895 (define-public r-lmoments
3902 (uri (cran-uri "Lmoments" version))
3905 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
3906 (properties `((upstream-name . "Lmoments")))
3907 (build-system r-build-system)
3909 (list r-rcpp r-rcpparmadillo))
3910 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
3911 (synopsis "L-moments and quantile mixtures")
3913 "This package contains functions to estimate L-moments and trimmed
3914 L-moments from the data. It also contains functions to estimate the
3915 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
3916 quantile mixture from L-moments and trimmed L-moments.")
3917 (license license:gpl2)))
3919 (define-public r-distillery
3921 (name "r-distillery")
3926 (uri (cran-uri "distillery" version))
3929 "1ymmxyamkq0zbz2m4gllln1ihks2hcib6gs0mls92as79srz122b"))))
3930 (build-system r-build-system)
3931 (home-page "https://ral.ucar.edu/staff/ericg/")
3932 (synopsis "Functions for confidence intervals and object information")
3934 "This package provides some very simple method functions for confidence
3935 interval calculation and to distill pertinent information from a potentially
3936 complex object; primarily used in common with the packages extRemes and
3938 (license license:gpl2+)))
3940 (define-public r-etrunct
3946 (uri (cran-uri "etrunct" version))
3949 "0ayazgyqlc8jcqr03cwfmfhm4pck6xri1r6vkgqy4arqkrrnrcqr"))))
3950 (properties `((upstream-name . "etrunct")))
3951 (build-system r-build-system)
3952 (home-page "https://cran.r-project.org/web/packages/etrunct")
3953 (synopsis "Computes moments of univariate truncated T distribution")
3954 (description "This package computes moments of univariate truncated
3955 T distribution. There is only one exported function, @code{e_trunct},
3956 which should be seen for details.")
3957 (license license:expat)))
3959 (define-public r-extremes
3966 (uri (cran-uri "extRemes" version))
3969 "00ps7yggp89sx1j0w6c8dk0la3k95rwjv1iz7rdfqy7i46xjf6as"))))
3970 (properties `((upstream-name . "extRemes")))
3971 (build-system r-build-system)
3973 (list r-distillery r-lmoments))
3974 (home-page "https://www.assessment.ucar.edu/toolkit/")
3975 (synopsis "Extreme value analysis")
3977 "ExtRemes is a suite of functions for carrying out analyses on the
3978 extreme values of a process of interest; be they block maxima over long blocks
3979 or excesses over a high threshold.")
3980 (license license:gpl2+)))
3982 (define-public r-lmtest
3989 (uri (cran-uri "lmtest" version))
3992 "126l0y7j2iy6g1w4zii1qkfcjq6wrnc3w2li0bz376smpryddy3i"))))
3993 (build-system r-build-system)
3998 (home-page "https://cran.r-project.org/web/packages/lmtest")
3999 (synopsis "Testing linear regression models")
4001 "This package provides a collection of tests, data sets, and examples for
4002 diagnostic checking in linear regression models. Furthermore, some generic
4003 tools for inference in parametric models are provided.")
4004 ;; Either version is okay
4005 (license (list license:gpl2 license:gpl3))))
4007 (define-public r-idr
4013 (uri (cran-uri "idr" version))
4016 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
4017 (build-system r-build-system)
4018 (home-page "https://cran.r-project.org/web/packages/idr/")
4019 (synopsis "Irreproducible discovery rate")
4021 "This is a package for estimating the copula mixture model and plotting
4022 correspondence curves in \"Measuring reproducibility of high-throughput
4023 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
4024 by Li, Brown, Huang, and Bickel")
4025 (license license:gpl2+)))
4027 (define-public r-inline
4033 (uri (cran-uri "inline" version))
4036 "1mcr9hgq6kkq03n7pkcccxa7vg8jma0q7lfxc5vvkc6snydk1s8f"))))
4037 (build-system r-build-system)
4038 (home-page "https://cran.r-project.org/web/packages/inline")
4039 (synopsis "Functions to inline C, C++, Fortran function calls from R")
4041 "This package provides functionality to dynamically define R functions
4042 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
4043 @code{.Call} calling conventions.")
4044 ;; Any version of the LGPL.
4045 (license license:lgpl3+)))
4047 (define-public r-inum
4053 (uri (cran-uri "inum" version))
4056 "1khkzja8lwn9075864vbyajqina9m588ahf1fsrrajrsqilyzssz"))))
4057 (build-system r-build-system)
4060 (home-page "https://cran.r-project.org/web/packages/inum/")
4061 (synopsis "Interval and enum-type representation of vectors")
4063 "This package provides an enum-type representation of vectors and
4064 representation of intervals, including a method of coercing variables
4066 (license license:gpl2)))
4067 (define-public r-invgamma
4073 (uri (cran-uri "invgamma" version))
4076 "12ga2y4wc9bc5zz6vimvxwgjpsx3ys3209nq63gscbw559ydxa5a"))))
4077 (properties `((upstream-name . "invgamma")))
4078 (build-system r-build-system)
4079 (home-page "https://github.com/dkahle/invgamma")
4080 (synopsis "Inverse gamma distribution")
4081 (description "This package provides a light weight implementation of the
4082 standard distribution functions for the inverse gamma distribution, wrapping
4083 those for the gamma distribution in the @code{stats} package.")
4084 (license license:gpl2)))
4086 (define-public r-bdsmatrix
4088 (name "r-bdsmatrix")
4093 (uri (cran-uri "bdsmatrix" version))
4096 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
4097 (properties `((upstream-name . "bdsmatrix")))
4098 (build-system r-build-system)
4099 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
4100 (synopsis "Routines for block diagonal symmetric matrices")
4102 "This package provides procedures to work with block diagonal symmetric
4103 matrices, a special case of sparse matrices.")
4104 (license license:lgpl2.0)))
4106 (define-public r-bbmle
4113 (uri (cran-uri "bbmle" version))
4116 "1bck8rmink4wsk8pcbnj4d60svxymp29pxbzwj8p9gzsg42c1v81"))))
4117 (build-system r-build-system)
4127 (home-page "https://cran.r-project.org/web/packages/bbmle")
4128 (synopsis "Tools for General Maximum Likelihood Estimation")
4130 "This package provides methods and functions for fitting maximum
4131 likelihood models in R. This package modifies and extends the @code{mle}
4132 classes in the @code{stats4} package.")
4133 ;; Any version of the GPL
4134 (license license:gpl2+)))
4136 (define-public r-emdbook
4143 (uri (cran-uri "emdbook" version))
4146 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
4147 (build-system r-build-system)
4149 (list r-bbmle r-coda r-lattice r-mass r-plyr))
4150 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
4151 (synopsis "Support functions and data for \"Ecological Models and Data\"")
4153 "This package provides auxiliary functions and data sets for \"Ecological
4154 Models and Data\", a book presenting maximum likelihood estimation and related
4155 topics for ecologists (ISBN 978-0-691-12522-0).")
4157 (license (list license:gpl2 license:gpl3))))
4159 (define-public r-lpsolve
4166 (uri (cran-uri "lpSolve" version))
4169 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
4170 (properties `((upstream-name . "lpSolve")))
4171 (build-system r-build-system)
4172 (home-page "https://cran.r-project.org/web/packages/lpSolve")
4173 (synopsis "R interface to Lp_solve to solve linear/integer programs")
4175 "Lp_solve is software for solving linear, integer and mixed integer
4176 programs. This implementation supplies a \"wrapper\" function in C and some R
4177 functions that solve general linear/integer problems, assignment problems, and
4178 transportation problems.")
4179 (license license:lgpl2.0)))
4181 (define-public r-limsolve
4188 (uri (cran-uri "limSolve" version))
4191 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
4192 (properties `((upstream-name . "limSolve")))
4193 (build-system r-build-system)
4195 (list r-lpsolve r-mass r-quadprog))
4196 (native-inputs (list gfortran))
4197 (home-page "https://cran.r-project.org/web/packages/limSolve")
4198 (synopsis "Solving linear inverse models")
4200 "This package provides functions that:
4203 @item find the minimum/maximum of a linear or quadratic function,
4204 @item sample an underdetermined or overdetermined system,
4205 @item solve a linear system Ax=B for the unknown x.
4208 It includes banded and tridiagonal linear systems. The package calls Fortran
4209 functions from LINPACK.")
4211 (license (list license:gpl2+ license:gpl3+))))
4213 (define-public r-fitdistrplus
4215 (name "r-fitdistrplus")
4220 (uri (cran-uri "fitdistrplus" version))
4223 "1glnbcm1gghzgvzpxcfsmn7dp2f9jqyx39n3ydwp9fx38409khhp"))))
4224 (build-system r-build-system)
4226 (list r-mass r-survival))
4229 (home-page "http://riskassessment.r-forge.r-project.org")
4230 (synopsis "Fitting a parametric distribution from data")
4232 "This package extends the @code{fitdistr} function of the MASS package
4233 with several functions to help the fit of a parametric distribution to
4234 non-censored or censored data. Censored data may contain left-censored,
4235 right-censored and interval-censored values, with several lower and upper
4236 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
4237 provides moment matching (MME), quantile matching (QME) and maximum
4238 goodness-of-fit estimation (MGE) methods (available only for non-censored
4239 data). Weighted versions of MLE, MME and QME are available.")
4240 (license license:gpl2+)))
4242 (define-public r-energy
4249 (uri (cran-uri "energy" version))
4252 "12a7gy681aq3l55iys044cs6sn1s2l5qihghpdl01cvv0ggfh26y"))))
4253 (build-system r-build-system)
4255 (list r-boot r-gsl r-rcpp))
4256 (home-page "https://cran.r-project.org/web/packages/energy")
4257 (synopsis "Multivariate inference via the energy of data")
4259 "This package provides e-statistics (energy) tests and statistics for
4260 multivariate and univariate inference, including distance correlation,
4261 one-sample, two-sample, and multi-sample tests for comparing multivariate
4262 distributions, are implemented. Measuring and testing multivariate
4263 independence based on distance correlation, partial distance correlation,
4264 multivariate goodness-of-fit tests, clustering based on energy distance,
4265 testing for multivariate normality, distance components (disco) for
4266 non-parametric analysis of structured data, and other energy
4267 statistics/methods are implemented.")
4268 (license license:gpl2+)))
4270 (define-public r-suppdists
4272 (name "r-suppdists")
4277 (uri (cran-uri "SuppDists" version))
4280 "1i3iq12a5x5k49ac01mikzcrrq9gc148xq3m08h4xm07bha6f2v8"))))
4281 (properties `((upstream-name . "SuppDists")))
4282 (build-system r-build-system)
4283 (home-page "https://cran.r-project.org/web/packages/SuppDists")
4284 (synopsis "Supplementary distributions")
4286 "This package provides ten distributions supplementing those built into
4287 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
4288 Spearman's rho, maximum F ratio, the Pearson product moment correlation
4289 coefficient, Johnson distributions, normal scores and generalized
4290 hypergeometric distributions. In addition two random number generators of
4291 George Marsaglia are included.")
4292 (license license:gpl2+)))
4294 (define-public r-ksamples
4301 (uri (cran-uri "kSamples" version))
4304 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
4305 (properties `((upstream-name . "kSamples")))
4306 (build-system r-build-system)
4309 (home-page "https://cran.r-project.org/web/packages/kSamples")
4310 (synopsis "K-Sample rank tests and their combinations")
4312 "This package provides tools to compares k samples using the
4313 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
4314 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
4315 test. It computes asymptotic, simulated or (limited) exact P-values, all
4316 valid under randomization, with or without ties, or conditionally under random
4317 sampling from populations, given the observed tie pattern. Except for Steel's
4318 test and the JT test it also combines these tests across several blocks of
4320 (license license:gpl2+)))
4322 (define-public r-cvst
4329 (uri (cran-uri "CVST" version))
4332 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
4333 (properties `((upstream-name . "CVST")))
4334 (build-system r-build-system)
4336 (list r-kernlab r-matrix))
4337 (home-page "https://cran.r-project.org/web/packages/CVST")
4338 (synopsis "Fast cross-validation via sequential testing")
4340 "This package implements the fast cross-validation via sequential
4341 testing (CVST) procedure. CVST is an improved cross-validation procedure
4342 which uses non-parametric testing coupled with sequential analysis to
4343 determine the best parameter set on linearly increasing subsets of the data.
4344 Additionally to the CVST the package contains an implementation of the
4345 ordinary k-fold cross-validation with a flexible and powerful set of helper
4346 objects and methods to handle the overall model selection process. The
4347 implementations of the Cochran's Q test with permutations and the sequential
4348 testing framework of Wald are generic and can therefore also be used in other
4350 (license license:gpl2+)))
4352 (define-public r-squarem
4359 (uri (cran-uri "SQUAREM" version))
4362 "0n1s32l9p4vdm3h5q6g43s0qbpzry08difsh0yay80wrla6f3rb6"))))
4363 (properties `((upstream-name . "SQUAREM")))
4364 (build-system r-build-system)
4365 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
4366 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
4368 "This package provides algorithms for accelerating the convergence of
4369 slow, monotone sequences from smooth, contraction mapping such as the EM
4370 algorithm. It can be used to accelerate any smooth, linearly convergent
4371 acceleration scheme. A tutorial style introduction to this package is
4372 available in a vignette.")
4373 (license license:gpl2+)))
4375 (define-public r-progressr
4377 (name "r-progressr")
4382 (uri (cran-uri "progressr" version))
4384 (base32 "03sk5cv8cywahlszjkd8pfqmhbj6cv0j54d3lassa7h44f20zryg"))))
4385 (properties `((upstream-name . "progressr")))
4386 (build-system r-build-system)
4389 (home-page "https://progressr.futureverse.org")
4390 (synopsis "Inclusive, unifying API for progress updates")
4392 "This package provides a minimal, unifying API for scripts and packages
4393 to report progress updates from anywhere including when using parallel
4394 processing. The package is designed such that the developer can to focus on
4395 what progress should be reported on without having to worry about how to
4396 present it. The end user has full control of how, where, and when to render
4397 these progress updates.")
4398 (license license:gpl3+)))
4400 (define-public r-lava
4407 (uri (cran-uri "lava" version))
4410 "0bi3c1aqwlq7jbz4raz6vga4r264w7lldi0i62xjlbl7hnlgi23s"))))
4411 (build-system r-build-system)
4413 (list r-future-apply r-numderiv r-progressr r-squarem r-survival))
4416 (home-page "https://github.com/kkholst/lava")
4417 (synopsis "Latent variable models")
4419 "This package provides tools for the estimation and simulation of latent
4421 (license license:gpl3)))
4423 (define-public r-drr
4430 (uri (cran-uri "DRR" version))
4433 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
4434 (properties `((upstream-name . "DRR")))
4435 (build-system r-build-system)
4437 (list r-cvst r-kernlab r-matrix))
4438 (home-page "https://cran.r-project.org/web/packages/DRR")
4439 (synopsis "Dimensionality reduction via regression")
4441 "This package provides an implementation of dimensionality reduction via
4442 regression using Kernel Ridge Regression.")
4443 (license license:gpl3)))
4445 (define-public r-prodlim
4448 (version "2019.11.13")
4452 (uri (cran-uri "prodlim" version))
4455 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
4456 (build-system r-build-system)
4458 (list r-kernsmooth r-lava r-rcpp r-survival))
4459 (home-page "https://cran.r-project.org/web/packages/prodlim")
4460 (synopsis "Product-limit estimation for censored event history analysis")
4462 "This package provides a fast and user-friendly implementation of
4463 nonparametric estimators for censored event history (survival) analysis with
4464 the Kaplan-Meier and Aalen-Johansen methods.")
4465 (license license:gpl2+)))
4467 (define-public r-dimred
4474 (uri (cran-uri "dimRed" version))
4477 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
4478 (properties `((upstream-name . "dimRed")))
4479 (build-system r-build-system)
4481 (list r-drr r-magrittr))
4482 (home-page "https://github.com/gdkrmr/dimRed")
4483 (synopsis "Framework for dimensionality reduction")
4485 "This package provides a collection of dimensionality reduction
4486 techniques from R packages and provides a common interface for calling the
4488 (license license:gpl3)))
4490 (define-public r-timedate
4493 (version "3043.102")
4497 (uri (cran-uri "timeDate" version))
4500 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
4501 (properties `((upstream-name . "timeDate")))
4502 (build-system r-build-system)
4503 (home-page "https://www.rmetrics.org")
4504 (synopsis "Chronological and calendar objects")
4506 "This package provides an environment for teaching \"Financial
4507 Engineering and Computational Finance\" and for managing chronological and
4509 (license license:gpl2+)))
4511 (define-public r-magic
4518 (uri (cran-uri "magic" version))
4521 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
4522 (build-system r-build-system)
4525 (home-page "https://github.com/RobinHankin/magic.git")
4526 (synopsis "Create and investigate magic squares")
4528 "This package provides a collection of efficient, vectorized algorithms
4529 for the creation and investigation of magic squares and hypercubes, including
4530 a variety of functions for the manipulation and analysis of arbitrarily
4531 dimensioned arrays.")
4532 (license license:gpl2)))
4534 (define-public r-rmysql
4541 (uri (cran-uri "RMySQL" version))
4544 "05hiwqakhz11kra24yyxrss8b8n32wg7k39j7hwdnvhh1n96scnl"))))
4545 (properties `((upstream-name . "RMySQL")))
4546 (build-system r-build-system)
4548 `(("mariadb-dev" ,mariadb "dev")
4552 (home-page "https://github.com/r-dbi/RMySQL")
4553 (synopsis "Database interface and MySQL driver for R")
4555 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
4556 package contains an old implementation based on legacy code from S-PLUS which
4557 is being phased out. A modern MySQL client based on Rcpp is available from
4558 the RMariaDB package.")
4559 (license license:gpl2)))
4561 (define-public r-rpostgresql
4563 (name "r-rpostgresql")
4568 (uri (cran-uri "RPostgreSQL" version))
4571 "1fbixmnjp1kh6yiv8zhg8zi5ryvdf5j2jxv4agq5gcxf541s3g5x"))))
4572 (properties `((upstream-name . "RPostgreSQL")))
4573 (build-system r-build-system)
4578 (home-page "https://github.com/tomoakin/RPostgreSQL")
4579 (synopsis "R interface to the PostgreSQL database system")
4581 "This package provides a Database Interface (DBI) compliant driver for R
4582 to access PostgreSQL database systems.")
4583 ;; The whole package is released under GPL version 2. It includes code
4584 ;; under the PostgreSQL license.
4585 (license license:gpl2)))
4587 (define-public r-linprog
4594 (uri (cran-uri "linprog" version))
4597 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
4598 (build-system r-build-system)
4599 (propagated-inputs (list r-lpsolve))
4600 (home-page "http://linprog.r-forge.r-project.org/")
4601 (synopsis "Linear programming and optimization")
4603 "This package can be used to solve Linear Programming / Linear
4604 Optimization problems by using the simplex algorithm.")
4605 (license license:gpl2+)))
4607 (define-public r-geometry
4614 (uri (cran-uri "geometry" version))
4617 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
4618 (build-system r-build-system)
4620 (list r-magic r-linprog r-lpsolve r-rcpp r-rcppprogress))
4621 (home-page "http://geometry.r-forge.r-project.org/")
4622 (synopsis "Mesh generator and surface tessellator")
4624 "This package makes the qhull library available in R, in a similar manner
4625 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
4626 intersections about a point, Voronoi diagrams, furthest-site Delaunay
4627 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
4628 and higher dimensions. It implements the Quickhull algorithm for computing
4629 the convex hull. Qhull does not support constrained Delaunay triangulations,
4630 or mesh generation of non-convex objects, but the package does include some R
4631 functions that allow for this. Currently the package only gives access to
4632 Delaunay triangulation and convex hull computation.")
4633 ;; The Qhull sources are included and are distributed under a custom
4634 ;; non-copyleft license. The R sources are released under GPL version 2.
4635 (license (list license:gpl2
4636 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
4638 (define-public r-ddalpha
4645 (uri (cran-uri "ddalpha" version))
4648 "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3"))))
4649 (build-system r-build-system)
4660 (home-page "https://cran.r-project.org/web/packages/ddalpha")
4661 (synopsis "Depth-Based classification and calculation of data depth")
4663 "This package contains procedures for depth-based supervised learning,
4664 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
4665 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
4666 statistical depth function to a compact low-dimensional space, where the final
4667 classification is done. It also offers an extension to functional data and
4668 routines for calculating certain notions of statistical depth functions. 50
4669 multivariate and 5 functional classification problems are included.")
4670 (license license:gpl2)))
4672 (define-public r-gower
4679 (uri (cran-uri "gower" version))
4682 "0c9n921wn4hhlvjq96r4nkk96s5788376cbldr7y7bwz348200iz"))))
4683 (build-system r-build-system)
4684 (home-page "https://github.com/markvanderloo/gower")
4685 (synopsis "Gower's distance")
4687 "This package provides tools to compute Gower's distance (or similarity)
4688 coefficient between records, and to compute the top-n matches between records.
4689 Core algorithms are executed in parallel on systems supporting OpenMP.")
4690 (license license:gpl3)))
4692 (define-public r-rcpproll
4699 (uri (cran-uri "RcppRoll" version))
4702 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
4703 (properties `((upstream-name . "RcppRoll")))
4704 (build-system r-build-system)
4707 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
4708 (synopsis "Efficient rolling and windowed operations")
4710 "This package provides fast and efficient routines for common rolling /
4711 windowed operations. Routines for the efficient computation of windowed mean,
4712 median, sum, product, minimum, maximum, standard deviation and variance are
4714 (license license:gpl2+)))
4716 (define-public r-ipred
4723 (uri (cran-uri "ipred" version))
4726 "0hsq00382pfd9hzpcgphjxazbxm4zx0k2r6pk6kib56k0ibm7qfn"))))
4727 (build-system r-build-system)
4735 (home-page "https://cran.r-project.org/web/packages/ipred")
4736 (synopsis "Improved predictors")
4738 "This package provides improved predictive models by indirect
4739 classification and bagging for classification, regression and survival
4740 problems as well as resampling based estimators of prediction error.")
4741 (license license:gpl2+)))
4743 (define-public r-psych
4750 (uri (cran-uri "psych" version))
4753 "032h33i2qlwsw2iq82nri5y8hs7d593w40aghcvnibpi2wxf0x8l"))))
4754 (build-system r-build-system)
4756 (list r-lattice r-mnormt r-nlme))
4759 (home-page "https://cran.r-project.org/web/packages/psych/")
4760 (synopsis "Procedures for psychological, psychometric, and personality research")
4762 "This package provides a general purpose toolbox for personality,
4763 psychometric theory and experimental psychology. Functions are primarily for
4764 multivariate analysis and scale construction using factor analysis, principal
4765 component analysis, cluster analysis and reliability analysis, although others
4766 provide basic descriptive statistics. Item Response Theory is done using
4767 factor analysis of tetrachoric and polychoric correlations. Functions for
4768 analyzing data at multiple levels include within and between group statistics,
4769 including correlations and factor analysis. Functions for simulating and
4770 testing particular item and test structures are included. Several functions
4771 serve as a useful front end for structural equation modeling. Graphical
4772 displays of path diagrams, factor analysis and structural equation models are
4773 created using basic graphics.")
4774 (license license:gpl2+)))
4776 (define-public r-generics
4783 (uri (cran-uri "generics" version))
4786 "04hrn6g5m5vi3znrcha3jw2q16lnmm3ygx2jl5aqiahg3azqwix2"))))
4787 (build-system r-build-system)
4788 (home-page "https://github.com/r-lib/generics")
4789 (synopsis "Common S3 generics not provided by base R methods")
4791 "In order to reduce potential package dependencies and conflicts,
4792 generics provides a number of commonly used S3 generics that are not provided
4793 by base R methods related to model fitting.")
4794 (license license:gpl2)))
4796 (define-public r-broom
4803 (uri (cran-uri "broom" version))
4806 "0ks64xwkaqh5cinq8j56d89rn9kipm7cdipsgqmz9xxy7ajxb7qj"))))
4807 (build-system r-build-system)
4822 (home-page "https://github.com/tidyverse/broom")
4823 (synopsis "Convert statistical analysis objects into tidy data frames")
4825 "This package provides tools to convert statistical analysis objects from
4826 R into tidy data frames, so that they can more easily be combined, reshaped
4827 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
4828 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
4829 summarizes a model's statistical findings such as coefficients of a
4830 regression; @code{augment}, which adds columns to the original data such as
4831 predictions, residuals and cluster assignments; and @code{glance}, which
4832 provides a one-row summary of model-level statistics.")
4833 (license license:expat)))
4835 (define-public r-recipes
4842 (uri (cran-uri "recipes" version))
4845 "0gbdc5kvbn14s5zrf4vrdjvkfajs00p7vvb433ii0lqnl07bl87d"))))
4846 (build-system r-build-system)
4868 (home-page "https://github.com/topepo/recipes")
4869 (synopsis "Preprocessing tools to create design matrices")
4871 "Recipes is an extensible framework to create and preprocess design
4872 matrices. Recipes consist of one or more data manipulation and analysis
4873 \"steps\". Statistical parameters for the steps can be estimated from an
4874 initial data set and then applied to other data sets. The resulting design
4875 matrices can then be used as inputs into statistical or machine learning
4877 (license license:gpl2)))
4879 (define-public r-pdist
4886 (uri (cran-uri "pdist" version))
4889 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
4890 (build-system r-build-system)
4891 (home-page "https://github.com/jeffwong/pdist")
4892 (synopsis "Partitioned distance function")
4894 "Pdist computes the euclidean distance between rows of a matrix X and
4895 rows of another matrix Y. Previously, this could be done by binding the two
4896 matrices together and calling @code{dist}, but this creates unnecessary
4897 computation by computing the distances between a row of X and another row of
4898 X, and likewise for Y. Pdist strictly computes distances across the two
4899 matrices, not within the same matrix, making computations significantly faster
4900 for certain use cases.")
4901 (license license:gpl3+)))
4903 (define-public r-ggrepel
4910 (uri (cran-uri "ggrepel" version))
4913 "1z5xyr5f4aryy0v1gzz9m8m4s5fzzwbrf0fxll1nbflr8xnr3yr9"))))
4914 (build-system r-build-system)
4916 (list r-ggplot2 r-rcpp r-rlang r-scales))
4918 (list r-knitr)) ; for vignettes
4919 (home-page "https://github.com/slowkow/ggrepel")
4920 (synopsis "Repulsive text and label geometries for ggplot2")
4922 "This package provides text and label geometries for ggplot2 that help to
4923 avoid overlapping text labels. Labels repel away from each other and away
4924 from the data points.")
4925 (license license:gpl3)))
4927 (define-public r-corrplot
4934 (uri (cran-uri "corrplot" version))
4937 "1g98jk6xsl08z4n6sy5vriif99m31zhbz7j3dh1kfj4w7yb9zh78"))))
4938 (build-system r-build-system)
4941 (home-page "https://github.com/taiyun/corrplot")
4942 (synopsis "Visualization of a correlation matrix")
4944 "This package provides a graphical display of a correlation matrix or
4945 general matrix. It also contains some algorithms to do matrix reordering. In
4946 addition, corrplot is good at details, including choosing color, text labels,
4947 color labels, layout, etc.")
4948 ;; Any version of the GPL
4949 (license license:gpl2+)))
4951 (define-public r-stringdist
4953 (name "r-stringdist")
4958 (uri (cran-uri "stringdist" version))
4960 (base32 "1fv1hbdlm8qwx57b2aj50mw0say5k48awzavx65mfk67qp6ddk7g"))))
4961 (build-system r-build-system)
4962 (home-page "https://github.com/markvanderloo/stringdist")
4963 (synopsis "Approximate string matching and string distance functions")
4965 "This package implements an approximate string matching version of R's
4966 native @code{match} function. It can calculate various string distances based
4967 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal string alignment),
4968 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
4969 Jaro-Winkler). An implementation of soundex is provided as well. Distances
4970 can be computed between character vectors while taking proper care of encoding
4971 or between integer vectors representing generic sequences.")
4972 (license license:gpl3+)))
4974 (define-public r-ucminf
4981 (uri (cran-uri "ucminf" version))
4984 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
4985 (build-system r-build-system)
4986 (native-inputs (list gfortran))
4987 (home-page "https://cran.r-project.org/web/packages/ucminf/")
4988 (synopsis "General-purpose unconstrained non-linear optimization")
4990 "This package provides an implementation of an algorithm for
4991 general-purpose unconstrained non-linear optimization. The algorithm is of
4992 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
4993 search with a trust region type monitoring of the input to the line search
4994 algorithm. The interface of @code{ucminf} is designed for easy interchange
4995 with the package @code{optim}.")
4996 (license license:gpl2+)))
4998 (define-public r-useful
5004 (uri (cran-uri "useful" version))
5007 "0n50v1q75k518sq23id14jphwla35q4sasahrnrnllwrachl67v1"))))
5008 (properties `((upstream-name . "useful")))
5009 (build-system r-build-system)
5019 (home-page "https://github.com/jaredlander/useful")
5020 (synopsis "Collection of handy, useful functions")
5021 (description "This package provides a set of little functions that have been
5022 found useful to do little odds and ends such as plotting the results of K-means
5023 clustering, substituting special text characters, viewing parts of a
5024 @code{data.frame}, constructing formulas from text and building design and
5025 response matrices.")
5026 (license license:bsd-3)))
5028 (define-public r-ordinal
5031 (version "2019.12-10")
5035 (uri (cran-uri "ordinal" version))
5038 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
5039 (build-system r-build-system)
5041 (list r-mass r-matrix r-numderiv r-ucminf))
5042 (home-page "https://github.com/runehaubo/ordinal")
5043 (synopsis "Regression models for ordinal data")
5045 "This package provides an implementation of cumulative link (mixed)
5046 models also known as ordered regression models, proportional odds models,
5047 proportional hazards models for grouped survival times and ordered models.
5048 Estimation is via maximum likelihood and mixed models are fitted with the
5049 Laplace approximation and adaptive Gauss-Hermite quadrature.")
5050 (license license:gpl2+)))
5052 (define-public r-jomo
5059 (uri (cran-uri "jomo" version))
5062 "1sbcpacxnxbzwa8rr9x2bq7hh0s3sw6yznr90dkp43n6xk5xaqir"))))
5063 (build-system r-build-system)
5065 (list r-lme4 r-mass r-ordinal r-survival))
5066 (home-page "https://cran.r-project.org/web/packages/jomo/")
5067 (synopsis "Multilevel Joint Modelling Multiple Imputation")
5069 "Similarly to Schafer's package pan, jomo is a package for multilevel
5070 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
5071 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
5072 possibility of handling binary and categorical data through latent normal
5073 variables, the option to use cluster-specific covariance matrices and to
5074 impute compatibly with the substantive model.")
5075 (license license:gpl2)))
5077 (define-public r-pan
5084 (uri (cran-uri "pan" version))
5087 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
5088 (build-system r-build-system)
5089 (native-inputs (list gfortran))
5090 (home-page "https://cran.r-project.org/web/packages/pan/")
5091 (synopsis "Multiple imputation for multivariate panel or clustered data")
5093 "This package implements multiple imputation for multivariate panel or
5095 (license license:gpl3)))
5097 (define-public r-mitml
5104 (uri (cran-uri "mitml" version))
5107 "00i18nnvrdrg91crgcp2a431xs71cawaip3xkqk2myv0iav3xga9"))))
5108 (build-system r-build-system)
5110 (list r-haven r-jomo r-pan))
5113 (home-page "https://cran.r-project.org/web/packages/mitml/")
5114 (synopsis "Tools for multiple imputation in multilevel modeling")
5116 "This package provides tools for multiple imputation of missing data in
5117 multilevel modeling. It includes a user-friendly interface to the packages
5118 pan and jomo, and several functions for visualization, data management and the
5119 analysis of multiply imputed data sets.")
5120 (license license:gpl2+)))
5122 (define-public r-mice
5129 (uri (cran-uri "mice" version))
5132 "11cpyqlilakan2pwjzacb9jjlazazsqdngy237nnrj8j6mky822i"))))
5133 (build-system r-build-system)
5143 (home-page "https://cran.r-project.org/web/packages/mice/")
5144 (synopsis "Multivariate imputation by chained equations")
5146 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
5147 implemented by the MICE algorithm as described in @url{Van Buuren and
5148 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
5149 variable has its own imputation model. Built-in imputation models are
5150 provided for continuous data (predictive mean matching, normal), binary
5151 data (logistic regression), unordered categorical data (polytomous logistic
5152 regression) and ordered categorical data (proportional odds). MICE can also
5153 impute continuous two-level data (normal model, pan, second-level variables).
5154 Passive imputation can be used to maintain consistency between variables.
5155 Various diagnostic plots are available to inspect the quality of the
5157 ;; Any of these two versions.
5158 (license (list license:gpl2 license:gpl3))))
5160 (define-public r-truncnorm
5162 (name "r-truncnorm")
5167 (uri (cran-uri "truncnorm" version))
5170 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
5171 (build-system r-build-system)
5172 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
5173 (synopsis "Truncated normal distribution")
5174 (description "This package provides functions for the truncated normal
5175 distribution with mean equal to @code{mean} and standard deviation equal to
5176 @code{sd}. It includes density, distribution, quantile, and expected value
5177 functions, as well as a random generation function.")
5178 (license license:gpl2)))
5180 (define-public r-rsolnp
5187 (uri (cran-uri "Rsolnp" version))
5190 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
5191 (properties `((upstream-name . "Rsolnp")))
5192 (build-system r-build-system)
5195 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
5196 (synopsis "General non-linear optimization")
5197 (description "The Rsolnp package implements a general non-linear augmented
5198 Lagrange multiplier method solver, a @dfn{sequential quadratic
5199 programming} (SQP) based solver).")
5200 ;; Any version of the GPL.
5201 (license license:gpl2+)))
5203 (define-public r-hardyweinberg
5205 (name "r-hardyweinberg")
5210 (uri (cran-uri "HardyWeinberg" version))
5213 "0ppkzbhrb83dj796pm6gn5ypsf1ql8d9b3fv47w63i0snkhxfiv4"))))
5214 (properties `((upstream-name . "HardyWeinberg")))
5215 (build-system r-build-system)
5217 (list r-mice r-rcpp r-rsolnp))
5218 (home-page "https://cran.r-project.org/package=HardyWeinberg")
5219 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
5221 "This package contains tools for exploring Hardy-Weinberg equilibrium for
5222 diallelic genetic marker data. All classical tests (chi-square, exact,
5223 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
5224 included in the package, as well as functions for power computation and for
5225 the simulation of marker data under equilibrium and disequilibrium. Routines
5226 for dealing with markers on the X-chromosome are included. Functions for
5227 testing equilibrium in the presence of missing data by using multiple
5228 imputation are also provided. Implements several graphics for exploring the
5229 equilibrium status of a large set of diallelic markers: ternary plots with
5230 acceptance regions, log-ratio plots and Q-Q plots.")
5231 (license license:gpl2+)))
5240 (uri (cran-uri "sm" version))
5243 "03z8igsjqr32x407asxvkrbayvm6yhv9xyfs0n8fkmv8zk5a41r6"))))
5244 (build-system r-build-system)
5245 (native-inputs (list gfortran))
5246 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
5247 (synopsis "Smoothing methods for nonparametric regression and density estimation")
5249 "This is software accompanying the book 'Applied Smoothing Techniques for
5250 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
5251 University Press. It provides smoothing methods for nonparametric regression
5252 and density estimation")
5253 (license license:gpl2+)))
5255 (define-public r-venndiagram
5257 (name "r-venndiagram")
5261 (uri (cran-uri "VennDiagram" version))
5264 "1l9mmc8wwn885l2b13kshhrkz53pqigcw6d8gklvv92fx5m5cdvm"))))
5265 (properties `((upstream-name . "VennDiagram")))
5266 (build-system r-build-system)
5268 (list r-futile-logger))
5269 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
5270 (synopsis "Generate High-Resolution Venn and Euler Plots")
5272 "This package provides a set of functions to generate high-resolution
5273 Venn and Euler plots. It includes handling for several special cases,
5274 including two-case scaling, and extensive customization of plot shape and
5276 (license license:gpl2+)))
5278 (define-public r-vioplot
5285 (uri (cran-uri "vioplot" version))
5288 "1dmdasp3jldc41233z6r08w3j76vyyp9m3jrj7n4ahk48yd5siq6"))))
5289 (build-system r-build-system)
5294 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
5295 (synopsis "Violin plot")
5297 "This package provides a violin plot, which is a combination of a box
5298 plot and a kernel density plot.")
5299 (license license:bsd-3)))
5301 (define-public r-rsofia
5307 ;; This package has been removed from CRAN, so we can
5308 ;; only fetch it from the archives.
5309 (uri (string-append "https://cran.r-project.org/src/"
5310 "contrib/Archive/RSofia/RSofia_"
5314 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
5315 (properties `((upstream-name . "RSofia")))
5316 (build-system r-build-system)
5319 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
5320 (synopsis "Port of sofia-ml to R")
5321 (description "This package is a port of sofia-ml to R. Sofia-ml is a
5322 suite of fast incremental algorithms for machine learning that can be used for
5323 training models for classification or ranking.")
5324 (license license:asl2.0)))
5326 (define-public r-xts
5333 (uri (cran-uri "xts" version))
5336 "0b6a7mpyk9aw6axas7nz01gadczprwwfhii01fz31z26z555i06n"))))
5337 (build-system r-build-system)
5338 (propagated-inputs (list r-zoo))
5339 (home-page "https://github.com/joshuaulrich/xts")
5340 (synopsis "Extensible time series")
5342 "This package provides for uniform handling of R's different time-based
5343 data classes by extending @code{zoo}, maximizing native format information
5344 preservation and allowing for user-level customization and extension, while
5345 simplifying cross-class interoperability.")
5346 (license license:gpl2+)))
5348 (define-public r-performanceanalytics
5350 (name "r-performanceanalytics")
5355 (uri (cran-uri "PerformanceAnalytics" version))
5358 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
5360 `((upstream-name . "PerformanceAnalytics")))
5361 (build-system r-build-system)
5363 (list r-quadprog r-xts r-zoo))
5364 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
5365 (synopsis "Econometric tools for performance and risk analysis")
5366 (description "This is a collection of econometric functions for
5367 performance and risk analysis. This package aims to aid practitioners and
5368 researchers in utilizing the latest research in analysis of non-normal return
5369 streams. In general, it is most tested on return (rather than price) data on
5370 a regular scale, but most functions will work with irregular return data as
5371 well, and increasing numbers of functions will work with P&L or price data
5373 ;; Either version may be picked.
5374 (license (list license:gpl2 license:gpl3))))
5376 (define-public r-laeken
5383 (uri (cran-uri "laeken" version))
5386 "1p3ccbaydlr52p8qmgmm2l6kryvq6jjjx7mqn2vv0gpjaxqhyy92"))))
5387 (build-system r-build-system)
5389 (list r-boot r-mass))
5390 (home-page "https://cran.r-project.org/web/packages/laeken/")
5391 (synopsis "Estimation of indicators on social exclusion and poverty")
5392 (description "This package provides tools for the estimation of indicators
5393 on social exclusion and poverty, as well as an implementation of Pareto tail
5394 modeling for empirical income distributions.")
5395 (license license:gpl2+)))
5397 (define-public r-vcd
5404 (uri (cran-uri "vcd" version))
5407 "13sn77qdcyll9lz7nab0bxzfvpgj8f5rl2cq5ylpz8pibynj1d55"))))
5408 (build-system r-build-system)
5410 (list r-colorspace r-lmtest r-mass))
5411 (home-page "https://cran.r-project.org/web/packages/vcd/")
5412 (synopsis "Visualizing categorical data")
5413 (description "This package provides visualization techniques, data sets,
5414 summary and inference procedures aimed particularly at categorical data.
5415 Special emphasis is given to highly extensible grid graphics. The package was
5416 originally inspired by the book \"Visualizing Categorical Data\" by Michael
5417 Friendly and is now the main support package for a new book, \"Discrete Data
5418 Analysis with R\" by Michael Friendly and David Meyer (2015).")
5419 (license license:gpl2)))
5421 (define-public r-vcfr
5427 (uri (cran-uri "vcfR" version))
5430 "0lhxb3ac4fafwik9q3cds46svzf0hyca8k54chw3dpk50c0zz1yx"))))
5431 (build-system r-build-system)
5447 (home-page "https://github.com/knausb/vcfR")
5448 (synopsis "Manipulate and visualize VCF data")
5449 (description "This package facilitates easy manipulation of variant call
5450 format (VCF) data. Functions are provided to rapidly read from and write to
5451 VCF files. Once VCF data is read into R, a parser function extracts matrices
5452 of data. This information can then be used for quality control or other
5453 purposes. Additional functions provide visualization of genomic data. Once
5454 processing is complete data may be written to a VCF file. It also may be
5455 converted into other popular R objects. This package provides a link between
5456 VCF data and familiar R software.")
5457 (license license:gpl3)))
5459 (define-public r-ica
5466 (uri (cran-uri "ica" version))
5469 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
5470 (build-system r-build-system)
5471 (home-page "https://cran.r-project.org/web/packages/ica/")
5472 (synopsis "Independent component analysis")
5473 (description "This package provides tools for @dfn{Independent Component
5474 Analysis} (ICA) using various algorithms: FastICA,
5475 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
5476 of Eigenmatrices} (JADE).")
5477 (license license:gpl2+)))
5479 (define-public r-dtw
5486 (uri (cran-uri "dtw" version))
5489 "004gm4mzgdzdj807j3bwqsv5lizmnmz5jq514bdjshhkysnzjz6z"))))
5490 (build-system r-build-system)
5491 (propagated-inputs (list r-proxy))
5492 (home-page "http://dtw.r-forge.r-project.org/")
5493 (synopsis "Dynamic Time Warping Algorithms")
5494 (description "This package provides a comprehensive implementation of
5495 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
5496 optimal (least cumulative distance) alignment between points of two time
5497 series. Common DTW variants covered include local (slope) and global (window)
5498 constraints, subsequence matches, arbitrary distance definitions,
5499 normalizations, minimum variance matching, and so on.")
5500 (license license:gpl2+)))
5502 (define-public r-sdmtools
5505 (version "1.1-221.2")
5509 (uri (cran-uri "SDMTools" version))
5512 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
5513 (properties `((upstream-name . "SDMTools")))
5514 (build-system r-build-system)
5515 (propagated-inputs (list r-r-utils))
5516 (home-page "https://www.rforge.net/SDMTools/")
5517 (synopsis "Species distribution modelling tools")
5518 (description "This package provides a set of tools for post processing
5519 the outcomes of species distribution modeling exercises. It includes novel
5520 methods for comparing models and tracking changes in distributions through
5521 time. It further includes methods for visualizing outcomes, selecting
5522 thresholds, calculating measures of accuracy and landscape fragmentation
5524 (license license:gpl3+)))
5526 (define-public r-scatterplot3d
5528 (name "r-scatterplot3d")
5533 (uri (cran-uri "scatterplot3d" version))
5536 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
5537 (build-system r-build-system)
5538 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
5539 (synopsis "3D scatter plot")
5540 (description "This package provides an implementation of scatter plots for
5541 plotting. a three dimensional point cloud.")
5542 (license license:gpl2)))
5544 (define-public r-ggridges
5551 (uri (cran-uri "ggridges" version))
5554 "0bmlqy1p6rac90af97ffpdi6php7dblx66l2hcm8ljidgyqzmspm"))))
5555 (build-system r-build-system)
5557 (list r-ggplot2 r-plyr r-scales r-withr))
5560 (home-page "https://github.com/clauswilke/ggridges")
5561 (synopsis "Ridgeline plots in ggplot2")
5563 "Ridgeline plots provide a convenient way of visualizing changes in
5564 distributions over time or space. This package enables the creation of such
5565 plots in @code{ggplot2}.")
5566 (license license:gpl2)))
5568 (define-public r-ggjoy
5575 (uri (cran-uri "ggjoy" version))
5578 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
5579 (build-system r-build-system)
5581 (list r-ggplot2 r-ggridges))
5582 (home-page "https://github.com/clauswilke/ggjoy")
5583 (synopsis "Joyplots in ggplot2")
5584 (description "Joyplots provide a convenient way of visualizing changes in
5585 distributions over time or space. This package enables the creation of such
5586 plots in @code{ggplot2}.")
5587 (license license:gpl2)))
5589 (define-public r-cli
5596 (uri (cran-uri "cli" version))
5599 "04ff3bgsahi736s8l6a26zlwwil8jw4shx7bb56ah1pp1f1n22n7"))))
5600 (build-system r-build-system)
5603 (home-page "https://github.com/r-lib/cli#readme")
5604 (synopsis "Helpers for developing command line interfaces")
5605 (description "This package provides a suite of tools designed to build
5606 attractive command line interfaces (CLIs). It includes tools for drawing
5607 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
5608 (license license:expat)))
5610 (define-public r-argparser
5612 (name "r-argparser")
5617 (uri (cran-uri "argparser" version))
5620 "0xcl0ivsbc4iw8s7027q4cx68j6s5lihbby0xa9pmlv4wjmcvdr6"))))
5621 (build-system r-build-system)
5622 (home-page "https://bitbucket.org/djhshih/argparser")
5623 (synopsis "Command-line argument parser")
5625 "This package provides a cross-platform command-line argument parser
5626 written purely in R with no external dependencies. It is useful with the
5627 Rscript front-end and facilitates turning an R script into an executable
5629 (license license:gpl3+)))
5631 (define-public r-debugme
5638 (uri (cran-uri "debugme" version))
5641 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
5642 (build-system r-build-system)
5643 (propagated-inputs (list r-crayon))
5644 (home-page "https://github.com/r-lib/debugme#readme")
5645 (synopsis "Debug R packages")
5647 "This package allows the user to specify debug messages as special string
5648 constants, and control debugging of packages via environment variables.")
5649 (license license:expat)))
5651 (define-public r-processx
5658 (uri (cran-uri "processx" version))
5660 (base32 "0azw8sx6nv6pp8m8jrwq01b9na2swrnznn7dwrhn07268w82svzd"))))
5661 (build-system r-build-system)
5664 (home-page "https://github.com/r-lib/processx3")
5665 (synopsis "Execute and control system processes")
5667 "This package provides portable tools to run system processes in the
5668 background. It can check if a background process is running; wait on a
5669 background process to finish; get the exit status of finished processes; kill
5670 background processes and their children; restart processes. It can read the
5671 standard output and error of the processes, using non-blocking connections.
5672 @code{processx} can poll a process for standard output or error, with a
5673 timeout. It can also poll several processes at once.")
5674 (license license:expat)))
5676 (define-public r-tsp
5683 (uri (cran-uri "TSP" version))
5686 "0gdwxbj2gria7jhsswmfvc32r43sdd63z3lyy21gbvmfcakvb8j9"))))
5687 (properties `((upstream-name . "TSP")))
5688 (build-system r-build-system)
5689 (propagated-inputs (list r-foreach))
5690 (home-page "https://cran.r-project.org/web/packages/TSP/")
5691 (synopsis "Traveling salesperson problem (TSP)")
5692 (description "This package provides basic infrastructure and some
5693 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
5694 traveling salesman problem).")
5695 (license license:gpl3)))
5697 (define-public r-qap
5704 (uri (cran-uri "qap" version))
5707 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
5708 (build-system r-build-system)
5709 (native-inputs (list gfortran))
5710 (home-page "https://cran.r-project.org/web/packages/qap/")
5711 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
5712 (description "This package implements heuristics for the @dfn{quadratic
5713 assignment problem} (QAP). Currently only a simulated annealing heuristic is
5715 (license license:gpl3)))
5717 (define-public r-gclus
5724 (uri (cran-uri "gclus" version))
5727 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
5728 (build-system r-build-system)
5729 (propagated-inputs (list r-cluster))
5730 (home-page "https://cran.r-project.org/web/packages/gclus/")
5731 (synopsis "Clustering graphics")
5732 (description "This package orders panels in scatterplot matrices and
5733 parallel coordinate displays by some merit index. It contains various indices
5734 of merit, ordering functions, and enhanced versions of @code{pairs} and
5735 @code{parcoord} which color panels according to their merit level.")
5736 (license license:gpl2+)))
5738 (define-public r-webshot
5745 (uri (cran-uri "webshot" version))
5748 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
5749 (build-system r-build-system)
5751 (list r-callr r-jsonlite r-magrittr))
5752 (home-page "https://github.com/wch/webshot/")
5753 (synopsis "Take screenshots of web pages")
5755 "Webshot makes it easy to take screenshots of web pages from within R.
5756 It can also run Shiny applications locally and take screenshots of the
5757 application; and it can render and screenshot static as well as interactive R
5758 Markdown documents.")
5759 (license license:gpl2)))
5761 (define-public r-seriation
5763 (name "r-seriation")
5768 (uri (cran-uri "seriation" version))
5771 "08c37n3xxc4n4vbkw38k3l3hdlmck8drqpl6z274vkgi2sqv8qyf"))))
5772 (build-system r-build-system)
5781 (native-inputs (list gfortran))
5782 (home-page "https://s2.smu.edu/IDA/seriation/")
5783 (synopsis "Infrastructure for ordering objects using seriation")
5785 "This package provides infrastructure for seriation with an
5786 implementation of several seriation/sequencing techniques to reorder matrices,
5787 dissimilarity matrices, and dendrograms. It also provides (optimally)
5788 reordered heatmaps, color images and clustering visualizations like
5789 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
5791 (license license:gpl3)))
5793 (define-public r-xfun
5800 (uri (cran-uri "xfun" version))
5802 (base32 "0civd050r94w2vwfx3xgz1w36wkwrkm5dscdv5kb3klbvqwy8nqb"))))
5803 (build-system r-build-system)
5804 ;; knitr itself depends on xfun
5807 `(("r-knitr" ,r-knitr)))
5808 (home-page "https://github.com/yihui/xfun")
5809 (synopsis "Miscellaneous functions")
5811 "This package provides miscellaneous functions commonly used in other
5812 packages maintained by Yihui Xie.")
5813 (license license:expat)))
5815 (define-public r-utf8
5822 (uri (cran-uri "utf8" version))
5825 "1x6qg19z4qih9lk3mvnmx0vailm1khp5lylw4hlwz6rssj3yw6m7"))))
5826 (build-system r-build-system)
5828 (list r-knitr r-rmarkdown)) ; for vignettes
5829 (home-page "https://github.com/patperry/r-utf8")
5830 (synopsis "Unicode text processing")
5832 "This package provides tools to process and print UTF-8 encoded
5833 international text (Unicode). Input, validate, normalize, encode, format, and
5835 (license license:asl2.0)))
5837 (define-public r-zeallot
5844 (uri (cran-uri "zeallot" version))
5847 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
5848 (build-system r-build-system)
5849 (home-page "https://github.com/nteetor/zeallot")
5850 (synopsis "Multiple, unpacking, and destructuring assignment")
5852 "This package provides a @code{%<-%} operator to perform multiple,
5853 unpacking, and destructuring assignment in R. The operator unpacks the
5854 right-hand side of an assignment into multiple values and assigns these values
5855 to variables on the left-hand side of the assignment.")
5856 (license license:expat)))
5858 (define-public r-vctrs
5865 (uri (cran-uri "vctrs" version))
5868 "1c8v5lmap6iq4jpi7p3w05hsv2dq7rjg057pvnfyc5d1xmsqnkkz"))))
5869 (build-system r-build-system)
5871 (list r-ellipsis r-glue r-rlang))
5874 (home-page "https://github.com/r-lib/vctrs")
5875 (synopsis "Vector helpers")
5877 "There are three main goals to the @code{vctrs} package:
5880 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
5881 @code{length()} and @code{class()}. These definitions are paired with a
5882 framework for type-coercion and size-recycling.
5883 @item To define type- and size-stability as desirable function properties, use
5884 them to analyse existing base function, and to propose better alternatives.
5885 This work has been particularly motivated by thinking about the ideal
5886 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
5887 @item To provide a new @code{vctr} base class that makes it easy to create new
5888 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
5889 a few new @code{vctrs} generics, making implementation considerably simpler
5892 (license license:gpl3)))
5894 (define-public r-pillar
5901 (uri (cran-uri "pillar" version))
5904 "17m13rzgwdddwa0n3gpmax6wmfaphbg71l13ffhw5vnxf6i94fh3"))))
5905 (build-system r-build-system)
5917 (home-page "https://github.com/r-lib/pillar")
5918 (synopsis "Coloured formatting for columns")
5920 "This package provides a @code{pillar} generic designed for formatting
5921 columns of data using the full range of colours provided by modern
5923 (license license:gpl3)))
5925 (define-public r-pinfsc50
5931 (uri (cran-uri "pinfsc50" version))
5934 "1547xyxmfb7zi8h9bsm6k67dcw4hpp129xzvmgwfw7r6p4af47zd"))))
5935 (build-system r-build-system)
5936 (home-page "https://cran.r-project.org/web/packages/pinfsc50/")
5937 (synopsis "Genomic data for the plant pathogen Phytophthora infestans")
5938 (description "This package contains genomic data for the plant pathogen
5939 Phytophthora infestans. It includes a variant file, a sequence file and an
5940 annotation file. This package is intended to be used as example data for
5941 packages that work with genomic data.")
5942 (license license:gpl2+)))
5944 (define-public r-uuid
5951 (uri (cran-uri "uuid" version))
5954 "0il35jnci537r8zkinyiy5jp5q530p85ln6dswpj884zclrlcvj5"))))
5955 (build-system r-build-system)
5956 (home-page "https://www.rforge.net/uuid")
5957 (synopsis "Tools for generating and handling of UUIDs")
5959 "This package provides tools for generating and handling of
5960 @dfn{Universally Unique Identifiers} (UUIDs).")
5961 (license license:expat)))
5963 (define-public r-tinytex
5970 (uri (cran-uri "tinytex" version))
5973 "04ng34kfds2isz4j9ch1xlii0dfclqay9fsc6wvr6sfifzv9fqyk"))))
5974 (build-system r-build-system)
5977 (home-page "https://github.com/yihui/tinytex")
5978 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
5980 "This package provides helper functions to install and maintain the LaTeX
5981 distribution named TinyTeX, a lightweight, cross-platform, portable, and
5982 easy-to-maintain version of TeX Live. This package also contains helper
5983 functions to compile LaTeX documents, and install missing LaTeX packages
5985 (license license:expat)))
5987 (define-public r-tinytest
5994 (uri (cran-uri "tinytest" version))
5997 "1mq31f7bzcz5bkgzl9khm1i80axfzra7gcjqxd2yqb4wrw1m3x4s"))))
5998 (properties `((upstream-name . "tinytest")))
5999 (build-system r-build-system)
6000 (home-page "https://github.com/markvanderloo/tinytest")
6001 (synopsis "Lightweight unit testing framework")
6003 "This package provides a lightweight unit testing framework. Main
6007 @item install tests with the package;
6008 @item test results are treated as data that can be stored and manipulated;
6009 @item test files are R scripts interspersed with test commands, that can be
6011 @item fully automated build-install-test sequence for packages;
6012 @item skip tests when not run locally (e.g. on CRAN);
6013 @item flexible and configurable output printing;
6014 @item compare computed output with output stored with the package;
6015 @item run tests in parallel;
6016 @item extensible by other packages;
6017 @item report side effects.
6020 (license license:gpl3)))
6022 (define-public r-network
6029 (uri (cran-uri "network" version))
6032 "19q563v5xfkbmr0ws9nhqx4wrxkf9jsck51rqc8mm2gq2h03lg7w"))))
6033 (build-system r-build-system)
6035 (list r-magrittr r-statnet-common r-tibble))
6036 (home-page "https://statnet.org/")
6037 (synopsis "Classes for relational data")
6039 "This package provides tools to create and modify network objects. The
6040 @code{network} class can represent a range of relational data types, and
6041 supports arbitrary vertex/edge/graph attributes.")
6042 (license license:gpl2+)))
6044 (define-public r-stabs
6051 (uri (cran-uri "stabs" version))
6054 "1nf1yg14cgxrs4np1yghpzw1nczaslfv3rvf3918wrlzg0vp6l7q"))))
6055 (build-system r-build-system)
6058 (home-page "https://github.com/hofnerb/stabs")
6059 (synopsis "Stability selection with error control")
6061 "This package provides resampling procedures to assess the stability of
6062 selected variables with additional finite sample error control for
6063 high-dimensional variable selection procedures such as Lasso or boosting.
6064 Both, standard stability selection (Meinshausen & Buhlmann, 2010) and
6065 complementary pairs stability selection with improved error bounds
6066 (Shah & Samworth, 2013) are implemented. The package can be combined with
6067 arbitrary user specified variable selection approaches.")
6068 (license license:gpl2)))
6070 (define-public r-rle
6077 (uri (cran-uri "rle" version))
6080 "0sagl0jggg40lihzy7pfq4593rfvc3b3f7g6ggi85s7n18qvwg40"))))
6081 (properties `((upstream-name . "rle")))
6082 (build-system r-build-system)
6083 (home-page "https://cran.r-project.org/web/packages/rle/")
6084 (synopsis "Common functions for run-length encoded vectors")
6086 "This package provides common @code{base} and @code{stats} methods for
6087 @code{rle} objects, aiming to make it possible to treat them transparently as
6089 (license license:gpl3)))
6091 (define-public r-statnet-common
6093 (name "r-statnet-common")
6098 (uri (cran-uri "statnet.common" version))
6101 "0bw8dwnv568i60xrj6d7gv0hnna1x7rvqaayy5i0827khvdj7nrw"))))
6103 `((upstream-name . "statnet.common")))
6104 (build-system r-build-system)
6107 (home-page "https://statnet.org")
6108 (synopsis "R scripts and utilities used by the Statnet software")
6109 (description "This package provides non-statistical utilities used by the
6110 software developed by the Statnet Project.")
6111 (license license:gpl3)))
6113 (define-public r-statcheck
6115 (name "r-statcheck")
6120 (uri (cran-uri "statcheck" version))
6123 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
6124 (build-system r-build-system)
6126 (list r-ggplot2 r-plyr r-rmarkdown))
6127 (home-page "https://cran.r-project.org/web/packages/statcheck/")
6128 (synopsis "Extract statistics from articles and recompute p-values")
6129 (description "This package can automatically extract statistical
6130 null-hypothesis significant testing (NHST) results from articles and recompute
6131 the p-values based on the reported test statistic and degrees of freedom to
6132 detect possible inconsistencies.")
6133 (license license:gpl2)))
6135 (define-public r-sna
6142 (uri (cran-uri "sna" version))
6145 "0ai0v4538d30m4wks5s3lch1yfmx1ml0nnrz7ihs097lv586a09s"))))
6146 (build-system r-build-system)
6148 (list r-network r-statnet-common))
6149 (home-page "https://statnet.org")
6150 (synopsis "Tools for social network analysis")
6152 "This package provides a range of tools for social network analysis,
6153 including node and graph-level indices, structural distance and covariance
6154 methods, structural equivalence detection, network regression, random graph
6155 generation, and 2D/3D network visualization.")
6156 (license license:gpl2+)))
6158 (define-public r-tfisher
6165 (uri (cran-uri "TFisher" version))
6168 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
6169 (properties `((upstream-name . "TFisher")))
6170 (build-system r-build-system)
6172 (list r-matrix r-mvtnorm r-sn))
6173 (home-page "https://cran.r-project.org/web/packages/TFisher/")
6174 (synopsis "Optimal thresholding Fisher's p-value combination method")
6176 "This package provides the @dfn{cumulative distribution function} (CDF),
6177 quantile, and statistical power calculator for a collection of thresholding
6178 Fisher's p-value combination methods, including Fisher's p-value combination
6179 method, truncated product method and, in particular, soft-thresholding
6180 Fisher's p-value combination method which is proven to be optimal in some
6181 context of signal detection. The p-value calculator for the omnibus version
6182 of these tests are also included.")
6183 (license license:gpl2)))
6185 (define-public r-ttr
6192 (uri (cran-uri "TTR" version))
6195 "06vicgbhwpsww09hhha5mbcd0cwip6cvkfbhjjhp950rv64bk1r5"))))
6196 (properties `((upstream-name . "TTR")))
6197 (build-system r-build-system)
6199 (list r-curl r-xts r-zoo))
6200 (home-page "https://github.com/joshuaulrich/TTR")
6201 (synopsis "Technical trading rules")
6203 "This package provides functions and data to construct technical trading
6205 (license license:gpl2)))
6207 (define-public r-leaps
6214 (uri (cran-uri "leaps" version))
6217 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
6218 (build-system r-build-system)
6219 (native-inputs (list gfortran))
6220 (home-page "https://cran.r-project.org/web/packages/leaps/")
6221 (synopsis "Regression subset selection")
6223 "This package provides tools for regression subset selection, including
6224 exhaustive search.")
6225 (license license:gpl2+)))
6227 (define-public r-splus2r
6234 (uri (cran-uri "splus2R" version))
6237 "035zd22zcpkh74rik9ws6g8al6vjz7jgrqs5si361bzb5n290p3x"))))
6238 (properties `((upstream-name . "splus2R")))
6239 (build-system r-build-system)
6240 (home-page "https://cran.r-project.org/web/packages/splus2R/")
6241 (synopsis "Supplemental S-PLUS functionality in R")
6243 "Currently there are many functions in S-PLUS that are missing in R. To
6244 facilitate the conversion of S-PLUS packages to R packages, this package
6245 provides some missing S-PLUS functionality in R.")
6246 (license license:gpl2)))
6248 (define-public r-ifultools
6250 (name "r-ifultools")
6255 (uri (cran-uri "ifultools" version))
6258 "16a7rbvlym3bnfm93ikr5kl0l86ppk0s41fva6idvcx765g3fqkk"))))
6259 (build-system r-build-system)
6261 (list r-mass r-splus2r))
6262 (home-page "https://cran.r-project.org/web/packages/ifultools/")
6263 (synopsis "Insightful research tools")
6264 (description "This package provides C code used by the wmtsa, fractal, and
6266 (license license:gpl2)))
6268 (define-public r-sapa
6275 (uri (cran-uri "sapa" version))
6278 "0kj681rd4c2lvqr926lb6f4qwp281x5274dg6vbk8pf5y7s0qlpc"))))
6279 (build-system r-build-system)
6281 (list r-ifultools r-splus2r))
6282 (home-page "https://cran.r-project.org/web/packages/sapa/")
6283 (synopsis "Spectral analysis for physical applications")
6284 (description "This package provides software for the book Spectral
6285 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
6286 Cambridge University Press, 1993.")
6287 (license license:gpl2)))
6289 (define-public r-aggregation
6291 (name "r-aggregation")
6296 (uri (cran-uri "aggregation" version))
6299 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
6300 (build-system r-build-system)
6301 (home-page "https://cran.r-project.org/web/packages/aggregation/")
6302 (synopsis "Methods for p-value aggregation")
6304 "This package contains functionality for performing the following methods
6305 of p-value aggregation: Fisher's method, the Lancaster method (weighted
6306 Fisher's method), and Sidak correction.")
6307 (license license:gpl3)))
6309 (define-public r-quantmod
6316 (uri (cran-uri "quantmod" version))
6319 "0dbcrncv06iqcbkky95dd7l32xq0hhbnkb0kj8wwzym1jf748h5a"))))
6320 (build-system r-build-system)
6322 (list r-curl r-ttr r-xts r-zoo))
6323 (home-page "https://cran.r-project.org/web/packages/quantmod/")
6324 (synopsis "Quantitative financial modelling framework")
6325 (description "This package provides a quantitative financial modelling
6326 framework to allow users to specify, build, trade, and analyse quantitative
6327 financial trading strategies.")
6328 (license license:gpl3)))
6330 (define-public r-tseries
6337 (uri (cran-uri "tseries" version))
6340 "1fhldj95d16cwygw8xg0kvr4xk569mpzprdvahlsf4hzykc2dgs5"))))
6341 (build-system r-build-system)
6343 (list r-quadprog r-quantmod r-zoo))
6346 (home-page "https://cran.r-project.org/web/packages/tseries/")
6347 (synopsis "Time series analysis and computational finance")
6349 "This package provides functions relating to time series analysis and
6350 computational finance.")
6351 (license license:gpl2)))
6353 (define-public r-wmtsa
6360 (uri (cran-uri "wmtsa" version))
6363 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
6364 (build-system r-build-system)
6366 (list r-ifultools r-mass r-splus2r))
6367 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
6368 (synopsis "Wavelet methods for time series analysis")
6370 "This package provides software to accompany the book \"Wavelet Methods
6371 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
6372 University Press, 2000.")
6373 (license license:gpl2)))
6375 (define-public r-tsa
6382 (uri (cran-uri "TSA" version))
6385 "1bv5q609lhmrcxnjnvcj497fbjlv89zwa8q918hw4iki5nkvwwdb"))))
6386 (properties `((upstream-name . "TSA")))
6387 (build-system r-build-system)
6389 (list r-leaps r-locfit r-mgcv r-tseries))
6390 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
6391 (synopsis "Time series analysis")
6393 "This package contains R functions and datasets detailed in the book
6394 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
6395 Cryer and Kung-Sik Chan.")
6396 (license license:gpl2+)))
6398 (define-public r-extradistr
6400 (name "r-extradistr")
6405 (uri (cran-uri "extraDistr" version))
6408 "1gypnbvdzczl0mvznvy8r7hzsvc5gvdvi2mmzj21cqdw9n63944r"))))
6409 (properties `((upstream-name . "extraDistr")))
6410 (build-system r-build-system)
6413 (home-page "https://github.com/twolodzko/extraDistr")
6414 (synopsis "Additional univariate and multivariate distributions")
6416 "This package implements density, distribution functions, quantile
6417 functions and random generation functions for a large number of univariate and
6418 multivariate distributions.")
6419 (license license:gpl2)))
6421 (define-public r-fractal
6428 (uri (cran-uri "fractal" version))
6431 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
6432 (build-system r-build-system)
6440 (home-page "https://cran.r-project.org/web/packages/fractal/")
6441 (synopsis "Fractal time series modeling and analysis")
6443 "This package provides tools for stochastic fractal and deterministic
6444 chaotic time series analysis.")
6445 (license license:gpl2)))
6447 (define-public r-urca
6454 (uri (cran-uri "urca" version))
6457 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
6458 (build-system r-build-system)
6459 (propagated-inputs (list r-nlme))
6460 (native-inputs (list gfortran))
6461 (home-page "https://cran.r-project.org/web/packages/urca/")
6462 (synopsis "Unit root and cointegration tests for time series data")
6464 "This package provides unit root and cointegration tests encountered in
6465 applied econometric analysis.")
6466 (license license:gpl2+)))
6468 (define-public r-cubature
6475 (uri (cran-uri "cubature" version))
6478 "0kk9lw3s66h0sayza3in8rdj7bmgqn4v5lfckhslarpvj2fxsnv0"))))
6479 (build-system r-build-system)
6484 (home-page "https://github.com/bnaras/cubature")
6485 (synopsis "Adaptive multivariate integration over hypercubes")
6487 "This package is an R wrapper around the cubature C library for adaptive
6488 multivariate integration over hypercubes. This version provides both
6489 @code{hcubature} and @code{pcubature} routines in addition to a vector
6491 ;; The included cubature C library is released under GPLv2+, but the
6492 ;; wrapper declares the license to be GPLv3+.
6493 (license (list license:gpl2+ license:gpl3+))))
6495 (define-public r-trend
6502 (uri (cran-uri "trend" version))
6505 "1mr5g5gaxiqj6x83ngcbwwh57vhrhcz0x9dh0rmvs9y2ivk29ccs"))))
6506 (build-system r-build-system)
6508 (list r-extradistr))
6511 (home-page "https://cran.r-project.org/web/packages/trend/")
6512 (synopsis "Non-parametric trend tests and change-point detection")
6514 "The analysis of environmental data often requires the detection of
6515 trends and change-points. This package includes tests for trend
6516 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
6517 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
6518 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
6519 correlation trend test), change-point detection (Lanzante's test procedures,
6520 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
6521 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
6522 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
6523 sample Robust Rank-Order Distributional Test.")
6524 (license license:gpl3)))
6526 (define-public r-expm
6533 (uri (cran-uri "expm" version))
6536 "1p5dapwv8ycxaysgi6imnby04i4kh1c5a2czqa4wygz0s8pr2y9c"))))
6537 (build-system r-build-system)
6538 (propagated-inputs (list r-matrix))
6539 (native-inputs (list gfortran))
6540 (home-page "https://r-forge.r-project.org/projects/expm/")
6541 (synopsis "Tools for matrix exponentials and related quantities")
6543 "This package provides tools for the computation of the matrix
6544 exponential, logarithm, square root, and related quantities.")
6545 (license license:gpl2+)))
6547 (define-public r-complexplus
6549 (name "r-complexplus")
6554 (uri (cran-uri "complexplus" version))
6557 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
6558 (build-system r-build-system)
6560 (list r-expm r-matrix))
6561 (home-page "https://cran.r-project.org/web/packages/complexplus/")
6562 (synopsis "Functions of complex or real variables")
6564 "This package extends several functions to the complex domain, including
6565 the matrix exponential and logarithm, and the determinant.")
6566 (license license:gpl2)))
6568 (define-public r-phontools
6570 (name "r-phontools")
6575 (uri (cran-uri "phonTools" version))
6578 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
6579 (properties `((upstream-name . "phonTools")))
6580 (build-system r-build-system)
6581 (home-page "http://www.santiagobarreda.com/rscripts.html")
6582 (synopsis "Tools for phonetic and acoustic analyses")
6584 "This package contains tools for the organization, display, and analysis
6585 of the sorts of data frequently encountered in phonetics research and
6586 experimentation, including the easy creation of IPA vowel plots, and the
6587 creation and manipulation of WAVE audio files.")
6588 (license license:bsd-2)))
6597 (uri (cran-uri "np" version))
6600 "1a9kzn37cddwfdki5zjmzanxp75pccdjnsvqfrh84hhcsy51pcx3"))))
6601 (build-system r-build-system)
6603 (list r-boot r-cubature r-quadprog r-quantreg))
6604 (home-page "https://github.com/JeffreyRacine/R-Package-np")
6605 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
6606 (description "This package provides non-parametric (and semi-parametric)
6607 kernel methods that seamlessly handle a mix of continuous, unordered, and
6608 ordered factor data types.")
6609 ;; Any version of the GPL.
6610 (license license:gpl3+)))
6612 (define-public r-powerplus
6614 (name "r-powerplus")
6619 (uri (cran-uri "powerplus" version))
6622 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
6623 (build-system r-build-system)
6625 (list r-complexplus r-expm r-mass r-matrix r-phontools))
6626 (home-page "https://cran.r-project.org/web/packages/powerplus/")
6627 (synopsis "Exponentiation operations")
6629 "This package provides tools for the computation of matrix and scalar
6631 (license license:gpl2)))
6633 (define-public r-egg
6640 (uri (cran-uri "egg" version))
6643 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
6644 (properties `((upstream-name . "egg")))
6645 (build-system r-build-system)
6647 (list r-ggplot2 r-gridextra r-gtable))
6648 (home-page "https://cran.r-project.org/web/packages/egg")
6649 (synopsis "Extensions for ggplot2")
6651 "This package provides miscellaneous functions to help customize ggplot2
6652 objects. High-level functions are provided to post-process ggplot2 layouts
6653 and allow alignment between plot panels, as well as setting panel sizes to
6654 fixed values. Other functions include a custom @code{geom}, and helper
6655 functions to enforce symmetric scales or add tags to facetted plots.")
6656 (license license:gpl3)))
6658 (define-public r-heatmap3
6665 (uri (cran-uri "heatmap3" version))
6668 "0sfvizmmwfk1bjhn6zfx5a4qqfgj1ldg8x90b65crqibgfa36k2r"))))
6669 (build-system r-build-system)
6671 (list r-fastcluster))
6674 (home-page "https://cran.r-project.org/web/packages/heatmap3/")
6675 (synopsis "Improved heatmap package")
6677 "This package provides an improved heatmap package. It is completely
6678 compatible with the original R function @code{heatmap}, and provides more
6679 powerful and convenient features.")
6680 (license license:gpl2+)))
6682 (define-public r-heatmaply
6684 (name "r-heatmaply")
6689 (uri (cran-uri "heatmaply" version))
6692 "1w8yyzb68laxd4zxycvgmpqj5wnyidjgv1vbzbxndp9p92f2cp8a"))))
6693 (build-system r-build-system)
6711 (home-page "https://cran.r-project.org/package=heatmaply")
6712 (synopsis "Interactive cluster heat maps using plotly")
6714 "This package enables you to create interactive cluster heatmaps that can
6715 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
6716 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
6717 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
6718 a popular graphical method for visualizing high-dimensional data, in which a
6719 table of numbers is encoded as a grid of colored cells. The rows and columns
6720 of the matrix are ordered to highlight patterns and are often accompanied by
6722 ;; Either version of the license.
6723 (license (list license:gpl2 license:gpl3))))
6732 (uri (cran-uri "h5" version))
6735 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
6736 (build-system r-build-system)
6743 (home-page "https://github.com/mannau/h5")
6744 (synopsis "Interface to the HDF5 Library")
6746 "This package provides an S4 interface to the HDF5 library supporting
6747 fast storage and retrieval of R-objects like vectors, matrices and arrays to
6748 binary files in a language independent format. The HDF5 format can therefore
6749 be used as an alternative to R's save/load mechanism. Since h5 is able to
6750 access only subsets of stored data it can also handle data sets which do not
6752 (license license:bsd-2)))
6754 (define-public r-cgdsr
6761 (uri (cran-uri "cgdsr" version))
6764 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
6765 (build-system r-build-system)
6767 (list r-httr r-r-methodss3 r-r-oo))
6768 (home-page "https://github.com/cBioPortal/cgdsr")
6769 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
6771 "This package provides a basic set of R functions for querying the Cancer
6772 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
6773 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
6774 (license license:lgpl3)))
6776 (define-public r-import
6783 (uri (cran-uri "import" version))
6786 "018s0x224gqnv4cjfh0fwliyfg6ma9vslmwybrlizfsmqcc5wp37"))))
6787 (build-system r-build-system)
6790 (home-page "https://github.com/smbache/import")
6791 (synopsis "Import mechanism for R")
6793 "This is an alternative mechanism for importing objects from packages.
6794 The syntax allows for importing multiple objects from a package with a single
6795 command in an expressive way. The import package bridges some of the gap
6796 between using @code{library} (or @code{require}) and direct (single-object)
6797 imports. Furthermore the imported objects are not placed in the current
6798 environment. It is also possible to import objects from stand-alone @code{.R}
6800 (license license:expat)))
6802 (define-public r-shinyace
6809 (uri (cran-uri "shinyAce" version))
6812 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
6813 (properties `((upstream-name . "shinyAce")))
6814 (build-system r-build-system)
6816 (list r-shiny r-jsonlite))
6817 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
6818 (synopsis "Ace editor bindings for Shiny")
6820 "This package provides Ace editor bindings to enable a rich text editing
6821 environment within Shiny.")
6822 (license license:expat)))
6824 (define-public r-randomizr
6826 (name "r-randomizr")
6831 (uri (cran-uri "randomizr" version))
6834 "0dljyfldnardaps3fq6vi5wcs9x6qfaq5apapa78c51lnaa6fn9h"))))
6835 (properties `((upstream-name . "randomizr")))
6836 (build-system r-build-system)
6839 (home-page "https://declaredesign.org/r/randomizr/")
6840 (synopsis "Tools for common forms of random assignment and sampling")
6842 "This package provides tools for generating random assignments for common
6843 experimental designs and random samples for common sampling designs.")
6844 (license license:expat)))
6846 (define-public r-base64url
6848 (name "r-base64url")
6853 (uri (cran-uri "base64url" version))
6856 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
6857 (build-system r-build-system)
6860 (home-page "https://github.com/mllg/base64url")
6861 (synopsis "Fast and URL-safe base64 encoder and decoder")
6863 "This package provides a URL-safe base64 encoder and decoder. In
6864 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
6865 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
6866 encoder does not fill the string with trailing @code{=}. The resulting
6867 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
6868 and thus are safe to use in URLs or for file names. The package also comes
6869 with a simple base32 encoder/decoder suited for case insensitive file
6871 (license license:gpl3)))
6873 (define-public r-radiant-data
6875 (name "r-radiant-data")
6880 (uri (cran-uri "radiant.data" version))
6883 "12x4nz5n6yz1a67ji79pwvznp9flmn50hpp9y9sfhixir7dvwy27"))
6884 (modules '((guix build utils)))
6887 ;; Delete files that are under CC-NC-SA.
6888 (delete-file-recursively "inst/app/tools/help")
6890 (properties `((upstream-name . "radiant.data")))
6891 (build-system r-build-system)
6925 (home-page "https://github.com/radiant-rstats/radiant.data")
6926 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
6928 "The Radiant Data menu includes interfaces for loading, saving, viewing,
6929 visualizing, summarizing, transforming, and combining data. It also contains
6930 functionality to generate reproducible reports of the analyses conducted in
6932 (license license:agpl3)))
6934 (define-public r-algdesign
6936 (name "r-algdesign")
6941 (uri (cran-uri "AlgDesign" version))
6943 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
6944 (properties `((upstream-name . "AlgDesign")))
6945 (build-system r-build-system)
6946 (home-page "https://github.com/jvbraun/AlgDesign")
6947 (synopsis "Algorithmic experimental design")
6949 "This package provides tools to calculate exact and approximate theory
6950 experimental designs for D, A, and I criteria. Very large designs may be
6951 created. Experimental designs may be blocked or blocked designs created from
6952 a candidate list, using several criteria. The blocking can be done when whole
6953 and within plot factors interact.")
6954 (license license:gpl2+)))
6956 (define-public r-alluvial
6963 (uri (cran-uri "alluvial" version))
6965 (base32 "039frwrsxq1lb97s7vf2vbyyadimkigs628ymym06fxka53drdkp"))))
6966 (properties `((upstream-name . "alluvial")))
6967 (build-system r-build-system)
6968 (native-inputs (list r-knitr))
6969 (home-page "https://github.com/mbojan/alluvial")
6970 (synopsis "Create parallel sets plots (Alluvial Diagrams)")
6972 "This package creates alluvial diagrams (also known as parallel sets
6973 plots) for multivariate and time series-like data.")
6974 (license license:expat)))
6976 (define-public r-signal
6983 (uri (cran-uri "signal" version))
6986 "0qaf39vfmhn3d0bdjqd805ayfkaj48dkmf5dqd47bpk7dp21b837"))))
6987 (build-system r-build-system)
6988 (propagated-inputs (list r-mass))
6989 (native-inputs (list gfortran))
6990 (home-page "https://cran.r-project.org/web/packages/signal/")
6991 (synopsis "Signal processing")
6993 "This package provides a set of signal processing functions originally
6994 written for Matlab and GNU Octave. It includes filter generation utilities,
6995 filtering functions, resampling routines, and visualization of filter models.
6996 It also includes interpolation functions.")
6997 (license license:gpl2)))
6999 (define-public r-gsubfn
7006 (uri (cran-uri "gsubfn" version))
7009 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
7010 (build-system r-build-system)
7011 (propagated-inputs (list r-proto))
7012 (home-page "https://code.google.com/archive/p/gsubfn/")
7013 (synopsis "Utilities for strings and function arguments.")
7015 "This package provides @code{gsubfn} which is like @code{gsub} but can
7016 take a replacement function or certain other objects instead of the
7017 replacement string. Matches and back references are input to the replacement
7018 function and replaced by the function output. @code{gsubfn} can be used to
7019 split strings based on content rather than delimiters and for quasi-perl-style
7020 string interpolation. The package also has facilities for translating
7021 formulas to functions and allowing such formulas in function calls instead of
7023 (license license:gpl2+)))
7025 (define-public r-sqldf
7032 (uri (cran-uri "sqldf" version))
7035 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
7036 (build-system r-build-system)
7038 (list r-chron r-dbi r-gsubfn r-proto r-rsqlite))
7039 (home-page "https://github.com/ggrothendieck/sqldf")
7040 (synopsis "Manipulate R data frames using SQL")
7042 "The @code{sqldf} function is typically passed a single argument which is
7043 an SQL select statement where the table names are ordinary R data frame names.
7044 @code{sqldf} transparently sets up a database, imports the data frames into
7045 that database, performs the SQL statement and returns the result using a
7046 heuristic to determine which class to assign to each column of the returned
7047 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
7048 used to read filtered files into R even if the original files are larger than
7049 R itself can handle.")
7050 (license license:gpl2)))
7052 (define-public r-abind
7059 (uri (cran-uri "abind" version))
7062 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
7063 (build-system r-build-system)
7064 (home-page "https://cran.r-project.org/web/packages/abind/")
7065 (synopsis "Combine multidimensional arrays")
7067 "This package provides tools to combine multidimensional arrays into a
7068 single array. This is a generalization of @code{cbind} and @code{rbind}. It
7069 works with vectors, matrices, and higher-dimensional arrays. It also provides
7070 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
7071 extracting and replacing data in arrays.")
7072 (license license:lgpl2.0+)))
7074 (define-public r-prroc
7081 (uri (cran-uri "PRROC" version))
7084 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
7085 (properties `((upstream-name . "PRROC")))
7086 (build-system r-build-system)
7087 (home-page "https://cran.r-project.org/web/packages/PRROC/")
7088 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
7090 "This package computes the areas under the @dfn{precision-recall} (PR)
7091 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
7092 contrast to other implementations, the interpolation between points of the PR
7093 curve is done by a non-linear piecewise function. In addition to the areas
7094 under the curves, the curves themselves can also be computed and plotted by a
7095 specific S3-method.")
7096 (license license:gpl3)))
7098 (define-public r-vim
7105 (uri (cran-uri "VIM" version))
7108 "0fbpm6y3hhiw8srnbc38k19b859jcqzsh78ib8yvj86gck5av0bm"))))
7109 (properties `((upstream-name . "VIM")))
7110 (build-system r-build-system)
7127 (home-page "https://github.com/alexkowa/VIM")
7128 (synopsis "Visualization and imputation of missing values")
7130 "This package provides tools for the visualization of missing and/or
7131 imputed values are introduced, which can be used for exploring the data and
7132 the structure of the missing and/or imputed values. Depending on this
7133 structure of the missing values, the corresponding methods may help to
7134 identify the mechanism generating the missing values and explore the
7135 data including missing values. In addition, the quality of imputation can be
7136 visually explored using various univariate, bivariate, multiple and
7137 multivariate plot methods.")
7138 (license license:gpl2+)))
7140 (define-public r-fnn
7147 (uri (cran-uri "FNN" version))
7150 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
7151 (properties `((upstream-name . "FNN")))
7152 (build-system r-build-system)
7153 (home-page "https://cran.r-project.org/web/packages/FNN")
7154 (synopsis "Fast nearest neighbor search algorithms and applications")
7156 "This package provides cover-tree and kd-tree fast k-nearest neighbor
7157 search algorithms. Related applications including KNN classification,
7158 regression and information measures are implemented.")
7159 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
7160 ;; later can be used.
7161 (license license:gpl2+)))
7163 (define-public r-smoother
7170 (uri (cran-uri "smoother" version))
7173 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
7174 (build-system r-build-system)
7177 (home-page "https://cran.r-project.org/web/packages/smoother")
7178 (synopsis "Functions relating to the smoothing of numerical data")
7180 "This package provides a collection of methods for smoothing numerical
7181 data, commencing with a port of the Matlab gaussian window smoothing function.
7182 In addition, several functions typically used in smoothing of financial data
7184 (license license:gpl2)))
7186 (define-public r-riverplot
7188 (name "r-riverplot")
7193 (uri (cran-uri "riverplot" version))
7196 "04ap1dsa7fx03l73jhv1ql3adaaaz2100qawdplxa9xmrllgcgbj"))))
7197 (build-system r-build-system)
7199 (list r-rcolorbrewer))
7202 (home-page "https://logfc.wordpress.com")
7203 (synopsis "Sankey or ribbon plots")
7205 "Sankey plots are a type of diagram that is convenient to illustrate how
7206 flow of information, resources etc. separates and joins, much like observing
7207 how rivers split and merge. For example, they can be used to compare
7208 different clusterings. This package provides an implementation of Sankey
7210 (license license:gpl2+)))
7212 (define-public r-dyn
7219 (uri (cran-uri "dyn" version))
7222 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
7223 (build-system r-build-system)
7226 (home-page "https://cran.r-project.org/web/packages/dyn")
7227 (synopsis "Time series regression")
7229 "This package provides the dyn class interfaces @code{ts}, @code{irts},
7230 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
7231 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
7232 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
7233 @code{randomForest::randomForest()} and other regression functions, allowing
7234 those functions to be used with time series including specifications that may
7235 contain lags, diffs and missing values.")
7237 (license license:gpl2+)))
7239 (define-public r-catdap
7246 (uri (cran-uri "catdap" version))
7249 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
7250 (build-system r-build-system)
7253 (home-page "https://cran.r-project.org/web/packages/catdap/")
7254 (synopsis "Tools for categorical data analysis")
7256 "This package provides functions for analyzing multivariate data.
7257 Dependencies of the distribution of the specified variable (response
7258 variable) to other variables (explanatory variables) are derived and
7259 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
7260 (license license:gpl2+)))
7262 (define-public r-arules
7269 (uri (cran-uri "arules" version))
7272 "0zzwr1mg92ha5l6razdb04da8ik3z3k74rm0rah44l1j2a6d30sk"))))
7273 (build-system r-build-system)
7275 (list r-generics r-matrix))
7276 (home-page "https://github.com/mhahsler/arules")
7277 (synopsis "Mining association rules and frequent itemsets")
7279 "This package provides an infrastructure for representing, manipulating
7280 and analyzing transaction data and patterns (frequent itemsets and association rules).
7281 It also provides C implementations of the association mining algorithms Apriori
7283 (license license:gpl3)))
7285 (define-public r-parsedate
7287 (name "r-parsedate")
7292 (uri (cran-uri "parsedate" version))
7295 "05l6f1n3dsm383w7jfg3j38klvmzzfvc7qi9zr5ij13rljj8s1vb"))))
7296 (build-system r-build-system)
7299 (home-page "https://github.com/gaborcsardi/parsedate")
7301 "Recognize and parse dates in various formats")
7303 "This package provides three functions for dealing with dates:
7304 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
7305 time formats, @code{parse_date} parses dates in unspecified formats,
7306 and @code{format_iso_8601} formats a date in ISO 8601 format.")
7307 (license license:gpl2)))
7309 (define-public r-abc-data
7316 (uri (cran-uri "abc.data" version))
7319 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
7320 (properties `((upstream-name . "abc.data")))
7321 (build-system r-build-system)
7322 (home-page "https://cran.r-project.org/web/packages/abc.data/")
7323 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
7325 "This package contains data which are used by functions of the abc
7326 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
7327 algorithms for performing parameter estimation, model selection, and
7329 (license license:gpl3+)))
7331 (define-public r-abc
7338 (uri (cran-uri "abc" version))
7341 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
7342 (build-system r-build-system)
7344 (list r-abc-data r-locfit r-mass r-nnet r-quantreg))
7345 (home-page "https://cran.r-project.org/web/packages/abc/")
7346 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
7348 "This package implements several @dfn{Approximate Bayesian
7349 Computation} (ABC) algorithms for performing parameter estimation, model
7350 selection, and goodness-of-fit. Cross-validation tools are also available for
7351 measuring the accuracy of ABC estimates, and to calculate the
7352 misclassification probabilities of different models.")
7353 (license license:gpl3+)))
7355 (define-public r-zip
7362 (uri (cran-uri "zip" version))
7365 "1n5ryjdj3i16b4mdp29wapgaklz3yzas5k8ffx7q6fa0jry9i5cz"))))
7366 (build-system r-build-system)
7367 (home-page "https://github.com/gaborcsardi/zip")
7368 (synopsis "Cross-platform Zip compression")
7370 "This package provides a cross-platform Zip compression library for R.
7371 It is a replacement for the @code{zip} function, that does not require any
7372 additional external tools on any platform.")
7373 (license license:cc0)))
7375 (define-public r-openxlsx
7382 (uri (cran-uri "openxlsx" version))
7385 "0vn8ifxb7ccip6b1ijf5lpa6c0n5y5ll8fbabybsb8nfc0y1nmxg"))))
7386 (build-system r-build-system)
7388 (list r-rcpp r-stringi r-zip))
7391 (home-page "https://github.com/awalker89/openxlsx")
7392 (synopsis "Read, write and edit XLSX files")
7394 "This package simplifies the creation of Excel @code{.xlsx} files by
7395 providing a high level interface to writing, styling and editing worksheets.
7396 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
7397 and @code{XLConnect} packages with the added benefit of removing the
7398 dependency on Java.")
7399 (license license:gpl3)))
7401 (define-public r-rio
7408 (uri (cran-uri "rio" version))
7411 "04jlrhyl0791yxwcpp1s8p1hhkljnijlc5iaxpk56h41w63k39lz"))))
7412 (build-system r-build-system)
7423 (home-page "https://github.com/leeper/rio")
7424 (synopsis "Swiss-army knife for data I/O")
7426 "This package provides streamlined data import and export infrastructure
7427 by making assumptions that the user is probably willing to make: @code{import}
7428 and @code{export} determine the data structure from the file extension,
7429 reasonable defaults are used for data import and export (e.g.,
7430 @code{stringsAsFactors=FALSE}), web-based import is natively
7431 supported (including from SSL/HTTPS), compressed files can be read directly
7432 without explicit decompression, and fast import packages are used where
7433 appropriate. An additional convenience function, @code{convert}, provides a
7434 simple method for converting between file types.")
7435 (license license:gpl2)))
7437 (define-public r-maptools
7444 (uri (cran-uri "maptools" version))
7447 "0fa4a43zax8gn3jdp4ngqav61x4g6l33bg9wzqbngkbjhipck59r"))))
7448 (build-system r-build-system)
7450 (list r-foreign r-lattice r-sp))
7451 (home-page "https://r-forge.r-project.org/projects/maptools/")
7452 (synopsis "Tools for reading and handling spatial objects")
7454 "This package provides a set of tools for manipulating and reading
7455 geographic data, in particular ESRI Shapefiles. It includes binary access to
7456 GSHHG shoreline files. The package also provides interface wrappers for
7457 exchanging spatial objects with other R packages.")
7458 ;; The C source files from shapelib are released under the Expat license.
7459 ;; The R code is released under GPL version 2 or later.
7460 (license (list license:gpl2+
7463 (define-public r-later
7470 (uri (cran-uri "later" version))
7473 "0acqg29hcm2iq1418b54np7zb5pnr3xzrwc3ijv2pz9wra10ix88"))))
7474 (build-system r-build-system)
7476 (list r-rcpp r-rlang))
7479 (home-page "https://github.com/r-lib/later")
7480 (synopsis "Utilities for delaying function execution")
7482 "This package provides tools to execute arbitrary R or C functions some
7483 time after the current time, after the R execution stack has emptied.")
7484 (license license:gpl2+)))
7486 (define-public r-promises
7493 (uri (cran-uri "promises" version))
7496 "1dy4cbqw17awh4q8m7cy3anaj0n9iynabfzflb1g94cyj0bq4fld"))))
7497 (build-system r-build-system)
7499 (list r-later r-magrittr r-r6 r-rcpp r-rlang))
7502 (home-page "https://rstudio.github.io/promises")
7503 (synopsis "Abstractions for promise-based asynchronous programming")
7505 "This package provides fundamental abstractions for doing asynchronous
7506 programming in R using promises. Asynchronous programming is useful for
7507 allowing a single R process to orchestrate multiple tasks in the background
7508 while also attending to something else. Semantics are similar to JavaScript
7509 promises, but with a syntax that is idiomatic R.")
7510 (license license:expat)))
7512 (define-public r-dosnow
7519 (uri (cran-uri "doSNOW" version))
7522 "0f07b38cl7s61vwzkyqkzzsic9g4sw9k6ndbxk3g90l4ca0d1ljc"))))
7523 (properties `((upstream-name . "doSNOW")))
7524 (build-system r-build-system)
7526 (list r-foreach r-iterators r-snow))
7527 (home-page "https://cran.r-project.org/web/packages/doSNOW")
7528 (synopsis "Foreach parallel adaptor for the snow package")
7530 "This package provides a parallel backend for the @code{%dopar%} function
7531 using the @code{snow} package.")
7532 (license license:gpl2)))
7534 (define-public r-fst
7541 (uri (cran-uri "fst" version))
7544 "0vwclzxww8mw9nnpyj29bn71mrr8jjg7ka03979h9rbzw6d9bjrr"))))
7545 (properties `((upstream-name . "fst")))
7546 (build-system r-build-system)
7547 (propagated-inputs (list r-rcpp))
7548 (home-page "http://www.fstpackage.org")
7549 (synopsis "Fast serialization of data frames")
7551 "The fst package for R provides a fast, easy and flexible way to
7552 serialize data frames. With access speeds of multiple GB/s, fst is
7553 specifically designed to unlock the potential of high speed solid state disks.
7554 Data frames stored in the fst format have full random access, both in column
7555 and rows. The fst format allows for random access of stored data and
7556 compression with the LZ4 and ZSTD compressors.")
7557 (license license:agpl3)))
7559 (define-public r-snowfall
7562 (version "1.84-6.1")
7565 (uri (cran-uri "snowfall" version))
7567 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
7568 (build-system r-build-system)
7571 (home-page "https://cran.r-project.org/web/packages/snowfall/")
7572 (synopsis "Easier cluster computing")
7573 (description "This package is a usability wrapper around snow for easier
7574 development of parallel R programs. This package offers e.g. extended error
7575 checks, and additional functions. All functions work in sequential mode, too,
7576 if no cluster is present or wished. The package is also designed as connector
7577 to the cluster management tool @code{sfCluster}, but can also used without
7579 (license license:gpl2+)))
7581 (define-public r-rgexf
7588 (uri (cran-uri "rgexf" version))
7591 "00c2zka1n3k7p1l0mlchr063s6x58p9r3fb64d4wgl4rvsq55q3f"))
7592 ;; Delete minified JavaScript files
7594 '(for-each delete-file
7595 '("inst/gexf-js/js/jquery-2.0.2.min.js"
7596 "inst/gexf-js/js/jquery-ui-1.10.3.custom.min.js"
7597 "inst/gexf-js/js/jquery.mousewheel.min.js")))))
7598 (properties `((upstream-name . "rgexf")))
7599 (build-system r-build-system)
7601 `(#:modules ((guix build utils)
7602 (guix build r-build-system)
7606 (modify-phases %standard-phases
7607 (add-after 'unpack 'process-javascript
7608 (lambda* (#:key inputs #:allow-other-keys)
7609 (invoke "unzip" "-d" "/tmp" (assoc-ref inputs "js-jquery-ui"))
7610 (with-directory-excursion "inst/gexf-js/js/"
7614 `((,(assoc-ref inputs "js-jquery")
7615 "jquery-2.0.2.min.js")
7616 ("/tmp/jquery-ui-1.10.3/ui/jquery-ui.js"
7617 "jquery-ui-1.10.3.custom.min.js")
7618 (,(assoc-ref inputs "js-jquery-mousewheel")
7619 "jquery.mousewheel.min.js"))))
7620 (lambda (sources targets)
7621 (for-each (lambda (source target)
7622 (format #true "Processing ~a --> ~a~%"
7624 (invoke "esbuild" source "--minify"
7625 (string-append "--outfile=" target)))
7626 sources targets)))))))))
7628 (list r-igraph r-servr r-xml))
7630 `(("r-knitr" ,r-knitr)
7631 ("esbuild" ,esbuild)
7636 (uri "https://code.jquery.com/jquery-2.0.2.js")
7639 "0v818bxpw48gdk8i95qqqij80r9jcgisi2r4ac6xnxca20h0gvfj"))))
7643 (uri "https://jqueryui.com/resources/download/jquery-ui-1.10.3.zip")
7646 "00xpfy0l69nj2yan4s8k65ldsrlfsjkmyw2dwcg93dc8mv454vxx"))))
7647 ("js-jquery-mousewheel"
7650 (uri "https://raw.githubusercontent.com/jquery/jquery-mousewheel/\
7651 3.0.6/jquery.mousewheel.js")
7654 "19lk5xy2s47bx8hsa7j6bg012f8yw6d770g230bcnm559kf4nc6v"))))))
7655 (home-page "https://gvegayon.github.io/rgexf")
7656 (synopsis "Build, import and export GEXF graph files")
7658 "Create, read and write GEXF (Graph Exchange XML Format) graph
7659 files (used in Gephi and others). It allows the user to easily build/read
7660 graph files including attributes, GEXF visual attributes (such as color, size,
7661 and position), network dynamics (for both edges and nodes) and edge weighting.
7662 Users can build/handle graphs element-by-element or massively through
7663 data-frames, visualize the graph on a web browser through gexf-js (a
7664 JavaScript library) and interact with the igraph package.")
7665 (license license:expat)))
7667 (define-public r-data-tree
7669 (name "r-data-tree")
7674 (uri (cran-uri "data.tree" version))
7677 "0pizmx2312zsym4m42b97q2184bg3hibvbdrblcga05xln84qrs0"))))
7678 (properties `((upstream-name . "data.tree")))
7679 (build-system r-build-system)
7681 (list r-r6 r-stringi))
7684 (home-page "https://github.com/gluc/data.tree")
7685 (synopsis "General purpose hierarchical data structure")
7687 "Create tree structures from hierarchical data, and traverse the tree in
7688 various orders. Aggregate, cumulate, print, plot, convert to and from
7689 data.frame and more. This is useful for decision trees, machine learning,
7690 finance, conversion from and to JSON, and many other applications.")
7691 (license license:gpl2+)))
7693 (define-public r-dtplyr
7700 (uri (cran-uri "dtplyr" version))
7703 "0cn7vxn92dcxrnabccla6ppf5x7pxfz6pjlmamp0imfphmr1ns4r"))))
7704 (properties `((upstream-name . "dtplyr")))
7705 (build-system r-build-system)
7719 (home-page "https://github.com/tidyverse/dtplyr")
7720 (synopsis "Data Table back-end for dplyr")
7722 "This package provides a @code{data.table} backend for @code{dplyr}. The
7723 goal of @code{dtplyr} is to allow you to write @code{dplyr} code that is
7724 automatically translated to the equivalent, but usually much faster,
7725 @code{data.table} code.")
7726 (license license:expat)))
7728 (define-public r-collapsibletree
7730 (name "r-collapsibletree")
7735 (uri (cran-uri "collapsibleTree" version))
7738 "0b65pbp1wnpsrayqi630ds4r98jvcvynnlp6wxdqrnnr9nzw5343"))
7741 ;; Delete minified JavaScript file
7742 (delete-file "inst/htmlwidgets/lib/d3-4.10.2/d3.min.js")
7745 `((upstream-name . "collapsibleTree")))
7746 (build-system r-build-system)
7749 (modify-phases %standard-phases
7750 (add-after 'unpack 'process-javascript
7751 (lambda* (#:key inputs #:allow-other-keys)
7752 (with-directory-excursion "inst/htmlwidgets/lib/d3-4.10.2/"
7753 (let ((source (assoc-ref inputs "d3.v4.js"))
7754 (target "d3.min.js"))
7755 (format #t "Processing ~a --> ~a~%"
7757 (invoke "esbuild" source "--minify"
7758 (string-append "--outfile=" target)))))))))
7760 (list r-data-tree r-htmlwidgets))
7762 `(("esbuild" ,esbuild)
7766 (uri "https://d3js.org/d3.v4.js")
7769 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
7770 (home-page "https://github.com/AdeelK93/collapsibleTree")
7771 (synopsis "Interactive collapsible tree diagrams using D3.js")
7773 "This is a package for interactive Reingold-Tilford tree diagrams created
7774 using D3.js, where every node can be expanded and collapsed by clicking on it.
7775 Tooltips and color gradients can be mapped to nodes using a numeric column in
7776 the source data frame.")
7777 (license license:gpl3+)))
7779 (define-public r-rappdirs
7786 (uri (cran-uri "rappdirs" version))
7789 "1161i3jgjvzjv4p8qbz9r976fnggkcrw3mlj4yd1h2svnijrz5a9"))))
7790 (build-system r-build-system)
7791 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
7792 (synopsis "Determine where to save data, caches, and logs")
7794 "This package provides an easy way to determine which directories on the
7795 user's computer should be used to save data, caches and logs. It is a port of
7796 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
7797 (license license:expat)))
7799 (define-public r-rastervis
7801 (name "r-rastervis")
7806 (uri (cran-uri "rasterVis" version))
7809 "1mg11njzajx9az6xjghjl2sna6wzs85ga8fhy9w43l2n8icsfbr2"))))
7810 (properties `((upstream-name . "rasterVis")))
7811 (build-system r-build-system)
7822 (home-page "https://oscarperpinan.github.io/rastervis/")
7823 (synopsis "Visualization methods for raster data")
7825 "This package provides methods for enhanced visualization and interaction
7826 with raster data. It implements visualization methods for quantitative data
7827 and categorical data, both for univariate and multivariate rasters. It also
7828 provides methods to display spatiotemporal rasters, and vector fields.")
7829 (license license:gpl3)))
7831 (define-public r-rentrez
7838 (uri (cran-uri "rentrez" version))
7841 "0x1g2f6hvkqqlb39z8m5qxhcvsizddic5i7rpqw0wy77xfbna9gv"))))
7842 (properties `((upstream-name . "rentrez")))
7843 (build-system r-build-system)
7845 (list r-httr r-jsonlite r-xml))
7848 (home-page "https://docs.ropensci.org/rentrez/")
7849 (synopsis "Entrez in R")
7851 "This package provides an R interface to the NCBI's EUtils API,
7852 allowing users to search databases like GenBank PubMed, process the results of
7853 those searches and pull data into their R sessions.")
7854 (license license:expat)))
7856 (define-public r-renv
7863 (uri (cran-uri "renv" version))
7866 "194hcxikdnna526bvyz9y60ccmmm9fib5g0w9dqivrg0fld23lyh"))))
7867 (properties `((upstream-name . "renv")))
7868 (build-system r-build-system)
7871 (home-page "https://rstudio.github.io/renv")
7872 (synopsis "Project environments")
7874 "This package provides a dependency management toolkit for R. Using
7875 renv, you can create and manage project-local R libraries, save the state of
7876 these libraries to a lockfile, and later restore your library as required.
7877 Together, these tools can help make your projects more isolated, portable, and
7879 (license license:expat)))
7881 (define-public r-learnr
7888 (uri (cran-uri "learnr" version))
7891 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
7892 (build-system r-build-system)
7908 (home-page "https://rstudio.github.io/learnr/")
7909 (synopsis "Interactive tutorials for R")
7911 "This package provides tools to create interactive tutorials using R
7912 Markdown. Use a combination of narrative, figures, videos, exercises, and
7913 quizzes to create self-paced tutorials for learning about R and R packages.")
7914 (license license:asl2.0)))
7916 (define-public r-analytics
7918 (name "r-analytics")
7923 (uri (cran-uri "analytics" version))
7926 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
7927 (build-system r-build-system)
7941 (home-page "https://cran.r-project.org/web/packages/analytics/")
7942 (synopsis "Collection of data analysis tools")
7944 "This package is a collection of data analysis tools. It includes tools
7945 for regression outlier detection in a fitted linear model, stationary
7946 bootstrap using a truncated geometric distribution, a comprehensive test for
7947 weak stationarity, column means by group, weighted biplots, and a heuristic to
7948 obtain a better initial configuration in non-metric MDS.")
7949 (license license:gpl2)))
7951 (define-public r-here
7958 (uri (cran-uri "here" version))
7960 (base32 "0srlr8h8qmr0wrmp7gs4g2ry5dni2hx8n947bik3s3a26f091v88"))))
7961 (properties `((upstream-name . "here")))
7962 (build-system r-build-system)
7963 (propagated-inputs (list r-rprojroot))
7964 (native-inputs (list r-knitr))
7965 (home-page "https://here.r-lib.org/")
7966 (synopsis "Simpler way to find files")
7968 "This package lets you construct paths to your project's files. Use the
7969 @code{here} function as a drop-in replacement for @code{file.path}, it will
7970 always locate the files relative to your project root.")
7971 (license license:expat)))
7973 (define-public r-reticulate
7975 (name "r-reticulate")
7980 (uri (cran-uri "reticulate" version))
7983 "0v7m2pv94lfqiw8rhz3c9g66vvz4qvih4vd29rhfk2phmcwpnvmh"))))
7984 (build-system r-build-system)
7985 (inputs (list python))
7996 (home-page "https://github.com/rstudio/reticulate")
7997 (synopsis "R interface to Python")
7999 "This package provides an interface from R to Python modules, classes,
8000 and functions. When calling into Python, R data types are automatically
8001 converted to their equivalent Python types. When values are returned from
8002 Python to R they are converted back to R types.")
8003 (license license:asl2.0)))
8005 (define-public r-bibtex
8012 (uri (cran-uri "bibtex" version))
8015 "0vdwx6808r73pk15263f33bkqbfmb08d8jkmr4d7h4ml414ikbbv"))))
8016 (build-system r-build-system)
8017 (propagated-inputs (list r-stringr))
8018 (home-page "https://github.com/romainfrancois/bibtex")
8019 (synopsis "Bibtex parser")
8020 (description "This package provides a utility for R to parse a bibtex
8022 (license license:gpl2+)))
8024 (define-public r-ggseqlogo
8026 (name "r-ggseqlogo")
8031 (uri (cran-uri "ggseqlogo" version))
8034 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
8035 (build-system r-build-system)
8036 (propagated-inputs (list r-ggplot2))
8037 (home-page "https://github.com/omarwagih/ggseqlogo")
8038 (synopsis "ggplot2 extension for drawing genetic sequence logos")
8040 "The range of functions provided by this package makes it possible to
8041 draw highly versatile genomic sequence logos. Features include, but are not
8042 limited to, modifying colour schemes and fonts used to draw the logo,
8043 generating multiple logo plots, and aiding the visualisation with annotations.
8044 Sequence logos can easily be combined with other ggplot2 plots.")
8045 ;; Unspecified version of the LGPL.
8046 (license license:lgpl3+)))
8048 (define-public r-ggsci
8055 (uri (cran-uri "ggsci" version))
8058 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
8059 (build-system r-build-system)
8061 (list r-ggplot2 r-scales))
8062 (home-page "https://nanx.me/ggsci/")
8063 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
8065 "This package provides a collection of ggplot2 color palettes inspired by
8066 plots in scientific journals, data visualization libraries, science fiction
8067 movies, and TV shows.")
8068 (license license:gpl3)))
8070 (define-public r-ggsignif
8077 (uri (cran-uri "ggsignif" version))
8080 "1ad774c7s7y4i00xd89lfigr9aybl94q98ch598k3rchanr4b1fa"))))
8081 (build-system r-build-system)
8086 (home-page "https://github.com/const-ae/ggsignif")
8087 (synopsis "Significance brackets for ggplot2")
8089 "Enrich your ggplots with group-wise comparisons. This package provides
8090 an easy way to indicate if two groups are significantly different. Commonly
8091 this is shown by a bracket on top connecting the groups of interest which
8092 itself is annotated with the level of significance. The package provides a
8093 single layer that takes the groups for comparison and the test as arguments
8094 and adds the annotation to the plot.")
8095 (license license:gpl3)))
8097 (define-public r-rstatix
8104 (uri (cran-uri "rstatix" version))
8107 "0330y8iziffqg8j9j5h9zv4qcdyf8ybhmzxrr9fzq9nc6bf1gbm5"))))
8108 (properties `((upstream-name . "rstatix")))
8109 (build-system r-build-system)
8122 (home-page "https://rpkgs.datanovia.com/rstatix/")
8123 (synopsis "Pipe-friendly framework for basic statistical tests")
8125 "This package provides a simple and intuitive pipe-friendly framework,
8126 coherent with the @code{tidyverse} design philosophy, for performing basic
8127 statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and
8128 correlation analyses. The output of each test is automatically transformed
8129 into a tidy data frame to facilitate visualization. Additional functions are
8130 available for reshaping, reordering, manipulating and visualizing correlation
8132 (license license:gpl2)))
8134 (define-public r-ggpubr
8141 (uri (cran-uri "ggpubr" version))
8144 "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb"))))
8145 (build-system r-build-system)
8163 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
8164 (synopsis "ggplot2-based publication-ready plots")
8166 "The ggplot2 package is an excellent and flexible package for elegant
8167 data visualization in R. However the default generated plots require some
8168 formatting before we can send them for publication. The ggpubr package
8169 provides some easy-to-use functions for creating and customizing ggplot2-based
8170 publication-ready plots.")
8171 (license license:gpl2)))
8173 (define-public r-ellipse
8180 (uri (cran-uri "ellipse" version))
8183 "1wm5v7zdv2drgdba7z96jwsx74mqhlq80qgrvdb4vb5r02dcw68p"))))
8184 (build-system r-build-system)
8185 (home-page "https://cran.r-project.org/web/packages/ellipse/")
8186 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
8188 "This package contains various routines for drawing ellipses and
8189 ellipse-like confidence regions, implementing the plots described in Murdoch
8190 and Chow (1996), A graphical display of large correlation matrices, The
8191 American Statistician 50, 178-180. There are also routines implementing the
8192 profile plots described in Bates and Watts (1988), Nonlinear Regression
8193 Analysis and its Applications.")
8194 (license license:gpl2+)))
8196 (define-public r-flashclust
8198 (name "r-flashclust")
8203 (uri (cran-uri "flashClust" version))
8206 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
8207 (properties `((upstream-name . "flashClust")))
8208 (build-system r-build-system)
8209 (native-inputs (list gfortran))
8210 (home-page "https://cran.r-project.org/web/packages/flashClust/")
8211 (synopsis "Implementation of optimal hierarchical clustering")
8213 "This package provides a fast implementation of hierarchical
8215 (license license:gpl2+)))
8217 (define-public r-factominer
8219 (name "r-factominer")
8224 (uri (cran-uri "FactoMineR" version))
8227 "0lg8n9fxxk46nchnj4pbpqqf4swxfsq7r9jzr36dmd36kb7avqxr"))))
8228 (properties `((upstream-name . "FactoMineR")))
8229 (build-system r-build-system)
8244 (home-page "http://factominer.free.fr")
8245 (synopsis "Multivariate exploratory data analysis and data mining")
8247 "This package provides exploratory data analysis methods to summarize,
8248 visualize and describe datasets. The main principal component methods are
8249 available, those with the largest potential in terms of applications:
8250 principal component analysis (PCA) when variables are quantitative,
8251 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
8252 variables are categorical, Multiple Factor Analysis when variables are
8253 structured in groups, etc. and hierarchical cluster analysis.")
8254 (license license:gpl2+)))
8256 (define-public r-factoextra
8258 (name "r-factoextra")
8263 (uri (cran-uri "factoextra" version))
8266 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
8267 (build-system r-build-system)
8278 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
8279 (synopsis "Extract and visualize the results of multivariate data analyses")
8281 "This package provides some easy-to-use functions to extract and
8282 visualize the output of multivariate data analyses, including
8283 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
8284 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
8285 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
8286 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
8287 packages. It contains also functions for simplifying some clustering analysis
8288 steps and provides ggplot2-based elegant data visualization.")
8289 (license license:gpl2)))
8291 (define-public r-fansi
8298 (uri (cran-uri "fansi" version))
8301 "0kx5kjhr8dvqz1mq1zkijkgp29jv8b0irm1xplx1d74n2v1zh6wx"))))
8302 (build-system r-build-system)
8304 (list r-knitr)) ; for vignettes
8305 (home-page "https://github.com/brodieG/fansi")
8306 (synopsis "ANSI control sequence aware string functions")
8308 "This package provides counterparts to R string manipulation functions
8309 that account for the effects of ANSI text formatting control sequences.")
8310 (license license:gpl2+)))
8312 (define-public r-nbclust
8319 (uri (cran-uri "NbClust" version))
8322 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
8323 (properties `((upstream-name . "NbClust")))
8324 (build-system r-build-system)
8325 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
8326 (synopsis "Determine the best number of clusters in a data set")
8328 "NbClust provides 30 indexes for determining the optimal number of
8329 clusters in a data set and offers the best clustering scheme from different
8330 results to the user.")
8331 (license license:gpl2)))
8333 (define-public r-hdf5r
8340 (uri (cran-uri "hdf5r" version))
8343 "0bv2q4ir73sbk5ra2q4mc8wbcmiwkws8k0mjlnx9ysi2mdrm3dw7"))))
8344 (build-system r-build-system)
8348 (list r-bit64 r-r6))
8351 (home-page "https://hhoeflin.github.io/hdf5r")
8352 (synopsis "Interface to the HDF5 binary data format")
8354 "HDF5 is a data model, library and file format for storing and managing
8355 large amounts of data. This package provides a nearly feature complete,
8356 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
8357 functionality is added so that HDF5 objects behave very similar to their
8358 corresponding R counterparts.")
8359 (license license:asl2.0)))
8361 (define-public r-itertools
8363 (name "r-itertools")
8368 (uri (cran-uri "itertools" version))
8371 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
8372 (build-system r-build-system)
8375 (home-page "https://cran.r-project.org/web/packages/itertools/")
8376 (synopsis "Iterator tools")
8378 "This package provides various tools for creating iterators, many
8379 patterned after functions in the Python @code{itertools} module, and others
8380 patterned after functions in the snow package.")
8381 (license license:gpl2)))
8383 (define-public r-polynom
8390 (uri (cran-uri "polynom" version))
8393 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
8394 (build-system r-build-system)
8395 (home-page "https://cran.r-project.org/web/packages/polynom/")
8396 (synopsis "Functions for univariate polynomial manipulations")
8398 "This package provides a collection of functions to implement a class for
8399 univariate polynomial manipulations.")
8400 (license license:gpl2)))
8402 (define-public r-gbrd
8409 (uri (cran-uri "gbRd" version))
8412 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
8413 (properties `((upstream-name . "gbRd")))
8414 (build-system r-build-system)
8415 (home-page "https://cran.r-project.org/web/packages/gbRd/")
8416 (synopsis "Utilities for processing Rd objects and files")
8418 "This package provides utilities for processing Rd objects and files.
8419 Extract argument descriptions and other parts of the help pages of
8421 (license license:gpl2+)))
8423 (define-public r-rjags
8430 (uri (cran-uri "rjags" version))
8433 "041y4zfr50y96g0kl857jcba0a3gpdpk8qfn9fj8zxzbz71k87xr"))))
8434 (build-system r-build-system)
8441 (home-page "http://mcmc-jags.sourceforge.net")
8442 (synopsis "Bayesian graphical models using MCMC")
8444 "This package provides an R interface to the JAGS MCMC library. JAGS is
8445 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
8446 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
8447 (license license:gpl2)))
8449 (define-public r-rbibutils
8451 (name "r-rbibutils")
8456 (uri (cran-uri "rbibutils" version))
8459 "15yyihk0dgz3yyqz28r5nc6m99zcywpabnabf18phbs7rb87p7mv"))))
8460 (properties `((upstream-name . "rbibutils")))
8461 (build-system r-build-system)
8462 (home-page "https://geobosh.github.io/rbibutils/")
8463 (synopsis "Convert between bibliography formats")
8465 "This package converts between a number of bibliography formats,
8466 including BibTeX, BibLaTeX and Bibentry. It includes a port of the bibutils
8467 utilities and supports all bibliography formats and character encodings
8468 implemented in bibutils.")
8469 (license license:gpl2)))
8471 (define-public r-rdpack
8478 (uri (cran-uri "Rdpack" version))
8481 "0s51c5fw1ka75b8cxk5bh27h6wcy5169yl93sjlxji2k27n9fj3i"))))
8482 (properties `((upstream-name . "Rdpack")))
8483 (build-system r-build-system)
8486 (home-page "https://github.com/GeoBosh/Rdpack")
8487 (synopsis "Update and manipulate Rd documentation objects")
8489 "This package provides functions for manipulation of R documentation
8490 objects, including functions @code{reprompt()} and @code{ereprompt()} for
8491 updating Rd documentation for functions, methods and classes; it also includes
8492 Rd macros for citations and import of references from bibtex files for use in
8493 Rd files and roxygen2 comments, as well as many functions for manipulation of
8494 references and Rd files.")
8495 (license license:gpl2+)))
8497 (define-public r-officer
8504 (uri (cran-uri "officer" version))
8507 "1gfx299zr4q2264q37994pirv5bd5isn1cszccz603ij3q40wajr"))))
8508 (build-system r-build-system)
8510 (list r-r6 r-uuid r-xml2 r-zip))
8513 (home-page "https://davidgohel.github.io/officer")
8514 (synopsis "Manipulation of Word and PowerPoint documents")
8516 "This package provides tools to access and manipulate Word and PowerPoint
8517 documents from R. The package focuses on tabular and graphical reporting from
8518 R; it also provides two functions that let users get document content into
8519 data objects. A set of functions lets add and remove images, tables and
8520 paragraphs of text in new or existing documents. When working with PowerPoint
8521 presentations, slides can be added or removed; shapes inside slides can also
8522 be added or removed. When working with Word documents, a cursor can be used
8523 to help insert or delete content at a specific location in the document.")
8524 (license license:gpl3)))
8526 (define-public r-profilemodel
8528 (name "r-profilemodel")
8533 (uri (cran-uri "profileModel" version))
8536 "01m5nb8cmq0aq555pxk2a99182si65hhmn68yn9nal2j3zl2bp4i"))))
8537 (properties `((upstream-name . "profileModel")))
8538 (build-system r-build-system)
8539 (home-page "https://github.com/ikosmidis/profileModel")
8540 (synopsis "Profiling inference functions for various model classes")
8542 "This package provides tools that can be used to calculate, evaluate,
8543 plot and use for inference the profiles of *arbitrary* inference functions for
8544 arbitrary @code{glm}-like fitted models with linear predictors. More information
8545 on the methods that are implemented can be found in Kosmidis (2008)
8546 @url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.")
8547 (license license:gpl2+)))
8549 (define-public r-brglm
8556 (uri (cran-uri "brglm" version))
8559 "08shcz0j1npdn7xkhsvlzs3z4rdwq3g4rk6a4xx8wirqw8n8s2an"))))
8560 (properties `((upstream-name . "brglm")))
8561 (build-system r-build-system)
8563 (list r-profilemodel))
8564 (home-page "https://github.com/ikosmidis/brglm")
8565 (synopsis "Bias reduction in binomial-response generalized linear models")
8567 "Fit generalized linear models with binomial responses using either an
8568 adjusted-score approach to bias reduction or maximum penalized likelihood
8569 where penalization is by Jeffreys invariant prior. These procedures return
8570 estimates with improved frequentist properties (bias, mean squared error) that
8571 are always finite even in cases where the maximum likelihood estimates are
8572 infinite (data separation). Fitting takes place by fitting generalized linear
8573 models on iteratively updated pseudo-data. The interface is essentially the
8574 same as @code{glm}. More flexibility is provided by the fact that custom
8575 pseudo-data representations can be specified and used for model fitting.
8576 Functions are provided for the construction of confidence intervals for the
8577 reduced-bias estimates.")
8578 (license license:gpl2+)))
8580 (define-public r-entropy
8587 (uri (cran-uri "entropy" version))
8590 "1f0j8jsn6pzf4gi5g0akixx6x5vc69ci5f4m2vnwp40frvsqjnkg"))))
8591 (properties `((upstream-name . "entropy")))
8592 (build-system r-build-system)
8593 (home-page "https://www.strimmerlab.org/software/entropy/")
8594 (synopsis "Estimation of entropy, mutual information and related quantities")
8596 "This package implements various estimators of entropy, such as the
8597 shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the
8598 Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen
8599 estimator. It also offers an R interface to the NSB estimator. Furthermore,
8600 it provides functions for estimating Kullback-Leibler divergence, chi-squared,
8601 mutual information, and chi-squared statistic of independence. In addition
8602 there are functions for discretizing continuous random variables.")
8603 (license license:gpl3+)))
8605 (define-public r-acd
8612 (uri (cran-uri "ACD" version))
8615 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
8616 (properties `((upstream-name . "ACD")))
8617 (build-system r-build-system)
8618 (home-page "https://cran.r-project.org/web/packages/ACD/")
8619 (synopsis "Categorical data analysis with complete or missing responses")
8621 "This package provides tools for categorical data analysis with complete
8622 or missing responses.")
8623 (license license:gpl2+)))
8625 (define-public r-acdm
8632 (uri (cran-uri "ACDm" version))
8635 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
8636 (properties `((upstream-name . "ACDm")))
8637 (build-system r-build-system)
8639 (list r-dplyr r-ggplot2 r-plyr r-rsolnp r-zoo))
8640 (home-page "https://cran.r-project.org/web/packages/ACDm/")
8641 (synopsis "Tools for Autoregressive Conditional Duration Models")
8643 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
8644 and Russell, 1998) models. It creates trade, price or volume durations from
8645 transactions (tic) data, performs diurnal adjustments, fits various ACD models
8647 (license license:gpl2+)))
8649 (define-public r-overlap
8656 (uri (cran-uri "overlap" version))
8659 "1arxprhz035ab78ks88n6scwnlwmnb97mlac5gsx90ipb6gkgcyk"))))
8660 (build-system r-build-system)
8661 (home-page "https://cran.r-project.org/web/packages/overlap/")
8662 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
8664 "This package provides functions to fit kernel density functions to data
8665 on temporal activity patterns of animals; estimate coefficients of overlapping
8666 of densities for two species; and calculate bootstrap estimates of confidence
8668 (license license:gpl3+)))
8670 (define-public r-snakecase
8672 (name "r-snakecase")
8677 (uri (cran-uri "snakecase" version))
8680 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
8681 (build-system r-build-system)
8683 (list r-stringi r-stringr))
8684 (home-page "https://github.com/Tazinho/snakecase")
8685 (synopsis "Convert strings into any case")
8687 "This package provides a consistent, flexible and easy to use tool to
8688 parse and convert strings into cases like snake or camel among others.")
8689 (license license:gpl3)))
8691 (define-public r-prediction
8693 (name "r-prediction")
8698 (uri (cran-uri "prediction" version))
8701 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
8702 (build-system r-build-system)
8704 (list r-data-table))
8705 (home-page "https://github.com/leeper/prediction")
8706 (synopsis "Tidy, type-safe prediction methods")
8708 "This package provides the @code{prediction()} function, a type-safe
8709 alternative to @code{predict()} that always returns a data frame. The package
8710 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
8711 from the @code{stats} package, as well as numerous other model classes from
8712 other add-on packages.")
8713 (license license:expat)))
8715 (define-public r-insight
8722 (uri (cran-uri "insight" version))
8725 "10kc72g2hfsiipba4kalda1wxsb01nq2ax2yim386bkk0vjszwfx"))))
8726 (build-system r-build-system)
8729 (home-page "https://easystats.github.io/insight/")
8730 (synopsis "Easy access to model information for various model objects")
8732 "This package provides a tool to provide an easy, intuitive and
8733 consistent access to information contained in various R models, like model
8734 formulas, model terms, information about random effects, data that was used to
8735 fit the model or data from response variables. The package mainly revolves
8736 around two types of functions: Functions that find (the names of) information,
8737 starting with @code{find_}, and functions that get the underlying data,
8738 starting with @code{get_}. The package has a consistent syntax and works with
8739 many different model objects, where otherwise functions to access these
8740 information are missing.")
8741 (license license:gpl3)))
8743 (define-public r-sjlabelled
8745 (name "r-sjlabelled")
8750 (uri (cran-uri "sjlabelled" version))
8753 "17gskxr43rgbg7syla3b78g2qgksq2kj07iad4139xycqxblxya0"))))
8754 (build-system r-build-system)
8759 (home-page "https://github.com/strengejacke/sjlabelled")
8760 (synopsis "Labelled data utility functions")
8762 "This package provides a collection of functions dealing with labelled
8763 data, like reading and writing data between R and other statistical software
8764 packages. This includes easy ways to get, set or change value and variable
8765 label attributes, to convert labelled vectors into factors or numeric (and
8766 vice versa), or to deal with multiple declared missing values.")
8767 (license license:gpl3)))
8769 (define-public r-sjmisc
8776 (uri (cran-uri "sjmisc" version))
8779 "17hcjb2j690qi2zrkwc14sr1wsid6dy6v7bfsf0bc94ql812k8g2"))))
8780 (build-system r-build-system)
8791 (home-page "https://github.com/strengejacke/sjmisc")
8792 (synopsis "Data and variable transformation functions")
8794 "This package is a collection of miscellaneous utility functions,
8795 supporting data transformation tasks like recoding, dichotomizing or grouping
8796 variables, setting and replacing missing values. The data transformation
8797 functions also support labelled data, and all integrate seamlessly into a
8798 tidyverse workflow.")
8799 (license license:gpl3)))
8801 (define-public r-nortest
8808 (uri (cran-uri "nortest" version))
8811 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
8812 (build-system r-build-system)
8813 (home-page "https://cran.r-project.org/web/packages/nortest/")
8814 (synopsis "Tests for normality")
8816 "This package provides five omnibus tests for testing the composite
8817 hypothesis of normality.")
8818 (license license:gpl2+)))
8820 (define-public r-moonbook
8827 (uri (cran-uri "moonBook" version))
8830 "0z78pzc8sr2g19xjdd9cmai4iqyifmh79gj8x40ddww6a27dalry"))))
8831 (properties `((upstream-name . "moonBook")))
8832 (build-system r-build-system)
8842 (home-page "https://github.com/cardiomoon/moonBook")
8843 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
8845 "This package provides several analysis-related functions for the book
8846 entitled \"R statistics and graph for medical articles\" (written in Korean),
8847 version 1, by Keon-Woong Moon with Korean demographic data with several plot
8849 (license license:gpl2)))
8851 (define-public r-flextable
8853 (name "r-flextable")
8858 (uri (cran-uri "flextable" version))
8861 "01nm0357b0z4dgrplbq9ms63j51n0rgvvxyy068zdsc5p7j3lql2"))))
8862 (build-system r-build-system)
8876 (home-page "https://davidgohel.github.io/flextable")
8877 (synopsis "Functions for tabular reporting")
8879 "This package provides tools to create pretty tables for HTML documents
8880 and other formats. Functions are provided to let users create tables, modify
8881 and format their content. It extends the @code{officer} package and can be
8882 used within R markdown documents when rendering to HTML and to Word
8884 (license license:gpl3)))
8886 (define-public r-writexl
8893 (uri (cran-uri "writexl" version))
8896 "0mfzyn8n5x5x5gf382bqgq61zpw9dymrp5kzdm2sbszplmxf6xry"))))
8897 (build-system r-build-system)
8898 (inputs (list zlib))
8899 (home-page "https://github.com/ropensci/writexl")
8900 (synopsis "Export data frames to xlsx format")
8902 "This package provides a data frame to xlsx exporter based on
8904 (license license:bsd-2)))
8906 (define-public r-biasedurn
8908 (name "r-biasedurn")
8913 (uri (cran-uri "BiasedUrn" version))
8916 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
8917 (properties `((upstream-name . "BiasedUrn")))
8918 (build-system r-build-system)
8919 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
8920 (synopsis "Biased Urn model distributions")
8922 "This package provides statistical models of biased sampling in the form
8923 of univariate and multivariate noncentral hypergeometric distributions,
8924 including Wallenius' noncentral hypergeometric distribution and Fisher's
8925 noncentral hypergeometric distribution (also called extended hypergeometric
8927 (license license:gpl3)))
8929 (define-public r-goplot
8936 (uri (cran-uri "GOplot" version))
8939 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
8940 (properties `((upstream-name . "GOplot")))
8941 (build-system r-build-system)
8943 (list r-ggdendro r-ggplot2 r-gridextra r-rcolorbrewer))
8944 (home-page "https://github.com/wencke/wencke.github.io")
8945 (synopsis "Visualization of functional analysis data")
8947 "This package provides an implementation of multilayered visualizations
8948 for enhanced graphical representation of functional analysis data. It
8949 combines and integrates omics data derived from expression and functional
8950 annotation enrichment analyses. Its plotting functions have been developed
8951 with an hierarchical structure in mind: starting from a general overview to
8952 identify the most enriched categories (modified bar plot, bubble plot) to a
8953 more detailed one displaying different types of relevant information for the
8954 molecules in a given set of categories (circle plot, chord plot, cluster plot,
8955 Venn diagram, heatmap).")
8956 (license license:gpl2)))
8958 (define-public r-getopt
8965 (uri (cran-uri "getopt" version))
8968 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
8969 (build-system r-build-system)
8970 (home-page "https://github.com/trevorld/getopt")
8971 (synopsis "Command-line option processor for R")
8973 "This package is designed to be used with Rscript to write shebang
8974 scripts that accept short and long options. Many users will prefer to
8975 use the packages @code{optparse} or @code{argparse} which add extra
8976 features like automatically generated help options and usage texts,
8977 support for default values, positional argument support, etc.")
8978 (license license:gpl2+)))
8980 (define-public r-findpython
8982 (name "r-findpython")
8987 (uri (cran-uri "findpython" version))
8990 "0jf10jpqla90x03kl3k77gnd255zmw9rvr8d724vb17cqawh9yar"))))
8991 (build-system r-build-system)
8992 (home-page "https://github.com/trevorld/findpython")
8993 (synopsis "Functions to find an acceptable Python binary")
8995 "This package was designed to find an acceptable Python binary that
8996 matches version and feature constraints.")
8997 (license license:expat)))
8999 ;; This in not the same as "r-argparser"
9000 (define-public r-argparse
9007 (uri (cran-uri "argparse" version))
9010 "1cz5qlxw3v8smd5vb00wlzy02mx5i0infm5hnq55hnakffd3b5wr"))))
9011 (build-system r-build-system)
9012 (inputs (list python))
9014 (list r-findpython r-jsonlite r-r6))
9017 (home-page "https://github.com/trevorld/argparse")
9018 (synopsis "Command line optional and positional argument parser")
9020 "This package provides a command line parser to be used with Rscript to
9021 write shebang scripts that gracefully accept positional and optional arguments
9022 and automatically generate usage notices.")
9023 (license license:gpl2+)))
9025 (define-public r-hash
9032 (uri (cran-uri "hash" version))
9035 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
9036 (build-system r-build-system)
9037 (home-page "https://cran.r-project.org/web/packages/hash/")
9038 (synopsis "Implementation of hash/associated arrays/dictionaries")
9040 "This package implements a data structure similar to hashes in Perl and
9041 dictionaries in Python but with a purposefully R flavor. For objects of
9042 appreciable size, access using hashes outperforms native named lists and
9044 (license license:gpl2+)))
9046 (define-public r-orddom
9053 (uri (cran-uri "orddom" version))
9056 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
9057 (build-system r-build-system)
9058 (propagated-inputs (list r-psych))
9059 (home-page "https://cran.r-project.org/web/packages/orddom/")
9060 (synopsis "Ordinal dominance statistics")
9062 "This package provides tools to compute ordinal, statistics and effect
9063 sizes as an alternative to mean comparison: Cliff's delta or success rate
9064 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
9065 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
9066 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
9067 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
9068 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
9069 Group (Non-)Overlap considerations.")
9070 (license license:gpl2)))
9072 (define-public r-deriv
9079 (uri (cran-uri "Deriv" version))
9082 "130g3mv0z9sqs6y23a0a94512iiw05yr6fp378vhdxxbignzbnyv"))))
9083 (properties `((upstream-name . "Deriv")))
9084 (build-system r-build-system)
9085 (home-page "https://cran.r-project.org/web/packages/Deriv")
9086 (synopsis "Symbolic differentiation")
9088 "This package provides an R-based solution for symbolic differentiation.
9089 It admits user-defined functions as well as function substitution in arguments
9090 of functions to be differentiated. Some symbolic simplification is part of
9092 (license license:gpl3+)))
9094 (define-public r-doby
9101 (uri (cran-uri "doBy" version))
9104 "1xhjh2d7zfgw8wbcj5yfscvmwbjar1w544ika13da69dydm44j81"))))
9105 (properties `((upstream-name . "doBy")))
9106 (build-system r-build-system)
9121 (home-page "https://people.math.aau.dk/~sorenh/software/doBy/")
9122 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
9124 "This package contains:
9127 @item facilities for working with grouped data: @code{do}
9128 something to data stratified @code{by} some variables.
9129 @item implementations of least-squares means, general linear contrasts, and
9130 @item miscellaneous other utilities.
9132 (license license:gpl2+)))
9134 (define-public r-refgenome
9136 (name "r-refgenome")
9141 (uri (cran-uri "refGenome" version))
9144 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
9145 (properties `((upstream-name . "refGenome")))
9146 (build-system r-build-system)
9148 (list r-dbi r-doby r-rsqlite))
9149 (home-page "https://cran.r-project.org/web/packages/refGenome/")
9151 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
9153 "This package contains functionality for importing and managing of
9154 downloaded genome annotation data from the Ensembl genome browser (European
9155 Bioinformatics Institute) and from the UCSC genome browser (University of
9156 California, Santa Cruz) and annotation routines for genomic positions and
9157 splice site positions.")
9158 (license license:gpl2)))
9160 (define-public r-basix
9167 (uri (cran-uri "BASIX" version))
9170 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
9171 (properties `((upstream-name . "BASIX")))
9172 (build-system r-build-system)
9173 (home-page "https://cran.r-project.org/web/packages/BASIX/")
9174 (synopsis "Efficient C/C++ toolset for R")
9176 "BASIX provides some efficient C/C++ implementations of native R
9177 procedures to speed up calculations in R.")
9178 (license license:gpl2)))
9180 (define-public r-blockfest
9182 (name "r-blockfest")
9187 (uri (cran-uri "BlockFeST" version))
9190 "1fcl3yc1cf09znqbj787d3fd2kl5rp63la7pxawsgmap7nxwkp65"))))
9191 (properties `((upstream-name . "BlockFeST")))
9192 (build-system r-build-system)
9193 (propagated-inputs (list r-basix))
9194 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
9195 (synopsis "Bayesian calculation of region-specific fixation index")
9197 "This package provides an R implementation of an extension of the
9198 BayeScan software for codominant markers, adding the option to group
9199 individual SNPs into pre-defined blocks. A typical application of this new
9200 approach is the identification of genomic regions, genes, or gene sets
9201 containing one or more SNPs that evolved under directional selection.")
9202 (license license:gpl2)))
9204 (define-public r-proc
9211 (uri (cran-uri "pROC" version))
9214 "1abvbzdss12n64pp9vlgnn0q3abh0nj4n0a8cinwwvhphjrm9vym"))))
9215 (properties `((upstream-name . "pROC")))
9216 (build-system r-build-system)
9218 (list r-plyr r-rcpp))
9219 (home-page "https://web.expasy.org/pROC/")
9220 (synopsis "Display and analyze ROC curves")
9222 "This package provides tools for visualizing, smoothing and comparing
9223 receiver operating characteristic (ROC curves). The area under the
9224 curve (AUC) can be compared with statistical tests based on U-statistics or
9225 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
9226 (license license:gpl3+)))
9228 (define-public r-rootsolve
9230 (name "r-rootsolve")
9235 (uri (cran-uri "rootSolve" version))
9238 "182bb727sgqi5f3pzmw8jnn328wdjrgj9lfvg49gv8s22rjd3cxm"))))
9239 (properties `((upstream-name . "rootSolve")))
9240 (build-system r-build-system)
9241 (native-inputs (list gfortran))
9242 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
9243 (synopsis "Tools for the analysis of ordinary differential equations")
9245 "This package provides routines to find the root of nonlinear functions,
9246 and to perform steady-state and equilibrium analysis of @dfn{ordinary
9247 differential equations} (ODE). It includes routines that:
9250 @item generate gradient and jacobian matrices (full and banded),
9251 @item find roots of non-linear equations by the Newton-Raphson method,
9252 @item estimate steady-state conditions of a system of (differential) equations
9253 in full, banded or sparse form, using the Newton-Raphson method, or by
9254 dynamically running,
9255 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
9256 and 3-D partial differential equations, that have been converted to ordinary
9257 differential equations by numerical differencing (using the method-of-lines
9260 (license license:gpl2+)))
9262 (define-public r-abcanalysis
9264 (name "r-abcanalysis")
9269 (uri (cran-uri "ABCanalysis" version))
9271 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
9272 (properties `((upstream-name . "ABCanalysis")))
9273 (build-system r-build-system)
9274 (propagated-inputs (list r-plotrix))
9275 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
9276 (synopsis "Computed ABC Analysis")
9278 "Multivariate data sets often differ in several factors or derived statistical
9279 parameters, which have to be selected for a valid interpretation. Basing this
9280 selection on traditional statistical limits leads occasionally to the perception
9281 of losing information from a data set. This package provides tools to calculate
9282 these limits on the basis of the mathematical properties of the distribution of
9283 the analyzed items.")
9284 (license license:gpl3)))
9286 (define-public r-slam
9293 (uri (cran-uri "slam" version))
9295 (base32 "044hnfqbx57v5zr64gl09b5arj45swn9ywqzrl9rsc8267ys0028"))))
9296 (build-system r-build-system)
9297 (home-page "https://cran.r-project.org/web/packages/slam/")
9298 (synopsis "Sparse lightweight arrays and matrices")
9300 "This package contains data structures and algorithms for sparse arrays and matrices,
9301 based on index arrays and simple triplet representations, respectively.")
9302 (license license:gpl2)))
9304 (define-public r-manipulatewidget
9306 (name "r-manipulatewidget")
9311 (uri (cran-uri "manipulateWidget" version))
9313 (base32 "1dpgzmiv08afm57yxr017b014lfn9h3pa4w65prk5k3dgn6p4wsv"))))
9315 `((upstream-name . "manipulateWidget")))
9316 (build-system r-build-system)
9329 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
9330 (synopsis "Add even more interactivity to interactive charts")
9332 "This package lets you create in just a few lines of R code a nice user interface to
9333 modify the data or the graphical parameters of one or multiple interactive
9334 charts. It is useful to quickly explore visually some data or for package
9335 developers to generate user interfaces easy to maintain.")
9336 (license license:gpl2+)))
9345 (uri (cran-uri "A3" version))
9347 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
9348 (properties `((upstream-name . "A3")))
9349 (build-system r-build-system)
9351 (list r-pbapply r-xtable))
9352 (home-page "https://cran.r-project.org/web/packages/A3/")
9353 (synopsis "Error metrics for predictive models")
9355 "This package supplies tools for tabulating and analyzing the results of predictive
9356 models. The methods employed are applicable to virtually any predictive model
9357 and make comparisons between different methodologies straightforward.")
9358 (license license:gpl2+)))
9360 (define-public r-infotheo
9367 (uri (cran-uri "infotheo" version))
9370 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
9371 (build-system r-build-system)
9372 (home-page "http://homepage.meyerp.com/software")
9373 (synopsis "Information-theoretic measures")
9375 "This package implements various measures of information theory based on
9376 several entropy estimators.")
9377 (license license:gpl3+)))
9379 (define-public r-nsprcomp
9386 (uri (cran-uri "nsprcomp" version))
9389 "1zlc1ximx96f235c0l8qfs6vbp1kpnbf943wxsfahnnlnxvwi59f"))))
9390 (properties `((upstream-name . "nsprcomp")))
9391 (build-system r-build-system)
9392 (home-page "https://sigg-iten.ch/research/")
9393 (synopsis "Non-negative and sparse PCA")
9395 "This package implements two methods for performing a constrained
9396 principal component analysis (PCA), where non-negativity and/or sparsity
9397 constraints are enforced on the principal axes (PAs). The function
9398 @code{nsprcomp} computes one principal component (PC) after the other. Each
9399 PA is optimized such that the corresponding PC has maximum additional variance
9400 not explained by the previous components. In contrast, the function
9401 @code{nscumcomp} jointly computes all PCs such that the cumulative variance is
9402 maximal. Both functions have the same interface as the @code{prcomp} function
9403 from the @code{stats} package (plus some extra parameters).")
9404 (license license:gpl2+)))
9406 (define-public r-cmplot
9413 (uri (cran-uri "CMplot" version))
9416 "0d6ww8pdrawdg5acbhiyi2jpmapf2ghixy9mi4kmsq8yg36pksfh"))))
9417 (properties `((upstream-name . "CMplot")))
9418 (build-system r-build-system)
9419 (home-page "https://github.com/YinLiLin/CMplot")
9420 (synopsis "Circle Manhattan plot")
9422 "Circle Manhattan Plot is an R package that can lay out genome-wide
9423 association study P-value results in both traditional rectangular patterns,
9424 QQ-plot and novel circular ones. United in only one bull's eye style plot,
9425 association results from multiple traits can be compared interactively,
9426 thereby to reveal both similarities and differences between signals.
9427 Additional functions include: highlight signals, a group of SNPs, chromosome
9428 visualization and candidate genes around SNPs.")
9429 (license license:gpl2+)))
9431 (define-public r-precrec
9438 (uri (cran-uri "precrec" version))
9441 "0vwzaqnh9ymrm52dd79bihwqprnygz0d71ay8fv51hdw0zg6saya"))))
9442 (properties `((upstream-name . "precrec")))
9443 (build-system r-build-system)
9451 (native-inputs (list r-knitr))
9452 (home-page "https://evalclass.github.io/precrec/")
9453 (synopsis "Calculate accurate precision-recall and ROC curves")
9455 "This package provides tools for accurate calculations and visualization
9456 of precision-recall and ROC (Receiver Operator Characteristics) curves.")
9457 (license license:gpl3)))
9459 (define-public r-netrep
9466 (uri (cran-uri "NetRep" version))
9469 "1swlb2k9bc7whvslxbklz864j9ynvna73hvq5rhv61cv5vy05ksd"))))
9470 (properties `((upstream-name . "NetRep")))
9471 (build-system r-build-system)
9481 (native-inputs (list r-knitr))
9482 (home-page "https://cran.r-project.org/package=NetRep")
9483 (synopsis "Permutation testing network module preservation across datasets")
9485 "This package provides functions for assessing the
9486 replication/preservation of a network module's topology across datasets
9487 through permutation testing.")
9488 (license license:gpl2)))
9490 (define-public r-intergraph
9492 (name "r-intergraph")
9497 (uri (cran-uri "intergraph" version))
9500 "18a7xgb2rp0w9jl2rkh8nzyjprrs5w7h2iidvc8c38bzx3qpggkc"))))
9501 (properties `((upstream-name . "intergraph")))
9502 (build-system r-build-system)
9504 (list r-igraph r-network))
9507 (home-page "http://mbojan.github.io/intergraph")
9508 (synopsis "Coercion routines for network data objects")
9510 "Functions implemented in this package allow to coerce (i.e. convert)
9511 network data between classes provided by other R packages. Currently
9512 supported classes are those defined in packages @code{network} and
9514 (license license:gpl3)))
9516 (define-public r-abcoptim
9523 (uri (cran-uri "ABCoptim" version))
9525 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
9526 (properties `((upstream-name . "ABCoptim")))
9527 (build-system r-build-system)
9528 (propagated-inputs (list r-rcpp))
9529 (home-page "https://github.com/gvegayon/ABCoptim/")
9530 (synopsis "Optimization of Artificial Bee Colony algorithm")
9532 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
9533 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
9534 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
9535 algorithms, and uses only common control parameters such as colony size and
9536 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
9537 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
9538 This version is a work-in-progress and is written in R code.")
9539 (license license:expat)))
9541 (define-public r-abcp2
9548 (uri (cran-uri "ABCp2" version))
9550 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
9551 (properties `((upstream-name . "ABCp2")))
9552 (build-system r-build-system)
9553 (propagated-inputs (list r-mass))
9554 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
9555 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
9557 "This package tests the goodness of fit of a distribution of offspring to the Normal,
9558 Poisson, and Gamma distribution and estimates the proportional paternity of the
9559 second male (P2) based on the best fit distribution.")
9560 (license license:gpl2)))
9562 (define-public r-abcrf
9569 (uri (cran-uri "abcrf" version))
9571 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
9572 (build-system r-build-system)
9583 (home-page "https://cran.r-project.org/web/packages/abcrf/")
9584 (synopsis "Approximate bayesian computation via random forests")
9586 "This package performs approximate bayesian computation (ABC) model choice and
9587 parameter inference via random forests. This machine learning tool named random
9588 forests (RF) can conduct selection among the highly complex models covered by
9590 (license license:gpl2+)))
9592 (define-public r-abctools
9599 (uri (cran-uri "abctools" version))
9601 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
9602 (build-system r-build-system)
9604 (list r-abc r-abind r-hmisc r-plyr))
9605 (home-page "https://github.com/dennisprangle/abctools/")
9606 (synopsis "Tools for ABC analyses")
9608 "This @code{r-abctools} package provides tools for approximate Bayesian computation
9609 including summary statistic selection and assessing coverage. This includes
9610 recent dimension reduction algorithms to tune the choice of summary statistics,
9611 and coverage methods to tune the choice of threshold.")
9612 (license license:gpl2+)))
9614 (define-public r-ggstance
9621 (uri (cran-uri "ggstance" version))
9623 (base32 "0jz9vvnmcc6a38n8nzr458r65sna23bgn5r8mxdhzdlyqibihr7d"))))
9624 (build-system r-build-system)
9626 (list r-ggplot2 r-plyr r-rlang r-withr))
9627 (home-page "https://cran.r-project.org/web/packages/ggstance/")
9628 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
9630 "This package is a @code{r-ggplot2} extension that provides flipped components:
9632 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
9633 @item vertical versions of @code{r-ggplot2} positions.
9635 (license license:gpl3)))
9637 (define-public r-ggnetwork
9639 (name "r-ggnetwork")
9644 (uri (cran-uri "ggnetwork" version))
9647 "0gqdgy5yh700dg0f7xb80hczlnqfisn8l55j7amd1n7fp2x5sr8v"))))
9648 (properties `((upstream-name . "ggnetwork")))
9649 (build-system r-build-system)
9651 (list r-ggplot2 r-ggrepel r-igraph r-network r-sna))
9652 (native-inputs (list r-knitr))
9653 (home-page "https://github.com/briatte/ggnetwork")
9654 (synopsis "Geometries to plot networks with ggplot2")
9656 "This package provides geometries to plot network objects with the
9658 (license license:gpl3)))
9660 (define-public r-cvauc
9667 (uri (cran-uri "cvAUC" version))
9670 "13bk97l5nn97h85iz93zxazhr63n21nwyrpnl856as9qp59yvn64"))))
9671 (properties `((upstream-name . "cvAUC")))
9672 (build-system r-build-system)
9674 (list r-data-table r-rocr))
9675 (home-page "https://github.com/ledell/cvAUC")
9676 (synopsis "Cross-validated area under the ROC curve confidence intervals")
9678 "This package contains various tools for working with and evaluating
9679 cross-validated area under the ROC curve (AUC) estimators. The primary
9680 functions of the package are @code{ci.cvAUC} and @code{ci.pooled.cvAUC}, which
9681 report cross-validated AUC and compute confidence intervals for
9682 cross-validated AUC estimates based on influence curves for i.i.d. and pooled
9683 repeated measures data, respectively.")
9684 (license license:asl2.0)))
9686 (define-public r-gam
9693 (uri (cran-uri "gam" version))
9696 "1zhy2fp7pxac8xp3z3hndhprj4s5gx3305b627vc78bal1ml3swi"))))
9697 (properties `((upstream-name . "gam")))
9698 (build-system r-build-system)
9703 (home-page "https://cran.r-project.org/package=gam")
9704 (synopsis "Generalized additive models")
9706 "This package provides functions for fitting and working with generalized
9707 additive models, as described in chapter 7 of \"Statistical Models in
9708 S\" (Chambers and Hastie (eds), 1991), and \"Generalized Additive
9709 Models\" (Hastie and Tibshirani, 1990).")
9710 (license license:gpl2)))
9712 (define-public r-superlearner
9714 (name "r-superlearner")
9719 (uri (cran-uri "SuperLearner" version))
9722 "00any24msgflyagy87nznpfjz5g9v15frqda6c679wa8plx26hjz"))))
9723 (properties `((upstream-name . "SuperLearner")))
9724 (build-system r-build-system)
9726 (list r-cvauc r-gam r-nnls))
9729 (home-page "https://github.com/ecpolley/SuperLearner")
9730 (synopsis "Super learner prediction")
9732 "This package implements the super learner prediction method and contains
9733 a library of prediction algorithms to be used in the super learner.")
9734 (license license:gpl3)))
9736 (define-public r-drtmle
9743 (uri (cran-uri "drtmle" version))
9746 "08a6k0nrg6mqdslwjc71583x52vnax87nbfalk98zczwvrrdwvxa"))))
9747 (properties `((upstream-name . "drtmle")))
9748 (build-system r-build-system)
9750 (list r-future-apply r-np r-superlearner))
9753 (home-page "https://github.com/benkeser/drtmle")
9754 (synopsis "Doubly-robust nonparametric estimation and inference")
9756 "This package implements targeted minimum loss-based estimators of
9757 counterfactual means and causal effects that are doubly-robust with respect
9758 both to consistency and asymptotic normality.")
9759 (license license:expat)))
9761 (define-public r-dofuture
9768 (uri (cran-uri "doFuture" version))
9771 "1hqzdlgcrc5l6xjwdylsc9iiysi2wx8k1j1vmw3wryj26057c9y4"))))
9772 (properties `((upstream-name . "doFuture")))
9773 (build-system r-build-system)
9776 (modify-phases %standard-phases
9777 (add-after 'unpack 'set-HOME
9778 (lambda _ (setenv "HOME" "/tmp"))))))
9780 (list r-foreach r-future r-globals r-iterators))
9782 (list r-r-rsp)) ; vignette builder
9783 (home-page "https://github.com/HenrikBengtsson/doFuture")
9784 (synopsis "Foreach parallel adapter using the future API")
9786 "This package provides a @code{%dopar%} adapter such that any type of
9787 futures can be used as backends for the @code{foreach} framework.")
9788 (license license:lgpl2.1+)))
9790 (define-public r-superheat
9792 (name "r-superheat")
9797 (uri (cran-uri "superheat" version))
9800 "01v8s6px1k5fajlm6py3ksr1i853kwwlky1yryzhy3p1cxhwgg83"))))
9801 (properties `((upstream-name . "superheat")))
9802 (build-system r-build-system)
9811 (home-page "https://cran.r-project.org/package=superheat")
9812 (synopsis "Graphical tool for exploring complex datasets using heatmaps")
9814 "This package provides a system for generating extendable and
9815 customizable heatmaps for exploring complex datasets, including big data and
9816 data with multiple data types.")
9817 (license license:cc0)))
9819 (define-public r-qualv
9826 (uri (cran-uri "qualV" version))
9829 "0rkjzva2h158d5c631jmjjh7qjibbyisl0503san80rk9fgxl45b"))))
9830 (properties `((upstream-name . "qualV")))
9831 (build-system r-build-system)
9833 (list r-kernsmooth))
9834 (home-page "http://qualV.R-Forge.R-Project.org/")
9835 (synopsis "Qualitative Validation Methods")
9837 "This package provides qualitative methods for the validation of dynamic
9841 @item an orthogonal set of deviance measures for absolute, relative and
9843 @item approaches accounting for time shifts.
9846 The first approach transforms time to take time delays and speed differences
9847 into account. The second divides the time series into interval units
9848 according to their main features and finds the @dfn{longest common
9849 subsequence} (LCS) using a dynamic programming algorithm.")
9850 (license license:gpl2+)))
9852 (define-public r-mosaiccore
9854 (name "r-mosaiccore")
9859 (uri (cran-uri "mosaicCore" version))
9861 (base32 "1h3ixzna4xy42rdnd89jj0v9q0riy3fnkd33z6l5c0zaidzm58fz"))))
9862 (properties `((upstream-name . "mosaicCore")))
9863 (build-system r-build-system)
9865 (list r-dplyr r-mass r-rlang r-tidyr))
9866 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
9867 (synopsis "Common utilities for mosaic family packages")
9869 "Common utilities used in other Mosaic family packages are collected here.")
9870 (license license:gpl2+)))
9872 (define-public r-labelled
9879 (uri (cran-uri "labelled" version))
9882 "0ffnhlr239nqcwb35m4hll21abnnhpmyy5wlxnyahrg0kqb0xb1n"))))
9883 (properties `((upstream-name . "labelled")))
9884 (build-system r-build-system)
9895 (home-page "http://larmarange.github.io/labelled/")
9896 (synopsis "Manipulating labelled data")
9898 "This package provides useful functions to deal with the
9899 @code{haven_labelled} and @code{haven_labelled_spss} classes introduced by the
9901 (license license:gpl3)))
9903 (define-public r-ggformula
9905 (name "r-ggformula")
9910 (uri (cran-uri "ggformula" version))
9912 (base32 "1ph5jd8svk8hmshi894vmmpq3zwgdmf4yn3gmdlkad68z8jynhsp"))))
9913 (build-system r-build-system)
9928 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
9929 (synopsis "Formula interface for the @code{r-ggplot2}")
9931 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
9932 gf_density(), and so on, bring the formula interface to ggplot(). This captures
9933 and extends the excellent simplicity of the lattice-graphics formula interface,
9934 while providing the intuitive capabilities of @code{r-ggplot2}.")
9935 (license license:expat)))
9937 (define-public r-mosaicdata
9939 (name "r-mosaicdata")
9944 (uri (cran-uri "mosaicData" version))
9946 (base32 "0h3f5fgzkzjfgf3ml0qa5j52921y6wy6jgggxmhs31bs8fd4srg4"))))
9947 (properties `((upstream-name . "mosaicData")))
9948 (build-system r-build-system)
9949 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
9950 (synopsis "Data sets for project Mosaic")
9952 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
9953 used to teach mathematics, statistics, computation and modeling.")
9954 (license license:gpl2+)))
9956 (define-public r-raster
9963 (uri (cran-uri "raster" version))
9966 "0wixw1ixnmcmkwczpj8m90c76727zira2rl4ighashggydkm2mlr"))))
9967 (build-system r-build-system)
9969 (list r-rcpp r-sp r-terra))
9970 (home-page "https://www.rspatial.org/")
9971 (synopsis "Geographic data analysis and modeling")
9973 "The package implements basic and high-level functions for reading,
9974 writing, manipulating, analyzing and modeling of gridded spatial data.
9975 Processing of very large files is supported.")
9976 (license license:gpl3+)))
9978 (define-public r-mosaic
9985 (uri (cran-uri "mosaic" version))
9987 (base32 "1y0isqbva0vi5zlx1xvixbq87n4xp66ljh43qnd0cpzaz0mn21cg"))))
9988 (build-system r-build-system)
10009 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
10010 (synopsis "Mathematics, statistics, and computation teaching utilities")
10012 "This package contain data sets and utilities from
10013 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
10014 statistics, computation and modeling. Project MOSAIC is a community of
10015 educators working to tie together aspects of quantitative work that students
10016 in science, technology, engineering and mathematics will need in their
10017 professional lives, but which are usually taught in isolation, if at all.")
10018 (license license:gpl2+)))
10020 (define-public r-abd
10027 (uri (cran-uri "abd" version))
10029 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
10030 (build-system r-build-system)
10032 (list r-lattice r-mosaic r-nlme))
10033 (home-page "https://cran.r-project.org/web/packages/abd/")
10034 (synopsis "Analysis of biological data")
10036 "The @code{r-abd} package contains data sets and sample code for the Analysis of
10037 biological data by Michael Whitlock and Dolph Schluter.")
10038 (license license:gpl2)))
10040 (define-public r-svgui
10047 (uri (cran-uri "svGUI" version))
10049 (base32 "0ch5gdfk834xj9w3vxpm3x4770fz3nnlyn8b0jsw9f3n2as7g979"))))
10050 (properties `((upstream-name . "svGUI")))
10051 (build-system r-build-system)
10054 (home-page "https://github.com/SciViews/svGUI/")
10055 (synopsis "Functions for managing GUI clients in R")
10057 "The SciViews @code{svGUI} package eases the management of Graphical User
10058 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
10059 centralizes info about GUI elements currently used, and it dispatches GUI
10060 calls to the particular toolkits in use in function of the context.")
10061 (license license:gpl2)))
10063 (define-public r-svdialogs
10065 (name "r-svdialogs")
10070 (uri (cran-uri "svDialogs" version))
10072 (base32 "0j00xjvkwv992ir48czhvyj29rb9vpd243vbyyj2binn0q0qa431"))))
10073 (properties `((upstream-name . "svDialogs")))
10074 (build-system r-build-system)
10078 (list r-rstudioapi r-svgui))
10081 (home-page "https://github.com/SciViews/svDialogs/")
10082 (synopsis "Portable dialog boxes")
10084 "This package helps to construct standard dialog boxes for your GUI, including
10085 message boxes, input boxes, list, file or directory selection, and others. In
10086 case R cannot display GUI dialog boxes, a simpler command line version of these
10087 interactive elements is also provided as a fallback solution.")
10088 (license license:gpl2)))
10090 (define-public r-abe
10097 (uri (cran-uri "abe" version))
10100 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
10101 (build-system r-build-system)
10102 (home-page "https://cran.r-project.org/web/packages/abe/")
10103 (synopsis "Augmented backward elimination")
10105 "This package performs augmented backward elimination and checks the
10106 stability of the obtained model. Augmented backward elimination combines
10107 significance or information based criteria with the change in estimate to
10108 either select the optimal model for prediction purposes or to serve as a tool
10109 to obtain a practically sound, highly interpretable model.")
10110 (license license:gpl2+)))
10112 (define-public r-abf2
10119 (uri (cran-uri "abf2" version))
10121 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
10122 (build-system r-build-system)
10123 (home-page "https://cran.r-project.org/web/packages/abf2/")
10124 (synopsis "Load gap-free axon @code{r-abf2} files")
10126 "This package loads electrophysiology data from ABF2 files, as created by
10127 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
10128 mode are currently supported.")
10129 (license license:artistic2.0)))
10131 (define-public r-abhgenotyper
10133 (name "r-abhgenotyper")
10138 (uri (cran-uri "ABHgenotypeR" version))
10140 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
10141 (properties `((upstream-name . "ABHgenotypeR")))
10142 (build-system r-build-system)
10144 (list r-ggplot2 r-reshape2))
10145 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
10146 (synopsis "Visualize and manipulate ABH genotypes")
10148 "The @code{r-abhgenotyper} package provides simple imputation,
10149 error-correction and plotting capacities for genotype data. The package is
10150 supposed to serve as an intermediate but independent analysis tool between the
10151 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
10152 not found in either TASSEL or @code{r-qtl} in addition to visualization of
10153 genotypes as \"graphical genotypes\".")
10154 (license license:gpl3)))
10156 (define-public r-furrr
10163 (uri (cran-uri "furrr" version))
10166 "001p2yhznrpnrjvdcmf2h3wpgdnw01wnqgid7wbq8bhavhi3888a"))))
10167 (build-system r-build-system)
10176 (home-page "https://github.com/DavisVaughan/furrr")
10177 (synopsis "Apply mapping functions in parallel using futures")
10179 "This package provides implementations of the family of @code{map()}
10180 functions from the @code{purrr} package that can be resolved using any
10181 @code{future}-supported backend, e.g. parallel on the local machine or
10182 distributed on a compute cluster.")
10183 (license license:lgpl2.1+)))
10185 (define-public r-abjutils
10187 (name "r-abjutils")
10192 (uri (cran-uri "abjutils" version))
10194 (base32 "18mmlkqsrjfclk8islfjdsp8sbw6dpjj5x45kqilxdiss69gg5zd"))))
10195 (build-system r-build-system)
10205 (home-page "https://github.com/abjur/abjutils/")
10206 (synopsis "Collection of tools for jurimetrical analysis")
10208 "This package implements general purpose tools, such as functions for
10209 sampling and basic manipulation of Brazilian lawsuits identification number.
10210 It also implements functions for text cleaning, such as accentuation
10212 (license license:expat)))
10214 (define-public r-abnormality
10216 (name "r-abnormality")
10221 (uri (cran-uri "abnormality" version))
10223 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
10224 (build-system r-build-system)
10226 (list r-mass r-matrix))
10227 (home-page "https://cran.r-project.org/web/packages/abnormality/")
10228 (synopsis "Measure a subject's abnormality with respect to a reference population")
10230 "This package contains functions to implement the methodology and
10231 considerations laid out by Marks et al. in the article \"Measuring abnormality
10232 in high dimensional spaces: applications in biomechanical gait analysis\".
10233 Using high-dimensional datasets to measure a subject's overall level of
10234 abnormality as compared to a reference population is often needed in outcomes
10236 (license license:expat)))
10238 (define-public r-abodoutlier
10240 (name "r-abodoutlier")
10245 (uri (cran-uri "abodOutlier" version))
10247 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
10248 (properties `((upstream-name . "abodOutlier")))
10249 (build-system r-build-system)
10252 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
10253 (synopsis "Angle-based outlier detection")
10255 "This package performs angle-based outlier detection on a given data
10256 frame. It offers three methods to process data:
10258 @item full but slow implementation using all the data that has cubic
10260 @item a fully randomized method;
10261 @item a method using k-nearest neighbours.
10263 These algorithms are well suited for high dimensional data outlier
10265 (license license:expat)))
10267 (define-public r-abps
10274 (uri (cran-uri "ABPS" version))
10276 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
10277 (properties `((upstream-name . "ABPS")))
10278 (build-system r-build-system)
10279 (propagated-inputs (list r-kernlab))
10280 (home-page "https://cran.r-project.org/web/packages/ABPS/")
10281 (synopsis "Abnormal blood profile score to detect blood doping")
10283 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
10284 The ABPS is a part of the Athlete biological passport program of the World
10285 anti-doping agency, which combines several blood parameters into a single
10286 score in order to detect blood doping. The package also contains functions to
10287 calculate other scores used in anti-doping programs, such as the ratio of
10288 hemoglobin to reticulocytes (OFF-score), as well as example data.")
10289 (license license:gpl2+)))
10291 (define-public r-parmigene
10293 (name "r-parmigene")
10298 (uri (cran-uri "parmigene" version))
10301 "067rqxqyzy1fsjj0s1g7af4527whwdhzjzc5b8a8n7683na59ns4"))))
10302 (build-system r-build-system)
10303 (home-page "https://cran.r-project.org/web/packages/parmigene/")
10304 (synopsis "Mutual information estimation for gene network reconstruction")
10306 "This package provides a parallel estimation of the mutual information
10307 based on entropy estimates from k-nearest neighbors distances and algorithms
10308 for the reconstruction of gene regulatory networks.")
10309 (license license:agpl3+)))
10311 (define-public r-pscl
10318 (uri (cran-uri "pscl" version))
10320 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
10321 (build-system r-build-system)
10324 (home-page "https://github.com/atahk/pscl/")
10325 (synopsis "Political science computational laboratory")
10327 "The @code{pscl} is an R package providing classes and methods for:
10329 @item Bayesian analysis of roll call data (item-response models);
10330 @item elementary Bayesian statistics;
10331 @item maximum likelihood estimation of zero-inflated and hurdle models for count
10333 @item utility functions.
10335 (license license:gpl2)))
10337 (define-public r-accelmissing
10339 (name "r-accelmissing")
10344 (uri (cran-uri "accelmissing" version))
10346 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
10347 (build-system r-build-system)
10349 (list r-mice r-pscl))
10350 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
10351 (synopsis "Missing value imputation for accelerometer data")
10353 "This package provides a statistical method to impute the missing values in
10354 accelerometer data. The methodology includes both parametric and
10355 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
10356 model. It also provides multiple functions to preprocess the accelerometer data
10357 previous to the missing data imputation. These include detecting the wearing
10358 and the non-wearing time, selecting valid days and subjects, and creating plots.")
10359 (license license:gpl2+)))
10361 (define-public r-mhsmm
10368 (uri (cran-uri "mhsmm" version))
10370 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
10371 (build-system r-build-system)
10372 (propagated-inputs (list r-mvtnorm))
10373 (home-page "https://github.com/jaredo/mhsmm/")
10374 (synopsis "Inference for hidden Markov and semi-Markov models")
10376 "The @code{r-mhsmm} package implements estimation and prediction methods for
10377 hidden Markov and semi-Markov models for multiple observation sequences. Such
10378 techniques are of interest when observed data is thought to be dependent on some
10379 unobserved (or hidden) state. Also, this package is suitable for equidistant
10380 time series data, with multivariate and/or missing data. Allows user defined
10381 emission distributions.")
10382 (license license:gpl2+)))
10384 (define-public r-nleqslv
10391 (uri (cran-uri "nleqslv" version))
10393 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
10394 (build-system r-build-system)
10395 (native-inputs (list gfortran))
10396 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
10397 (synopsis "Solve systems of nonlinear equations")
10399 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
10400 Broyden or a Newton method with a choice of global strategies such as line
10401 search and trust region. There are options for using a numerical or user
10402 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
10403 singular or ill-conditioned Jacobian.")
10404 (license license:gpl2+)))
10406 (define-public r-physicalactivity
10408 (name "r-physicalactivity")
10413 (uri (cran-uri "PhysicalActivity" version))
10415 (base32 "0b27prkv3x6v2afz0y53ccs9scibpc7nj54n0hpd9fgn1wyg4c40"))))
10417 `((upstream-name . "PhysicalActivity")))
10418 (build-system r-build-system)
10419 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
10420 (synopsis "Processing accelerometer data for physical activity measurement")
10422 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
10423 for classification of monitored wear and nonwear time intervals in accelerometer
10424 data collected to assess physical activity. The package also contains functions
10425 for making plots of accelerometer data and obtaining the summary of various
10426 information including daily monitor wear time and the mean monitor wear time
10427 during valid days. The revised package version 0.2-1 improved the functions
10428 regarding speed, robustness and add better support for time zones and daylight
10429 saving. In addition, several functions were added:
10431 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
10432 @item the @code{markPAI} can categorize physical activity intensity level based
10433 on user-defined cut-points of accelerometer counts.
10435 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
10436 @code{queryActigraph} functions.")
10437 (license license:gpl3+)))
10439 (define-public r-acc
10446 (uri (cran-uri "acc" version))
10448 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
10449 (build-system r-build-system)
10464 (home-page "https://cran.r-project.org/web/packages/acc/")
10465 (synopsis "Exploring accelerometer data")
10467 "This package processes accelerometer data from uni-axial and tri-axial devices
10468 and generates data summaries. Also, includes functions to plot, analyze, and
10469 simulate accelerometer data.")
10470 (license license:gpl2+)))
10472 (define-public r-rbenchmark
10474 (name "r-rbenchmark")
10479 (uri (cran-uri "rbenchmark" version))
10481 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
10482 (build-system r-build-system)
10483 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
10484 (synopsis "Benchmarking routine for R")
10486 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
10487 and is intended to facilitate benchmarking of arbitrary R code. The library
10488 consists of just one function, benchmark, which is a simple wrapper around
10489 system.time. Given a specification of the benchmarking process (counts of
10490 replications, evaluation environment) and an arbitrary number of expressions,
10491 benchmark evaluates each of the expressions in the specified environment,
10492 replicating the evaluation as many times as specified, and returning the results
10493 conveniently wrapped into a data frame.")
10494 (license license:gpl2+)))
10496 (define-public r-mitools
10503 (uri (cran-uri "mitools" version))
10506 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
10507 (build-system r-build-system)
10508 (propagated-inputs (list r-dbi))
10509 (home-page "https://cran.r-project.org/web/packages/mitools/")
10510 (synopsis "Tools for multiple imputation of missing data")
10512 "This package provides tools to perform analyses and combine results from
10513 multiple-imputation datasets.")
10514 (license license:gpl2)))
10516 (define-public r-mixsqp
10522 (uri (cran-uri "mixsqp" version))
10525 "1qics04w0swyp216d6g8dmsph8q2kpadpacp66h2qih3521js12q"))))
10526 (properties `((upstream-name . "mixsqp")))
10527 (build-system r-build-system)
10529 (list r-irlba r-rcpp r-rcpparmadillo))
10532 (home-page "https://github.com/stephenslab/mixsqp")
10534 "Sequential quadratic programming for maximum-likelihood estimation")
10536 "This package provides an optimization method based on sequential
10537 quadratic programming for maximum likelihood estimation of the mixture
10538 proportions in a finite mixture model where the component densities are
10539 known. The algorithm is expected to obtain solutions that are at least
10540 as accurate as the state-of-the-art MOSEK interior-point solver, and they
10541 are expected to arrive at solutions more quickly when the number of
10542 samples is large and the number of mixture components is not too large.")
10543 (license license:expat)))
10545 (define-public r-magick
10552 (uri (cran-uri "magick" version))
10555 "0h942bn7wfnzbbgq9hrs75c7igmg5r1c5sad2v0znhza4cp7p1w3"))))
10556 (build-system r-build-system)
10558 (list imagemagick zlib))
10560 (list r-curl r-magrittr r-rcpp))
10562 (list pkg-config r-knitr))
10563 (home-page "https://github.com/ropensci/magick")
10564 (synopsis "Advanced graphics and image-processing in R")
10566 "This package provides bindings to ImageMagick, a comprehensive image
10567 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
10568 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
10569 operations are vectorized via the Magick++ STL meaning they operate either on
10570 a single frame or a series of frames for working with layers, collages, or
10571 animation. In RStudio, images are automatically previewed when printed to the
10572 console, resulting in an interactive editing environment.")
10573 (license license:expat)))
10575 (define-public r-survey
10582 (uri (cran-uri "survey" version))
10585 "0ljsszybzri531q6xab04r6zq11vchfs7y0snjzk57m3g0b9ms05"))))
10586 (build-system r-build-system)
10594 (home-page "http://r-survey.r-forge.r-project.org/survey/")
10595 (synopsis "Analysis of complex survey samples")
10597 "This package provides tools for the analysis of complex survey samples.
10598 The provided features include: summary statistics, two-sample tests, rank
10599 tests, generalised linear models, cumulative link models, Cox models,
10600 loglinear models, and general maximum pseudolikelihood estimation for
10601 multistage stratified, cluster-sampled, unequally weighted survey samples;
10602 variances by Taylor series linearisation or replicate weights;
10603 post-stratification, calibration, and raking; two-phase subsampling designs;
10604 graphics; PPS sampling without replacement; principal components, and factor
10606 ;; Either version of the GPL.
10607 (license (list license:gpl2 license:gpl3))))
10609 (define-public r-gee
10612 (version "4.13-20")
10616 (uri (cran-uri "gee" version))
10619 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
10620 (properties `((upstream-name . "gee")))
10621 (build-system r-build-system)
10624 (home-page "https://cran.r-project.org/web/packages/gee/")
10625 (synopsis "Generalized estimation equation solver")
10627 "This package provides a solver for generalized estimation equations.")
10628 (license license:gpl2)))
10630 (define-public r-tab
10637 (uri (cran-uri "tab" version))
10640 "1kg8c1safi9klkx2mdkmsf5dn9piy4jljwd4ma7g4jz2rwl4jzhv"))))
10641 (properties `((upstream-name . "tab")))
10642 (build-system r-build-system)
10644 (list r-dplyr r-kableextra r-knitr r-mass r-survey))
10647 (home-page "https://cran.r-project.org/web/packages/tab/")
10648 (synopsis "Create summary tables for statistical reports")
10650 "This package contains functions for creating various types of summary
10651 tables, e.g. comparing characteristics across levels of a categorical variable
10652 and summarizing fitted generalized linear models, generalized estimating
10653 equations, and Cox proportional hazards models. Functions are available to
10654 handle data from simple random samples as well as complex surveys.")
10655 (license license:gpl3+)))
10657 (define-public r-dvmisc
10664 (uri (cran-uri "dvmisc" version))
10666 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
10667 (build-system r-build-system)
10680 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
10681 (synopsis "Faster computation of common statistics and miscellaneous functions")
10683 "This package implements faster versions of base R functions (e.g. mean, standard
10684 deviation, covariance, weighted mean), mostly written in C++, along with
10685 miscellaneous functions for various purposes (e.g. create the histogram with
10686 fitted probability density function or probability mass function curve, create
10687 the body mass index groups, assess the linearity assumption in logistic
10689 (license license:gpl2)))
10691 (define-public r-accelerometry
10693 (name "r-accelerometry")
10698 (uri (cran-uri "accelerometry" version))
10700 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
10701 (build-system r-build-system)
10703 (list r-dvmisc r-rcpp))
10704 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
10705 (synopsis "Functions for processing accelerometer data")
10707 "This package provides a collection of functions that perform operations on
10708 time-series accelerometer data, such as identify the non-wear time, flag minutes
10709 that are part of an activity bout, and find the maximum 10-minute average count
10710 value. The functions are generally very flexible, allowing for a variety of
10711 algorithms to be implemented.")
10712 (license license:gpl3)))
10714 (define-public r-absim
10721 (uri (cran-uri "AbSim" version))
10723 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
10724 (properties `((upstream-name . "AbSim")))
10725 (build-system r-build-system)
10727 (list r-ape r-powerlaw))
10728 (home-page "https://cran.r-project.org/web/packages/AbSim/")
10729 (synopsis "Time resolved simulations of antibody repertoires")
10731 "This package provides simulation methods for the evolution of antibody repertoires.
10732 The heavy and light chain variable region of both human and C57BL/6 mice can
10733 be simulated in a time-dependent fashion. Both single lineages using one set of
10734 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
10735 with an initial V-D-J recombination event, starting the first phylogenetic tree.
10736 Upon completion, the main loop of the algorithm begins, with each iteration
10737 representing one simulated time step. Various mutation events are possible at
10738 each time step, contributing to a diverse final repertoire.")
10739 (license license:gpl2)))
10741 (define-public r-quic
10748 (uri (cran-uri "QUIC" version))
10750 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
10751 (properties `((upstream-name . "QUIC")))
10752 (build-system r-build-system)
10753 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
10754 (synopsis "Regularized sparse inverse covariance matrix estimation")
10756 "This package implements the regularized Gaussian maximum likelihood
10757 estimation of the inverse of a covariance matrix. It uses Newton's method and
10758 coordinate descent to solve the regularized inverse covariance matrix
10759 estimation problem.")
10760 ;; The project home page states that the release is under GPLv3 or later.
10761 ;; The CRAN page only says GPL-3.
10762 (license license:gpl3+)))
10764 (define-public r-abundant
10766 (name "r-abundant")
10771 (uri (cran-uri "abundant" version))
10773 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
10774 (build-system r-build-system)
10777 (home-page "https://cran.r-project.org/web/packages/abundant/")
10778 (synopsis "Abundant regression and high-dimensional principal fitted components")
10780 "This package provides tools to fit and predict with the high-dimensional
10781 principal fitted components model. This model is described by Cook, Forzani,
10782 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
10783 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
10784 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
10785 (license license:gpl2+)))
10787 (define-public r-ac3net
10794 (uri (cran-uri "Ac3net" version))
10796 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
10797 (properties `((upstream-name . "Ac3net")))
10798 (build-system r-build-system)
10800 (list r-data-table))
10801 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
10802 (synopsis "Inferring directional conservative causal core gene networks")
10803 (description "This package infers directional Conservative causal core
10804 (gene) networks (C3NET). This is a version of the algorithm C3NET with
10805 directional network.")
10806 (license license:gpl3+)))
10808 (define-public r-aca
10815 (uri (cran-uri "ACA" version))
10817 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
10818 (properties `((upstream-name . "ACA")))
10819 (build-system r-build-system)
10820 (home-page "https://cran.r-project.org/web/packages/ACA/")
10821 (synopsis "Abrupt change-point or aberration detection in point series")
10823 "This package offers an interactive function for the detection of breakpoints in
10825 ;; Any version of the GPL
10826 (license (list license:gpl2+ license:gpl3+))))
10828 (define-public r-acceptancesampling
10830 (name "r-acceptancesampling")
10835 (uri (cran-uri "AcceptanceSampling" version))
10837 (base32 "13k3zczjycw24n5yp0qmrm233id5j8h6fvra57f1n6js7ljxiiq2"))))
10839 `((upstream-name . "AcceptanceSampling")))
10840 (build-system r-build-system)
10841 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
10842 (synopsis "Creation and evaluation of acceptance sampling plans")
10844 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
10845 acceptance sampling plans. Acceptance sampling is a methodology commonly used
10846 in quality control and improvement. International standards of acceptance
10847 sampling provide sampling plans for specific circumstances. The aim of this
10848 package is to provide an easy-to-use interface to visualize single, double or
10849 multiple sampling plans. In addition, methods have been provided to enable the
10850 user to assess sampling plans against pre-specified levels of performance, as
10851 measured by the probability of acceptance for a given level of quality in the
10853 (license license:gpl3+)))
10855 (define-public r-acclma
10862 (uri (cran-uri "ACCLMA" version))
10864 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
10865 (properties `((upstream-name . "ACCLMA")))
10866 (build-system r-build-system)
10867 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
10868 (synopsis "ACC & LMA graph plotting")
10870 "This package contains a function that imports data from a @acronym{CSV,
10871 Comma-Separated Values} file, or uses manually entered data from the format (x,
10872 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
10873 Curve} vs @acronym{LOI, Line of Independence} graph and
10874 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
10875 function is @code{plotLMA} (source file, header) that takes a data set and plots the
10876 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
10877 string) was passed, a manual data entry window is opened. The header parameter
10878 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
10879 a header row or not. The dataset should contain only one independent variable
10880 (x) and one dependent variable (y) and can contain a weight for each
10882 (license license:gpl2)))
10884 (define-public r-aspi
10891 (uri (cran-uri "aspi" version))
10893 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
10894 (build-system r-build-system)
10896 "https://cran.r-project.org/web/packages/aspi/")
10898 "Analysis of symmetry of parasitic infections")
10900 "This package provides tools for the analysis and visualization of bilateral
10901 asymmetry in parasitic infections.")
10902 (license license:gpl3+)))
10904 (define-public r-sandwich
10906 (name "r-sandwich")
10911 (uri (cran-uri "sandwich" version))
10914 "12aa5083k3sfrfq1jy3l94wffss9h0rga8j71jy3n8pkhiq4nn7n"))))
10915 (build-system r-build-system)
10918 (home-page "https://cran.r-project.org/web/packages/sandwich/")
10919 (synopsis "Robust Covariance Matrix Estimators")
10921 "This package provides model-robust standard error estimators for
10922 cross-sectional, time series, clustered, panel, and longitudinal data.")
10923 ;; Either version of the license.
10924 (license (list license:gpl2 license:gpl3))))
10926 (define-public r-th-data
10933 (uri (cran-uri "TH.data" version))
10936 "0ghihfpk5d8gsdlzf6phw7dwwz3adx64pxk82vlmlqx53ljpxcr1"))))
10937 (properties `((upstream-name . "TH.data")))
10938 (build-system r-build-system)
10940 (list r-mass r-survival))
10943 (home-page "https://cran.r-project.org/web/packages/TH.data/")
10944 (synopsis "Shared data sets")
10946 "This package contains supporting data sets that are used in other
10947 packages maintained by Torsten Hothorn.")
10948 (license license:gpl3)))
10950 (define-public r-multcomp
10952 (name "r-multcomp")
10957 (uri (cran-uri "multcomp" version))
10960 "02zv739mbmx672yrqqx8am229h7ps476wphig7jrrbfgay29sl21"))))
10961 (build-system r-build-system)
10963 (list r-codetools r-mvtnorm r-sandwich r-survival r-th-data))
10964 (home-page "https://cran.r-project.org/web/packages/multcomp/")
10965 (synopsis "Simultaneous inference in general parametric models")
10967 "Simultaneous tests and confidence intervals for general linear
10968 hypotheses in parametric models, including linear, generalized linear, linear
10969 mixed effects, and survival models. The package includes demos reproducing
10970 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
10971 Hothorn, Westfall, 2010, CRC Press).")
10972 (license license:gpl2)))
10974 (define-public r-emmeans
10981 (uri (cran-uri "emmeans" version))
10984 "1ig94mjifhhygznv2xv1gl8hdvk618w5fcmkaj1xmpwpc64m9dnl"))))
10985 (build-system r-build-system)
10987 (list r-estimability r-mvtnorm r-numderiv r-xtable))
10990 (home-page "https://github.com/rvlenth/emmeans")
10991 (synopsis "Estimated marginal means, aka least-squares means")
10993 "This package provides tools to obtain @dfn{estimated marginal
10994 means} (EMMs) for many linear, generalized linear, and mixed models. It can
10995 be used to compute contrasts or linear functions of EMMs, trends, and
10996 comparisons of slopes.")
10997 ;; Either version of the license.
10998 (license (list license:gpl2 license:gpl3))))
11000 (define-public r-pwr
11007 (uri (cran-uri "pwr" version))
11010 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
11011 (build-system r-build-system)
11014 (home-page "https://github.com/heliosdrm/pwr")
11015 (synopsis "Basic functions for power analysis")
11017 "This package provides power analysis functions along the lines of
11019 (license license:gpl3+)))
11021 (define-public r-libcoin
11028 (uri (cran-uri "libcoin" version))
11030 (base32 "1syrcdj5qg5m3zd3dlxgpfklswbalfg42w058dr09hnzqsvx0z9d"))))
11031 (build-system r-build-system)
11032 (propagated-inputs (list r-mvtnorm))
11033 (home-page "https://cran.r-project.org/web/packages/libcoin")
11034 (synopsis "Linear test statistics for permutation inference")
11036 "This package provides basic infrastructure for linear test statistics
11037 and permutation inference in the framework of Strasser and Weber (1999).")
11038 (license license:gpl2)))
11040 (define-public r-coin
11047 (uri (cran-uri "coin" version))
11050 "1cpv7jx840inzg98bkhrb5yscx0gpag6br237r5qpnc2gbrd2ikm"))))
11051 (build-system r-build-system)
11059 (home-page "http://coin.r-forge.r-project.org")
11060 (synopsis "Conditional inference procedures in a permutation test framework")
11062 "This package provides conditional inference procedures for the general
11063 independence problem including two-sample, K-sample (non-parametric ANOVA),
11064 correlation, censored, ordered and multivariate problems.")
11065 (license license:gpl2)))
11067 (define-public r-bayesplot
11069 (name "r-bayesplot")
11074 (uri (cran-uri "bayesplot" version))
11077 "0aman4273i8hy3z0qay1nrsr7v27m4icm1j6f4w59ylix80l5myq"))))
11078 (build-system r-build-system)
11092 (home-page "https://mc-stan.org/bayesplot")
11093 (synopsis "Plotting for Bayesian models")
11095 "This package provides plotting functions for posterior analysis, model
11096 checking, and MCMC diagnostics. The package is designed not only to provide
11097 convenient functionality for users, but also a common set of functions that
11098 can be easily used by developers working on a variety of R packages for
11099 Bayesian modeling.")
11100 (license license:gpl3+)))
11102 (define-public r-tmb
11109 (uri (cran-uri "TMB" version))
11112 "116k7ffgadhkqq4lckfd4403qvybcls1hcs1ap1b7lkylghjahf2"))))
11113 (properties `((upstream-name . "TMB")))
11114 (build-system r-build-system)
11116 (list r-matrix r-rcppeigen))
11117 (home-page "http://tmb-project.org")
11118 (synopsis "Template model builder: a general random effect tool")
11120 "With this tool, a user should be able to quickly implement complex
11121 random effect models through simple C++ templates. The package combines
11122 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
11123 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
11124 from R) to obtain an efficient implementation of the applied Laplace
11125 approximation with exact derivatives. Key features are: Automatic sparseness
11126 detection, parallelism through BLAS and parallel user templates.")
11127 (license license:gpl2)))
11129 (define-public r-sjstats
11136 (uri (cran-uri "sjstats" version))
11138 (base32 "1cv80yjnyh6qihxf57zivihhia20gibr5f03x8aspy6382wnwlka"))))
11139 (build-system r-build-system)
11158 (home-page "https://github.com/strengejacke/sjstats")
11159 (synopsis "Functions for common statistical computations")
11161 "This package provides a collection of convenient functions for common
11162 statistical computations, which are not directly provided by R's @code{base}
11163 or @code{stats} packages. This package aims at providing, first, shortcuts
11164 for statistical measures, which otherwise could only be calculated with
11165 additional effort. Second, these shortcut functions are generic, and can be
11166 applied not only to vectors, but also to other objects as well. The focus of
11167 most functions lies on summary statistics or fit measures for regression
11168 models, including generalized linear models, mixed effects models and Bayesian
11170 (license license:gpl3)))
11172 (define-public r-glmmtmb
11175 (version "1.1.2.3")
11179 (uri (cran-uri "glmmTMB" version))
11182 "1yfwwz2dhd34vgagg8hi7irkqw8padavbc7337jdiwgk3w01wqsm"))))
11183 (properties `((upstream-name . "glmmTMB")))
11184 (build-system r-build-system)
11193 (list r-knitr)) ; for vignettes
11194 (home-page "https://github.com/glmmTMB")
11195 (synopsis "Generalized linear mixed models")
11197 "Fit linear and generalized linear mixed models with various extensions,
11198 including zero-inflation. The models are fitted using maximum likelihood
11199 estimation via the Template Model Builder. Random effects are assumed to be
11200 Gaussian on the scale of the linear predictor and are integrated out using the
11201 Laplace approximation. Gradients are calculated using automatic
11203 (license license:agpl3+)))
11205 (define-public r-bayestestr
11207 (name "r-bayestestr")
11212 (uri (cran-uri "bayestestR" version))
11215 "0lz8mzacxgmll576p88654mrvlk4pzvhwwghvn5pm7zxisgx0kq0"))))
11216 (properties `((upstream-name . "bayestestR")))
11217 (build-system r-build-system)
11219 (list r-datawizard r-insight))
11222 (home-page "https://github.com/easystats/bayestestR")
11223 (synopsis "Describe Bayesian models and posterior distributions")
11225 "This package provides utilities to understand and describe posterior
11226 distributions and Bayesian models. It includes point-estimates such as
11227 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
11228 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
11229 ROPE percentage and pd).")
11230 (license license:gpl3)))
11232 (define-public r-performance
11234 (name "r-performance")
11239 (uri (cran-uri "performance" version))
11242 "1xjjnhqmwfflm5yfgjhycjn0fj0manvsvkk2ppifn0373bajp5n2"))))
11243 (build-system r-build-system)
11245 (list r-bayestestr r-datawizard r-insight))
11246 (home-page "https://easystats.github.io/performance/")
11247 (synopsis "Assessment of regression models performance")
11249 "This package provides utilities for computing measures to assess model
11250 quality, which are not directly provided by R's @code{base} or @code{stats}
11251 packages. These include e.g. measures like r-squared, intraclass correlation
11252 coefficient, root mean squared error or functions to check models for
11253 overdispersion, singularity or zero-inflation and more. Functions apply to a
11254 large variety of regression models, including generalized linear models, mixed
11255 effects models and Bayesian models.")
11256 (license license:gpl3)))
11258 (define-public r-ggeffects
11260 (name "r-ggeffects")
11265 (uri (cran-uri "ggeffects" version))
11268 "0xrb105kblkj3l9zlj9yy52rjlmx5x2aai1wwb5zvjr1f6nlc84l"))))
11269 (build-system r-build-system)
11271 (list r-insight r-mass r-sjlabelled))
11274 (home-page "https://github.com/strengejacke/ggeffects")
11275 (synopsis "Create tidy data frames of marginal effects for ggplot")
11277 "This package provides tools to compute marginal effects from statistical
11278 models and return the result as tidy data frames. These data frames are ready
11279 to use with the @code{ggplot2} package. Marginal effects can be calculated
11280 for many different models. Interaction terms, splines and polynomial terms
11281 are also supported. The two main functions are @code{ggpredict()} and
11282 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
11283 results using @code{ggplot2}.")
11284 (license license:gpl3)))
11286 (define-public r-effectsize
11288 (name "r-effectsize")
11293 (uri (cran-uri "effectsize" version))
11296 "0w7m3hzmwral9cycpvknrkbdvgk230b3vg5sxbm84x72mw534hnh"))))
11297 (properties `((upstream-name . "effectsize")))
11298 (build-system r-build-system)
11300 (list r-bayestestr r-datawizard r-insight r-parameters
11304 (home-page "https://github.com/easystats/effectsize")
11305 (synopsis "Indices of effect size and standardized parameters")
11307 "This package provides utilities to work with indices of effect size and
11308 standardized parameters for a wide variety of models, allowing computation and
11309 conversion of indices such as Cohen's d, r, odds, etc.")
11310 (license license:gpl3)))
11312 (define-public r-sjplot
11319 (uri (cran-uri "sjPlot" version))
11321 (base32 "07b9p5wbb6xmyapg9j6i4cdcj7j9wj9gi30gljj6j2lj1flgdd7q"))))
11322 (properties `((upstream-name . "sjPlot")))
11323 (build-system r-build-system)
11345 (home-page "https://strengejacke.github.io/sjPlot/")
11346 (synopsis "Data visualization for statistics in social science")
11348 "This package represents a collection of plotting and table output
11349 functions for data visualization. Results of various statistical
11350 analyses (that are commonly used in social sciences) can be visualized using
11351 this package, including simple and cross tabulated frequencies, histograms,
11352 box plots, (generalized) linear models, mixed effects models, principal
11353 component analysis and correlation matrices, cluster analyses, scatter plots,
11354 stacked scales, effects plots of regression models (including interaction
11355 terms) and much more. This package supports labelled data.")
11356 (license license:gpl3)))
11358 (define-public r-ini
11365 (uri (cran-uri "ini" version))
11368 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
11369 (build-system r-build-system)
11370 (home-page "https://github.com/dvdscripter/ini")
11371 (synopsis "Read and write configuration files")
11373 "This package provides tools to parse simple @code{.ini} configuration
11374 files to an structured list. Users can manipulate this resulting list with
11375 @code{lapply()} functions. This same structured list can be used to write
11376 back to file after modifications.")
11377 (license license:gpl3)))
11379 (define-public r-gitcreds
11381 (name "r-gitcreds")
11386 (uri (cran-uri "gitcreds" version))
11389 "1snzn7nxy0rwz0bzjsg6k04c0n811dgn8gn9cmn2v78aj57ayjmi"))))
11390 (properties `((upstream-name . "gitcreds")))
11391 (build-system r-build-system)
11392 (inputs `(("git" ,git-minimal)))
11393 (native-inputs (list r-knitr))
11394 (home-page "https://github.com/r-lib/gitcreds")
11395 (synopsis "Query git credentials from R")
11397 "Query, set, and delete credentials from the git credential store.
11398 Manage GitHub tokens and other git credentials. This package is to be used by
11399 other packages that need to authenticate to GitHub and/or other git
11401 (license license:expat)))
11403 (define-public r-gh
11410 (uri (cran-uri "gh" version))
11413 "077drbxz3rx7idv6w24ipj1p6jnzv86a3iyryab699cc9q2kjh54"))))
11414 (build-system r-build-system)
11416 (list r-cli r-gitcreds r-httr r-ini r-jsonlite))
11419 (home-page "https://github.com/r-lib/gh#readme")
11420 (synopsis "Access the GitHub API via R")
11422 "This package provides a minimal R client to access the GitHub API.")
11423 (license license:expat)))
11425 (define-public r-fs
11432 (uri (cran-uri "fs" version))
11435 "15rqc3ljmcmgfvadj1j1kq7kvibagxic8sgplhlcdqqxax9idprn"))))
11436 (build-system r-build-system)
11439 (home-page "https://fs.r-lib.org")
11440 (synopsis "Cross-platform file system operations based on libuv")
11442 "This package provides a cross-platform interface to file system
11443 operations, built on top of the libuv C library.")
11444 (license license:gpl3)))
11446 (define-public r-clisymbols
11448 (name "r-clisymbols")
11453 (uri (cran-uri "clisymbols" version))
11456 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
11457 (build-system r-build-system)
11458 (home-page "https://github.com/gaborcsardi/clisymbols")
11459 (synopsis "Unicode symbols at the R prompt")
11461 "This package provides a small subset of Unicode symbols, that are useful
11462 when building command line applications. They fall back to alternatives on
11463 terminals that do not support Unicode.")
11464 (license license:expat)))
11466 (define-public r-credentials
11468 (name "r-credentials")
11473 (uri (cran-uri "credentials" version))
11476 "0q3s1bibwvw1p541k8a5cjx4dj1iabl4crg61fgjxkniclxag5c7"))))
11477 (properties `((upstream-name . "credentials")))
11478 (build-system r-build-system)
11481 (modify-phases %standard-phases
11482 (add-after 'unpack 'setenv-HOME
11484 ;; This is necessary because git looks for $HOME/.gitconfig
11485 (setenv "HOME" "/tmp")
11488 `(("git" ,git-minimal)))
11490 (list r-askpass r-curl r-jsonlite r-openssl r-sys))
11493 (home-page "https://docs.ropensci.org/credentials/")
11494 (synopsis "Tools for managing SSH and Git credentials")
11496 "This package assists you in setting up and retrieving of HTTPS and SSH
11497 credentials for use with git and other services. For HTTPS remotes the
11498 package interfaces the @command{git-credential} utility which @command{git}
11499 uses to store HTTP usernames and passwords. For SSH remotes this package
11500 provides convenient functions to find or generate appropriate SSH keys. The
11501 package both helps the user to setup a local git installation, and also
11502 provides a back-end for git/ssh client libraries to authenticate with existing
11503 user credentials.")
11504 (license license:expat)))
11506 (define-public r-gert
11513 (uri (cran-uri "gert" version))
11516 "06g3gy4260y4f43zgahamckisjs8dvl06rb0kyinrwlm675dqppm"))))
11517 (properties `((upstream-name . "gert")))
11518 (build-system r-build-system)
11520 (list libgit2 zlib))
11529 (list pkg-config r-knitr))
11530 (home-page "https://docs.ropensci.org/gert/")
11531 (synopsis "Simple Git client for R")
11533 "This package provides a simple git client for R based on libgit2 with
11534 support for SSH and HTTPS remotes. All functions in gert use basic R data
11535 types (such as vectors and data-frames) for their arguments and return values.
11536 User credentials are shared with command line git through the
11537 @code{git-credential} store and SSH keys stored on disk or ssh-agent.")
11538 (license license:expat)))
11540 (define-public r-usethis
11547 (uri (cran-uri "usethis" version))
11550 "1gwvirp53pa0zychd7d47d56a2vfdzz7l3p61l8m9n270ac7bc1d"))))
11551 (build-system r-build-system)
11572 (home-page "https://github.com/r-lib/usethis")
11573 (synopsis "Automate R package and project setup")
11575 "This package helps you to automate R package and project setup tasks
11576 that are otherwise performed manually. This includes setting up unit testing,
11577 test coverage, continuous integration, Git, GitHub integration, licenses,
11578 Rcpp, RStudio projects, and more.")
11579 (license license:gpl3)))
11581 (define-public r-sessioninfo
11583 (name "r-sessioninfo")
11588 (uri (cran-uri "sessioninfo" version))
11591 "0w3vhp652524348a4cfyvvs8z9xpxkcznw8x406nvkwfh0gdyka2"))))
11592 (build-system r-build-system)
11595 (home-page "https://github.com/r-lib/sessioninfo#readme")
11596 (synopsis "R session information")
11598 "This package provides tools to query and print information about the
11599 current R session. It is similar to @code{utils::sessionInfo()}, but includes
11600 more information about packages, and where they were installed from.")
11601 (license license:gpl2)))
11603 (define-public r-remotes
11610 (uri (cran-uri "remotes" version))
11613 "0xij8x4ga0r7rp2lxx9hw1zlzv48mfg56v8nf03gsw0dw6r7gmym"))))
11614 (build-system r-build-system)
11617 (home-page "https://github.com/r-lib/remotes#readme")
11618 (synopsis "R package installation from remote repositories")
11620 "Download and install R packages stored in GitHub, BitBucket, or plain
11621 subversion or git repositories. This package is a lightweight replacement of
11622 the @code{install_*} functions in the @code{devtools} package. Indeed most of
11623 the code was copied over from @code{devtools}.")
11624 (license license:gpl2+)))
11626 (define-public r-xopen
11633 (uri (cran-uri "xopen" version))
11636 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
11637 (build-system r-build-system)
11640 (home-page "https://github.com/r-lib/xopen#readme")
11641 (synopsis "Open system files, URLs, anything")
11643 "This package provides a cross-platform solution to open files,
11644 directories or URLs with their associated programs.")
11645 (license license:expat)))
11647 (define-public r-rcmdcheck
11649 (name "r-rcmdcheck")
11654 (uri (cran-uri "rcmdcheck" version))
11657 "1l696byn3kjq2xvz4wxybzaj6ink85h4lz3a35v2132ba5yyzm5v"))))
11658 (build-system r-build-system)
11672 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
11673 (synopsis "Run R CMD check from R and capture results")
11675 "Run @code{R CMD check} from R programmatically, and capture the results
11676 of the individual checks.")
11677 (license license:expat)))
11679 (define-public r-rapportools
11681 (name "r-rapportools")
11686 (uri (cran-uri "rapportools" version))
11689 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
11690 (build-system r-build-system)
11692 (list r-pander r-plyr r-reshape))
11693 (home-page "https://cran.r-project.org/web/packages/rapportools/")
11694 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
11696 "This package provides helper functions that act as wrappers to more
11697 advanced statistical methods with the advantage of having sane defaults for
11699 (license license:agpl3+)))
11701 (define-public r-pander
11708 (uri (cran-uri "pander" version))
11711 "1knjcr50xxns3w3kh15myjpsizn4d7fdqx071a4yj90imif07qjh"))))
11712 (build-system r-build-system)
11714 (list r-digest r-rcpp))
11717 (home-page "https://rapporter.github.io/pander")
11718 (synopsis "Render R objects into Pandoc's markdown")
11720 "The main aim of the pander R package is to provide a minimal and easy
11721 tool for rendering R objects into Pandoc's markdown. The package is also
11722 capable of exporting/converting complex Pandoc documents (reports) in various
11724 ;; This package is licensed under either the AGPLv3+ or the very rarely
11726 (license license:agpl3+)))
11728 (define-public r-summarytools
11730 (name "r-summarytools")
11735 (uri (cran-uri "summarytools" version))
11738 "04qcysfywljnqkcz2b7kzpy0xv3ykkvvb14vnda63z1wvmadyhkn"))))
11739 (build-system r-build-system)
11755 (home-page "https://github.com/dcomtois/summarytools")
11756 (synopsis "Tools to quickly and neatly summarize data")
11758 "This package provides tools for data frame summaries, cross-tabulations,
11759 weight-enabled frequency tables and common univariate statistics in concise
11760 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
11761 good point-of-entry for exploring data, both for experienced and new R
11763 (license license:gpl2)))
11765 (define-public r-lsei
11772 (uri (cran-uri "lsei" version))
11775 "1dka0rigfw4vj809qma2dkiwjb3nw5635ynnba5cm299cn7hb2b2"))))
11776 (build-system r-build-system)
11779 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
11780 (synopsis "Solve regression problems under equality/inequality constraints")
11782 "It contains functions that solve least squares linear regression
11783 problems under linear equality/inequality constraints. Functions for solving
11784 quadratic programming problems are also available, which transform such
11785 problems into least squares ones first.")
11786 (license license:gpl2+)))
11788 (define-public r-npsurv
11795 (uri (cran-uri "npsurv" version))
11798 "1ihxhb42cga1hssj2jv4ah0f4hlwsky899ij5261fzh1wxvdp1xw"))))
11799 (build-system r-build-system)
11802 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
11803 (synopsis "Nonparametric survival analysis")
11805 "This package contains functions for non-parametric survival analysis of
11806 exact and interval-censored observations.")
11807 (license license:gpl2+)))
11809 (define-public r-clusteval
11811 (name "r-clusteval")
11816 (uri (cran-uri "clusteval" version))
11819 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
11820 (build-system r-build-system)
11822 (list r-mvtnorm r-rcpp))
11823 (home-page "https://cran.r-project.org/web/packages/clusteval/")
11824 (synopsis "Evaluation of clustering algorithms")
11826 "This R package provides a suite of tools to evaluate clustering
11827 algorithms, clusterings, and individual clusters.")
11828 (license license:expat)))
11830 (define-public r-tweedie
11837 (uri (cran-uri "tweedie" version))
11840 "1nfhaqblvm62j8gfkyrgba5ai0pb2fsnrxp63637mhys2bawlcm0"))))
11841 (build-system r-build-system)
11842 (native-inputs (list gfortran))
11843 (home-page "https://cran.r-project.org/web/packages/tweedie/")
11844 (synopsis "Evaluation of Tweedie exponential family models")
11846 "Maximum likelihood computations for Tweedie families, including the
11847 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
11848 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
11849 and related methods.")
11850 (license license:gpl2+)))
11852 (define-public r-rcppgsl
11859 (uri (cran-uri "RcppGSL" version))
11861 (base32 "0lalz51q31qqy0cr227vc3msi0h47p111lzy4zs93drgl1yhh4l6"))))
11862 (properties `((upstream-name . "RcppGSL")))
11863 (build-system r-build-system)
11866 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
11867 (synopsis "Rcpp integration for GSL vectors and matrices")
11869 "The GNU Scientific Library (or GSL) is a collection of numerical
11870 routines for scientific computing. It is particularly useful for C and C++
11871 programs as it provides a standard C interface to a wide range of mathematical
11872 routines. There are over 1000 functions in total with an extensive test
11873 suite. The RcppGSL package provides an easy-to-use interface between GSL data
11874 structures and R using concepts from Rcpp which is itself a package that eases
11875 the interfaces between R and C++.")
11876 (license license:gpl2+)))
11878 (define-public r-mvabund
11885 (uri (cran-uri "mvabund" version))
11888 "107pwv2bwird1a98chcnbld2wqj9prkf4pkncyrrp304zpdkkby1"))))
11889 (build-system r-build-system)
11891 (list r-mass r-rcpp r-rcppgsl r-statmod r-tweedie))
11892 (home-page "https://cran.r-project.org/web/packages/mvabund/")
11893 (synopsis "Statistical methods for analysing multivariate abundance data")
11895 "This package provides a set of tools for displaying, modeling and
11896 analysing multivariate abundance data in community ecology.")
11897 (license license:lgpl2.1+)))
11899 (define-public r-afex
11906 (uri (cran-uri "afex" version))
11909 "1k04n6gwk2n8kg0l3yk5j3wrqgkv5f6w04yjpif9y451hx5w7svg"))))
11910 (build-system r-build-system)
11912 (list r-car r-lme4 r-lmertest r-pbkrtest r-reshape2))
11915 (home-page "https://afex.singmann.science/")
11916 (synopsis "Analysis of factorial experiments")
11918 "This package provides convenience functions for analyzing factorial
11919 experiments using ANOVA or mixed models.")
11920 (license license:gpl2+)))
11922 (define-public r-lmertest
11924 (name "r-lmertest")
11929 (uri (cran-uri "lmerTest" version))
11932 "1zd8gqjkazhxgpnnr484xwsq30p62fq8592nzyc171zjyplpbaim"))))
11933 (properties `((upstream-name . "lmerTest")))
11934 (build-system r-build-system)
11936 (list r-ggplot2 r-lme4 r-mass r-numderiv))
11937 (home-page "https://github.com/runehaubo/lmerTestR")
11938 (synopsis "Tests in linear mixed effects models")
11940 "This package provides p-values in type I, II or III anova and summary
11941 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
11942 method. A Kenward-Roger method is also available via the @code{pbkrtest}
11943 package. Model selection methods include step, drop1 and anova-like tables
11944 for random effects (ranova). Methods for Least-Square means (LS-means) and
11945 tests of linear contrasts of fixed effects are also available.")
11946 (license license:gpl2+)))
11948 (define-public r-r2glmm
11955 (uri (cran-uri "r2glmm" version))
11958 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
11959 (build-system r-build-system)
11971 (home-page "https://github.com/bcjaeger/r2glmm")
11972 (synopsis "Compute R squared for mixed (multilevel) models")
11974 "This package computes model and semi partial R squared with confidence
11975 limits for the linear and generalized linear mixed model (LMM and GLMM). The
11976 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
11977 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
11979 (license license:gpl2)))
11981 (define-public r-cmdfun
11988 (uri (cran-uri "cmdfun" version))
11991 "1pbcq7hi2lcmqnghmy3q2fsk0c9fy5m0637acyzmc096fxbx723j"))))
11992 (properties `((upstream-name . "cmdfun")))
11993 (build-system r-build-system)
12003 (home-page "https://snystrom.github.io/cmdfun/")
12004 (synopsis "Framework for building interfaces to shell commands")
12006 "Writing interfaces to command line software is cumbersome. The cmdfun
12007 package provides a framework for building function calls to seamlessly
12008 interface with shell commands by allowing lazy evaluation of command line
12009 arguments. It also provides methods for handling user-specific paths to tool
12010 installs or secrets like API keys. Its focus is to equally serve package
12011 builders who wish to wrap command line software, and to help analysts stay
12012 inside R when they might usually leave to execute non-R software.")
12013 (license license:expat)))
12015 (define-public r-rslurm
12022 (uri (cran-uri "rslurm" version))
12025 "19451icfh7snjbbmpzpr1hrdf52q8ijv0ag1di3y55r2la3jxxcf"))))
12026 (properties `((upstream-name . "rslurm")))
12027 (build-system r-build-system)
12028 (propagated-inputs (list r-whisker))
12029 (native-inputs (list r-knitr))
12030 (home-page "http://cyberhelp.sesync.org/rslurm/")
12031 (synopsis "Submit R calculations to a Slurm cluster")
12033 "This package provides functions that simplify submitting R scripts to a
12034 Slurm workload manager, in part by automating the division of embarrassingly
12035 parallel calculations across cluster nodes.")
12036 (license license:gpl3)))
12038 (define-public r-chk
12045 (uri (cran-uri "chk" version))
12048 "1fxsxgvd08lkb6amjgs4x48dhqr046mmjngjfgy2ya9cl2shd7ls"))))
12049 (properties `((upstream-name . "chk")))
12050 (build-system r-build-system)
12052 (list r-lifecycle r-rlang))
12053 (native-inputs (list r-knitr))
12054 (home-page "https://github.com/poissonconsulting/chk")
12055 (synopsis "Check user-supplied function arguments")
12057 "This is a package for developers to check user-supplied function
12058 arguments. It is designed to be simple, fast and customizable. Error
12059 messages follow the tidyverse style guide.")
12060 (license license:expat)))
12062 (define-public r-weights
12069 (uri (cran-uri "weights" version))
12072 "1fnchf7f0hyl514bk8sc3l884kg25kb5xm4mc2l28n6hm7l6bgpg"))))
12073 (build-system r-build-system)
12075 (list r-gdata r-hmisc r-lme4 r-mice))
12076 (home-page "https://cran.r-project.org/web/packages/weights/")
12077 (synopsis "Weighting and weighted statistics")
12078 (description "This package Provides a variety of functions for producing
12079 simple weighted statistics, such as weighted Pearson's correlations, partial
12080 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
12081 includes some software for quickly recoding survey data and plotting point
12082 estimates from interaction terms in regressions (and multiply imputed
12083 regressions). NOTE: Weighted partial correlation calculations pulled to
12085 (license license:gpl2+)))
12087 (define-public r-rcppannoy
12089 (name "r-rcppannoy")
12094 (uri (cran-uri "RcppAnnoy" version))
12097 "12k8ny981dmky5js8yl6bih5r5mq3w43f2f9admhkwqn0n80kcl9"))))
12098 (properties `((upstream-name . "RcppAnnoy")))
12099 (build-system r-build-system)
12102 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
12103 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
12105 "Annoy is a small C++ library for Approximate Nearest Neighbors written
12106 for efficient memory usage as well an ability to load from and save to disk.
12107 This package provides an R interface.")
12108 ;; Annoy is released under ASL 2.0, but this wrapper is released under
12110 (license (list license:gpl2+ license:asl2.0))))
12112 (define-public r-rcpphnsw
12114 (name "r-rcpphnsw")
12119 (uri (cran-uri "RcppHNSW" version))
12122 "01z0plf1i6dyibw4ica8shmijyk1grpqb886hcga72z2cpm4xsx0"))))
12123 (properties `((upstream-name . "RcppHNSW")))
12124 (build-system r-build-system)
12125 (propagated-inputs (list r-rcpp))
12126 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
12127 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
12129 "Hnswlib is a C++ library for approximate nearest neighbors. This
12130 package provides a minimal R interface by relying on the Rcpp package.")
12131 ;; hnswlib is released under Version 2.0 of the Apache License.
12132 (license (list license:gpl3 license:asl2.0))))
12134 (define-public r-rcppparallel
12136 (name "r-rcppparallel")
12141 (uri (cran-uri "RcppParallel" version))
12144 "10pa9vaz7p4m6hjca2cpy6vj7rvgly4zv0q1g2xfsmcchyk4bdbn"))))
12145 (properties `((upstream-name . "RcppParallel")))
12146 (build-system r-build-system)
12147 (home-page "https://rcppcore.github.io/RcppParallel/")
12148 (synopsis "Parallel programming tools for Rcpp")
12150 "This package provides high level functions for parallel programming with
12151 Rcpp. For example, the @code{parallelFor()} function can be used to convert
12152 the work of a standard serial @code{for} loop into a parallel one and the
12153 @code{parallelReduce()} function can be used for accumulating aggregates or
12155 (license license:gpl2)))
12157 (define-public r-ncdf4
12164 (uri (cran-uri "ncdf4" version))
12167 "1fyjhp2zkvp7ls1sxn623far7473lpkfsqqvj3a1fczpmqs6iw4m"))))
12168 (build-system r-build-system)
12170 (list netcdf zlib))
12171 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
12172 (synopsis "R interface to Unidata netCDF format data files")
12174 "This package provides a high-level R interface to data files written
12175 using Unidata's netCDF library (version 4 or earlier), which are binary data
12176 files that are portable across platforms and include metadata information in
12177 addition to the data sets. Using this package, netCDF files can be opened and
12178 data sets read in easily. It is also easy to create new netCDF dimensions,
12179 variables, and files, in either version 3 or 4 format, and manipulate existing
12181 (license license:gpl3+)))
12183 (define-public r-biocmanager
12185 (name "r-biocmanager")
12186 (version "1.30.16")
12190 (uri (cran-uri "BiocManager" version))
12192 (base32 "0m9qxwqajg8lp0z06blbpgk3zw0z73aly1cvmjk6mvwja6jm99vm"))))
12193 (properties `((upstream-name . "BiocManager")))
12194 (build-system r-build-system)
12197 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
12198 (synopsis "Access the Bioconductor project package repository")
12200 "This package provides a convenient tool to install and update
12201 Bioconductor packages.")
12202 (license license:artistic2.0)))
12204 (define-public r-rgl
12207 (version "0.108.3")
12211 (uri (cran-uri "rgl" version))
12214 "0fqkx079z9y5b1gdg6qfz2wpw2j8q3ddflfkd9wwrkyacas6xyc9"))))
12215 (build-system r-build-system)
12217 (list pkg-config r-knitr))
12232 (home-page "https://r-forge.r-project.org/projects/rgl/")
12233 (synopsis "3D visualization using OpenGL")
12235 "This package provides medium to high level functions for 3D interactive graphics,
12236 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
12237 as functions for constructing representations of geometric
12238 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
12239 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
12240 image formats, including PNG, Postscript, SVG, PGF.")
12241 ;; Any version of the GPL.
12242 (license (list license:gpl2+ license:gpl3+))))
12244 (define-public r-multicool
12246 (name "r-multicool")
12251 (uri (cran-uri "multicool" version))
12254 "0djacq0irfqz4nlnx238kja73yvr1n5qybbfyl6bw1n6qgcjhza8"))))
12255 (build-system r-build-system)
12256 (propagated-inputs (list r-rcpp))
12257 (home-page "https://cran.r-project.org/web/packages/multicool/")
12258 (synopsis "Permutations of multisets in cool-lex order")
12260 "This package provides a set of tools to permute multisets without loops
12261 or hash tables and to generate integer partitions. Cool-lex order is similar
12262 to colexicographical order.")
12263 (license license:gpl2)))
12265 (define-public r-misc3d
12272 (uri (cran-uri "misc3d" version))
12275 "0r9x57s63kx9f6dgam2nhbziq8nrs9wd8pk7g76hds2kw46vnyx0"))))
12276 (build-system r-build-system)
12277 (home-page "https://cran.r-project.org/web/packages/misc3d/")
12278 (synopsis "Miscellaneous 3D Plots")
12280 "This package provides a collection of miscellaneous 3d plots, including
12282 ;; Any version of the GPL.
12283 (license (list license:gpl2+ license:gpl3+))))
12285 (define-public r-ks
12292 (uri (cran-uri "ks" version))
12294 (base32 "02gnpyjqdlj6dl2x9i7mmks4f5nrh85j3h0kfa0v1v6wi8blx7kw"))))
12295 (build-system r-build-system)
12307 (home-page "https://www.mvstat.net/tduong/")
12308 (synopsis "Kernel smoothing")
12310 "This package provides kernel smoothers for univariate and multivariate
12311 data, including density functions, density derivatives, cumulative
12312 distributions, modal clustering, discriminant analysis, and two-sample
12313 hypothesis testing.")
12314 ;; Either version of the GPL.
12315 (license (list license:gpl2 license:gpl3))))
12317 (define-public r-feature
12324 (uri (cran-uri "feature" version))
12327 "0yzn1w1sasilcp8v0pcjnxjv9l6lspkskqi412i6h040gqmjjf6y"))))
12328 (build-system r-build-system)
12330 (list r-ks r-plot3d))
12333 (home-page "https://www.mvstat.net/tduong/")
12334 (synopsis "Inferential feature significance for kernel density estimation")
12336 "The feature package contains functions to display and compute kernel
12337 density estimates, significant gradient and significant curvature regions.
12338 Significant gradient and/or curvature regions often correspond to significant
12339 features (e.g. local modes).")
12340 ;; Either version of the GPL.
12341 (license (list license:gpl2 license:gpl3))))
12343 (define-public r-arm
12350 (uri (cran-uri "arm" version))
12353 "0pagrc1vkaz460d0lvrgb4xj6gcd920f4mrc8zpzw07c3v1s2sw1"))))
12354 (build-system r-build-system)
12362 (home-page "https://cran.r-project.org/web/packages/arm/")
12363 (synopsis "Data analysis using regression and multilevel/hierarchical models")
12365 "This package provides functions to accompany A. Gelman and J. Hill,
12366 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
12367 University Press, 2007.")
12368 (license license:gpl3+)))
12370 (define-public r-circular
12372 (name "r-circular")
12377 (uri (cran-uri "circular" version))
12380 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
12381 (build-system r-build-system)
12383 (list r-boot r-mvtnorm))
12386 (home-page "https://cran.r-project.org/web/packages/circular/")
12387 (synopsis "Circular statistics")
12389 "This package provides tools for circular statistics, from \"Topics in
12390 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
12392 (license license:gpl2+)))
12394 (define-public r-activity
12396 (name "r-activity")
12401 (uri (cran-uri "activity" version))
12404 "1wn2a0hx7wfr2jyj1b772w5fgl6bcqkkw8cybais2s1wyjx8kjr5"))))
12405 (build-system r-build-system)
12407 (list r-circular r-insol r-pbapply))
12408 (home-page "https://cran.r-project.org/web/packages/activity/")
12409 (synopsis "Animal activity statistics")
12411 "This package provides functions to fit kernel density functions to
12412 animal activity time data; plot activity distributions; quantify overall
12413 levels of activity; statistically compare activity metrics through
12414 bootstrapping; and evaluate variation in linear variables with time (or other
12415 circular variables).")
12416 (license license:gpl3)))
12418 (define-public r-ouch
12425 (uri (cran-uri "ouch" version))
12428 "1a7r24j59xz3lxa5wc694j6b80j8m5l86zd1sw9pvs66l8gd98kf"))))
12429 (build-system r-build-system)
12430 (propagated-inputs (list r-subplex))
12431 (home-page "https://kingaa.github.io/ouch/")
12432 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
12434 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
12435 for evolution along a phylogenetic tree.")
12436 (license license:gpl2+)))
12438 (define-public r-fmsb
12445 (uri (cran-uri "fmsb" version))
12448 "09pq7p7i6vkq9av7l7x9hicl9sqh7xn96f9pac117hy6z852jvi2"))))
12449 (build-system r-build-system)
12450 (home-page "http://minato.sip21c.org/msb/")
12451 (synopsis "Functions for medical statistics book with demographic data")
12453 "This package provides several utility functions for the book entitled
12454 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
12455 Japan, 2007) with Japanese demographic data and some demographic analysis
12456 related functions.")
12457 (license license:gpl2+)))
12459 (define-public r-stabledist
12461 (name "r-stabledist")
12466 (uri (cran-uri "stabledist" version))
12469 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
12470 (build-system r-build-system)
12471 (home-page "https://www.rmetrics.org")
12472 (synopsis "Stable distribution functions")
12474 "This package provides density, probability and quantile functions, and
12475 random number generation for (skew) stable distributions, using the
12476 parametrizations of Nolan.")
12477 (license license:gpl2+)))
12479 (define-public r-gsl
12482 (version "2.1-7.1")
12486 (uri (cran-uri "gsl" version))
12489 "118rj9kjx9rzlynvhrly19qz3yxg8jzws35971ssgzrp5lwd367f"))))
12490 (build-system r-build-system)
12493 (home-page "https://cran.r-project.org/web/packages/gsl")
12494 (synopsis "Wrapper for the GNU Scientific Library")
12496 "This package provides an R wrapper for the special functions and quasi
12497 random number generators of the GNU Scientific Library.")
12498 (license license:gpl2+)))
12500 (define-public r-adgoftest
12502 (name "r-adgoftest")
12507 (uri (cran-uri "ADGofTest" version))
12510 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
12511 (properties `((upstream-name . "ADGofTest")))
12512 (build-system r-build-system)
12513 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
12514 (synopsis "Anderson-Darling GoF test")
12516 "This package provides an implementation of the Anderson-Darling GoF test
12517 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
12518 Anderson-Darling Distribution\".")
12519 ;; Any version of the GPL.
12520 (license license:gpl3+)))
12522 (define-public r-sodium
12529 (uri (cran-uri "sodium" version))
12532 "0x4jb3cf1nv1spz1jc9xp8hly2b4a7nj48xr4s33jnfcpdjkmn5q"))))
12533 (properties `((upstream-name . "sodium")))
12534 (build-system r-build-system)
12538 (list pkg-config r-knitr))
12539 (home-page "https://github.com/jeroen/sodium")
12540 (synopsis "R bindings to the libsodium crypto library")
12542 "This package provides bindings to libsodium: a library for encryption,
12543 decryption, signatures, password hashing and more. Sodium uses curve25519, a
12544 Diffie-Hellman function by Daniel Bernstein, which has become very popular
12545 after it was discovered that the NSA had backdoored Dual EC DRBG.")
12546 (license license:expat)))
12548 (define-public r-softimpute
12550 (name "r-softimpute")
12555 (uri (cran-uri "softImpute" version))
12558 "1v2a4d688ij5zcvkzpra9yx40xckdfnllnfnyq2450zf3n1kjk7a"))))
12559 (properties `((upstream-name . "softImpute")))
12560 (build-system r-build-system)
12564 (list gfortran r-knitr))
12565 (home-page "https://cran.r-project.org/web/packages/softImpute")
12566 (synopsis "Matrix completion via iterative soft-thresholded SVD")
12568 "This package provides iterative methods for matrix completion that use
12569 nuclear-norm regularization. The package includes procedures for centering
12570 and scaling rows, columns or both, and for computing low-rank @dfn{single
12571 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
12573 (license license:gpl2)))
12575 (define-public r-fftwtools
12577 (name "r-fftwtools")
12582 (uri (cran-uri "fftwtools" version))
12585 "0zrchp4l0jdbir2gibjf00x225y9giqk80zvqmr2yyvc12lwkw7i"))))
12586 (build-system r-build-system)
12587 (inputs (list fftw))
12590 (home-page "https://github.com/krahim/fftwtools")
12591 (synopsis "Wrapper for FFTW3")
12593 "This package provides a wrapper for several FFTW functions. It provides
12594 access to the two-dimensional FFT, the multivariate FFT, and the
12595 one-dimensional real to complex FFT using the FFTW3 library. The package
12596 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
12597 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
12598 The FFT functions have a parameter that allows them to not return the
12599 redundant complex conjugate when the input is real data.")
12600 (license license:gpl2+)))
12602 (define-public r-tiff
12609 (uri (cran-uri "tiff" version))
12612 "1zha6bzb1rmfl6n2xjkygs9wfi3ah9cjr7a6jzk4zqc5kvl58lak"))))
12613 (build-system r-build-system)
12615 `(("libtiff" ,libtiff)
12616 ("libjpeg" ,libjpeg-turbo)
12620 (home-page "https://www.rforge.net/tiff/")
12621 (synopsis "Read and write TIFF images")
12623 "This package provides an easy and simple way to read, write and display
12624 bitmap images stored in the TIFF format. It can read and write both files and
12625 in-memory raw vectors.")
12626 ;; Either of these two license versions.
12627 (license (list license:gpl2 license:gpl3))))
12629 (define-public r-nlp
12636 (uri (cran-uri "NLP" version))
12639 "1dpj04fmld2lnhg072ahgjbhmciqqy9h1lrz0wf32mr7mm9s9sh5"))))
12640 (properties `((upstream-name . "NLP")))
12641 (build-system r-build-system)
12642 (home-page "https://cran.r-project.org/web/packages/NLP/")
12643 (synopsis "Natural language processing infrastructure")
12645 "This package provides basic classes and methods for Natural Language
12647 (license license:gpl3)))
12649 (define-public r-tm
12656 (uri (cran-uri "tm" version))
12659 "0mk2lsplynms15nw92vbdgsafg4bw1m0ik31gch1mnsnv61idsxi"))))
12660 (properties `((upstream-name . "tm")))
12661 (build-system r-build-system)
12663 (list r-bh r-nlp r-rcpp r-slam r-xml2))
12664 (home-page "http://tm.r-forge.r-project.org/")
12665 (synopsis "Text mining package")
12667 "This package provides a framework for text mining applications within R.")
12668 (license license:gpl3)))
12670 (define-public r-waveslim
12672 (name "r-waveslim")
12677 (uri (cran-uri "waveslim" version))
12680 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
12681 (build-system r-build-system)
12684 (home-page "http://waveslim.blogspot.com")
12685 (synopsis "Basic wavelet routines for signal processing")
12687 "This package provides basic wavelet routines for time series (1D),
12688 image (2D) and array (3D) analysis. The code provided here is based on
12689 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
12690 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
12691 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
12692 pairs (Selesnick 2001, 2002).")
12693 (license license:bsd-3)))
12695 (define-public r-wordcloud
12697 (name "r-wordcloud")
12702 (uri (cran-uri "wordcloud" version))
12705 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
12706 (build-system r-build-system)
12708 (list r-rcolorbrewer r-rcpp
12709 ;; The "tm" package is only "suggested" according to CRAN, but the
12710 ;; wordcloud package cannot be loaded without it.
12712 (home-page "https://cran.r-project.org/web/packages/wordcloud")
12713 (synopsis "Word clouds")
12715 "This package provides functionality to create pretty word clouds,
12716 visualize differences and similarity between documents, and avoid
12717 over-plotting in scatter plots with text.")
12718 (license license:lgpl2.1)))
12720 (define-public r-colorramps
12722 (name "r-colorramps")
12727 (uri (cran-uri "colorRamps" version))
12730 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
12731 (properties `((upstream-name . "colorRamps")))
12732 (build-system r-build-system)
12733 (home-page "https://cran.r-project.org/web/packages/colorRamps")
12734 (synopsis "Build color tables")
12735 (description "This package provides features to build gradient color
12737 ;; Any version of the GPL
12738 (license license:gpl3+)))
12740 (define-public r-tidytree
12742 (name "r-tidytree")
12747 (uri (cran-uri "tidytree" version))
12749 (base32 "1gnpm4zz0kvqng5s179301q0h5993ajynm8y0zbdz38qcmzfpsdk"))))
12750 (build-system r-build-system)
12763 (home-page "https://github.com/GuangchuangYu/tidytree")
12764 (synopsis "Tidy tool for phylogenetic tree data manipulation")
12766 "Phylogenetic trees generally contain multiple components including nodes,
12767 edges, branches and associated data. This package provides an approach to
12768 convert tree objects to tidy data frames. It also provides tidy interfaces to
12769 manipulate tree data.")
12770 (license license:artistic2.0)))
12772 (define-public r-rvcheck
12779 (uri (cran-uri "rvcheck" version))
12781 (base32 "09khjklvzbafd7r55496by01a9g3y291d87hpy43w44dmz9fzn9a"))))
12782 (build-system r-build-system)
12784 (list r-biocmanager r-yulab-utils))
12785 (home-page "https://cran.r-project.org/web/packages/rvcheck")
12786 (synopsis "R package version check")
12788 "This package provides tools to check the latest release version of R and
12789 R packages (on CRAN, Bioconductor or Github).")
12790 (license license:artistic2.0)))
12792 (define-public r-docopt
12799 (uri (cran-uri "docopt" version))
12802 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz"))))
12803 (build-system r-build-system)
12804 (home-page "https://github.com/docopt/docopt.R")
12805 (synopsis "Command-line interface specification language")
12807 "This package enables you to define a command-line interface by just
12808 giving it a description in the specific format.")
12809 (license license:expat)))
12811 (define-public r-sparsesvd
12813 (name "r-sparsesvd")
12818 (uri (cran-uri "sparsesvd" version))
12821 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
12822 (build-system r-build-system)
12823 (propagated-inputs (list r-matrix))
12824 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
12825 (synopsis "Sparse truncated singular value decomposition")
12827 "This package provides a Wrapper around the SVDLIBC library
12828 for (truncated) singular value decomposition of a sparse matrix. Currently,
12829 only sparse real matrices in Matrix package format are supported.")
12830 ;; SVDLIBC is released under BSD-2. The R interface is released under
12832 (license (list license:bsd-3 license:bsd-2))))
12834 (define-public r-speedglm
12836 (name "r-speedglm")
12841 (uri (cran-uri "speedglm" version))
12844 "0f37w4lj8dpcg1sfkd7cv6qpdkanmb97mnd8zih2fxzv8bpd0rfh"))))
12845 (build-system r-build-system)
12847 (list r-mass r-matrix))
12848 (home-page "https://cran.r-project.org/web/packages/speedglm")
12849 (synopsis "Fit linear and generalized linear models to large data sets")
12851 "This package provides tools for fitting linear models and generalized
12852 linear models to large data sets by updating algorithms.")
12853 ;; Any version of the GPL
12854 (license license:gpl2+)))
12856 (define-public r-densityclust
12858 (name "r-densityclust")
12863 (uri (cran-uri "densityClust" version))
12866 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
12867 (properties `((upstream-name . "densityClust")))
12868 (build-system r-build-system)
12877 (home-page "https://cran.r-project.org/web/packages/densityClust")
12878 (synopsis "Clustering by fast search and find of density peaks")
12880 "This package provides an improved implementation (based on k-nearest
12881 neighbors) of the density peak clustering algorithm, originally described by
12882 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
12883 large datasets (> 100,000 samples) very efficiently.")
12884 (license license:gpl2+)))
12886 (define-public r-combinat
12888 (name "r-combinat")
12893 (uri (cran-uri "combinat" version))
12896 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
12897 (build-system r-build-system)
12898 (home-page "https://cran.r-project.org/web/packages/combinat")
12899 (synopsis "Combinatorics utilities")
12900 (description "This package provides assorted routines for combinatorics.")
12901 (license license:gpl2)))
12903 (define-public r-qlcmatrix
12905 (name "r-qlcmatrix")
12910 (uri (cran-uri "qlcMatrix" version))
12913 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
12914 (properties `((upstream-name . "qlcMatrix")))
12915 (build-system r-build-system)
12917 (list r-docopt r-matrix r-slam r-sparsesvd))
12918 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
12919 (synopsis "Sparse matrix functions for quantitative language comparison")
12921 "This package provides an extension of the functionality of the Matrix
12922 package for using sparse matrices. Some of the functions are very general,
12923 while other are highly specific for the special data format used for
12924 @dfn{quantitative language comparison} (QLC).")
12925 (license license:gpl3)))
12927 (define-public r-ddrtree
12934 (uri (cran-uri "DDRTree" version))
12937 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
12938 (properties `((upstream-name . "DDRTree")))
12939 (build-system r-build-system)
12941 (list r-bh r-irlba r-rcpp r-rcppeigen))
12942 (home-page "https://cran.r-project.org/web/packages/DDRTree")
12943 (synopsis "Learning principal graphs with DDRTree")
12945 "This package provides an implementation of the framework of
12946 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
12947 dimensional space while constructs a principal tree which passes through the
12948 middle of the data simultaneously. DDRTree shows superiority to
12949 alternatives (Wishbone, DPT) for inferring the ordering as well as the
12950 intrinsic structure of single cell genomics data. In general, it could be
12951 used to reconstruct the temporal progression as well as the bifurcation
12952 structure of any data type.")
12953 (license license:asl2.0)))
12955 (define-public r-corpcor
12962 (uri (cran-uri "corpcor" version))
12965 "028fw61n61i79fhnaqx7gmdifdpbvp3yiaq9vvfrbv4k7i84r83i"))))
12966 (build-system r-build-system)
12967 (home-page "http://strimmerlab.org/software/corpcor/")
12968 (synopsis "Efficient estimation of covariance and (partial) correlation")
12970 "This package implements a James-Stein-type shrinkage estimator for the
12971 covariance matrix, with separate shrinkage for variances and correlations.
12972 Furthermore, functions are available for fast singular value decomposition,
12973 for computing the pseudoinverse, and for checking the rank and positive
12974 definiteness of a matrix.")
12975 (license license:gpl3+)))
12977 (define-public r-rspectra
12979 (name "r-rspectra")
12984 (uri (cran-uri "RSpectra" version))
12987 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
12988 (properties `((upstream-name . "RSpectra")))
12989 (build-system r-build-system)
12991 (list r-matrix r-rcpp r-rcppeigen))
12992 (home-page "https://github.com/yixuan/RSpectra")
12993 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
12995 "This package provides an R interface to the Spectra library for
12996 large-scale eigenvalue and SVD problems. It is typically used to compute a
12997 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
12998 which is usually more efficient than @code{eigen()} if k << n.")
13000 (license license:mpl2.0)))
13002 (define-public r-vbsr
13009 (uri (cran-uri "vbsr" version))
13012 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
13013 (build-system r-build-system)
13014 (home-page "https://cran.r-project.org/web/packages/vbsr")
13015 (synopsis "Variational Bayes spike regression regularized linear models")
13017 "This package provides an efficient algorithm for solving ultra-sparse
13018 regularized regression models using a variational Bayes algorithm with a spike
13019 prior. The algorithm is solved on a path, with coordinate updates, and is
13020 capable of generating very sparse models. Very general model
13021 diagnostics for controlling type-1 errors are also provided.")
13022 (license license:gpl2)))
13024 (define-public r-flare
13031 (uri (cran-uri "flare" version))
13034 "0f992dmgnr6s8g3386i9bjfyf08q8srgw7sjz2yx7snj8znq7251"))))
13035 (build-system r-build-system)
13037 (list r-igraph r-lattice r-mass r-matrix))
13038 (home-page "https://cran.r-project.org/web/packages/flare")
13039 (synopsis "Family of Lasso regression implementations")
13041 "This package provides implementations of a family of Lasso variants
13042 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
13043 high dimensional sparse linear models.")
13044 (license license:gpl2)))
13046 (define-public r-lassopv
13053 (uri (cran-uri "lassopv" version))
13056 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
13057 (build-system r-build-system)
13058 (propagated-inputs (list r-lars))
13059 (home-page "https://github.com/lingfeiwang/lassopv")
13060 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
13062 "This package enables you to estimate the p-values for predictors x
13063 against target variable y in Lasso regression, using the regularization
13064 strength when each predictor enters the active set of regularization path for
13065 the first time as the statistic.")
13066 (license license:gpl3)))
13068 (define-public r-splitstackshape
13070 (name "r-splitstackshape")
13075 (uri (cran-uri "splitstackshape" version))
13078 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
13079 (build-system r-build-system)
13081 (list r-data-table))
13082 (home-page "https://github.com/mrdwab/splitstackshape")
13083 (synopsis "Stack and reshape datasets after splitting concatenated values")
13085 "Online data collection tools like Google Forms often export
13086 multiple-response questions with data concatenated in cells. The
13087 @code{concat.split} (cSplit) family of functions provided by this package
13088 splits such data into separate cells. This package also includes functions to
13089 stack groups of columns and to reshape wide data, even when the data are
13090 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
13091 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
13093 (license license:gpl3)))
13095 (define-public r-tfmpvalue
13097 (name "r-tfmpvalue")
13102 (uri (cran-uri "TFMPvalue" version))
13105 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
13106 (properties `((upstream-name . "TFMPvalue")))
13107 (build-system r-build-system)
13108 (propagated-inputs (list r-rcpp))
13109 (home-page "https://github.com/ge11232002/TFMPvalue")
13110 (synopsis "P-value computation for position weight matrices")
13112 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
13113 identification from sequence/alignments, we are interested in the significance
13114 of certain match scores. TFMPvalue provides the accurate calculation of a
13115 p-value with a score threshold for position weight matrices, or the score with
13116 a given p-value. It is an interface to code originally made available by
13117 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
13118 Touzet and Varre (2007).")
13119 (license license:gpl2)))
13121 (define-public r-rncl
13127 (uri (cran-uri "rncl" version))
13130 "0ss9jqrvv7bhvl5j74cjrp8r866d9dlavrbbfscwz3mhkgfx06bb"))))
13131 (build-system r-build-system)
13133 (list r-progress r-rcpp))
13134 (home-page "https://github.com/fmichonneau/rncl")
13135 (synopsis "Interface to the Nexus class library")
13136 (description "This package provides an interface to the Nexus class
13137 library which allows parsing of NEXUS, Newick and other phylogenetic tree
13138 file formats. It provides elements of the file that can be used to build
13139 phylogenetic objects such as @code{ape}'s @code{phylo} or @code{phylobase}'s
13140 @code{phylo4(d)}. This functionality is demonstrated with
13141 @code{read_newick_phylo()} and @code{read_nexus_phylo()}.")
13142 (license license:bsd-2)))
13144 (define-public r-phylobase
13146 (name "r-phylobase")
13150 (uri (cran-uri "phylobase" version))
13153 "0jzr1gdvmi4l640hwwzh9bxqmpja69bn3ygnaqx37awvyh7khi2s"))))
13154 (build-system r-build-system)
13156 (list r-ade4 r-ape r-rcpp r-rncl r-rnexml))
13159 (home-page "https://github.com/fmichonneau/phylobase")
13160 (synopsis "Base package for phylogenetic structures and comparative data")
13161 (description "This package provides a base @code{S4} class for comparative
13162 methods, incorporating one or more trees and trait data.")
13163 (license license:gpl2+)))
13165 (define-public r-rnexml
13171 (uri (cran-uri "RNeXML" version))
13174 "1wsl4xq9w5bp3wk69dw57bg0qcw1vs6ajwya4p0w1r00ck5pwrib"))))
13175 (build-system r-build-system)
13191 (home-page "https://docs.ropensci.org/RNeXML/")
13192 (synopsis "Semantically rich I/O for the NeXML Format")
13193 (description "This package provides access to phyloinformatic data in
13194 NeXML format. The package should add new functionality to R such as the
13195 possibility to manipulate NeXML objects in more various and refined way
13196 and compatibility with @code{ape} objects.")
13197 (license license:bsd-3)))
13199 (define-public r-rnifti
13206 (uri (cran-uri "RNifti" version))
13209 "0bz10ar6hrgkvlzh9j2im24kwi3s2nnax668z40a2wj6s5xghqlr"))))
13210 (properties `((upstream-name . "RNifti")))
13211 (build-system r-build-system)
13212 (propagated-inputs (list r-rcpp))
13213 (home-page "https://github.com/jonclayden/RNifti")
13214 (synopsis "Fast R and C++ access to NIfTI images")
13216 "This package provides very fast read and write access to images stored
13217 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
13218 compiled C and interpreted R code. It also provides a C/C++ API that can be
13219 used by other packages.")
13220 (license license:gpl2)))
13222 (define-public r-shades
13229 (uri (cran-uri "shades" version))
13232 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
13233 (build-system r-build-system)
13234 (home-page "https://github.com/jonclayden/shades")
13235 (synopsis "Simple color manipulation")
13237 "This package provides functions for easily manipulating colors,
13238 creating color scales and calculating color distances.")
13239 (license license:bsd-3)))
13241 (define-public r-ore
13244 (version "1.7.1.1")
13248 (uri (cran-uri "ore" version))
13250 (base32 "0rs5r5h11x4l4nsbl4xqzbl4ahajd5374fq05abcmfjnjr9j64w5"))))
13251 (build-system r-build-system)
13252 (home-page "https://github.com/jonclayden/ore")
13253 (synopsis "R interface to the Onigmo regular expression library")
13255 "This package provides an alternative to R's built-in functionality for
13256 handling regular expressions, based on the Onigmo library. It offers
13257 first-class compiled regex objects, partial matching and function-based
13258 substitutions, amongst other features.")
13259 (license license:bsd-3)))
13261 (define-public r-reportr
13268 (uri (cran-uri "reportr" version))
13271 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
13272 (build-system r-build-system)
13273 (propagated-inputs (list r-ore))
13274 (home-page "https://github.com/jonclayden/reportr")
13275 (synopsis "General message and error reporting system")
13277 "This package provides a system for reporting messages, which offers
13278 certain useful features over the standard R system, such as the incorporation
13279 of output consolidation, message filtering, assertions, expression
13280 substitution, automatic generation of stack traces for debugging, and
13281 conditional reporting based on the current \"output level\".")
13282 (license license:gpl2)))
13284 (define-public r-tractor-base
13286 (name "r-tractor-base")
13287 (version "3.3.3.1")
13291 (uri (cran-uri "tractor.base" version))
13294 "0w5jw7pf77npkgig7667yikpbwv4dfk1dcq63qm88l409ga2f95p"))))
13295 (properties `((upstream-name . "tractor.base")))
13296 (build-system r-build-system)
13298 (list r-ore r-reportr r-rnifti r-shades))
13299 (home-page "https://www.tractor-mri.org.uk")
13300 (synopsis "Read, manipulate and visualize magnetic resonance images")
13302 "This package provides functions for working with magnetic resonance
13303 images. It supports reading and writing of popular file formats (DICOM,
13304 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
13305 visualization; flexible image manipulation; metadata and sparse image
13307 (license license:gpl2)))
13309 (define-public r-grimport
13311 (name "r-grimport")
13316 (uri (cran-uri "grImport" version))
13319 "0pbzc45wgp0cpycnw0bzn65ckdszzay0zrp7c7ssxdkifp8bai3a"))))
13320 (properties `((upstream-name . "grImport")))
13321 (build-system r-build-system)
13323 (list ghostscript))
13326 (home-page "https://cran.r-project.org/web/packages/grImport")
13327 (synopsis "Convert, import, and draw PostScript pictures")
13329 "This package provides functions for converting, importing, and drawing
13330 PostScript pictures in R plots.")
13331 (license license:gpl2+)))
13333 (define-public r-grimport2
13335 (name "r-grimport2")
13340 (uri (cran-uri "grImport2" version))
13343 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
13344 (properties `((upstream-name . "grImport2")))
13345 (build-system r-build-system)
13347 (list r-base64enc r-jpeg r-png r-xml))
13348 (home-page "https://cran.r-project.org/web/packages/grImport2/")
13349 (synopsis "Import SVG graphics")
13351 "This package provides functions for importing external vector images and
13352 drawing them as part of R plots. This package is different from the
13353 @code{grImport} package because, where that package imports PostScript format
13354 images, this package imports SVG format images. Furthermore, this package
13355 imports a specific subset of SVG, so external images must be preprocessed
13356 using a package like @code{rsvg} to produce SVG that this package can import.
13357 SVG features that are not supported by R graphics, such as gradient fills, can
13358 be imported and then exported via the @code{gridSVG} package.")
13359 (license license:gpl2+)))
13361 (define-public r-kohonen
13368 (uri (cran-uri "kohonen" version))
13371 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
13372 (build-system r-build-system)
13375 (home-page "https://cran.r-project.org/web/packages/kohonen")
13376 (synopsis "Supervised and unsupervised self-organising maps")
13378 "This package provides functions to train @dfn{self-organising
13379 maps} (SOMs). Also interrogation of the maps and prediction using trained
13380 maps are supported. The name of the package refers to Teuvo Kohonen, the
13381 inventor of the SOM.")
13382 (license license:gpl2+)))
13384 (define-public r-nnls
13391 (uri (cran-uri "nnls" version))
13394 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
13395 (build-system r-build-system)
13396 (native-inputs (list gfortran))
13397 (home-page "https://cran.r-project.org/web/packages/nnls")
13398 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
13400 "This package provides an R interface to the Lawson-Hanson implementation
13401 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
13402 the combination of non-negative and non-positive constraints.")
13403 (license license:gpl2+)))
13405 (define-public r-iso
13408 (version "0.0-18.1")
13412 (uri (cran-uri "Iso" version))
13415 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g"))))
13416 (properties `((upstream-name . "Iso")))
13417 (build-system r-build-system)
13418 (native-inputs (list gfortran))
13419 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
13420 (synopsis "Functions to perform isotonic regression")
13422 "This package provides support for linear order and unimodal
13423 order (univariate) isotonic regression and bivariate isotonic regression with
13424 linear order on both variables.")
13425 (license license:gpl2+)))
13427 (define-public r-chemometricswithr
13429 (name "r-chemometricswithr")
13434 (uri (cran-uri "ChemometricsWithR" version))
13437 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
13439 `((upstream-name . "ChemometricsWithR")))
13440 (build-system r-build-system)
13442 (list r-devtools r-kohonen r-mass r-pls))
13443 (home-page "https://github.com/rwehrens/CWR")
13444 (synopsis "Chemometrics with R")
13446 "This package provides functions and scripts used in the book
13447 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
13448 Life Sciences\" by Ron Wehrens, Springer (2011).")
13449 (license license:gpl2+)))
13451 (define-public r-als
13458 (uri (cran-uri "ALS" version))
13461 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
13462 (properties `((upstream-name . "ALS")))
13463 (build-system r-build-system)
13465 (list r-iso r-nnls))
13466 (home-page "https://cran.r-project.org/web/packages/ALS")
13467 (synopsis "Multivariate curve resolution alternating least squares")
13469 "Alternating least squares is often used to resolve components
13470 contributing to data with a bilinear structure; the basic technique may be
13471 extended to alternating constrained least squares. This package provides an
13472 implementation of @dfn{multivariate curve resolution alternating least
13473 squares} (MCR-ALS).
13475 Commonly applied constraints include unimodality, non-negativity, and
13476 normalization of components. Several data matrices may be decomposed
13477 simultaneously by assuming that one of the two matrices in the bilinear
13478 decomposition is shared between datasets.")
13479 (license license:gpl2+)))
13481 (define-public r-strucchange
13483 (name "r-strucchange")
13488 (uri (cran-uri "strucchange" version))
13491 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
13492 (build-system r-build-system)
13494 (list r-sandwich r-zoo))
13495 (home-page "https://cran.r-project.org/web/packages/strucchange")
13496 (synopsis "Testing, monitoring, and dating structural changes")
13498 "This package provides tools for testing, monitoring and dating
13499 structural changes in (linear) regression models. It features tests/methods
13500 from the generalized fluctuation test framework as well as from the F
13501 test (Chow test) framework. This includes methods to fit, plot and test
13502 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
13503 statistics, respectively. It is possible to monitor incoming data online
13504 using fluctuation processes. Finally, the breakpoints in regression models
13505 with structural changes can be estimated together with confidence intervals.
13506 Emphasis is always given to methods for visualizing the data.")
13507 ;; Either of these two GPL versions
13508 (license (list license:gpl2 license:gpl3))))
13510 (define-public r-pixmap
13517 (uri (cran-uri "pixmap" version))
13520 "1v1a1adsgh5jlvvi98j4nhb1h681s97ip76zdrga12rlsjaahfw9"))))
13521 (build-system r-build-system)
13522 (home-page "https://cran.r-project.org/web/packages/pixmap")
13523 (synopsis "Tools for bitmap images")
13525 "This package provides functions for importing, exporting, plotting and
13526 other manipulations of bitmapped images.")
13527 (license license:gpl2)))
13529 (define-public r-rapidjsonr
13531 (name "r-rapidjsonr")
13536 (uri (cran-uri "rapidjsonr" version))
13539 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
13540 (build-system r-build-system)
13541 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
13542 (synopsis "JSON parser")
13544 "This package provides JSON parsing capability through the Rapidjson
13546 (license license:expat)))
13548 (define-public r-ontologyindex
13550 (name "r-ontologyindex")
13555 (uri (cran-uri "ontologyIndex" version))
13558 "0j3h1spqwjhh1wbmwivmqcyi042yy7d565c3kxgn70xrmy693x1k"))))
13559 (properties `((upstream-name . "ontologyIndex")))
13560 (build-system r-build-system)
13563 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
13564 (synopsis "Functions for processing ontologies in R")
13566 "This package provides functions for reading ontologies into R as lists
13567 and manipulating sets of ontological terms.")
13568 (license license:gpl2+)))
13570 (define-public r-gargle
13577 (uri (cran-uri "gargle" version))
13580 "0fypj70c1fjmvs57birik76wfx8a2fs4gzicbb52k57i6clwlijd"))))
13581 (build-system r-build-system)
13594 (home-page "https://gargle.r-lib.org")
13595 (synopsis "Utilities for working with Google APIs")
13597 "This package provides utilities for working with Google APIs. This
13598 includes functions and classes for handling common credential types and for
13599 preparing, executing, and processing HTTP requests.")
13600 (license license:expat)))
13602 (define-public r-bigrquery
13604 (name "r-bigrquery")
13609 (uri (cran-uri "bigrquery" version))
13612 "02msq61l7vamzpvbhvalh3qil1aa7pr68pwpsivbb6pvz6p4zyns"))))
13613 (build-system r-build-system)
13630 (home-page "https://github.com/rstats-db/bigrquery")
13631 (synopsis "R interface to Google's BigQuery API")
13633 "This package provides an R interface to Google's BigQuery database.")
13634 (license license:gpl3)))
13636 (define-public r-gmp
13639 (version "0.6-2.1")
13643 (uri (cran-uri "gmp" version))
13646 "1mj7hy6riaxl9n4q2cnyyjazwad90xbjszk25si968618rih4n64"))))
13647 (build-system r-build-system)
13650 (modify-phases %standard-phases
13651 (add-after 'unpack 'set-CC
13652 (lambda _ (setenv "CC" "gcc") #t)))))
13653 (inputs (list gmp))
13654 (home-page "https://cran.r-project.org/web/packages/gmp")
13655 (synopsis "Multiple precision arithmetic")
13657 "This package supports multiple precision arithmetic (big integers and
13658 rationals, prime number tests, matrix computation), \"arithmetic without
13659 limitations\" using the GNU Multiple Precision library.")
13660 ;; Any version of the GPL.
13661 (license license:gpl3+)))
13663 (define-public r-rmpfr
13670 (uri (cran-uri "Rmpfr" version))
13673 "1ljpbxvm4agbxnab5dfffbpw5k964hy3gw57dzydq1gpbxwdphlk"))))
13674 (properties `((upstream-name . "Rmpfr")))
13675 (build-system r-build-system)
13682 (home-page "http://rmpfr.r-forge.r-project.org/")
13683 (synopsis "R bindings to the MPFR library")
13685 "This package supports arithmetic (via S4 classes and methods) for
13686 arbitrary precision floating point numbers, including transcendental
13687 functions. To this end, the package interfaces with the @dfn{Multiple
13688 Precision Floating-Point Reliable} (MPFR) library.")
13689 (license license:gpl2+)))
13691 (define-public r-assertive-base
13693 (name "r-assertive-base")
13698 (uri (cran-uri "assertive.base" version))
13701 "07m0ddz092bgbl2fn1yk932h0iajdcqkri632477wl5a1q5r3w2b"))))
13703 `((upstream-name . "assertive.base")))
13704 (build-system r-build-system)
13705 (home-page "https://bitbucket.org/richierocks/assertive.base")
13706 (synopsis "Core of the assertive package")
13708 "This package provides a minimal set of predicates and assertions used by
13709 the assertive package. This is mainly for use by other package developers who
13710 want to include run-time testing features in their own packages.")
13711 (license license:gpl3+)))
13713 (define-public r-assertive-properties
13715 (name "r-assertive-properties")
13720 (uri (cran-uri "assertive.properties" version))
13723 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
13725 `((upstream-name . "assertive.properties")))
13726 (build-system r-build-system)
13728 (list r-assertive-base))
13729 (home-page "https://bitbucket.org/richierocks/assertive.properties")
13730 (synopsis "Assertions to check properties of variables")
13732 "This package provides a set of predicates and assertions for checking
13733 the properties of variables, such as length, names and attributes. This is
13734 mainly for use by other package developers who want to include run-time
13735 testing features in their own packages.")
13736 (license license:gpl3+)))
13738 (define-public r-assertive-numbers
13740 (name "r-assertive-numbers")
13745 (uri (cran-uri "assertive.numbers" version))
13748 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
13750 `((upstream-name . "assertive.numbers")))
13751 (build-system r-build-system)
13753 (list r-assertive-base))
13754 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
13755 (synopsis "Assertions to check properties of numbers")
13757 "This package provides a set of predicates and assertions for checking
13758 the properties of numbers. This is mainly for use by other package developers
13759 who want to include run-time testing features in their own packages.")
13760 (license license:gpl3+)))
13762 (define-public r-assertive-sets
13764 (name "r-assertive-sets")
13769 (uri (cran-uri "assertive.sets" version))
13772 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
13774 `((upstream-name . "assertive.sets")))
13775 (build-system r-build-system)
13777 (list r-assertive-base))
13778 (home-page "https://bitbucket.org/richierocks/assertive.sets")
13779 (synopsis "Assertions to check properties of sets")
13781 "This package provides a set of predicates and assertions for checking
13782 the properties of sets. This is mainly for use by other package developers
13783 who want to include run-time testing features in their own packages.")
13784 (license license:gpl3+)))
13786 (define-public r-assertive-matrices
13788 (name "r-assertive-matrices")
13793 (uri (cran-uri "assertive.matrices" version))
13796 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
13798 `((upstream-name . "assertive.matrices")))
13799 (build-system r-build-system)
13801 (list r-assertive-base))
13802 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
13803 (synopsis "Assertions to check properties of matrices")
13805 "This package provides a set of predicates and assertions for checking
13806 the properties of matrices. This is mainly for use by other package
13807 developers who want to include run-time testing features in their own
13809 (license license:gpl3+)))
13811 (define-public r-assertive-models
13813 (name "r-assertive-models")
13818 (uri (cran-uri "assertive.models" version))
13821 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
13823 `((upstream-name . "assertive.models")))
13824 (build-system r-build-system)
13826 (list r-assertive-base))
13827 (home-page "https://bitbucket.org/richierocks/assertive.models")
13828 (synopsis "Assertions to check properties of models")
13830 "This package provides a set of predicates and assertions for checking
13831 the properties of models. This is mainly for use by other package developers
13832 who want to include run-time testing features in their own packages.")
13833 (license license:gpl3+)))
13835 (define-public r-assertive-reflection
13837 (name "r-assertive-reflection")
13842 (uri (cran-uri "assertive.reflection" version))
13845 "1g9lpwzy6r2xmyi2mlbcccnfgyzhzbmx5bsicf3vkffxrlkrpjn2"))))
13847 `((upstream-name . "assertive.reflection")))
13848 (build-system r-build-system)
13850 (list r-assertive-base))
13851 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
13852 (synopsis "Assertions for checking the state of R")
13854 "This package provides a set of predicates and assertions for checking
13855 the state and capabilities of R, the operating system it is running on, and
13856 the IDE being used. This is mainly for use by other package developers who
13857 want to include run-time testing features in their own packages.")
13858 (license license:gpl3+)))
13860 (define-public r-assertive-types
13862 (name "r-assertive-types")
13867 (uri (cran-uri "assertive.types" version))
13870 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
13872 `((upstream-name . "assertive.types")))
13873 (build-system r-build-system)
13875 (list r-assertive-base r-assertive-properties r-codetools))
13876 (home-page "https://bitbucket.org/richierocks/assertive.types")
13877 (synopsis "Assertions to check types of variables")
13879 "This package provides a set of predicates and assertions for checking
13880 the types of variables. This is mainly for use by other package developers
13881 who want to include run-time testing features in their own packages.")
13882 (license license:gpl3+)))
13884 (define-public r-assertive-files
13886 (name "r-assertive-files")
13891 (uri (cran-uri "assertive.files" version))
13894 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
13896 `((upstream-name . "assertive.files")))
13897 (build-system r-build-system)
13899 (list r-assertive-base r-assertive-numbers))
13900 (home-page "https://bitbucket.org/richierocks/assertive.files")
13901 (synopsis "Assertions to check properties of files")
13903 "This package provides a set of predicates and assertions for checking
13904 the properties of files and connections. This is mainly for use by other
13905 package developers who want to include run-time testing features in their own
13907 (license license:gpl3+)))
13909 (define-public r-assertive-code
13911 (name "r-assertive-code")
13916 (uri (cran-uri "assertive.code" version))
13919 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
13921 `((upstream-name . "assertive.code")))
13922 (build-system r-build-system)
13924 (list r-assertive-base r-assertive-properties r-assertive-types))
13925 (home-page "https://bitbucket.org/richierocks/assertive.code")
13926 (synopsis "Assertions to check properties of code")
13928 "This package provides a set of predicates and assertions for checking
13929 the properties of code. This is mainly for use by other package developers
13930 who want to include run-time testing features in their own packages.")
13931 (license license:gpl3+)))
13933 (define-public r-assertive-datetimes
13935 (name "r-assertive-datetimes")
13940 (uri (cran-uri "assertive.datetimes" version))
13943 "151d05z8n6dpl44pqsa1jfi0ijbigr3zfc43xlw53nd8ymi22kh1"))))
13945 `((upstream-name . "assertive.datetimes")))
13946 (build-system r-build-system)
13948 (list r-assertive-base r-assertive-types))
13949 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
13950 (synopsis "Assertions to check properties of dates and times")
13952 "This package provides a set of predicates and assertions for checking
13953 the properties of dates and times. This is mainly for use by other package
13954 developers who want to include run-time testing features in their own
13956 (license license:gpl3+)))
13958 (define-public r-assertive-strings
13960 (name "r-assertive-strings")
13965 (uri (cran-uri "assertive.strings" version))
13968 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
13970 `((upstream-name . "assertive.strings")))
13971 (build-system r-build-system)
13973 (list r-assertive-base r-assertive-types r-stringi))
13974 (home-page "https://bitbucket.org/richierocks/assertive.strings")
13975 (synopsis "Assertions to check properties of strings")
13977 "This package provides a set of predicates and assertions for checking
13978 the properties of strings. This is mainly for use by other package developers
13979 who want to include run-time testing features in their own packages.")
13980 (license license:gpl3+)))
13982 (define-public r-assertive-data-us
13984 (name "r-assertive-data-us")
13989 (uri (cran-uri "assertive.data.us" version))
13992 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
13994 `((upstream-name . "assertive.data.us")))
13995 (build-system r-build-system)
13997 (list r-assertive-base r-assertive-strings))
13998 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
13999 (synopsis "Assertions to check properties of strings")
14001 "This package provides a set of predicates and assertions for checking
14002 the properties of US-specific complex data types. This is mainly for use by
14003 other package developers who want to include run-time testing features in
14004 their own packages.")
14005 (license license:gpl3+)))
14007 (define-public r-assertive-data-uk
14009 (name "r-assertive-data-uk")
14014 (uri (cran-uri "assertive.data.uk" version))
14017 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
14019 `((upstream-name . "assertive.data.uk")))
14020 (build-system r-build-system)
14022 (list r-assertive-base r-assertive-strings))
14023 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
14024 (synopsis "Assertions to check properties of strings")
14026 "This package provides a set of predicates and assertions for checking
14027 the properties of UK-specific complex data types. This is mainly for use by
14028 other package developers who want to include run-time testing features in
14029 their own packages.")
14030 (license license:gpl3+)))
14032 (define-public r-assertive-data
14034 (name "r-assertive-data")
14039 (uri (cran-uri "assertive.data" version))
14042 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
14044 `((upstream-name . "assertive.data")))
14045 (build-system r-build-system)
14047 (list r-assertive-base r-assertive-strings))
14048 (home-page "https://bitbucket.org/richierocks/assertive.data")
14049 (synopsis "Assertions to check properties of data")
14051 "This package provides a set of predicates and assertions for checking
14052 the properties of (country independent) complex data types. This is mainly
14053 for use by other package developers who want to include run-time testing
14054 features in their own packages.")
14055 (license license:gpl3+)))
14057 (define-public r-assertive
14059 (name "r-assertive")
14064 (uri (cran-uri "assertive" version))
14067 "02palil82idqhhshcdjsfsja9qkqnd0dczqzj5gbccy4hfg1c0y4"))))
14068 (build-system r-build-system)
14070 (list r-assertive-base
14073 r-assertive-data-uk
14074 r-assertive-data-us
14075 r-assertive-datetimes
14077 r-assertive-matrices
14079 r-assertive-numbers
14080 r-assertive-properties
14081 r-assertive-reflection
14083 r-assertive-strings
14088 (home-page "https://bitbucket.org/richierocks/assertive")
14089 (synopsis "Readable check functions to ensure code integrity")
14091 "This package provides lots of predicates (@code{is_*} functions) to
14092 check the state of your variables, and assertions (@code{assert_*} functions)
14093 to throw errors if they aren't in the right form.")
14094 (license license:gpl3+)))
14096 (define-public r-dotcall64
14098 (name "r-dotcall64")
14103 (uri (cran-uri "dotCall64" version))
14106 "1im5k8jbviwj2i42mq1kmjskh80isa7jr9w8i0fknidrzzy2h2zi"))))
14107 (properties `((upstream-name . "dotCall64")))
14108 (build-system r-build-system)
14109 (native-inputs (list gfortran))
14110 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
14111 (synopsis "Enhanced foreign function interface supporting long vectors")
14113 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
14114 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
14115 supports long vectors, arguments of type 64-bit integer, and provides a
14116 mechanism to avoid unnecessary copies of read-only and write-only arguments.
14117 This makes it a convenient and fast interface to C/C++ and Fortran code.")
14118 (license license:gpl2+)))
14120 (define-public r-spam
14127 (uri (cran-uri "spam" version))
14129 (base32 "03c50wfyrzcmrcv9mkgj8dmdg2cwkh4p4ys8gaclr8w7ym45qav3"))))
14130 (build-system r-build-system)
14132 (list r-dotcall64))
14134 (list gfortran r-knitr))
14135 (home-page "https://www.math.uzh.ch/pages/spam/")
14136 (synopsis "Sparse matrix algebra")
14138 "This package provides a set of functions for sparse matrix algebra.
14139 Differences with other sparse matrix packages are:
14142 @item it only supports (essentially) one sparse matrix format;
14143 @item it is based on transparent and simple structure(s);
14144 @item it is tailored for MCMC calculations within G(M)RF;
14145 @item and it is fast and scalable (with the extension package @code{spam64}).
14147 ;; Either of these licenses
14148 (license (list license:bsd-3 license:lgpl2.0))))
14150 (define-public r-fields
14157 (uri (cran-uri "fields" version))
14159 (base32 "1hs4k5a9hh0r5fsrnpnvs6wvf78xpjzj8a2j6643dsz73a5q6ln6"))))
14160 (build-system r-build-system)
14162 (list r-maps r-spam r-viridis))
14165 (home-page "https://www.image.ucar.edu/fields")
14166 (synopsis "Tools for spatial data")
14168 "This is a package for curve, surface and function fitting with an
14169 emphasis on splines, spatial data and spatial statistics. The major methods
14170 include cubic, and thin plate splines, Kriging, and compactly supported
14171 covariance functions for large data sets.")
14172 (license license:gpl2+)))
14174 (define-public r-spatialextremes
14176 (name "r-spatialextremes")
14181 (uri (cran-uri "SpatialExtremes" version))
14184 "1mhn1c8n3bmgf0fjyac3wji4790zswzkqliqcv3n8kv9806crb0y"))))
14186 `((upstream-name . "SpatialExtremes")))
14187 (build-system r-build-system)
14189 (list r-fields r-maps))
14190 (home-page "http://spatialextremes.r-forge.r-project.org/")
14191 (synopsis "Modelling spatial extremes")
14193 "This package provides tools for the statistical modelling of spatial
14194 extremes using max-stable processes, copula or Bayesian hierarchical models.
14195 More precisely, this package allows (conditional) simulations from various
14196 parametric max-stable models, analysis of the extremal spatial dependence, the
14197 fitting of such processes using composite likelihoods or least square (simple
14198 max-stable processes only), model checking and selection and prediction.")
14199 (license license:gpl2+)))
14201 (define-public r-drc
14208 (uri (cran-uri "drc" version))
14211 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
14212 (build-system r-build-system)
14220 (home-page "https://cran.r-project.org/web/packages/drc")
14221 (synopsis "Analysis of dose-response curves")
14223 "This package provides a suite of flexible and versatile model fitting
14224 and after-fitting functions for the analysis of dose-response data.")
14225 (license license:gpl2+)))
14227 (define-public r-rmeta
14234 (uri (cran-uri "rmeta" version))
14237 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
14238 (build-system r-build-system)
14239 (home-page "https://cran.r-project.org/web/packages/rmeta")
14240 (synopsis "Tools for meta-analysis")
14242 "This package provides functions for simple fixed and random effects
14243 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
14244 draws standard summary plots, funnel plots, and computes summaries and tests
14245 for association and heterogeneity.")
14246 (license license:gpl2)))
14248 (define-public r-bootstrap
14250 (name "r-bootstrap")
14255 (uri (cran-uri "bootstrap" version))
14258 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
14259 (build-system r-build-system)
14260 (native-inputs (list gfortran))
14261 (home-page "https://cran.r-project.org/web/packages/bootstrap")
14262 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
14264 "This package provides software and data for the book \"An Introduction
14265 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
14266 This package is primarily provided for projects already based on it, and for
14267 support of the book. New projects should preferentially use the recommended
14268 package \"boot\".")
14269 (license license:bsd-3)))
14271 (define-public r-survivalroc
14273 (name "r-survivalroc")
14278 (uri (cran-uri "survivalROC" version))
14281 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
14282 (properties `((upstream-name . "survivalROC")))
14283 (build-system r-build-system)
14284 (home-page "https://cran.r-project.org/web/packages/survivalROC")
14285 (synopsis "Time-dependent ROC curve estimation from censored survival data")
14287 "Compute time-dependent ROC curve from censored survival data using
14288 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
14289 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
14290 (license license:gpl2+)))
14292 (define-public r-locfdr
14298 (uri (cran-uri "locfdr" version))
14301 "1falkbp2xz07am8jlhwlvyqvxnli4nwl188kd0g58vdfjcjy3mj2"))))
14302 (build-system r-build-system)
14303 (home-page "https://cran.r-project.org/web/packages/locfdr/")
14304 (synopsis "Computes local false discovery rates")
14305 (description "This package can be used to compute local false
14307 (license license:gpl2)))
14309 (define-public r-longitudinal
14311 (name "r-longitudinal")
14316 (uri (cran-uri "longitudinal" version))
14319 "046w3xbr535c5jyd68adv42a7limxp1mv57b5w6w673w707lmw2p"))))
14320 (build-system r-build-system)
14321 (propagated-inputs (list r-corpcor))
14322 (home-page "http://strimmerlab.org/software/longitudinal/")
14323 (synopsis "Analysis of multiple time course data")
14325 "This package contains general data structures and functions for
14326 longitudinal data with multiple variables, repeated measurements, and
14327 irregularly spaced time points. It also implements a shrinkage estimator of
14328 dynamical correlation and dynamical covariance.")
14329 (license license:gpl3+)))
14331 (define-public r-genenet
14338 (uri (cran-uri "GeneNet" version))
14341 "1r1khga3nxxjghs4vnbymzp0cwb1q17zw2v3a94qz8fsrirq1sf1"))))
14342 (properties `((upstream-name . "GeneNet")))
14343 (build-system r-build-system)
14345 (list r-corpcor r-fdrtool r-longitudinal))
14346 (home-page "http://strimmerlab.org/software/genenet/")
14347 (synopsis "Modeling and inferring gene networks")
14349 "This package analyzes gene expression (time series) data with focus on
14350 the inference of gene networks. In particular, GeneNet implements the methods
14351 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
14352 for learning large-scale gene association networks (including assignment of
14353 putative directions).")
14354 (license license:gpl3+)))
14356 (define-public r-rbamtools
14358 (name "r-rbamtools")
14359 (version "2.16.17")
14363 (uri (cran-uri "rbamtools" version))
14366 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
14367 (build-system r-build-system)
14368 (inputs (list zlib))
14370 (list r-refgenome))
14371 (home-page "https://cran.r-project.org/web/packages/rbamtools")
14372 (synopsis "Read and write BAM (binary alignment) files")
14374 "This package provides an R interface to functions of the SAMtools
14376 (license license:artistic2.0)))
14378 (define-public r-protviz
14385 (uri (cran-uri "protViz" version))
14388 "0l1pmfr9kmc90rl5s9b0141451rxrjmiiasp3lsvl2x3ps0smqaj"))))
14389 (properties `((upstream-name . "protViz")))
14390 (build-system r-build-system)
14391 (propagated-inputs (list r-rcpp))
14392 (home-page "https://github.com/protViz/protViz/")
14393 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
14395 "This package helps with quality checks, visualizations and analysis of
14396 mass spectrometry data, coming from proteomics experiments. The package is
14397 developed, tested and used at the Functional Genomics Center Zurich, where it
14398 is used mainly for prototyping, teaching, and having fun with proteomics data.
14399 But it can also be used to do data analysis for small scale data sets.")
14400 (license license:gpl3)))
14402 (define-public r-cmprsk
14409 (uri (cran-uri "cmprsk" version))
14411 (base32 "1xnx2zanw548prxsw2zw5cddkkg6kj97jgyzw67achq5mnsvfbg8"))))
14412 (build-system r-build-system)
14417 (home-page "https://cran.r-project.org/web/packages/cmprsk")
14418 (synopsis "Subdistribution analysis of competing risks")
14420 "This package provides tool for estimation, testing and regression
14421 modeling of subdistribution functions in competing risks, as described in
14422 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
14423 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
14424 A proportional hazards model for the subdistribution of a competing risk,
14425 JASA, 94:496-509.")
14426 (license license:gpl2+)))
14428 (define-public r-etm
14435 (uri (cran-uri "etm" version))
14438 "1hvrplmdpjjpjji663rw0vjbbrzj2nvr04d1nkc8bf46p4ixyxgy"))))
14439 (build-system r-build-system)
14441 (list r-data-table r-lattice r-rcpp r-rcpparmadillo r-survival))
14442 (home-page "https://cran.r-project.org/web/packages/etm")
14443 (synopsis "Empirical transition matrix")
14445 "The @dfn{empirical transition matrix} (etm) package estimates
14446 the matrix of transition probabilities for any time-inhomogeneous multistate
14447 model with finite state space using the Aalen-Johansen estimator.")
14448 (license license:expat)))
14450 (define-public r-epi
14457 (uri (cran-uri "Epi" version))
14460 "1wcxr1f7irgfdwzz4vf67114yhxrhxxxnhy4hfaww0zy91vzxx10"))))
14461 (properties `((upstream-name . "Epi")))
14462 (build-system r-build-system)
14476 (home-page "https://BendixCarstensen.com/Epi/")
14477 (synopsis "Statistical analysis in epidemiology")
14479 "This package provides functions for demographic and epidemiological
14480 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
14481 particular representation, manipulation and simulation of multistate data -
14482 the Lexis suite of functions, which includes interfaces to the @code{mstate},
14483 @code{etm} and @code{cmprsk} packages. It also contains functions for
14484 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
14485 data and some useful functions for tabulation and plotting, as well as a
14486 number of epidemiological data sets.")
14487 (license license:gpl2)))
14489 (define-public r-ppls
14492 (version "1.6-1.1")
14496 (uri (cran-uri "ppls" version))
14499 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
14500 (build-system r-build-system)
14501 (propagated-inputs (list r-mass))
14502 (home-page "https://cran.r-project.org/web/packages/ppls")
14503 (synopsis "Penalized partial least squares")
14505 "This package contains linear and nonlinear regression methods based on
14506 partial least squares and penalization techniques. Model parameters are
14507 selected via cross-validation, and confidence intervals ans tests for the
14508 regression coefficients can be conducted via jackknifing.")
14509 (license license:gpl2+)))
14511 (define-public r-huge
14518 (uri (cran-uri "huge" version))
14520 (base32 "1sl457a1lndrx98y2j9a2smanawx2iqlhl82iand0g3p5xp8ch4j"))))
14521 (build-system r-build-system)
14523 (list r-igraph r-mass r-matrix r-rcpp r-rcppeigen))
14524 (home-page "https://cran.r-project.org/web/packages/huge")
14525 (synopsis "High-dimensional undirected graph estimation")
14527 "This package provides a general framework for high-dimensional
14528 undirected graph estimation. It integrates data preprocessing, neighborhood
14529 screening, graph estimation, and model selection techniques into a pipeline.")
14530 (license license:gpl2)))
14532 (define-public r-parcor
14539 (uri (cran-uri "parcor" version))
14542 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
14543 (build-system r-build-system)
14545 (list r-epi r-genenet r-glmnet r-mass r-ppls))
14546 (home-page "https://cran.r-project.org/web/packages/parcor")
14547 (synopsis "Regularized estimation of partial correlation matrices")
14549 "This package estimates the matrix of partial correlations based on
14550 different regularized regression methods: lasso, adaptive lasso, PLS, and
14551 Ridge Regression. In addition, the package provides model selection for
14552 lasso, adaptive lasso and Ridge regression based on cross-validation.")
14553 (license license:gpl2+)))
14555 (define-public r-mcmc
14562 (uri (cran-uri "mcmc" version))
14565 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
14566 (build-system r-build-system)
14567 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
14568 (synopsis "Markov chain Monte Carlo")
14570 "This package simulates continuous distributions of random vectors using
14571 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
14572 function that evaluates the log unnormalized density. Algorithms are random
14573 walk Metropolis algorithm (function @code{metrop}), simulated
14574 tempering (function @code{temper}), and morphometric random walk
14575 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
14576 by change of variable.")
14577 (license license:expat)))
14579 (define-public r-listenv
14586 (uri (cran-uri "listenv" version))
14589 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
14590 (build-system r-build-system)
14593 (modify-phases %standard-phases
14594 (add-after 'unpack 'set-HOME
14595 (lambda _ (setenv "HOME" "/tmp"))))))
14597 (list r-r-rsp)) ; vignette builder
14598 (home-page "https://github.com/HenrikBengtsson/listenv")
14599 (synopsis "Environments behaving (almost) as lists")
14601 "This package implements list environments. List environments are
14602 environments that have list-like properties. For instance, the elements of a
14603 list environment are ordered and can be accessed and iterated over using index
14605 (license license:lgpl2.1+)))
14607 (define-public r-globals
14614 (uri (cran-uri "globals" version))
14617 "1wrjiiif6rpc268zz79pvpw33si6n6ffgxdnxmmcracwhb5vqg90"))))
14618 (build-system r-build-system)
14620 (list r-codetools))
14621 (home-page "https://github.com/HenrikBengtsson/globals")
14622 (synopsis "Identify global objects in R expressions")
14624 "This package provides tools to identify global (\"unknown\" or \"free\")
14625 objects in R expressions by code inspection using various strategies, e.g.
14626 conservative or liberal. The objective of this package is to make it as
14627 simple as possible to identify global objects for the purpose of exporting
14628 them in distributed compute environments.")
14629 (license license:lgpl2.1+)))
14631 (define-public r-parallelly
14633 (name "r-parallelly")
14638 (uri (cran-uri "parallelly" version))
14641 "0a84lr2jqqnvmdayb9v9kv7m8rffp65s4s1wcalr96sl3cxypyc7"))))
14642 (properties `((upstream-name . "parallelly")))
14643 (build-system r-build-system)
14644 (home-page "https://github.com/HenrikBengtsson/parallelly")
14645 (synopsis "Enhancements of the parallel package")
14647 "This package provides utility functions that enhance the @code{parallel}
14648 package and support the built-in parallel backends of the @code{future}
14649 package. For example, @code{availableCores} gives the number of CPU cores
14650 available to your R process as given by R options and environment variables,
14651 including those set by job schedulers on high-performance compute clusters.
14652 If none is set, it will fall back to @code{parallel::detectCores}. Another
14653 example is @code{makeClusterPSOCK}, which is backward compatible with
14654 @code{parallel::makePSOCKcluster} while doing a better job in setting up
14655 remote cluster workers without the need for configuring the firewall to do
14656 port-forwarding to your local computer.")
14657 (license license:lgpl2.1+)))
14659 (define-public r-future
14666 (uri (cran-uri "future" version))
14669 "1y5qzpsg0r2dccynyybbb2ngxbl1y3phs1dq2jj3f2bwhc7chsfq"))))
14670 (build-system r-build-system)
14673 (modify-phases %standard-phases
14674 (add-after 'unpack 'set-HOME
14675 (lambda _ (setenv "HOME" "/tmp"))))))
14677 (list r-digest r-globals r-listenv r-parallelly))
14679 (list r-r-rsp)) ; vignette builder
14680 (home-page "https://github.com/HenrikBengtsson/future")
14681 (synopsis "Unified parallel and distributed processing in R")
14683 "The purpose of this package is to provide a lightweight and unified
14684 Future API for sequential and parallel processing of R expression via futures.
14685 This package implements sequential, multicore, multisession, and cluster
14686 futures. With these, R expressions can be evaluated on the local machine, in
14687 parallel a set of local machines, or distributed on a mix of local and remote
14688 machines. Extensions to this package implement additional backends for
14689 processing futures via compute cluster schedulers etc. Because of its unified
14690 API, there is no need to modify any code in order to switch from sequential on
14691 the local machine to, say, distributed processing on a remote compute cluster.")
14692 (license license:lgpl2.1+)))
14694 (define-public r-future-apply
14696 (name "r-future-apply")
14701 (uri (cran-uri "future.apply" version))
14704 "1ix61bfbk43pwnjb0wk8lkfgdsy5zi8svk74gar5nrl90b5w6nqd"))))
14705 (properties `((upstream-name . "future.apply")))
14706 (build-system r-build-system)
14709 (modify-phases %standard-phases
14710 (add-after 'unpack 'set-HOME
14711 (lambda _ (setenv "HOME" "/tmp"))))))
14713 (list r-future r-globals))
14715 (list r-r-rsp)) ; vignette builder
14716 (home-page "https://github.com/HenrikBengtsson/future.apply")
14717 (synopsis "Apply function to elements in parallel using futures")
14719 "This package provides implementations of @code{apply()},
14720 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
14721 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
14722 can be resolved using any future-supported backend, e.g. parallel on the local
14723 machine or distributed on a compute cluster.")
14724 (license license:gpl2+)))
14726 (define-public r-rsvd
14733 (uri (cran-uri "rsvd" version))
14736 "07p2hjmpcwcsang8z9sjkpy94rydcin7m3hyvcgzgm5cd6w8c1p4"))))
14737 (build-system r-build-system)
14740 (home-page "https://github.com/erichson/rSVD")
14741 (synopsis "Randomized singular value decomposition")
14743 "Low-rank matrix decompositions are fundamental tools and widely used for
14744 data analysis, dimension reduction, and data compression. Classically, highly
14745 accurate deterministic matrix algorithms are used for this task. However, the
14746 emergence of large-scale data has severely challenged our computational
14747 ability to analyze big data. The concept of randomness has been demonstrated
14748 as an effective strategy to quickly produce approximate answers to familiar
14749 problems such as the @dfn{singular value decomposition} (SVD). This package
14750 provides several randomized matrix algorithms such as the randomized singular
14751 value decomposition (@code{rsvd}), randomized principal component
14752 analysis (@code{rpca}), randomized robust principal component
14753 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
14754 and the randomized CUR decomposition (@code{rcur}). In addition several plot
14755 functions are provided.")
14756 (license license:gpl3+)))
14758 (define-public r-sloop
14765 (uri (cran-uri "sloop" version))
14768 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
14769 (build-system r-build-system)
14771 (list r-codetools r-crayon r-purrr r-rlang r-tibble))
14772 (home-page "https://github.com/r-lib/sloop")
14773 (synopsis "Helpers for object-oriented programming in R")
14775 "This package provides a collection of helper functions designed to
14776 help you to better understand object oriented programming in R, particularly
14778 (license license:gpl3)))
14780 (define-public r-capushe
14787 (uri (cran-uri "capushe" version))
14790 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
14791 (build-system r-build-system)
14792 (propagated-inputs (list r-mass))
14793 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
14794 (synopsis "Calibrating penalties using slope heuristics")
14796 "This package provides tools for the calibration of penalized criteria
14797 for model selection. The calibration methods available are based on the slope
14799 (license license:gpl2+)))
14801 (define-public r-dorng
14808 (uri (cran-uri "doRNG" version))
14811 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
14812 (properties `((upstream-name . "doRNG")))
14813 (build-system r-build-system)
14815 (list r-foreach r-iterators r-rngtools))
14816 (home-page "https://renozao.github.io/doRNG/")
14817 (synopsis "Generic reproducible parallel backend for foreach loops")
14819 "This package provides functions to perform reproducible parallel
14820 @code{foreach} loops, using independent random streams as generated by
14821 L'Ecuyer's combined multiple-recursive generator. It enables to easily
14822 convert standard @code{%dopar%} loops into fully reproducible loops,
14823 independently of the number of workers, the task scheduling strategy, or the
14824 chosen parallel environment and associated foreach backend.")
14825 (license license:gpl2+)))
14827 (define-public r-blockmodeling
14829 (name "r-blockmodeling")
14834 (uri (cran-uri "blockmodeling" version))
14837 "1vc8gy4slsywcwxq532373i0dq73fhs5cac9mr6zz2pjaaxjghhq"))))
14838 (build-system r-build-system)
14841 (native-inputs (list gfortran))
14842 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
14843 (synopsis "Generalized and classical blockmodeling of valued networks")
14845 "This package is primarily meant as an implementation of generalized
14846 blockmodeling for valued networks. In addition, measures of similarity or
14847 dissimilarity based on structural equivalence and regular equivalence (REGE
14848 algorithms) can be computed and partitioned matrices can be plotted.")
14849 (license license:gpl2+)))
14851 (define-public r-upsetr
14858 (uri (cran-uri "UpSetR" version))
14861 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
14862 (properties `((upstream-name . "UpSetR")))
14863 (build-system r-build-system)
14865 (list r-ggplot2 r-gridextra r-plyr r-scales))
14866 (home-page "https://github.com/hms-dbmi/UpSetR")
14867 (synopsis "Visualize intersecting sets")
14869 "This package provides a more scalable alternative to Venn and Euler
14870 diagrams for visualizing intersecting sets. Create visualizations of
14871 intersecting sets using a novel matrix design, along with visualizations of
14872 several common set, element and attribute related tasks.")
14873 (license license:expat)))
14875 ;; This package includes a JavaScript file, which is not minified. When
14876 ;; upgrading please check that there are no new minified JavaScript files.
14877 (define-public r-shinybs
14884 (uri (cran-uri "shinyBS" version))
14887 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
14888 (properties `((upstream-name . "shinyBS")))
14889 (build-system r-build-system)
14890 ;; The tests spawn Shiny browser apps. They cannot be run
14891 ;; non-interactively.
14892 (arguments '(#:tests? #f))
14894 (list r-htmltools r-shiny))
14895 (home-page "https://ebailey78.github.io/shinyBS/")
14896 (synopsis "Twitter Bootstrap components for Shiny")
14898 "This package adds additional Twitter Bootstrap components to Shiny.")
14899 (license license:gpl3)))
14901 (define-public r-shinyjqui
14903 (name "r-shinyjqui")
14908 (uri (cran-uri "shinyjqui" version))
14911 "0ins0pmfis34jr0rimsp1k1aw856r3xjdnsvv8lkwqhvp58nzqah"))
14914 (delete-file "inst/www/shinyjqui.min.js")))))
14915 (properties `((upstream-name . "shinyjqui")))
14916 (build-system r-build-system)
14919 (modify-phases %standard-phases
14920 (add-after 'unpack 'process-javascript
14921 (lambda* (#:key inputs #:allow-other-keys)
14922 (with-directory-excursion "inst/www/"
14923 (let ((source "shinyjqui.js")
14924 (target "shinyjqui.min.js"))
14925 (format #true "Processing ~a --> ~a~%"
14927 (invoke "esbuild" source "--minify"
14928 (string-append "--outfile=" target)))))))))
14930 (list r-htmltools r-htmlwidgets r-jsonlite r-shiny))
14932 (list r-knitr esbuild))
14933 (home-page "https://github.com/yang-tang/shinyjqui")
14934 (synopsis "jQuery UI interactions and effects for Shiny")
14936 "This is an extension to Shiny that brings interactions and animation
14937 effects from the jQuery UI library.")
14938 (license license:expat)))
14940 (define-public r-outliers
14942 (name "r-outliers")
14947 (uri (cran-uri "outliers" version))
14950 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
14951 (build-system r-build-system)
14952 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
14953 (synopsis "Tests for outliers")
14955 "This package provides a collection of some tests commonly used for
14956 identifying outliers.")
14957 (license license:gpl2+)))
14959 (define-public r-bayesm
14966 (uri (cran-uri "bayesm" version))
14968 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
14969 (build-system r-build-system)
14971 (list r-rcpp r-rcpparmadillo))
14972 (home-page "http://www.perossi.org/home/bsm-1")
14973 (synopsis "Bayesian inference for marketing/micro-econometrics")
14975 "This package covers many important models used in marketing and
14976 micro-econometrics applications, including Bayes Regression (univariate or
14977 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
14978 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
14979 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
14980 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
14981 Estimation with normal base, Hierarchical Linear Models with normal prior and
14982 covariates, Hierarchical Linear Models with a mixture of normals prior and
14983 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
14984 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
14985 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
14986 analysis of choice-based conjoint data, Bayesian treatment of linear
14987 instrumental variables models, Analysis of Multivariate Ordinal survey data
14988 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
14989 Coefficient Logit Models.")
14990 (license license:gpl2+)))
14992 (define-public r-tensora
14999 (uri (cran-uri "tensorA" version))
15002 "19wwh654qlja4z1n7afjpzsrrm53p8ddysa2vra5mdnkddb4g2cf"))))
15003 (properties `((upstream-name . "tensorA")))
15004 (build-system r-build-system)
15005 (home-page "http://www.stat.boogaart.de/tensorA")
15006 (synopsis "Advanced tensor arithmetic with named indices")
15008 "This package provides convenience functions for advanced linear algebra
15009 with tensors and computation with datasets of tensors on a higher level
15010 abstraction. It includes Einstein and Riemann summing conventions, dragging,
15011 co- and contravariate indices, and parallel computations on sequences of
15013 (license license:gpl2+)))
15015 (define-public r-rarpack
15022 (uri (cran-uri "rARPACK" version))
15025 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
15026 (properties `((upstream-name . "rARPACK")))
15027 (build-system r-build-system)
15028 (propagated-inputs (list r-rspectra))
15029 (home-page "https://github.com/yixuan/rARPACK")
15030 (synopsis "Solvers for large scale eigenvalue and SVD problems")
15032 "This package was previously an R wrapper of the ARPACK library, and now
15033 a shell of the R package RSpectra, an R interface to the Spectra library for
15034 solving large scale eigenvalue/vector problems. The current version of
15035 rARPACK simply imports and exports the functions provided by RSpectra. New
15036 users of rARPACK are advised to switch to the RSpectra package.")
15037 (license license:bsd-3)))
15039 (define-public r-compositions
15041 (name "r-compositions")
15046 (uri (cran-uri "compositions" version))
15049 "05pji62pzgfk9dyiybmr16q0h6mdzsmvyzxdni3hn0dvl4a7mr5m"))))
15050 (build-system r-build-system)
15052 (list r-bayesm r-mass r-robustbase r-tensora))
15055 (home-page "http://www.stat.boogaart.de/compositions")
15056 (synopsis "Compositional data analysis")
15058 "This package provides functions for the consistent analysis of
15059 compositional data (e.g. portions of substances) and positive
15060 numbers (e.g. concentrations).")
15061 (license license:gpl2+)))
15063 (define-public r-cobs
15070 (uri (cran-uri "cobs" version))
15073 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
15074 (build-system r-build-system)
15076 (list r-quantreg r-sparsem))
15077 (home-page "https://cran.r-project.org/web/packages/cobs")
15078 (synopsis "Constrained B-Splines (sparse matrix based)")
15080 "This package provides qualitatively constrained (regression) smoothing
15081 splines via linear programming and sparse matrices.")
15082 (license license:gpl2+)))
15084 (define-public r-drimpute
15086 (name "r-drimpute")
15091 (uri (cran-uri "DrImpute" version))
15094 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
15095 (properties `((upstream-name . "DrImpute")))
15096 (build-system r-build-system)
15098 (list r-rcpp r-rcpparmadillo))
15099 (home-page "https://github.com/ikwak2/DrImpute")
15100 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
15102 "This is an R package for imputing dropout events. Many statistical
15103 methods in cell type identification, visualization and lineage reconstruction
15104 do not account for dropout events. DrImpute can improve the performance of
15105 such software by imputing dropout events.")
15106 (license license:gpl3)))
15108 (define-public r-gamlss-dist
15110 (name "r-gamlss-dist")
15115 (uri (cran-uri "gamlss.dist" version))
15117 (base32 "0m41n7zf7m0mh1w9ql70wqnzsf2f013ql699im7zmp6fdggb8qxm"))))
15118 (properties `((upstream-name . "gamlss.dist")))
15119 (build-system r-build-system)
15120 (propagated-inputs (list r-mass))
15121 (home-page "http://www.gamlss.org/")
15122 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
15124 "This package provides a set of distributions which can be used for
15125 modelling the response variables in Generalized Additive Models for Location
15126 Scale and Shape. The distributions can be continuous, discrete or mixed
15127 distributions. Extra distributions can be created, by transforming, any
15128 continuous distribution defined on the real line, to a distribution defined on
15129 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
15130 transformation, respectively.")
15131 ;; Either version of the GPL.
15132 (license (list license:gpl2 license:gpl3))))
15134 ;; This package includes JavaScript files, which are not minified. When
15135 ;; upgrading please check that there are no new minified JavaScript files.
15136 (define-public r-shinyjs
15143 (uri (cran-uri "shinyjs" version))
15146 "1zzq356dvd8ciajy6r5n4ybgx9xk7ydwv25j86xlcsqznkxdkkf2"))))
15147 (build-system r-build-system)
15149 (list r-digest r-htmltools r-jsonlite r-shiny))
15152 (home-page "https://deanattali.com/shinyjs")
15153 (synopsis "Improve the user experience of your Shiny apps")
15155 "Perform common useful JavaScript operations in Shiny apps that will
15156 greatly improve your apps without having to know any JavaScript. Examples
15157 include: hiding an element, disabling an input, resetting an input back to its
15158 original value, delaying code execution by a few seconds, and many more useful
15159 functions for both the end user and the developer. Shinyjs can also be used
15160 to easily call your own custom JavaScript functions from R.")
15161 (license license:agpl3+)))
15163 ;; This package includes minified JavaScript files. When upgrading please
15164 ;; check that there are no new minified JavaScript files.
15165 (define-public r-colourpicker
15167 (name "r-colourpicker")
15172 (uri (cran-uri "colourpicker" version))
15175 "1q1wi3g403fbzp4ys3gsjbwdc86x770cx323qgi47ca8n219kl50"))))
15176 (build-system r-build-system)
15179 (modify-phases %standard-phases
15180 (add-after 'unpack 'process-javascript
15181 (lambda* (#:key inputs #:allow-other-keys)
15182 (with-directory-excursion "inst"
15184 `((,(assoc-ref inputs "js-salvattore")
15185 . "examples/colourInput/www/salvattore.min.js")
15186 (,(assoc-ref inputs "js-jquery")
15187 . "htmlwidgets/lib/jquery/jquery.min.js")
15188 ("www/shared/colourpicker/js/colourpicker.js"
15189 . "www/shared/colourpicker/js/colourpicker.min.js"))))
15190 (for-each (lambda (source target)
15191 (format #true "Processing ~a --> ~a~%"
15193 (delete-file target)
15194 (invoke "esbuild" source "--minify"
15195 (string-append "--outfile=" target)))
15197 (map cdr mapping)))))))))
15207 `(("esbuild" ,esbuild)
15211 (uri "https://code.jquery.com/jquery-1.11.3.js")
15214 "1v956yf5spw0156rni5z77hzqwmby7ajwdcd6mkhb6zvl36awr90"))))
15218 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
15221 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
15222 (home-page "https://github.com/daattali/colourpicker")
15223 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
15225 "This package provides a color picker that can be used as an input in
15226 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
15227 custom color palettes, and many more options. A plot color helper tool is
15228 available as an RStudio Addin, which helps you pick colors to use in your
15229 plots. A more generic color picker RStudio Addin is also provided to let you
15230 select colors to use in your R code.")
15231 (license license:expat)))
15233 (define-public r-ggextra
15240 (uri (cran-uri "ggExtra" version))
15243 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
15244 (properties `((upstream-name . "ggExtra")))
15245 (build-system r-build-system)
15247 (list r-colourpicker
15257 (home-page "https://github.com/daattali/ggExtra")
15258 (synopsis "Marginal histograms for ggplot2 and other enhancements")
15260 "This package is a collection of functions and layers to enhance ggplot2.
15261 The flagship function is @code{ggMarginal()}, which can be used to add
15262 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
15263 (license license:expat)))
15265 (define-public r-minpack-lm
15267 (name "r-minpack-lm")
15272 (uri (cran-uri "minpack.lm" version))
15275 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
15276 (properties `((upstream-name . "minpack.lm")))
15277 (build-system r-build-system)
15278 (native-inputs (list gfortran))
15279 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
15280 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
15282 "The @code{nls.lm} function provides an R interface to @code{lmder} and
15283 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
15284 problems by a modification of the Levenberg-Marquardt algorithm, with support
15285 for lower and upper parameter bounds. The implementation can be used via
15286 @code{nls}-like calls using the @code{nlsLM} function.")
15287 (license license:gpl3)))
15289 (define-public r-moments
15296 (uri (cran-uri "moments" version))
15299 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
15300 (build-system r-build-system)
15301 (home-page "https://cran.r-project.org/web/packages/moments")
15302 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
15304 "This package provides functions to calculate: moments, Pearson's
15305 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
15306 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
15307 (license license:gpl2+)))
15309 (define-public r-msir
15316 (uri (cran-uri "msir" version))
15319 "1wm83m3cqd6llxb9p2jwim0wb81v84pgdmgcznygzaaq6kbn3n84"))))
15320 (build-system r-build-system)
15325 (home-page "https://cran.r-project.org/web/packages/msir")
15326 (synopsis "Model-based sliced inverse regression")
15328 "This is an R package for dimension reduction based on finite Gaussian
15329 mixture modeling of inverse regression.")
15330 (license license:gpl2+)))
15332 (define-public r-pbivnorm
15334 (name "r-pbivnorm")
15339 (uri (cran-uri "pbivnorm" version))
15342 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
15343 (build-system r-build-system)
15344 (native-inputs (list gfortran))
15345 (home-page "https://github.com/brentonk/pbivnorm")
15346 (synopsis "Vectorized bivariate normal CDF")
15348 "This package provides a vectorized R function for calculating
15349 probabilities from a standard bivariate normal CDF.")
15350 (license license:gpl2+)))
15352 (define-public r-lavaan
15359 (uri (cran-uri "lavaan" version))
15362 "12hhbwxaiprs9bmclwhhdpv42h4mrl4gj92zq3wk8rb883mw816l"))))
15363 (build-system r-build-system)
15365 (list r-mass r-mnormt r-numderiv r-pbivnorm))
15366 (home-page "https://lavaan.ugent.be")
15367 (synopsis "Latent variable analysis")
15369 "This package provides tools to fit a variety of latent variable models,
15370 including confirmatory factor analysis, structural equation modeling and
15371 latent growth curve models.")
15372 (license license:gpl2+)))
15374 (define-public r-nonnest2
15376 (name "r-nonnest2")
15381 (uri (cran-uri "nonnest2" version))
15384 "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2"))))
15385 (build-system r-build-system)
15387 (list r-compquadform r-lavaan r-mvtnorm r-sandwich))
15390 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
15391 (synopsis "Tests of non-nested models")
15393 "This package allows for testing of non-nested models. It includes tests
15394 of model distinguishability and of model fit that can be applied to both
15395 nested and non-nested models. The package also includes functionality to
15396 obtain confidence intervals associated with AIC and BIC.")
15397 ;; Either version of the GPL.
15398 (license (list license:gpl2 license:gpl3))))
15400 (define-public r-penalized
15402 (name "r-penalized")
15407 (uri (cran-uri "penalized" version))
15410 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
15411 (build-system r-build-system)
15413 (list r-rcpp r-rcpparmadillo r-survival))
15414 (home-page "https://cran.r-project.org/web/packages/penalized/")
15415 (synopsis "Penalized estimation in GLMs and in the Cox model")
15417 "This package provides tools for fitting possibly high dimensional
15418 penalized regression models. The penalty structure can be any combination of
15419 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
15420 constraint on the regression coefficients. The supported regression models
15421 are linear, logistic and Poisson regression and the Cox Proportional Hazards
15422 model. Cross-validation routines allow optimization of the tuning
15424 (license license:gpl2+)))
15426 (define-public r-zim
15433 (uri (cran-uri "ZIM" version))
15436 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
15437 (properties `((upstream-name . "ZIM")))
15438 (build-system r-build-system)
15439 (propagated-inputs (list r-mass))
15440 (home-page "https://github.com/biostatstudio/ZIM")
15441 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
15443 "Analyze count time series with excess zeros. Two types of statistical
15444 models are supported: Markov regression and state-space models. They are also
15445 known as observation-driven and parameter-driven models respectively in the
15446 time series literature. The functions used for Markov regression or
15447 observation-driven models can also be used to fit ordinary regression models
15448 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
15449 negative binomial (ZINB) assumption. The package also contains miscellaneous
15450 functions to compute density, distribution, quantile, and generate random
15451 numbers from ZIP and ZINB distributions.")
15452 (license license:gpl3)))
15454 (define-public r-nor1mix
15461 (uri (cran-uri "nor1mix" version))
15464 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
15465 (build-system r-build-system)
15466 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
15467 (synopsis "Normal (1-d) mixture models")
15469 "This package provides S3 classes and methods for one-dimensional normal
15470 mixture models, for, e.g., density estimation or clustering algorithms
15471 research and teaching; it provides the widely used Marron-Wand densities. It
15472 also provides tools for efficient random number generation and graphics.")
15473 (license license:gpl2+)))
15475 (define-public r-beanplot
15477 (name "r-beanplot")
15482 (uri (cran-uri "beanplot" version))
15485 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
15486 (build-system r-build-system)
15487 (home-page "https://cran.r-project.org/web/packages/beanplot/")
15488 (synopsis "Visualization via beanplots")
15490 "This package provides beanplots, an alternative to
15491 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
15493 (license license:gpl2)))
15495 (define-public r-pbdzmq
15502 (uri (cran-uri "pbdZMQ" version))
15505 "0yy3x3l04vx13jbjbvkvsc8jdbf0abndjfknszdx3bi18b2chi4r"))))
15506 (properties `((upstream-name . "pbdZMQ")))
15507 (build-system r-build-system)
15509 (list zeromq zlib))
15512 (home-page "https://pbdr.org/")
15513 (synopsis "R interface to ZeroMQ")
15515 "ZeroMQ is a well-known library for high-performance asynchronous
15516 messaging in scalable, distributed applications. This package provides high
15517 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
15518 interactive client/server programming frameworks. A few wrapper functions
15519 compatible with @code{rzmq} are also provided.")
15520 (license license:gpl3)))
15522 (define-public r-repr
15529 (uri (cran-uri "repr" version))
15532 "0qimllv9pn8wsl550bjkp5dkknbmr69j85mrwfbbq75m2ga466sk"))))
15533 (build-system r-build-system)
15535 (list r-base64enc r-htmltools r-jsonlite r-pillar))
15536 (home-page "https://cran.r-project.org/web/packages/repr/")
15537 (synopsis "Serializable representations")
15539 "This package provides string and binary representations of objects for
15540 several formats and MIME types.")
15541 (license license:gpl3)))
15543 (define-public r-irdisplay
15545 (name "r-irdisplay")
15550 (uri (cran-uri "IRdisplay" version))
15553 "15jbjrihm1mk899357h9xb08iq3xyagds1xb40fmdpkfcmcfqrw9"))))
15554 (properties `((upstream-name . "IRdisplay")))
15555 (build-system r-build-system)
15558 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
15559 (synopsis "Jupyter display machinery")
15561 "This package provides an interface to the rich display capabilities of
15562 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
15563 running IRkernel session.")
15564 (license license:expat)))
15566 (define-public r-irkernel
15568 (name "r-irkernel")
15573 (uri (cran-uri "IRkernel" version))
15576 "14gz3790iv6gg6yi9wslk1yn0jq57yvhxgm840qh818xfkdxpd2z"))))
15577 (properties `((upstream-name . "IRkernel")))
15578 (build-system r-build-system)
15581 (modify-phases %standard-phases
15582 (add-after 'install 'install-kernelspec
15583 (lambda* (#:key outputs #:allow-other-keys)
15584 (let ((out (assoc-ref outputs "out")))
15585 (setenv "HOME" "/tmp")
15586 (invoke "jupyter" "kernelspec" "install"
15589 (string-append out "/site-library/IRkernel/kernelspec"))
15590 ;; Record the absolute file name of the 'R' executable in
15592 (substitute* (string-append out "/share/jupyter"
15593 "/kernels/ir/kernel.json")
15595 (string-append "[\"" (which "R") "\",")))
15605 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
15610 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
15611 (synopsis "Native R kernel for Jupyter")
15613 "The R kernel for the Jupyter environment executes R code which the
15614 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
15616 (license license:expat)))
15618 (define-public r-gmodels
15625 (uri (cran-uri "gmodels" version))
15628 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
15629 (build-system r-build-system)
15631 (list r-gdata r-mass))
15632 (home-page "https://cran.r-project.org/web/packages/gmodels/")
15633 (synopsis "Various R programming tools for model fitting")
15635 "This package provides various R programming tools for model fitting.")
15636 (license license:gpl2)))
15638 (define-public r-apcluster
15640 (name "r-apcluster")
15645 (uri (cran-uri "apcluster" version))
15648 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
15649 (build-system r-build-system)
15651 (list r-matrix r-rcpp))
15652 (home-page "https://cran.r-project.org/web/packages/apcluster/")
15653 (synopsis "Affinity propagation clustering")
15655 "This package implements affinity propagation clustering introduced by
15656 Frey and Dueck (2007). The package further provides leveraged affinity
15657 propagation and an algorithm for exemplar-based agglomerative clustering that
15658 can also be used to join clusters obtained from affinity propagation. Various
15659 plotting functions are available for analyzing clustering results.")
15660 (license license:gpl2+)))
15662 (define-public r-valr
15669 (uri (cran-uri "valr" version))
15672 "1lzdlw0mw06rymyjzwf4i8rx1z6zxpwxxqfsc9ggqlnhq6bfhy93"))))
15673 (build-system r-build-system)
15685 (home-page "https://github.com/rnabioco/valr")
15686 (synopsis "Genome interval arithmetic in R")
15688 "This package enables you to read and manipulate genome intervals and
15689 signals. It provides functionality similar to command-line tool suites within
15690 R, enabling interactive analysis and visualization of genome-scale data.")
15691 (license license:expat)))
15693 (define-public r-rematch2
15695 (name "r-rematch2")
15700 (uri (cran-uri "rematch2" version))
15703 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y"))))
15704 (build-system r-build-system)
15707 (home-page "https://github.com/r-lib/rematch2")
15708 (synopsis "Tidy output from regular expression matching")
15710 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
15711 return the match results in tidy data frames.")
15712 (license license:expat)))
15714 (define-public r-picante
15721 (uri (cran-uri "picante" version))
15724 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn"))))
15725 (build-system r-build-system)
15727 (list r-ape r-nlme r-vegan))
15728 (home-page "https://cran.r-project.org/web/packages/picante/")
15729 (synopsis "Integrating phylogenies and ecology")
15731 "This package provides functions for phylocom integration, community
15732 analyses, null-models, traits and evolution. It implements numerous
15733 ecophylogenetic approaches including measures of community phylogenetic and
15734 trait diversity, phylogenetic signal, estimation of trait values for
15735 unobserved taxa, null models for community and phylogeny randomizations, and
15736 utility functions for data input/output and phylogeny plotting. A full
15737 description of package functionality and methods are provided by Kembel et
15739 (license license:gpl2)))
15741 (define-public r-reinforcelearn
15743 (name "r-reinforcelearn")
15748 (uri (cran-uri "reinforcelearn" version))
15751 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
15752 (build-system r-build-system)
15754 (list r-checkmate r-nnet r-purrr r-r6))
15755 (home-page "https://markusdumke.github.io/reinforcelearn")
15756 (synopsis "Reinforcement learning")
15758 "This package implements reinforcement learning environments and
15759 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
15760 can be used with function approximation, eligibility traces (Singh & Sutton,
15761 1996) and experience replay (Mnih et al., 2013).")
15762 (license license:expat)))
15764 (define-public r-lemon
15771 (uri (cran-uri "lemon" version))
15774 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4"))))
15775 (build-system r-build-system)
15787 (home-page "https://github.com/stefanedwards/lemon")
15788 (synopsis "Freshen up your ggplot2 plots")
15790 "This package provides functions for working with legends and axis lines
15791 of ggplot2, facets that repeat axis lines on all panels, and some knitr
15793 (license license:gpl3)))
15795 (define-public r-wgaim
15802 (uri (cran-uri "wgaim" version))
15804 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
15805 (build-system r-build-system)
15807 (list r-ggplot2 r-qtl))
15808 (home-page "https://cran.r-project.org/web/packages/wgaim")
15809 (synopsis "Whole genome average interval mapping for QTL detection")
15811 "This package integrates sophisticated mixed modelling methods with a
15812 whole genome approach to detecting significant QTL in linkage maps.")
15813 (license license:gpl2+)))
15815 (define-public r-bedr
15822 (uri (cran-uri "bedr" version))
15825 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
15826 (build-system r-build-system)
15835 htslib)) ; for tabix
15837 (list r-knitr)) ; for vignettes
15838 (home-page "https://cran.r-project.org/web/packages/bedr")
15839 (synopsis "Genomic region processing")
15841 "This package is for genomic regions processing using command line tools
15842 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
15843 utilities to perform genome arithmetic e.g indexing, formatting and merging.
15844 The bedr package's API enhances access to these tools as well as offers
15845 additional utilities for genomic regions processing.")
15846 (license license:gpl2)))
15848 (define-public r-sets
15855 (uri (cran-uri "sets" version))
15858 "18185rm458nlifzrp73fjrjvksmm5dvn5ygs949kdzdln1myb4xf"))))
15859 (properties `((upstream-name . "sets")))
15860 (build-system r-build-system)
15861 (home-page "https://cran.r-project.org/web/packages/sets")
15862 (synopsis "Sets, generalized sets, customizable sets and intervals")
15864 "This package provides data structures and basic operations for ordinary
15865 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
15866 customizable sets, and intervals.")
15867 (license license:gpl2)))
15869 (define-public r-partitions
15871 (name "r-partitions")
15876 (uri (cran-uri "partitions" version))
15879 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
15880 (build-system r-build-system)
15882 (list r-gmp r-polynom r-sets))
15883 (home-page "https://cran.r-project.org/web/packages/partitions")
15884 (synopsis "Additive partitions of integers")
15886 "This package provides tools to enumerates the partitions, unequal
15887 partitions, and restricted partitions of an integer; the three corresponding
15888 partition functions are also given.")
15889 ;; Any version of the GPL
15890 (license license:gpl2+)))
15892 (define-public r-brobdingnag
15894 (name "r-brobdingnag")
15899 (uri (cran-uri "Brobdingnag" version))
15902 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
15903 (properties `((upstream-name . "Brobdingnag")))
15904 (build-system r-build-system)
15905 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
15906 (synopsis "Very large numbers in R")
15908 "This package handles very large numbers in R. Real numbers are held
15909 using their natural logarithms, plus a logical flag indicating sign. The
15910 package includes a vignette that gives a step-by-step introduction to using S4
15912 ;; Any version of the GPL
15913 (license license:gpl2+)))
15915 (define-public r-untb
15922 (uri (cran-uri "untb" version))
15925 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
15926 (build-system r-build-system)
15928 (list r-brobdingnag r-partitions r-polynom))
15929 (home-page "https://github.com/RobinHankin/untb.git")
15930 (synopsis "Ecological drift under the UNTB")
15932 "This package provides numerical simulations, and visualizations, of
15933 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
15934 (license license:gpl2+)))
15936 (define-public r-stepwise
15938 (name "r-stepwise")
15943 (uri (cran-uri "stepwise" version))
15946 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
15947 (build-system r-build-system)
15948 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
15949 (synopsis "Stepwise detection of recombination breakpoints")
15951 "This package provides a stepwise approach to identifying recombination
15952 breakpoints in a genomic sequence alignment.")
15953 (license license:gpl2+)))
15955 (define-public r-snpmaxsel
15957 (name "r-snpmaxsel")
15962 (uri (cran-uri "SNPmaxsel" version))
15965 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
15966 (properties `((upstream-name . "SNPmaxsel")))
15967 (build-system r-build-system)
15969 (list r-combinat r-mvtnorm))
15970 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
15971 (synopsis "Maximally selected statistics for SNP data")
15973 "This package implements asymptotic methods related to maximally selected
15974 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
15976 (license license:gpl2+)))
15978 (define-public r-acsnminer
15980 (name "r-acsnminer")
15981 (version "0.16.8.25")
15984 (uri (cran-uri "ACSNMineR" version))
15987 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
15988 (properties `((upstream-name . "ACSNMineR")))
15989 (build-system r-build-system)
15991 (list r-ggplot2 r-gridextra))
15992 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
15993 (synopsis "Gene enrichment analysis")
15995 "This package provides tools to compute and represent gene set enrichment
15996 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
15997 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
15998 enrichment can be run with hypergeometric test or Fisher exact test, and can
15999 use multiple corrections. Visualization of data can be done either by
16000 barplots or heatmaps.")
16001 (license license:gpl2+)))
16003 (define-public r-seqinr
16010 (uri (cran-uri "seqinr" version))
16013 "1xz9spln6s9mcwpgcv1m4jymn4gnl1bb6vh90bphqcn0vvlk8jsq"))))
16014 (build-system r-build-system)
16016 (list r-ade4 r-segmented))
16019 (home-page "http://seqinr.r-forge.r-project.org/")
16020 (synopsis "Biological sequences retrieval and analysis")
16022 "This package provides tools for exploratory data analysis and data
16023 visualization of biological sequence (DNA and protein) data. It also includes
16024 utilities for sequence data management under the ACNUC system.")
16025 (license license:gpl2+)))
16027 (define-public r-units
16034 (uri (cran-uri "units" version))
16037 "1ss0f15h4yqzk488ilsa5d2ibrj3wzwplx4160mn600i8ciy02xr"))))
16038 (build-system r-build-system)
16045 (home-page "https://github.com/r-quantities/units/")
16046 (synopsis "Measurement Units for R Vectors")
16048 "This package provides support for measurement units in R vectors,
16049 matrices and arrays: automatic propagation, conversion, derivation and
16050 simplification of units; raising errors in case of unit incompatibility. It
16051 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
16053 (license license:gpl2)))
16055 (define-public r-udunits2
16057 (name "r-udunits2")
16062 (uri (cran-uri "udunits2" version))
16065 "1l889f8iy8qaacxfs6ll62d6hs8g8qsr5ynn24grpvp8dk8l888w"))))
16066 (properties `((upstream-name . "udunits2")))
16067 (build-system r-build-system)
16070 (home-page "https://cran.r-project.org/package=udunits2")
16071 (synopsis "Udunits-2 bindings for R")
16073 "This package provides simple bindings to Unidata's udunits library.")
16074 (license license:gpl2)))
16076 (define-public r-classint
16078 (name "r-classint")
16083 (uri (cran-uri "classInt" version))
16086 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
16087 (properties `((upstream-name . "classInt")))
16088 (build-system r-build-system)
16090 (list r-class r-e1071 r-kernsmooth))
16092 (list gfortran r-knitr))
16093 (home-page "https://github.com/r-spatial/classInt/")
16094 (synopsis "Choose univariate class intervals")
16096 "This package provides selected commonly used methods for choosing
16097 univariate class intervals for mapping or other graphics purposes.")
16098 (license license:gpl2+)))
16100 (define-public r-spdata
16107 (uri (cran-uri "spData" version))
16110 "1z4hp5ivwzyvl8mkp98j2ng1cl1xksqbjxv85vdlqfqjwpia6df6"))))
16111 (properties `((upstream-name . "spData")))
16112 (build-system r-build-system)
16114 (list r-raster r-sp))
16115 (home-page "https://github.com/Nowosad/spData")
16116 (synopsis "Datasets for spatial analysis")
16118 "This a package containing diverse spatial datasets for demonstrating,
16119 benchmarking and teaching spatial data analysis. It includes R data of class
16120 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
16121 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
16122 of the datasets are designed to illustrate specific analysis techniques.
16123 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
16124 illustrate point pattern analysis techniques.")
16125 (license license:cc0)))
16127 (define-public r-learnbayes
16129 (name "r-learnbayes")
16134 (uri (cran-uri "LearnBayes" version))
16137 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
16138 (properties `((upstream-name . "LearnBayes")))
16139 (build-system r-build-system)
16140 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
16141 (synopsis "Functions for learning Bayesian inference")
16143 "This package provides a collection of functions helpful in learning the
16144 basic tenets of Bayesian statistical inference. It contains functions for
16145 summarizing basic one and two parameter posterior distributions and predictive
16146 distributions. It contains MCMC algorithms for summarizing posterior
16147 distributions defined by the user. It also contains functions for regression
16148 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
16150 (license license:gpl2+)))
16152 (define-public r-deldir
16159 (uri (cran-uri "deldir" version))
16162 "1igq0l2knsbhizncgydcsidgkvvlwwlkrifbcdyhnzk0bhrdixkd"))))
16163 (build-system r-build-system)
16164 (native-inputs (list gfortran))
16165 (home-page "https://cran.r-project.org/web/packages/deldir")
16166 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
16168 "This package provides tools for calculating the Delaunay triangulation
16169 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
16170 of a planar point set. It plots triangulations and tessellations in various
16171 ways, clips tessellations to sub-windows, calculates perimeters of
16172 tessellations, and summarizes information about the tiles of the
16174 (license license:gpl2+)))
16176 (define-public r-wk
16183 (uri (cran-uri "wk" version))
16186 "0fj2wzswv3dfninsyw9irf52fc2d0lag5b822x841vdfpvh01mbi"))))
16187 (properties `((upstream-name . "wk")))
16188 (build-system r-build-system)
16191 (home-page "https://paleolimbot.github.io/wk/")
16192 (synopsis "Lightweight well-known geometry parsing")
16194 "This package provides a minimal R and C++ API for parsing well-known
16195 binary and well-known text representation of geometries to and from R-native
16196 formats. Well-known binary is compact and fast to parse; well-known text is
16197 human-readable and is useful for writing tests. These formats are only useful
16198 in R if the information they contain can be accessed in R, for which
16199 high-performance functions are provided here.")
16200 (license license:expat)))
16202 (define-public r-s2
16209 (uri (cran-uri "s2" version))
16212 "0gwydn6wdl675ydkcckrci6ylcx30qn8nfhmrp4qx4r9mv3c2410"))))
16213 (properties `((upstream-name . "s2")))
16214 (build-system r-build-system)
16216 (list r-rcpp r-wk))
16221 (home-page "https://r-spatial.github.io/s2/")
16222 (synopsis "Spherical geometry operators using the S2 geometry library")
16224 "This package provides R bindings for Google's s2 library for geometric
16225 calculations on the sphere. High-performance constructors and exporters
16226 provide high compatibility with existing spatial packages, transformers
16227 construct new geometries from existing geometries, predicates provide a means
16228 to select geometries based on spatial relationships, and accessors extract
16229 information about geometries.")
16230 (license license:asl2.0)))
16232 (define-public r-sf
16239 (uri (cran-uri "sf" version))
16242 "0dxln3ikqmwczz0ri63xwj05v09hkpljw2qvma6n03nzczyg2713"))))
16243 (build-system r-build-system)
16245 (list gdal geos proj sqlite zlib))
16254 (list pkg-config r-knitr))
16255 (home-page "https://github.com/r-spatial/sf/")
16256 (synopsis "Simple features for R")
16258 "This package provides support for simple features, a standardized way to
16259 encode spatial vector data. It binds to GDAL for reading and writing data, to
16260 GEOS for geometrical operations, and to PROJ for projection conversions and
16261 datum transformations.")
16262 ;; Either of these licenses
16263 (license (list license:gpl2 license:expat))))
16265 (define-public r-spdep
16271 (uri (cran-uri "spdep" version))
16274 "1dykhsk5djh62b3zcvpmvm3s87rn8ywzbwblhzivhln0y6pzk9hv"))
16276 '(for-each delete-file '("inst/doc/nb_igraph.html"
16277 "inst/doc/nb_igraph.R"
16278 "inst/doc/nb_igraph.Rmd"
16279 "inst/doc/sids.html"
16283 "inst/doc/CO69.html"
16285 "inst/doc/nb_sf.html"
16287 "inst/doc/nb_sf.Rmd")))))
16288 (build-system r-build-system)
16307 (home-page "https://github.com/r-spatial/spdep/")
16308 (synopsis "Spatial dependence: weighting schemes, statistics and models")
16310 "This package provides a collection of functions to create spatial
16311 weights matrix objects from polygon contiguities, from point patterns by
16312 distance and tessellations, for summarizing these objects, and for permitting
16313 their use in spatial data analysis, including regional aggregation by minimum
16315 (license license:gpl2+)))
16317 (define-public r-adegenet
16319 (name "r-adegenet")
16324 (uri (cran-uri "adegenet" version))
16327 "1wjp31634n6z6wglf4z3ydrhhn5jmpwwckmp3n2b0v5f3p2fivp4"))))
16328 (build-system r-build-system)
16341 (home-page "https://github.com/thibautjombart/adegenet")
16342 (synopsis "Exploratory analysis of genetic and genomic data")
16344 "This package provides a toolset for the exploration of genetic and
16345 genomic data. Adegenet provides formal (S4) classes for storing and handling
16346 various genetic data, including genetic markers with varying ploidy and
16347 hierarchical population structure (@code{genind} class), alleles counts by
16348 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
16349 also implements original multivariate methods (DAPC, sPCA), graphics,
16350 statistical tests, simulation tools, distance and similarity measures, and
16351 several spatial methods. A range of both empirical and simulated datasets is
16352 also provided to illustrate various methods.")
16353 (license license:gpl2+)))
16355 (define-public r-pegas
16362 (uri (cran-uri "pegas" version))
16364 (base32 "0ykx84p7c8cad5d1mj8cm1d5cz2paacdjx4ll4qzmq827lcyycz1"))))
16365 (build-system r-build-system)
16367 (list r-adegenet r-ape))
16368 (home-page "http://ape-package.ird.fr/pegas.html")
16369 (synopsis "Population and evolutionary genetics analysis system")
16371 "This package provides functions for reading, writing, plotting,
16372 analysing, and manipulating allelic and haplotypic data, including from VCF
16373 files, and for the analysis of population nucleotide sequences and
16374 micro-satellites including coalescent analyses, linkage disequilibrium,
16375 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
16376 minimum spanning tree and network, and median-joining networks.")
16377 (license license:gpl2+)))
16379 (define-public r-rmetasim
16381 (name "r-rmetasim")
16386 (uri (cran-uri "rmetasim" version))
16389 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
16390 (build-system r-build-system)
16392 (list r-ade4 r-adegenet r-gtools r-pegas))
16393 (home-page "https://cran.r-project.org/web/packages/rmetasim")
16394 (synopsis "Individual-based population genetic simulation environment")
16396 "This package provides an interface between R and the metasim simulation
16397 engine. The simulation environment is documented in: Strand, A.(2002),
16398 Metasim 1.0: an individual-based environment for simulating population
16399 genetics of complex population dynamics.")
16401 (license license:gpl2+)))
16403 (define-public r-genetics
16405 (name "r-genetics")
16406 (version "1.3.8.1.3")
16410 (uri (cran-uri "genetics" version))
16413 "0lljxvz7nc6y2z303icphar2niir0i407w5cyhy2pwspd9gwkwpy"))))
16414 (build-system r-build-system)
16416 (list r-combinat r-gdata r-gtools r-mass r-mvtnorm))
16417 (home-page "https://cran.r-project.org/web/packages/genetics/")
16418 (synopsis "Population genetics")
16420 "This package provides classes and methods for handling genetic data.
16421 It includes classes to represent genotypes and haplotypes at single markers up
16422 to multiple markers on multiple chromosomes. Function include allele
16423 frequencies, flagging homo/heterozygotes, flagging carriers of certain
16424 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
16425 and testing for linkage disequilibrium, ...")
16426 ;; Any GPL version.
16427 (license license:gpl2+)))
16429 (define-public r-snp-plotter
16431 (name "r-snp-plotter")
16436 (uri (cran-uri "snp.plotter" version))
16439 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
16440 (properties `((upstream-name . "snp.plotter")))
16441 (build-system r-build-system)
16442 (propagated-inputs (list r-genetics))
16443 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
16444 (synopsis "Plot p-values using single SNP and/or haplotype data")
16446 "This package helps you create plots of p-values using single SNP and/or
16447 haplotype data. Main features of the package include options to display a
16448 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
16449 datasets simultaneously. Plots can be created using global and/or individual
16450 haplotype p-values along with single SNP p-values. Images are created as
16451 either PDF/EPS files.")
16452 (license license:gpl2+)))
16454 (define-public r-polspline
16456 (name "r-polspline")
16461 (uri (cran-uri "polspline" version))
16463 (base32 "0rhzf735hmbqfn2xbgcln4sqx7m9far72g5gq9mghgkw016kqglm"))))
16464 (build-system r-build-system)
16465 (native-inputs (list gfortran))
16466 (home-page "https://cran.r-project.org/web/packages/polspline/")
16467 (synopsis "Polynomial spline routines")
16469 "This package provides routines for the polynomial spline fitting
16470 routines hazard regression, hazard estimation with flexible tails, logspline,
16471 lspec, polyclass, and polymars.")
16472 (license license:gpl2+)))
16474 (define-public r-rms
16481 (uri (cran-uri "rms" version))
16483 (base32 "1di4xvsx0rwkr77nfqiysbg4qf699199xqil70i39d4zwfzqrm8h"))))
16484 (build-system r-build-system)
16501 (native-inputs (list gfortran))
16502 (home-page "http://biostat.mc.vanderbilt.edu/rms")
16503 (synopsis "Regression modeling strategies")
16505 "This is a package for regression modeling, testing, estimation,
16506 validation, graphics, prediction, and typesetting by storing enhanced model
16507 design attributes in the fit. The rms package is a collection of functions
16508 that assist with and streamline modeling. It also contains functions for
16509 binary and ordinal logistic regression models, ordinal models for continuous Y
16510 with a variety of distribution families, and the Buckley-James multiple
16511 regression model for right-censored responses, and implements penalized
16512 maximum likelihood estimation for logistic and ordinary linear models. The
16513 package works with almost any regression model, but it was especially written
16514 to work with binary or ordinal regression models, Cox regression, accelerated
16515 failure time models, ordinary linear models, the Buckley-James model,
16516 generalized least squares for serially or spatially correlated observations,
16517 generalized linear models, and quantile regression.")
16518 (license license:gpl2+)))
16520 (define-public r-arsenal
16527 (uri (cran-uri "arsenal" version))
16530 "0qvs3ld28djnjnggdhqjwq8sbv8zz322qahlvf7dnx35yqf6xkms"))))
16531 (properties `((upstream-name . "arsenal")))
16532 (build-system r-build-system)
16533 (propagated-inputs (list r-knitr))
16534 (native-inputs (list r-knitr))
16535 (home-page "https://github.com/mayoverse/arsenal")
16536 (synopsis "Functions for large-scale statistical summaries")
16538 "This package provides an arsenal of R functions for large-scale
16539 statistical summaries, which are streamlined to work within the latest
16540 reporting tools in R and RStudio and which use formulas and versatile
16541 summary statistics for summary tables and models. The primary functions
16545 @item @code{tableby}, a Table-1-like summary of multiple variable types by the
16546 levels of one or more categorical variables;
16547 @item @code{paired}, a Table-1-like summary of multiple variable types paired
16548 across two time points;
16549 @item @code{modelsum}, which performs simple model fits on one or more
16550 endpoints for many variables (univariate or adjusted for covariates);
16551 @item @code{freqlist}, a powerful frequency table across many categorical
16553 @item @code{comparedf}, a function for comparing @code{data.frames}; and
16554 @item @code{write2}, a function to output tables to a document.
16557 (license license:gpl2+)))
16559 (define-public r-haplo-stats
16561 (name "r-haplo-stats")
16566 (uri (cran-uri "haplo.stats" version))
16569 "1q2zn72j92bwhcdswk4qqfgzch56p9pcy2xhkd3safvqp3l9rzpw"))))
16570 (properties `((upstream-name . "haplo.stats")))
16571 (build-system r-build-system)
16573 (list r-arsenal r-rms))
16575 (list r-r-rsp)) ; for vignettes
16576 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
16577 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
16579 "This package provides routines for the analysis of indirectly measured
16580 haplotypes. The statistical methods assume that all subjects are unrelated
16581 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
16582 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
16583 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
16584 examples in the vignette.")
16585 (license license:gpl2+)))
16587 (define-public r-bqtl
16594 (uri (cran-uri "bqtl" version))
16597 "1sbzpi9z94f010lw2y1gmifjrvpmiqs4m26za7vr1xz72azrqvs9"))))
16598 (build-system r-build-system)
16599 (native-inputs (list gfortran))
16600 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
16601 (synopsis "Bayesian QTL mapping toolkit")
16603 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
16604 lines. It includes maximum likelihood and Bayesian tools.")
16605 (license license:gpl2+)))
16607 (define-public r-ibdreg
16614 (uri (cran-uri "ibdreg" version))
16617 "1x8z0vr2cmdks12hxfm0wwxskb0cr669w5j5rpa2ln8q704yy41g"))))
16618 (build-system r-build-system)
16619 (home-page "https://www.mayo.edu/research/labs/\
16620 statistical-genetics-genetic-epidemiology/software")
16621 (synopsis "Regression methods for IBD linkage with covariates")
16623 "This package provides a method to test genetic linkage with covariates
16624 by regression methods with response IBD sharing for relative pairs. Account
16625 for correlations of IBD statistics and covariates for relative pairs within
16626 the same pedigree.")
16627 (license license:gpl2+)))
16629 (define-public r-dlmap
16636 (uri (cran-uri "dlmap" version))
16639 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
16640 (build-system r-build-system)
16642 (list r-ibdreg r-mgcv r-nlme r-qtl r-wgaim))
16643 (home-page "https://cran.r-project.org/web/packages/dlmap/")
16644 (synopsis "Detection localization mapping for QTL")
16646 "This is package for QTL mapping in a mixed model framework with separate
16647 detection and localization stages. The first stage detects the number of QTL
16648 on each chromosome based on the genetic variation due to grouped markers on
16649 the chromosome; the second stage uses this information to determine the most
16650 likely QTL positions. The mixed model can accommodate general fixed and
16651 random effects, including spatial effects in field trials and pedigree
16652 effects. It is applicable to backcrosses, doubled haploids, recombinant
16653 inbred lines, F2 intercrosses, and association mapping populations.")
16654 (license license:gpl2)))
16656 (define-public r-hwde
16663 (uri (cran-uri "hwde" version))
16666 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
16667 (build-system r-build-system)
16668 (home-page "https://cran.r-project.org/web/packages/hwde/")
16669 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
16671 "This package fits models for genotypic disequilibria, as described in
16672 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
16673 terms are available that account for first order interactions between loci.
16674 It also implements, for a single locus in a single population, a conditional
16675 exact test for Hardy-Weinberg equilibrium.")
16676 (license license:gpl2+)))
16678 (define-public r-tdthap
16685 (uri (cran-uri "tdthap" version))
16688 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
16689 (build-system r-build-system)
16690 (home-page "https://cran.r-project.org/web/packages/tdthap/")
16691 (synopsis "TDT tests for extended haplotypes")
16693 "Functions and examples are provided for transmission/disequilibrium
16694 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
16695 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
16696 (license license:artistic2.0)))
16698 (define-public r-sparql
16704 (uri (cran-uri "SPARQL" version))
16707 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
16708 (properties `((upstream-name . "SPARQL")))
16709 (build-system r-build-system)
16711 (list r-rcurl r-xml))
16712 (home-page "https://cran.r-project.org/web/packages/SPARQL")
16713 (synopsis "SPARQL client for R")
16714 (description "This package provides an interface to use SPARQL to pose
16715 SELECT or UPDATE queries to an end-point.")
16716 ;; The only license indication is found in the DESCRIPTION file,
16717 ;; which states GPL-3. So we cannot assume GPLv3+.
16718 (license license:gpl3)))
16720 (define-public r-bookdown
16722 (name "r-bookdown")
16726 (uri (cran-uri "bookdown" version))
16729 "1qqvvfbpbd6sin8vpvr3zzlhlyx1i6b98yp77xj5zl220nid5slb"))))
16730 (build-system r-build-system)
16740 ;; We cannot add knitr because this package depends on xfun, which is an
16744 `(("r-knitr" ,r-knitr)))
16745 (home-page "https://github.com/rstudio/bookdown")
16746 (synopsis "Authoring books and technical documents with R markdown")
16747 (description "This package provides output formats and utilities for
16748 authoring books and technical documents with R Markdown.")
16749 (license license:gpl3)))
16751 (define-public r-optparse
16753 (name "r-optparse")
16758 (uri (cran-uri "optparse" version))
16761 "1rqz0y4r94y3mwbb9kyz97cjqpnprka96qbncvbnbmgg2d630kij"))))
16762 (build-system r-build-system)
16767 (home-page "https://github.com/trevorld/optparse")
16768 (synopsis "Command line option parser")
16770 "This package provides a command line parser inspired by Python's
16771 @code{optparse} library to be used with Rscript to write shebang scripts
16772 that accept short and long options.")
16773 (license license:gpl2+)))
16775 (define-public r-kernlab
16782 (uri (cran-uri "kernlab" version))
16784 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
16785 (build-system r-build-system)
16786 (home-page "https://cran.r-project.org/web/packages/kernlab")
16787 (synopsis "Kernel-based machine learning tools")
16789 "This package provides kernel-based machine learning methods for
16790 classification, regression, clustering, novelty detection, quantile regression
16791 and dimensionality reduction. Among other methods @code{kernlab} includes
16792 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
16794 (license license:gpl2)))
16796 (define-public r-hierfstat
16798 (name "r-hierfstat")
16803 (uri (cran-uri "hierfstat" version))
16806 "1p4vlna185sa3b5xjbysiqxcj9aa5s7dmxy41hg79vlqdivf874r"))))
16807 (build-system r-build-system)
16809 (list r-ade4 r-adegenet r-gaston r-gtools))
16812 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
16813 (synopsis "Estimation and tests of hierarchical F-statistics")
16815 "This package allows the estimation of hierarchical F-statistics from
16816 haploid or diploid genetic data with any numbers of levels in the hierarchy,
16817 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
16818 are also given to test via randomisations the significance of each F and
16819 variance components, using the likelihood-ratio statistics G.")
16820 (license license:gpl2+)))
16822 (define-public r-hapassoc
16824 (name "r-hapassoc")
16829 (uri (cran-uri "hapassoc" version))
16832 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
16833 (build-system r-build-system)
16834 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
16835 (synopsis "Inference of trait associations with SNP haplotypes")
16837 "Hapassoc performs likelihood inference of trait associations with
16838 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
16839 functions are developed primarily for data collected in cohort or
16840 cross-sectional studies. They can accommodate uncertain haplotype phase and
16841 handle missing genotypes at some SNPs.")
16842 (license license:gpl2)))
16844 (define-public r-sampling
16846 (name "r-sampling")
16851 (uri (cran-uri "sampling" version))
16854 "11xis4vzn2ga8ml9xrgfgqzccvwbnabq35aidzdvpnvciybsanvz"))))
16855 (build-system r-build-system)
16857 (list r-lpsolve r-mass))
16858 (home-page "https://cran.r-project.org/web/packages/sampling/")
16859 (synopsis "Survey sampling")
16861 "This package provides functions for drawing and calibrating samples.")
16862 (license license:gpl2+)))
16864 (define-public r-r2html
16871 (uri (cran-uri "R2HTML" version))
16874 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
16875 (properties `((upstream-name . "R2HTML")))
16876 (build-system r-build-system)
16877 (home-page "https://github.com/nalimilan/R2HTML")
16878 (synopsis "HTML export for R objects")
16880 "This package includes HTML functions and methods to write in an HTML
16881 file. Thus, making HTML reports is easy. It includes a function that allows
16882 redirection on the fly, which appears to be very useful for teaching purposes,
16883 as the student can keep a copy of the produced output to keep all that they
16884 did during the course. The package comes with a vignette describing how to
16885 write HTML reports for statistical analysis. Finally, a driver for Sweave
16886 parses HTML flat files containing R code and to automatically write
16887 the corresponding outputs (tables and graphs).")
16888 (license license:gpl2+)))
16890 (define-public r-rjava
16897 (uri (cran-uri "rJava" version))
16900 "1pkgndppk498by44sai440l3i7vzndknbngn1q748cv39xvsbnrg"))))
16901 (properties `((upstream-name . "rJava")))
16902 (build-system r-build-system)
16904 `(#:modules ((guix build utils)
16905 (guix build r-build-system)
16908 (modify-phases %standard-phases
16909 (add-after 'unpack 'set-JAVA_HOME
16910 (lambda* (#:key inputs #:allow-other-keys)
16911 (let ((jdk (assoc-ref inputs "jdk")))
16912 (setenv "JAVA_HOME" jdk)
16913 (setenv "JAVA" (which "java"))
16914 (setenv "JAR" (which "jar"))
16915 (setenv "JAVAC" (which "javac"))
16916 (setenv "JAVAH" (which "javah"))
16917 (setenv "JAVA_CPPFLAGS"
16918 (string-append "-I" jdk "/include "
16919 "-I" jdk "/include/linux"))
16920 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
16921 ((lib) (setenv "JAVA_LIBS" lib))
16922 (_ (error "Could not find libjvm.so"))))
16926 ("jdk" ,icedtea-8 "jdk")
16928 (home-page "https://www.rforge.net/rJava/")
16929 (synopsis "Low-Level R to Java interface")
16931 "This package provides a low-level interface to the Java VM very much
16932 like .C/.Call and friends. It allows the creation of objects, calling methods
16933 and accessing fields.")
16934 (license license:gpl2)))
16936 (define-public r-svmisc
16943 (uri (cran-uri "svMisc" version))
16946 "1r3kih5bnr4plnzdn5f2gg3xl3krgyl7gkdlf58a2l8vk13j3m9d"))))
16947 (properties `((upstream-name . "svMisc")))
16948 (build-system r-build-system)
16951 (home-page "https://github.com/SciViews/svMisc")
16952 (synopsis "Miscellaneous functions for SciViews")
16954 "This package provides miscellaneous functions for SciViews or general
16955 use, including tools to manage a temporary environment attached to the search
16956 path for temporary variables you do not want to @code{save()} or
16957 @code{load()}; test the current platform; showing progress bars, etc.")
16958 (license license:gpl2)))
16960 (define-public r-xyz
16967 (uri (cran-uri "xyz" version))
16970 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
16971 (build-system r-build-system)
16974 (home-page "https://cran.r-project.org/web/packages/xyz/")
16975 (synopsis "Algorithm for fast interaction search in high-dimensional data")
16977 "High dimensional interaction search by brute force requires a quadratic
16978 computational cost in the number of variables. The xyz algorithm provably
16979 finds strong interactions in almost linear time. For details of the algorithm
16980 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
16981 interaction search in high-dimensional data.")
16982 ;; Any version of the GPL.
16983 (license license:gpl2+)))
16985 (define-public r-rttf2pt1
16987 (name "r-rttf2pt1")
16992 (uri (cran-uri "Rttf2pt1" version))
16995 "0w9ybqvr4bvpa2dyfkrscg4in0x2dkzmxdn1n6003j1rss7f8rw6"))))
16996 (properties `((upstream-name . "Rttf2pt1")))
16997 (build-system r-build-system)
16998 (home-page "https://github.com/wch/Rttf2pt1")
16999 (synopsis "Font conversion utility")
17001 "This package contains the program @code{ttf2pt1}, for use with the
17002 @code{extrafont} package.")
17003 ;; Most of the files are covered under the Expat license. Some files are
17004 ;; covered under BSD-3. Deviations for individual files are recorded in
17005 ;; the LICENSE file.
17006 (license (list license:bsd-3 license:expat
17007 (license:non-copyleft "file://LICENSE")))))
17009 (define-public r-extrafontdb
17011 (name "r-extrafontdb")
17016 (uri (cran-uri "extrafontdb" version))
17019 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
17020 (build-system r-build-system)
17021 (home-page "https://github.com/wch/extrafontdb")
17022 (synopsis "Database for the extrafont package")
17024 "This package holds the database for the @code{extrafont} package.")
17025 (license license:gpl2)))
17027 (define-public r-extrafont
17029 (name "r-extrafont")
17034 (uri (cran-uri "extrafont" version))
17037 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
17038 (build-system r-build-system)
17040 (list r-extrafontdb r-rttf2pt1))
17041 (home-page "https://github.com/wch/extrafont")
17042 (synopsis "Tools for using fonts in R")
17044 "The extrafont package makes it easier to use fonts other than the basic
17045 PostScript fonts that R uses. Fonts that are imported into extrafont can be
17046 used with PDF or PostScript output files. There are two hurdles for using
17047 fonts in PDF (or Postscript) output files:
17050 @item Making R aware of the font and the dimensions of the characters.
17051 @item Embedding the fonts in the PDF file so that the PDF can be displayed
17052 properly on a device that doesn't have the font. This is usually needed if
17053 you want to print the PDF file or share it with others.
17056 The extrafont package makes both of these things easier.")
17057 (license license:gpl2)))
17059 (define-public r-xkcd
17066 (uri (cran-uri "xkcd" version))
17069 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
17070 (build-system r-build-system)
17072 (list r-extrafont r-ggplot2 r-hmisc))
17073 (home-page "https://cran.r-project.org/web/packages/xkcd/")
17074 (synopsis "Plot ggplot2 graphics in the XKCD style")
17076 "This package provides the means to plot ggplot2 graphs in the style of
17077 the XKCD web comic.")
17078 (license license:gpl3)))
17080 (define-public r-babelgene
17082 (name "r-babelgene")
17087 (uri (cran-uri "babelgene" version))
17090 "1gk5pm3b3shr1id66a11ywc1b823gbj8yckg24szzfhj8g4ixyf0"))))
17091 (properties `((upstream-name . "babelgene")))
17092 (build-system r-build-system)
17094 (list r-dplyr r-rlang))
17098 "https://igordot.github.io/babelgene/")
17099 (synopsis "Gene orthologs for model organisms in a Tidy data format")
17101 "Genomic analysis of model organisms often requires the use of databases
17102 based on human data or making comparisons to patient-derived resources. This
17103 requires converting genes between human and non-human analogues. The
17104 babelgene R package provides predicted gene orthologs/homologs for frequently
17105 studied model organisms in an R-friendly tidy/long format. The package
17106 integrates orthology assertion predictions sourced from multiple databases as
17107 compiled by the HGNC Comparison of Orthology Predictions (HCOP).")
17108 (license license:expat)))
17110 (define-public r-msigdbr
17117 (uri (cran-uri "msigdbr" version))
17120 "103m52av68pkjfh8f81qh6j3cs1mj1lg831ciwybr34cax767jr1"))))
17121 (build-system r-build-system)
17131 (home-page "https://github.com/igordot/msigdbr")
17132 (synopsis "MSigDB gene sets for multiple organisms")
17134 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
17135 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
17136 software in a standard R data frame with key-value pairs. Included are the
17137 original human gene symbols and Entrez IDs as well as the equivalents for
17138 various frequently studied model organisms such as mouse, rat, pig, fly, and
17140 ;; The package is covered under the Expat license, but the upstream MSigDB
17141 ;; files are made available under the Creative Commons Attribution 4.0
17142 ;; International license.
17143 (license (list license:expat license:cc-by4.0))))
17145 (define-public r-gridgraphics
17147 (name "r-gridgraphics")
17152 (uri (cran-uri "gridGraphics" version))
17155 "12yswy02j3h5wir7m5jnkhpjmb0sa4snn61vjd68i49qwsa6w219"))))
17156 (properties `((upstream-name . "gridGraphics")))
17157 (build-system r-build-system)
17158 (home-page "https://github.com/pmur002/gridgraphics")
17159 (synopsis "Redraw base graphics using @code{grid} graphics")
17161 "This package provides functions to convert a page of plots drawn with
17162 the @code{graphics} package into identical output drawn with the @code{grid}
17163 package. The result looks like the original @code{graphics}-based plot, but
17164 consists of @code{grid} grobs and viewports that can then be manipulated with
17165 @code{grid} functions (e.g., edit grobs and revisit viewports).")
17166 (license license:gpl2+)))
17168 (define-public r-farver
17175 (uri (cran-uri "farver" version))
17178 "1x6ffwxqbrwlylnk995jz2a6nz2y9z59jaq0ncpni7q40w367j75"))))
17179 (build-system r-build-system)
17180 (home-page "https://github.com/thomasp85/farver")
17181 (synopsis "Vectorized color conversion and comparison")
17183 "The encoding of color can be handled in many different ways, using
17184 different color spaces. As different color spaces have different uses,
17185 efficient conversion between these representations are important. This
17186 package provides a set of functions that gives access to very fast color space
17187 conversion and comparisons implemented in C++, and offers 100-fold speed
17188 improvements over the @code{convertColor} function in the @code{grDevices}
17190 (license license:expat)))
17192 (define-public r-yulab-utils
17194 (name "r-yulab-utils")
17199 (uri (cran-uri "yulab.utils" version))
17202 "1bj93gnj7j4b7dgkbr5v22rsbwfcw5dvipl5irmidaakvrihd19q"))))
17203 (properties `((upstream-name . "yulab.utils")))
17204 (build-system r-build-system)
17205 (home-page "https://cran.r-project.org/package=yulab.utils")
17206 (synopsis "Supporting functions for packages maintained by YuLab-SMU")
17208 "Miscellaneous functions commonly used by YuLab-SMU, such as
17209 @code{install_zip_gh} to install R packages from Github ZIP files.")
17210 (license license:artistic2.0)))
17212 (define-public r-ggplotify
17214 (name "r-ggplotify")
17219 (uri (cran-uri "ggplotify" version))
17222 "12mk3fa8fdjxj7xxz21jkr7h91w5wdgwjqhszcz1qffwsgb773qp"))))
17223 (build-system r-build-system)
17225 (list r-ggplot2 r-gridgraphics r-yulab-utils))
17228 (home-page "https://github.com/GuangchuangYu/ggplotify")
17229 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
17231 "This package provides tools to convert plot function calls (using
17232 expression or formula) to @code{grob} or @code{ggplot} objects that are
17233 compatible with the @code{grid} and @code{ggplot2} environment. With this
17234 package, we are able to e.g. use @code{cowplot} to align plots produced by
17235 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
17236 converting them to @code{ggplot} objects.")
17237 (license license:artistic2.0)))
17239 (define-public r-triebeard
17241 (name "r-triebeard")
17246 (uri (cran-uri "triebeard" version))
17249 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
17250 (build-system r-build-system)
17251 (propagated-inputs (list r-rcpp))
17252 (home-page "https://github.com/Ironholds/triebeard/")
17253 (synopsis "Radix trees in Rcpp")
17255 "Radix trees, or tries, are key-value data structures optimized for
17256 efficient lookups, similar in purpose to hash tables. This package provides
17257 an implementation of radix trees for use in R programming and in developing
17258 packages with Rcpp.")
17259 (license license:expat)))
17261 (define-public r-tweenr
17268 (uri (cran-uri "tweenr" version))
17271 "17znizh4yabh2zs9mzyr0sl6p0pw49961i61br7cl1b7v9sza18q"))))
17272 (build-system r-build-system)
17274 (list r-farver r-magrittr r-rcpp r-rlang))
17275 (home-page "https://github.com/thomasp85/tweenr")
17276 (synopsis "Interpolate data for smooth animations")
17278 "In order to create smooth animation between states of data, tweening is
17279 necessary. This package provides a range of functions for creating tweened
17280 data that can be used as basis for animation. Furthermore it adds a number of
17281 vectorized interpolaters for common R data types such as numeric, date and
17283 (license license:expat)))
17285 (define-public r-polyclip
17287 (name "r-polyclip")
17292 (uri (cran-uri "polyclip" version))
17295 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
17296 (build-system r-build-system)
17297 (native-inputs (list pkg-config))
17298 (home-page "http://www.angusj.com/delphi/clipper.php")
17299 (synopsis "Polygon clipping")
17301 "This package provides an R port of the library Clipper. It performs
17302 polygon clipping operations (intersection, union, set minus, set difference)
17303 for polygonal regions of arbitrary complexity, including holes. It computes
17304 offset polygons (spatial buffer zones, morphological dilations, Minkowski
17305 dilations) for polygonal regions and polygonal lines. It computes the
17306 Minkowski Sum of general polygons. There is a function for removing
17307 self-intersections from polygon data.")
17308 (license license:boost1.0)))
17310 (define-public r-urltools
17312 (name "r-urltools")
17317 (uri (cran-uri "urltools" version))
17320 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
17321 (build-system r-build-system)
17323 (list r-rcpp r-triebeard))
17324 (home-page "https://github.com/Ironholds/urltools/")
17325 (synopsis "Vectorized tools for URL handling and parsing")
17327 "This package provides a toolkit for all URL-handling needs, including
17328 encoding and decoding, parsing, parameter extraction and modification. All
17329 functions are designed to be both fast and entirely vectorized. It is
17330 intended to be useful for people dealing with web-related datasets, such as
17331 server-side logs, although may be useful for other situations involving large
17333 (license license:expat)))
17335 (define-public r-ggforce
17342 (uri (cran-uri "ggforce" version))
17345 "0bwzjbjl678xvc2ihm80dwn9pidwafqjdab3k299csys16s3na1a"))))
17346 (build-system r-build-system)
17359 (home-page "https://ggforce.data-imaginist.com")
17360 (synopsis "Accelerating ggplot2")
17362 "The aim of the ggplot2 package is to aid in visual data investigations.
17363 This focus has led to a lack of facilities for composing specialized plots.
17364 This package aims to be a collection of mainly new statistics and geometries
17365 that fills this gap.")
17366 (license license:expat)))
17368 (define-public r-europepmc
17370 (name "r-europepmc")
17375 (uri (cran-uri "europepmc" version))
17378 "16japbndid34shqg8n0bmjrxn84xmhrylvz832zclcllm6i93fn1"))))
17379 (build-system r-build-system)
17394 (home-page "https://github.com/ropensci/europepmc/")
17395 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
17397 "This package provides an R Client for the
17398 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
17399 Service}. It gives access to both metadata on life science literature and
17400 open access full texts. Europe PMC indexes all PubMed content and other
17401 literature sources including Agricola, a bibliographic database of citations
17402 to the agricultural literature, or Biological Patents. In addition to
17403 bibliographic metadata, the client allows users to fetch citations and
17404 reference lists. Links between life-science literature and other EBI
17405 databases, including ENA, PDB or ChEMBL are also accessible.")
17406 (license license:gpl3)))
17408 (define-public r-ggraph
17415 (uri (cran-uri "ggraph" version))
17418 "0m4n8iw2b9jk8hcy5blg5w59zsqcpsbv27wbw598dvljpafx8sp3"))))
17419 (build-system r-build-system)
17438 (home-page "https://cran.r-project.org/web/packages/ggraph/")
17439 (synopsis "Implementation of grammar of graphics for graphs and networks")
17441 "The grammar of graphics as implemented in ggplot2 is a poor fit for
17442 graph and network visualizations due to its reliance on tabular data input.
17443 The ggraph package is an extension of the ggplot2 API tailored to graph
17444 visualizations and provides the same flexible approach to building up plots
17446 (license license:gpl3)))
17448 (define-public r-gkmsvm
17455 (uri (cran-uri "gkmSVM" version))
17458 "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj"))))
17459 (properties `((upstream-name . "gkmSVM")))
17460 (build-system r-build-system)
17462 (list r-kernlab r-rcpp r-rocr r-seqinr))
17463 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
17464 (synopsis "Gapped-kmer support vector machine")
17466 "This R package provides tools for training gapped-kmer SVM classifiers
17467 for DNA and protein sequences. This package supports several sequence
17468 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
17469 (license license:gpl2+)))
17471 (define-public r-varselrf
17473 (name "r-varselrf")
17478 (uri (cran-uri "varSelRF" version))
17481 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
17482 (properties `((upstream-name . "varSelRF")))
17483 (build-system r-build-system)
17485 (list r-randomforest))
17486 (home-page "https://www.ligarto.org/rdiaz/software/software")
17487 (synopsis "Variable selection using random forests")
17489 "This package provides tools for the variable selection from random
17490 forests using both backwards variable elimination (for the selection of small
17491 sets of non-redundant variables) and selection based on the importance
17492 spectrum (somewhat similar to scree plots; for the selection of large,
17493 potentially highly-correlated variables). The main applications are in
17494 high-dimensional data (e.g., microarray data, and other genomics and
17495 proteomics applications).")
17496 (license license:gpl2+)))
17498 (define-public r-pamr
17505 (uri (cran-uri "pamr" version))
17508 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
17509 (build-system r-build-system)
17511 (list r-cluster r-survival))
17512 (native-inputs (list gfortran))
17513 (home-page "https://cran.r-project.org/web/packages/pamr/")
17514 (synopsis "Prediction Analysis for Microarrays")
17516 "This package provides some functions for sample classification in
17518 (license license:gpl2)))
17520 (define-public r-rda
17523 (version "1.0.2-2.1")
17527 (uri (cran-uri "rda" version))
17530 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
17531 (build-system r-build-system)
17532 (home-page "https://cran.r-project.org/web/packages/rda/")
17533 (synopsis "Shrunken centroids regularized discriminant analysis")
17535 "This package provides tools for shrunken centroids regularized
17536 discriminant analysis for the purpose of classifying high dimensional data.")
17537 (license license:gpl2+)))
17539 (define-public r-ggvis
17546 (uri (cran-uri "ggvis" version))
17549 "1qv512pd4x5vmx15y9nvqmabbbw14h75fmi1sjbcg5yl25z0cswy"))))
17550 (build-system r-build-system)
17559 (home-page "https://ggvis.rstudio.com/")
17560 (synopsis "Interactive grammar of graphics")
17562 "This package is a data visualization package for R providing an
17563 implementation of an interactive grammar of graphics, taking the best parts of
17564 ggplot2, combining them with the reactive framework of Shiny and drawing web
17565 graphics using Vega.")
17566 (license license:gpl2)))
17568 (define-public r-gbm
17575 (uri (cran-uri "gbm" version))
17578 "1h9f4ww9yc3nsvghgr2q7jjrlz29ibabxjbax1sk5wmqh2wy6pbx"))))
17579 (build-system r-build-system)
17581 (list r-lattice r-survival))
17584 (home-page "https://github.com/gbm-developers/gbm")
17585 (synopsis "Generalized boosted regression models")
17587 "This package is an implementation of extensions to Freund and Schapire's
17588 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
17589 regression methods for least squares, absolute loss, t-distribution loss,
17590 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
17591 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
17592 and Learning to Rank measures (LambdaMart).")
17593 (license license:gpl2+)))
17595 (define-public r-threejs
17602 (uri (cran-uri "threejs" version))
17605 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
17606 (build-system r-build-system)
17608 `(#:modules ((guix build utils)
17609 (guix build r-build-system)
17613 (modify-phases %standard-phases
17614 (add-after 'unpack 'process-javascript
17615 (lambda* (#:key inputs #:allow-other-keys)
17616 (with-directory-excursion "inst"
17620 `((,(assoc-ref inputs "js-jquery")
17621 "htmlwidgets/lib/jquery/jquery.min.js")
17622 (,(assoc-ref inputs "js-threejs-111")
17623 "htmlwidgets/lib/threejs-111/three.min.js"))))
17624 (lambda (sources targets)
17625 (for-each (lambda (source target)
17626 (format #t "Processing ~a --> ~a~%"
17628 (delete-file target)
17629 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
17630 (call-with-output-file target
17632 (dump-port minified port)))))
17633 sources targets))))
17636 (list r-base64enc r-crosstalk r-htmlwidgets r-igraph))
17638 `(("uglifyjs" ,node-uglify-js)
17642 (uri "https://code.jquery.com/jquery-1.12.4.js")
17645 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
17649 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
17652 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
17653 (home-page "https://bwlewis.github.io/rthreejs")
17654 (synopsis "Interactive 3D scatter plots, networks and globes")
17656 "Create interactive 3D scatter plots, network plots, and globes in R
17657 using the three.js visualization library.")
17658 (license license:expat)))
17660 (define-public r-mlbench
17667 (uri (cran-uri "mlbench" version))
17670 "157iqsld0wj8g8cbs7nh6p2x6kasmkhs3078hsmqac946gk2pydi"))))
17671 (build-system r-build-system)
17672 (home-page "https://cran.r-project.org/web/packages/mlbench/")
17673 (synopsis "Machine learning benchmark problems")
17675 "This package provides a collection of artificial and real-world machine
17676 learning benchmark problems, including, e.g., several data sets from the UCI
17678 (license license:gpl2)))
17680 (define-public r-mpm
17687 (uri (cran-uri "mpm" version))
17690 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
17691 (build-system r-build-system)
17693 (list r-kernsmooth r-mass))
17694 (home-page "http://mpm.r-forge.r-project.org")
17695 (synopsis "Multivariate projection methods")
17697 "This is a package for exploratory graphical analysis of multivariate
17698 data, specifically gene expression data with different projection methods:
17699 principal component analysis, correspondence analysis, spectral map
17701 (license license:gpl2+)))
17703 (define-public r-png
17709 (uri (cran-uri "png" version))
17712 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
17713 (build-system r-build-system)
17715 (list libpng zlib))
17716 (home-page "https://www.rforge.net/png/")
17717 (synopsis "Read and write PNG images")
17719 "This package provides an easy and simple way to read, write and display
17720 bitmap images stored in the PNG format. It can read and write both files and
17721 in-memory raw vectors.")
17722 ;; Any of these GPL versions.
17723 (license (list license:gpl2 license:gpl3))))
17725 (define-public r-ggcorrplot
17727 (name "r-ggcorrplot")
17732 (uri (cran-uri "ggcorrplot" version))
17735 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
17736 (build-system r-build-system)
17738 (list r-ggplot2 r-reshape2))
17739 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
17740 (synopsis "Visualization of a correlation matrix using ggplot2")
17742 "The ggcorrplot package can be used to visualize easily a correlation
17743 matrix using ggplot2. It provides a solution for reordering the correlation
17744 matrix and displays the significance level on the plot. It also includes a
17745 function for computing a matrix of correlation p-values.")
17746 (license license:gpl2)))
17748 (define-public r-ggfun
17755 (uri (cran-uri "ggfun" version))
17758 "07njcjcj212zxanq8x3nkh7mgvqmym08rx5s41rz9flhk9gkc9jr"))))
17759 (properties `((upstream-name . "ggfun")))
17760 (build-system r-build-system)
17762 (list r-ggplot2 r-rlang))
17763 (native-inputs (list r-knitr))
17764 (home-page "https://cran.r-project.org/package=ggfun")
17765 (synopsis "Miscellaneous functions for ggplot2")
17767 "This package provides useful functions to edit ggplot object (e.g.,
17768 setting fonts for theme and layers, adding rounded rectangle as background for
17769 each of the legends).")
17770 (license license:artistic2.0)))
17772 (define-public r-gridtext
17774 (name "r-gridtext")
17779 (uri (cran-uri "gridtext" version))
17782 "131kw7nkfwksviwfifd2kk7lyvhxzzzv1nnj8rahkr3dik3akk61"))))
17783 (properties `((upstream-name . "gridtext")))
17784 (build-system r-build-system)
17794 (home-page "https://wilkelab.org/gridtext/")
17795 (synopsis "Improved text rendering support for Grid graphics")
17797 "This package provides support for rendering of formatted text using Grid
17798 graphics. Text can be formatted via a minimal subset of Markdown, HTML, and
17799 inline CSS directives, and it can be rendered both with and without word
17801 (license license:expat)))
17803 (define-public r-ggtext
17810 (uri (cran-uri "ggtext" version))
17813 "0n19dlcys8v7myfyckr6dnq0kx79k3sbh8nwx1jsx8pgzfbi8a2b"))))
17814 (properties `((upstream-name . "ggtext")))
17815 (build-system r-build-system)
17817 (list r-ggplot2 r-gridtext r-rlang r-scales))
17818 (native-inputs (list r-knitr))
17819 (home-page "https://wilkelab.org/ggtext/")
17820 (synopsis "Improved text rendering support for ggplot2")
17822 "This package provides a ggplot2 extension that enables the rendering of
17823 complex formatted plot labels (titles, subtitles, facet labels, axis labels,
17824 etc.). Text boxes with automatic word wrap are also supported.")
17825 (license license:gpl2)))
17827 ;; This package includes minified JavaScript files. When upgrading please
17828 ;; check that there are no new minified JavaScript files.
17829 (define-public r-flexdashboard
17831 (name "r-flexdashboard")
17836 (uri (cran-uri "flexdashboard" version))
17839 "1bh759llp15fxrx2rwvxd8p3w84vjmkid32ism7zg49a127fjib4"))
17840 (modules '((guix build utils)))
17843 ;; Delete bundled minified JavaScript files
17844 (delete-file "inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
17845 (delete-file "inst/www/sly/sly.min.js")
17846 (delete-file "inst/www/stickytableheaders/jquery.stickytableheaders.min.js")
17847 (delete-file "inst/www/prism/prism.js")
17849 (build-system r-build-system)
17851 `(#:modules ((guix build utils)
17852 (guix build r-build-system)
17856 (ice-9 textual-ports))
17858 (modify-phases %standard-phases
17859 (add-after 'unpack 'process-javascript
17860 (lambda* (#:key inputs #:allow-other-keys)
17861 (with-directory-excursion "inst"
17862 ;; Concatenate all components of prism.js
17863 (let ((contents (string-join
17864 (map (lambda (name)
17865 (call-with-input-file
17866 (assoc-ref inputs name)
17870 "js-prism-line-numbers"))
17872 (call-with-output-file "prism-src.js"
17873 (cut display contents <>)))
17877 `(("www/stickytableheaders/jquery.stickytableheaders.js"
17878 "www/stickytableheaders/jquery.stickytableheaders.min.js")
17880 "www/sly/sly.min.js")
17882 "www/prism/prism.js")
17883 (,(assoc-ref inputs "js-raphael")
17884 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
17885 (,(assoc-ref inputs "js-featherlight")
17886 "www/featherlight/featherlight.min.js"))))
17887 (lambda (sources targets)
17888 (for-each (lambda (source target)
17889 (format #t "Processing ~a --> ~a~%"
17891 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
17892 (call-with-output-file target
17894 (dump-port minified port)))))
17895 sources targets))))
17905 `(("uglifyjs" ,node-uglify-js)
17909 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
17912 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
17916 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
17919 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
17923 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
17926 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
17927 ("js-prism-line-numbers"
17930 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
17933 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
17937 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
17940 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
17941 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
17942 (synopsis "R Markdown format for flexible dashboards")
17944 "This package provides an R Markdown format for converting an R Markdown
17945 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
17946 of its components to the containing web page.")
17947 (license license:expat)))
17949 (define-public r-preseqr
17956 (uri (cran-uri "preseqR" version))
17959 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
17960 (properties `((upstream-name . "preseqR")))
17961 (build-system r-build-system)
17964 (home-page "https://cran.r-project.org/web/packages/preseqR/")
17965 (synopsis "Predicting species accumulation curves")
17967 "This package can be used to predict the r-species accumulation
17968 curve (r-SAC), which is the number of species represented at least r times as
17969 a function of the sampling effort. When r = 1, the curve is known as the
17970 species accumulation curve, or the library complexity curve in high-throughput
17971 genomic sequencing. The package includes both parametric and nonparametric
17972 methods, as described by Deng C, et al. (2018).")
17973 (license license:gpl3)))
17975 (define-public r-mapplots
17977 (name "r-mapplots")
17982 (uri (cran-uri "mapplots" version))
17985 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
17986 (build-system r-build-system)
17987 (home-page "https://cran.r-project.org/web/packages/mapplots/")
17988 (synopsis "Data visualization on maps")
17990 "This package helps you create simple maps; add sub-plots like pie plots
17991 to a map or any other plot; format, plot and export gridded data. The package
17992 was developed for displaying fisheries data but most functions can be used for
17993 more generic data visualisation.")
17994 (license license:gpl2+)))
17996 (define-public r-pmcmr
18003 (uri (cran-uri "PMCMR" version))
18006 "05n13pp5yff6pzk4ry07crddfaj3jlglrd1vkcnacyd8jpaxkd77"))))
18007 (properties `((upstream-name . "PMCMR")))
18008 (build-system r-build-system)
18009 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
18010 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
18012 "This is a deprecated package for calculating pairwise multiple
18013 comparisons of mean rank sums. This package is superseded by the novel
18014 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
18015 compatibility of dependent packages for some time.")
18016 (license license:gpl3+)))
18018 (define-public r-downloader
18020 (name "r-downloader")
18025 (uri (cran-uri "downloader" version))
18028 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
18029 (build-system r-build-system)
18032 (home-page "https://github.com/wch/downloader")
18033 (synopsis "Download files over HTTP and HTTPS")
18035 "This package provides a wrapper for the @code{download.file} function,
18036 making it possible to download files over HTTPS across platforms. The
18037 @code{RCurl} package provides this functionality (and much more) but has
18038 external dependencies. This package has is implemented purely in R.")
18039 (license license:gpl2)))
18041 (define-public r-aplot
18048 (uri (cran-uri "aplot" version))
18051 "067yzy35spvs6jbccqpmvnjilglxzda6qqlqhjv311kfvnppzsyf"))))
18052 (properties `((upstream-name . "aplot")))
18053 (build-system r-build-system)
18061 (home-page "https://github.com/YuLab-SMU/aplot")
18062 (synopsis "Decorate a ggplot with associated information")
18064 "Users may want to align plots with associated information that requires
18065 axes to be exactly matched in subplots, e.g. hierarchical clustering with a
18066 heatmap. This package provides utilities to align associated subplots to a
18067 main plot at different sides (left, right, top and bottom) with axes exactly
18069 (license license:artistic2.0)))
18071 (define-public r-ggnewscale
18073 (name "r-ggnewscale")
18078 (uri (cran-uri "ggnewscale" version))
18081 "1hjysfagd2lqy8yivqq9q7l6hbvyq8kasw3zqh5fk9xn18ikc702"))))
18082 (properties `((upstream-name . "ggnewscale")))
18083 (build-system r-build-system)
18086 (home-page "https://cran.r-project.org/package=ggnewscale")
18087 (synopsis "Multiple fill and color scales in ggplot2")
18089 "This package lets you use multiple fill and color scales in ggplot2.")
18090 (license license:gpl3)))
18092 (define-public r-ggpointdensity
18094 (name "r-ggpointdensity")
18099 (uri (cran-uri "ggpointdensity" version))
18102 "0c9a14j3b0hvamqylhzldw2hjdxmfbllwahjkf3gg2rw337ld9iy"))))
18104 `((upstream-name . "ggpointdensity")))
18105 (build-system r-build-system)
18108 (home-page "https://github.com/LKremer/ggpointdensity")
18109 (synopsis "Cross between a 2D density plot and a scatter plot")
18111 "This package provides a cross between a 2D density plot and a scatter
18112 plot, implemented as a ggplot2 @code{geom}. Points in the scatter plot are
18113 colored by the number of neighboring points. This is useful to visualize the
18114 2D-distribution of points in case of overplotting.")
18115 (license license:gpl3)))
18117 (define-public r-arrow
18124 (uri (cran-uri "arrow" version))
18127 "14fghz9xijcrck0c65crvfidgyhgzy9b2apwmg7qrgn2sy09xm0p"))))
18128 (properties `((upstream-name . "arrow")))
18129 (build-system r-build-system)
18131 (list `(,apache-arrow "lib") zlib))
18141 (list pkg-config r-knitr))
18142 (home-page "https://github.com/apache/arrow/")
18143 (synopsis "R integration to Apache Arrow")
18145 "Apache Arrow is a cross-language development platform for in-memory
18146 data. It specifies a standardized language-independent columnar memory format
18147 for flat and hierarchical data, organized for efficient analytic operations on
18148 modern hardware. This package provides an R interface to the Arrow C++
18150 (license license:asl2.0)))
18152 (define-public r-rex
18159 (uri (cran-uri "rex" version))
18162 "0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06"))))
18163 (build-system r-build-system)
18168 (home-page "https://github.com/kevinushey/rex")
18169 (synopsis "Friendly regular expressions")
18171 "This package provides a friendly interface for the construction of
18172 regular expressions. Regular expressions are a very powerful feature, however
18173 they are often difficult to interpret. Rex allows you to build complex
18174 regular expressions from human readable expressions")
18175 (license license:expat)))
18177 (define-public r-mlapi
18184 (uri (cran-uri "mlapi" version))
18187 "023vk5bp8cjcq88sapkl87kdxr92bay1dyxl6xirnyj699pyj51k"))))
18188 (properties `((upstream-name . "mlapi")))
18189 (build-system r-build-system)
18191 (list r-matrix r-r6))
18194 (home-page "https://cran.r-project.org/package=mlapi")
18195 (synopsis "Abstract classes for building scikit-learn like API")
18197 "This package provides R6 abstract classes for building machine learning
18198 models with a scikit-learn like API. Scikit-learn is a popular module for the
18199 Python programming language whose design became a de facto standard in
18200 industry for machine learning tasks.")
18201 (license license:expat)))
18203 (define-public r-float
18210 (uri (cran-uri "float" version))
18213 "1bx5yxkb123001v31jjk7h7f0qissmjydvbil5cj3jvmqkayq1a1"))))
18214 (properties `((upstream-name . "float")))
18215 (build-system r-build-system)
18218 (home-page "https://github.com/wrathematics/float")
18219 (synopsis "32-bit floats")
18221 "R comes with a suite of utilities for linear algebra with
18222 \"numeric\" (double precision) vectors/matrices. However, sometimes single
18223 precision (or less!) is more than enough for a particular task. This package
18224 extends R's linear algebra facilities to include 32-bit float (single
18225 precision) data. Float vectors/matrices have half the precision of their
18226 \"numeric\"-type counterparts but are generally faster to numerically operate
18227 on, for a performance vs accuracy trade-off.")
18228 (license license:bsd-2)))
18230 (define-public r-rsparse
18237 (uri (cran-uri "rsparse" version))
18240 "1blg59gsidh0sn6yy761pisz2phml0hzgqc24s5s8q9q903rddr9"))))
18241 (properties `((upstream-name . "rsparse")))
18242 (build-system r-build-system)
18251 (home-page "https://github.com/rexyai/rsparse")
18252 (synopsis "Statistical learning on sparse matrices")
18254 "This package implements many algorithms for statistical learning on
18255 sparse matrices: matrix factorizations, matrix completion, elastic net
18256 regressions, factorization machines. The rsparse package also enhances the
18257 Matrix package by providing methods for multithreaded <sparse, dense> matrix
18258 products and native slicing of the sparse matrices in @dfn{Compressed Sparse
18259 Row} (CSR) format.")
18260 (license license:gpl2+)))
18262 (define-public r-text2vec
18264 (name "r-text2vec")
18269 (uri (cran-uri "text2vec" version))
18272 "0r75cv77x2zm1z66s95hic71dpbqmybz39n48q6mz7gfd3m7312y"))))
18273 (properties `((upstream-name . "text2vec")))
18274 (build-system r-build-system)
18287 (home-page "http://text2vec.org")
18288 (synopsis "Text mining framework for R")
18290 "This package provides fast and memory-friendly tools for text
18291 vectorization, topic modeling (LDA, LSA), word embeddings (GloVe),
18292 similarities. It provides a source-agnostic streaming API, which allows
18293 researchers to perform analysis of collections of documents which are larger
18294 than available RAM. All core functions are parallelized to benefit from
18295 multicore machines.")
18296 (license license:gpl2+)))
18298 (define-public r-mcmcpack
18300 (name "r-mcmcpack")
18305 (uri (cran-uri "MCMCpack" version))
18308 "16zjx8yz29ii75wfxj3p562l657bng8jnwzp2b54s7fiaws4kfdm"))))
18309 (properties `((upstream-name . "MCMCpack")))
18310 (build-system r-build-system)
18312 (list r-coda r-lattice r-mass r-mcmc r-quantreg))
18313 (home-page "https://cran.r-project.org/package=MCMCpack")
18314 (synopsis "Markov Chain Monte Carlo (MCMC) package")
18316 "This package contains functions to perform Bayesian inference using
18317 posterior simulation for a number of statistical models. Most simulation is
18318 done in compiled C++ written in the Scythe Statistical Library. All models
18319 return @code{coda} @code{mcmc} objects that can then be summarized using the
18320 @code{coda} package. Some useful utility functions such as density functions,
18321 pseudo-random number generators for statistical distributions, a general
18322 purpose Metropolis sampling algorithm, and tools for visualization are
18324 (license license:gpl3)))
18326 (define-public r-xmlparsedata
18328 (name "r-xmlparsedata")
18333 (uri (cran-uri "xmlparsedata" version))
18336 "1c6bnz3ng1qw7sfip8wq3a4dn36a4d6rbja0sadn0a4pbsmk8q3n"))))
18337 (properties `((upstream-name . "xmlparsedata")))
18338 (build-system r-build-system)
18339 (home-page "https://github.com/r-lib/xmlparsedata#readme")
18340 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
18342 "This package provides tools to convert the output of
18343 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
18344 @code{XPath}, and is easier to manipulate in general.")
18345 (license license:expat)))
18347 (define-public r-cyclocomp
18349 (name "r-cyclocomp")
18354 (uri (cran-uri "cyclocomp" version))
18357 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
18358 (properties `((upstream-name . "cyclocomp")))
18359 (build-system r-build-system)
18361 (list r-callr r-crayon r-desc r-remotes r-withr))
18362 (home-page "https://github.com/MangoTheCat/cyclocomp")
18363 (synopsis "Cyclomatic complexity of R code")
18365 "Cyclomatic complexity is a software metric, used to indicate the
18366 complexity of a program. It is a quantitative measure of the number of
18367 linearly independent paths through a program's source code. This package
18368 provides tools to compute this metric.")
18369 (license license:expat)))
18371 (define-public r-lintr
18378 (uri (cran-uri "lintr" version))
18381 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
18382 (properties `((upstream-name . "lintr")))
18383 (build-system r-build-system)
18397 (home-page "https://github.com/jimhester/lintr")
18398 (synopsis "Linter for R code")
18399 (description "This package checks adherence to a given style, syntax
18400 errors and possible semantic issues. It supports on the fly checking of R
18401 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
18402 (license license:expat)))
18404 (define-public r-sctransform
18406 (name "r-sctransform")
18411 (uri (cran-uri "sctransform" version))
18414 "1p3m6i28nlxh6r609syn88cwlbdpl3dw44dy3gsijk2ibq20mfsx"))))
18415 (build-system r-build-system)
18427 (home-page "https://github.com/ChristophH/sctransform")
18428 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
18430 "This package provides a normalization method for single-cell UMI count
18431 data using a variance stabilizing transformation. The transformation is based
18432 on a negative binomial regression model with regularized parameters. As part
18433 of the same regression framework, this package also provides functions for
18434 batch correction, and data correction.")
18435 (license license:gpl3)))
18437 (define-public r-styler
18444 (uri (cran-uri "styler" version))
18447 "0p7p2mh4f469drfn5z4wc4xrg06mpnm9wkw76fghclf8m9vcqbx6"))))
18448 (build-system r-build-system)
18451 (modify-phases %standard-phases
18452 (add-after 'unpack 'set-HOME
18453 (lambda _ (setenv "HOME" "/tmp"))))))
18469 (home-page "https://github.com/r-lib/styler")
18470 (synopsis "Non-invasive pretty printing of R code")
18472 "This is a package for pretty-printing R code without changing the user's
18473 formatting intent.")
18474 (license license:gpl3)))
18476 (define-public r-scrime
18483 (uri (cran-uri "scrime" version))
18486 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
18487 (build-system r-build-system)
18488 (home-page "https://cran.r-project.org/web/packages/scrime/")
18489 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
18491 "This package provides tools for the analysis of high-dimensional data
18492 developed/implemented at the group \"Statistical Complexity Reduction In
18493 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
18494 the functions can also be applied to other types of categorical data.")
18495 (license license:gpl2)))
18497 (define-public r-pbmcapply
18499 (name "r-pbmcapply")
18504 (uri (cran-uri "pbmcapply" version))
18507 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
18508 (build-system r-build-system)
18509 (home-page "https://github.com/kvnkuang/pbmcapply")
18510 (synopsis "Track the progress of apply procedures with a progress bar")
18512 "This light-weight package helps you track and visualize the progress of
18513 parallel versions of vectorized R functions of the @code{mc*apply} family.")
18514 (license license:expat)))
18516 (define-public r-blme
18523 (uri (cran-uri "blme" version))
18526 "0413j7gwr5yj14jamkizj55q7xii1a0kgazzj0ilqn2ascclz6k7"))))
18527 (build-system r-build-system)
18528 (propagated-inputs (list r-lme4))
18529 (home-page "https://github.com/vdorie/blme")
18530 (synopsis "Bayesian linear mixed-effects models")
18532 "This package provides tools for maximum a posteriori estimation for
18533 linear and generalized linear mixed-effects models in a Bayesian setting. It
18534 extends the lme4 package.")
18535 (license license:gpl2+)))
18537 (define-public r-batchtools
18539 (name "r-batchtools")
18544 (uri (cran-uri "batchtools" version))
18547 "0d2xy77hkzhcnyz8zxcv98i80fx6ripjw4rvyx4ww1d0vjjgqf52"))))
18548 (build-system r-build-system)
18564 (home-page "https://github.com/mllg/batchtools")
18565 (synopsis "Tools for computation on batch systems")
18567 "As a successor of the packages BatchJobs and BatchExperiments, this
18568 package provides a parallel implementation of the Map function for high
18569 performance computing systems managed by various schedulers. A multicore and
18570 socket mode allow the parallelization on a local machines, and multiple
18571 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
18572 the package provides an abstraction mechanism to define large-scale computer
18573 experiments in a well-organized and reproducible way.")
18574 (license license:lgpl3)))
18576 (define-public r-clue
18583 (uri (cran-uri "clue" version))
18586 "0apgpdnn74mqg2bnr8yjyxgyvdl411h0r2b1r2xd67k21pyxs8bd"))))
18587 (build-system r-build-system)
18588 (propagated-inputs (list r-cluster))
18589 (home-page "https://cran.r-project.org/web/packages/clue/")
18590 (synopsis "Tools for analyzing cluster ensembles")
18591 (description "Cluster ensembles are collections of individual solutions to
18592 a given clustering problem which are useful or necessary to consider in a wide
18593 range of applications. This R package provides an extensible computational
18594 environment for creating and analyzing cluster ensembles, with basic data
18595 structures for representing partitions and hierarchies, and facilities for
18596 computing on them, including methods for measuring proximity and obtaining
18597 consensus and secondary clusterings.")
18598 (license license:gpl2)))
18600 (define-public r-sitmo
18607 (uri (cran-uri "sitmo" version))
18610 "1hm89zi38ldgbskyx1cn7gm87yqy7zrxli8q05a36y1ndvazi3j4"))))
18611 (build-system r-build-system)
18612 (propagated-inputs (list r-rcpp))
18615 (home-page "https://github.com/coatless/sitmo/")
18616 (synopsis "Parallel pseudo random number generator header files")
18618 "This package provides two high quality and fast PPRNGs that may be used
18619 in an OpenMP parallel environment. In addition, there is a generator for one
18620 dimensional low-discrepancy sequence.")
18621 (license license:expat)))
18623 (define-public r-dqrng
18630 (uri (cran-uri "dqrng" version))
18633 "1fwsldqcri2lccna4icbmmlqic3w4xyjm7rn0xmikrsw4kzapvjb"))))
18634 (build-system r-build-system)
18636 (list r-bh r-rcpp r-sitmo))
18639 (home-page "https://www.daqana.org/dqrng")
18640 (synopsis "Fast pseudo random number generators")
18642 "Several fast random number generators are provided as C++ header-only
18643 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
18644 Additionally, fast functions for generating random numbers according to a
18645 uniform, normal and exponential distribution are included. The latter two use
18646 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
18647 functions are exported to R and as a C++ interface and are enabled for use
18648 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
18649 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
18650 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
18651 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
18652 ;; whole is distributed under the terms of the AGPL 3.
18653 (license license:agpl3)))
18655 (define-public r-ingredients
18657 (name "r-ingredients")
18662 (uri (cran-uri "ingredients" version))
18665 "11bv4l4fn9kr7y2nfzrwnaya8fi9w3nwcm9vzlqb7dva83rkqbsc"))))
18666 (properties `((upstream-name . "ingredients")))
18667 (build-system r-build-system)
18669 (list r-ggplot2 r-gridextra r-scales))
18670 (native-inputs (list r-knitr))
18671 (home-page "https://ModelOriented.github.io/ingredients/")
18672 (synopsis "Effects and importances of model ingredients")
18674 "This is a collection of tools for assessment of feature importance and
18675 feature effects. Key functions are:
18678 @item @code{feature_importance()} for assessment of global level feature
18680 @item @code{ceteris_paribus()} for calculation of the what-if plots,
18681 @item @code{partial_dependence()} for partial dependence plots,
18682 @item @code{conditional_dependence()} for conditional dependence plots,
18683 @item @code{accumulated_dependence()} for accumulated local effects plots,
18684 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
18685 aggregation of ceteris paribus profiles,
18686 @item generic @code{print()} and @code{plot()} for better usability of
18687 selected explainers,
18688 @item generic @code{plotD3()} for interactive, D3 based explanations, and
18689 @item generic @code{describe()} for explanations in natural language.
18691 (license license:gpl3)))
18693 (define-public r-ibreakdown
18695 (name "r-ibreakdown")
18700 (uri (cran-uri "iBreakDown" version))
18703 "00jzrndb3ahsv6ihp2pvs732n9cc944m83vdinrl9v1pxd82prkh"))))
18704 (properties `((upstream-name . "iBreakDown")))
18705 (build-system r-build-system)
18706 (propagated-inputs (list r-ggplot2))
18707 (native-inputs (list r-knitr))
18708 (home-page "https://ModelOriented.github.io/iBreakDown/")
18709 (synopsis "Model agnostic instance level variable attributions")
18711 "This package provides a model agnostic tool for decomposition of
18712 predictions from black boxes. It supports additive attributions and
18713 attributions with interactions. The Break Down Table shows contributions of
18714 every variable to a final prediction. The Break Down Plot presents variable
18715 contributions in a concise graphical way. This package works for
18716 classification and regression models.")
18717 (license license:gpl3)))
18719 (define-public r-dae
18726 (uri (cran-uri "dae" version))
18729 "0mq94ah21p1glvsbvdmi2p7nlgz1bvq7w3rz2z3mdqq18kz6nkjw"))))
18730 (build-system r-build-system)
18732 (list r-ggplot2 r-plyr))
18734 (list r-r-rsp)) ; vignette builder
18735 (home-page "http://chris.brien.name")
18736 (synopsis "Functions useful in the design and ANOVA of experiments")
18738 "This package provides functions useful in the design and ANOVA of
18739 experiments. The content falls into the following groupings:
18743 @item factor manipulation functions,
18744 @item design functions,
18745 @item ANOVA functions,
18746 @item matrix functions,
18747 @item projector and canonical efficiency functions, and
18748 @item miscellaneous functions.
18751 There is a vignette called @code{DesignNotes} describing how to use the design
18752 functions for randomizing and assessing designs. The ANOVA functions
18753 facilitate the extraction of information when the @code{Error} function has
18754 been used in the call to @code{aov}.")
18755 (license license:gpl2)))
18757 (define-public r-dalex
18764 (uri (cran-uri "DALEX" version))
18767 "0x8rcl3p1h1dpzgsfnalfjhvv345gg5v0z8dxqwrk6i32xk5wmzb"))))
18768 (properties `((upstream-name . "DALEX")))
18769 (build-system r-build-system)
18771 (list r-ggplot2 r-ibreakdown r-ingredients))
18772 (home-page "https://pbiecek.github.io/DALEX/")
18773 (synopsis "Descriptive machine learning explanations")
18775 "Machine Learning models are widely used and have various applications in
18776 classification or regression. Models created with boosting, bagging, stacking
18777 or similar techniques are often used due to their high performance, but such
18778 black-box models usually lack interpretability. The DALEX package contains
18779 various explainers that help to understand the link between input variables
18780 and model output.")
18781 ;; Any version of the GPL
18782 (license license:gpl3+)))
18784 (define-public r-enrichr
18791 (uri (cran-uri "enrichR" version))
18794 "0i3kfq4fkmx47n61zj5f87iv8ci6gbgy90a7s8dy9zbndzvbgya3"))))
18795 (properties `((upstream-name . "enrichR")))
18796 (build-system r-build-system)
18798 (list r-ggplot2 r-httr r-rjson))
18801 (home-page "https://cran.r-project.org/web/packages/enrichR/")
18802 (synopsis "R Interface to Enrichr database for analyzing gene sets")
18804 "This package provides an R interface to all Enrichr databases, a
18805 web-based tool for analyzing gene sets and returns any enrichment of common
18806 annotated biological functions.")
18807 (license license:gpl2+)))
18809 (define-public r-plot3d
18816 (uri (cran-uri "plot3D" version))
18819 "1h59zlsyzbjylaziwavppl9bjmnba4iiq34772y3dys6fqclajnh"))))
18820 (properties `((upstream-name . "plot3D")))
18821 (build-system r-build-system)
18822 (propagated-inputs (list r-misc3d))
18823 (home-page "https://cran.r-project.org/web/packages/plot3D")
18824 (synopsis "Plot multi-dimensional data")
18826 "This package provides functions for viewing 2D and 3D data, including
18827 perspective plots, slice plots, surface plots, scatter plots, etc. It
18828 includes data sets from oceanography.")
18829 (license license:gpl3+)))
18831 (define-public r-ggfortify
18833 (name "r-ggfortify")
18838 (uri (cran-uri "ggfortify" version))
18841 "0qls8pyndrlwx75wzlc0xmk04qq263d7065r3d6kvay7haa4nm40"))))
18842 (build-system r-build-system)
18853 (home-page "https://github.com/sinhrks/ggfortify")
18854 (synopsis "Data visualization tools for statistical analysis results")
18856 "This package provides unified plotting tools for statistics commonly
18857 used, such as GLM, time series, PCA families, clustering and survival
18858 analysis. The package offers a single plotting interface for these analysis
18859 results and plots in a unified style using the @code{ggplot2} package.")
18860 (license license:gpl2)))
18862 (define-public r-refmanager
18864 (name "r-refmanager")
18869 (uri (cran-uri "RefManageR" version))
18872 "1spzdp5ni52dybcaxqnhwdphh27wjyrsfy4hsxsplpg9rqwfqfps"))))
18873 (properties `((upstream-name . "RefManageR")))
18874 (build-system r-build-system)
18884 (home-page "https://github.com/ropensci/RefManageR/")
18885 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
18887 "This package provides tools for importing and working with bibliographic
18888 references. It greatly enhances the @code{bibentry} class by providing a
18889 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
18890 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
18891 by various formats for name lists (author by last names, translator by full
18892 names, etc.). Entries can be updated, combined, sorted, printed in a number
18893 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
18894 into R and converted to @code{BibEntry} objects.")
18895 ;; Any of these licenses may be picked.
18896 (license (list license:gpl2 license:gpl3 license:bsd-3))))
18898 (define-public r-citr
18905 (uri (cran-uri "citr" version))
18908 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
18909 (build-system r-build-system)
18920 (home-page "https://github.com/crsh/citr")
18921 (synopsis "RStudio add-in to insert Markdown citations")
18923 "This package provides functions and an RStudio add-in that search a
18924 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
18925 the current document.")
18926 (license license:expat)))
18928 (define-public r-xgboost
18931 (version "1.5.0.2")
18935 (uri (cran-uri "xgboost" version))
18938 "04xbgrrb3aq067hrivslq5f2rd1v95yfv7lkj596ijyqi6ibjl27"))))
18939 (build-system r-build-system)
18941 (list r-data-table r-jsonlite r-matrix))
18944 (home-page "https://github.com/dmlc/xgboost")
18945 (synopsis "Extreme gradient boosting")
18947 "This package provides an R interface to Extreme Gradient Boosting, which
18948 is an efficient implementation of the gradient boosting framework from Chen
18949 and Guestrin (2016). The package includes efficient linear model solver and
18950 tree learning algorithms. The package can automatically do parallel
18951 computation on a single machine. It supports various objective functions,
18952 including regression, classification and ranking. The package is made to be
18953 extensible, so that users are also allowed to define their own objectives
18955 (license license:asl2.0)))
18957 (define-public r-umap
18960 (version "0.2.7.0")
18964 (uri (cran-uri "umap" version))
18967 "191vpy84s0bar06y9z1qx43x2kc4qp7lmrcmd0cvz2pnzq722jab"))))
18968 (build-system r-build-system)
18970 (list r-openssl r-rcpp r-reticulate r-rspectra))
18973 (home-page "https://github.com/tkonopka/umap")
18974 (synopsis "Uniform manifold approximation and projection")
18976 "Uniform manifold approximation and projection is a technique for
18977 dimension reduction. This package provides an interface to the UMAP algorithm
18978 in R, including a translation of the original algorithm into R.")
18979 (license license:expat)))
18981 (define-public r-uwot
18988 (uri (cran-uri "uwot" version))
18991 "08vxh085wnrxgwy35ksb4cr7ccjvd98pyr2zlgarqryfgc1bdqbf"))))
18992 (build-system r-build-system)
19002 (home-page "https://github.com/jlmelville/uwot")
19003 (synopsis "Uniform manifold approximation and projection")
19005 "This package provides an implementation of the Uniform Manifold
19006 Approximation and Projection dimensionality reduction by McInnes et
19007 al. (2018). It also provides means to transform new data and to carry out
19008 supervised dimensionality reduction. An implementation of the related
19009 LargeVis method of Tang et al. (2016) is also provided.")
19010 (license license:gpl3)))
19012 (define-public r-kableextra
19014 (name "r-kableextra")
19019 (uri (cran-uri "kableExtra" version))
19022 "1c5vzy95cbz36jwyssr927qicrayifinv861rvnmg4nghb1gl7q9"))))
19023 (properties `((upstream-name . "kableExtra")))
19024 (build-system r-build-system)
19042 (home-page "https://haozhu233.github.io/kableExtra/")
19043 (synopsis "Construct complex tables with pipe syntax")
19045 "Build complex HTML or LaTeX tables using @code{kable()} from
19046 @code{knitr} and the piping syntax from @code{magrittr}. The function
19047 @code{kable()} is a light weight table generator coming from @code{knitr}.
19048 This package simplifies the way to manipulate the HTML or LaTeX codes
19049 generated by @code{kable()} and allows users to construct complex tables and
19050 customize styles using a readable syntax.")
19051 (license license:expat)))
19053 (define-public r-glasso
19060 (uri (cran-uri "glasso" version))
19062 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
19063 (build-system r-build-system)
19064 (native-inputs (list gfortran))
19065 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
19066 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
19068 "This is a package for estimation of a sparse inverse covariance matrix
19069 using a lasso (L1) penalty. Facilities are provided for estimates along a
19070 path of values for the regularization parameter.")
19071 (license license:gpl2)))
19073 (define-public r-rhpcblasctl
19075 (name "r-rhpcblasctl")
19076 (version "0.21-247.1")
19080 (uri (cran-uri "RhpcBLASctl" version))
19083 "0scpr6jq25xx7wmqyc380ann4h536ll0g7wblikk25yqvpamzrav"))))
19084 (properties `((upstream-name . "RhpcBLASctl")))
19085 (build-system r-build-system)
19086 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
19087 (synopsis "Control the number of threads on BLAS")
19089 "This package allows you to control the number of threads the BLAS
19090 library uses. It is also possible to control the number of threads in
19092 (license license:agpl3+)))
19094 (define-public r-lda
19101 (uri (cran-uri "lda" version))
19104 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
19105 (build-system r-build-system)
19106 (home-page "https://cran.r-project.org/web/packages/lda/")
19107 (synopsis "Collapsed Gibbs sampling methods for topic models")
19109 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
19110 related models. This includes (but is not limited to) sLDA, corrLDA, and the
19111 mixed-membership stochastic blockmodel. Inference for all of these models is
19112 implemented via a fast collapsed Gibbs sampler written in C. Utility
19113 functions for reading/writing data typically used in topic models, as well as
19114 tools for examining posterior distributions are also included.")
19115 ;; Any version of the LGPL
19116 (license license:lgpl3+)))
19118 (define-public r-rann-l1
19125 (uri (cran-uri "RANN.L1" version))
19128 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
19129 (properties `((upstream-name . "RANN.L1")))
19130 (build-system r-build-system)
19131 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
19132 (synopsis "Fast nearest neighbour search using L1 metric")
19134 "This package provides tools to find the k nearest neighbours for every
19135 point in a given dataset in O(N log N) time using Arya and Mount's ANN
19136 library. There is support for approximate as well as exact searches, fixed
19137 radius searches and @code{bd} as well as @code{kd} trees. The distance is
19138 computed using the L1 (Manhattan, taxicab) metric.")
19139 (license license:gpl3+)))
19141 (define-public r-leiden
19148 (uri (cran-uri "leiden" version))
19151 "03gaxpcab3a1av5lk8r5ll1s858gvyx5ndknci1sia96w1v44xc1"))))
19152 (properties `((upstream-name . "leiden")))
19153 (build-system r-build-system)
19155 (list r-igraph r-matrix r-reticulate))
19158 (home-page "https://github.com/TomKellyGenetics/leiden")
19159 (synopsis "R implementation of Leiden clustering algorithm")
19161 "This package implements the Python @code{leidenalg} module to be called
19162 in R. It enables clustering using the Leiden algorithm for partitioning a
19163 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
19164 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
19165 (license license:gpl3)))
19167 (define-public r-patchwork
19169 (name "r-patchwork")
19174 (uri (cran-uri "patchwork" version))
19177 "10glgkf58lcykcwda1hj6xdps02m3i247qynk6s2jmwljagps3fg"))))
19178 (build-system r-build-system)
19180 (list r-ggplot2 r-gtable))
19183 (home-page "https://github.com/thomasp85/patchwork")
19184 (synopsis "Compose ggplot2 plots")
19186 "The @code{ggplot2} package provides a strong API for sequentially
19187 building up a plot, but does not concern itself with composition of multiple
19188 plots. Patchwork is a package that expands the API to allow for arbitrarily
19189 complex composition of plots by providing mathematical operators for combining
19191 (license license:expat)))
19193 (define-public r-liger
19200 (uri (git-reference
19201 (url "https://github.com/MacoskoLab/liger")
19202 (commit (string-append "v" version))))
19203 (file-name (git-file-name name version))
19206 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
19207 (modules '((guix build utils)))
19210 (delete-file "inst/java/ModularityOptimizer.jar")
19212 (build-system r-build-system)
19215 (modify-phases %standard-phases
19216 (add-after 'unpack 'build-java-part
19217 (lambda* (#:key inputs #:allow-other-keys)
19218 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
19219 (for-each (lambda (file) (invoke "javac" file))
19220 (find-files "." "\\.java$"))
19221 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
19222 (find-files "." "\\.class$"))
19246 `(("jdk" ,icedtea "jdk")
19247 ;; See https://github.com/MacoskoLab/liger/issues/96
19248 ;; The optimizer is released under the Expat license.
19252 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
19255 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
19257 ("r-knitr" ,r-knitr))) ; for vignettes
19258 (home-page "https://github.com/MacoskoLab/liger")
19259 (synopsis "Integrate and analyze multiple single-cell datasets")
19261 "LIGER is a package for integrating and analyzing multiple single-cell
19262 datasets, developed and maintained by the Macosko lab. It relies on
19263 integrative non-negative matrix factorization to identify shared and
19264 dataset-specific factors.")
19265 (license license:gpl3)))
19267 (define-public r-harmony
19274 (uri (git-reference
19275 (url "https://github.com/immunogenomics/harmony")
19277 (file-name (git-file-name name version))
19280 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
19281 (modules '((guix build utils)))
19284 (for-each delete-file '("config.status" "configure"))
19286 (build-system r-build-system)
19301 (home-page "https://github.com/immunogenomics/harmony")
19302 (synopsis "Integration of single cell sequencing data")
19304 "This package provides an implementation of the Harmony algorithm for
19305 single cell integration, described in Korsunsky et al
19306 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
19307 function and interfaces to external frameworks.")
19308 (license license:gpl3)))
19310 (define-public r-covr
19317 (uri (cran-uri "covr" version))
19319 (base32 "0v5cv3cw2kpdr6wxmkbd3wclavr17zipypdcb10hhmpa4cvgqk55"))))
19320 (properties `((upstream-name . "covr")))
19321 (build-system r-build-system)
19331 (list r-knitr)) ; for vignettes
19332 (home-page "https://github.com/r-lib/covr")
19333 (synopsis "Test coverage for R packages")
19335 "Thisp package enables you to track and report code coverage for your
19336 package and (optionally) upload the results to a coverage service. Code
19337 coverage is a measure of the amount of code being exercised by a set of tests.
19338 It is an indirect measure of test quality and completeness. This package is
19339 compatible with any testing methodology or framework and tracks coverage of
19340 both R code and compiled C/C++/FORTRAN code.")
19341 (license license:gpl3)))
19343 (define-public r-systemfonts
19345 (name "r-systemfonts")
19350 (uri (cran-uri "systemfonts" version))
19353 "1fmv1ni77ncz6rrm4iv8a7l6pbqnk2ri0yzad2bs943gxbarjz34"))))
19354 (properties `((upstream-name . "systemfonts")))
19355 (build-system r-build-system)
19359 `(("fontconfig" ,fontconfig)
19362 (list pkg-config r-knitr))
19363 (home-page "https://github.com/r-lib/systemfonts")
19364 (synopsis "System native font finding")
19366 "This package provides system native access to the font catalogue. As
19367 font handling varies between systems it is difficult to correctly locate
19368 installed fonts across different operating systems. The 'systemfonts' package
19369 provides bindings to the native libraries for finding font files that can then
19370 be used further by e.g. graphic devices.")
19371 (license license:expat)))
19373 (define-public r-graphlayouts
19375 (name "r-graphlayouts")
19380 (uri (cran-uri "graphlayouts" version))
19383 "0vncg1pfnwrfkjfwz5k86b0ir8vnjkbyd0kzpbgb0cpkdz7987pc"))))
19384 (properties `((upstream-name . "graphlayouts")))
19385 (build-system r-build-system)
19387 (list r-igraph r-rcpp r-rcpparmadillo))
19388 (home-page "https://github.com/schochastics/graphlayouts")
19389 (synopsis "Additional layout algorithms for network visualizations")
19391 "This package provides several layout algorithms to visualize networks
19392 which are not part of the igraph library. Most are based on the concept of
19393 stress majorization by Gansner et al. (2004)
19394 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
19395 emphasize hidden group structures in networks or focus on specific nodes.")
19396 (license license:expat)))
19398 (define-public r-terra
19405 (uri (cran-uri "terra" version))
19408 "0c4nx113sfympixy5rkvgzc7pprcfflnadkbwhcpzjlky8gmmsk4"))))
19409 (properties `((upstream-name . "terra")))
19410 (build-system r-build-system)
19415 sqlite ; needed for proj
19421 (home-page "https://rspatial.org/terra")
19422 (synopsis "Spatial data analysis")
19424 "This package provides methods for spatial data analysis, especially
19425 raster data. The included methods allow for low-level data manipulation as
19426 well as high-level global, local, zonal, and focal computation. The predict
19427 and interpolate methods facilitate the use of regression type (interpolation,
19428 machine learning) models for spatial prediction. Processing of very large
19429 files is supported.")
19430 (license license:gpl3+)))
19432 (define-public r-tidygraph
19434 (name "r-tidygraph")
19439 (uri (cran-uri "tidygraph" version))
19442 "17qjns33zcj82jcsl7bn7i4zxcm7ric50zyf7agi0i01zi16qz85"))))
19443 (properties `((upstream-name . "tidygraph")))
19444 (build-system r-build-system)
19455 (home-page "https://github.com/thomasp85/tidygraph")
19456 (synopsis "Tidy API for graph manipulation")
19458 "This package provides a graph implementation that can be thought of as
19459 two tidy data frames describing node and edge data respectively. It provides
19460 an approach to manipulate these two virtual data frames using the API defined
19461 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
19462 common graph algorithms.")
19463 (license license:expat)))
19465 (define-public r-soupx
19466 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
19470 (version (git-version "0.3.1" revision commit))
19474 (uri (git-reference
19475 (url "https://github.com/constantAmateur/SoupX")
19477 (file-name (git-file-name name version))
19480 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
19481 (properties `((upstream-name . "SoupX")))
19482 (build-system r-build-system)
19484 (list r-ggplot2 r-matrix r-seurat))
19485 (home-page "https://github.com/constantAmateur/SoupX")
19486 (synopsis "Single cell mRNA Soup eXterminator")
19488 "This package provides a package for quantifying, profiling and
19489 removing cell free mRNA contamination (the \"soup\") from droplet based single
19490 cell RNA-seq experiments.")
19491 (license license:gpl2))))
19493 (define-public r-assertr
19500 (uri (cran-uri "assertr" version))
19503 "00764vv86r3bn4r85in4w637harffyw605fgq0dj6mrbrwcfb650"))))
19504 (build-system r-build-system)
19506 (list r-dplyr r-mass r-rlang))
19508 (list r-knitr)) ; needed for vignette
19509 (home-page "https://github.com/ropensci/assertr")
19510 (synopsis "Assertive programming for R analysis pipelines")
19512 "This package provides functionality to assert conditions that have to be
19513 met so that errors in data used in analysis pipelines can fail quickly. It is
19514 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
19516 (license license:expat)))
19518 (define-public r-parameters
19520 (name "r-parameters")
19525 (uri (cran-uri "parameters" version))
19528 "0f06bwlc1g0xdyhdqzx8plfx1jwk8a9j4lcbl91wjsil8wja0bkl"))))
19529 (properties `((upstream-name . "parameters")))
19530 (build-system r-build-system)
19532 (list r-bayestestr r-datawizard r-insight))
19535 (home-page "https://cran.r-project.org/web/packages/parameters")
19536 (synopsis "Processing of model parameters")
19538 "This package provides utilities for processing the parameters of various
19539 statistical models. Beyond computing p values, CIs, and other indices for a
19540 wide variety of models, this package implements features like standardization
19541 or bootstrapping of parameters and models, feature reduction (feature
19542 extraction and variable selection) as well as conversion between indices of
19544 (license license:gpl3)))
19546 (define-public r-rgdal
19553 (uri (cran-uri "rgdal" version))
19555 (base32 "0mjpxs2dvbngbchlb0kfs0jcac7v88slwxmka81ds92lggnmb9b2"))))
19556 (properties `((upstream-name . "rgdal")))
19557 (build-system r-build-system)
19559 (list gdal proj zlib))
19563 (list pkg-config r-knitr))
19564 (home-page "http://rgdal.r-forge.r-project.org")
19565 (synopsis "Bindings for the Geospatial Data Abstraction Library")
19567 "This package provides bindings to the Geospatial Data Abstraction
19568 Library (GDAL) and access to projection/transformation operations from the
19570 (license license:gpl2+)))
19572 (define-public r-insol
19579 (uri (cran-uri "insol" version))
19582 "166kgxgzbh55y2qqya6c2si22x0v7asi70im054g6xxwc5187kh3"))))
19583 (properties `((upstream-name . "insol")))
19584 (build-system r-build-system)
19589 (home-page "https://meteoexploration.com/R/insol/index.html")
19590 (synopsis "Tools for calculating solar radiation")
19592 "This package provides functions to compute insolation on tilted
19593 surfaces, computes atmospheric transmittance and related parameters such as:
19594 Earth radius vector, declination, sunset and sunrise, daylength, equation of
19595 time, vector in the direction of the sun, vector normal to surface, and some
19596 atmospheric physics.")
19597 (license license:gpl2+)))
19599 (define-public r-lifecycle
19601 (name "r-lifecycle")
19606 (uri (cran-uri "lifecycle" version))
19609 "183v1z1h037pvsgrj6vakpwhnhsr29hsw8p16k59dgpi00f6x9qx"))))
19610 (properties `((upstream-name . "lifecycle")))
19611 (build-system r-build-system)
19613 (list r-glue r-rlang))
19615 (list r-knitr)) ; for vignettes
19616 (home-page "https://github.com/r-lib/lifecycle")
19617 (synopsis "Manage the life cycle of your package functions")
19619 "Manage the life cycle of your exported functions with shared
19620 conventions, documentation badges, and non-invasive deprecation warnings. The
19621 lifecycle package defines four development stages (experimental, maturing,
19622 stable, and questioning) and three deprecation stages (soft-deprecated,
19623 deprecated, and defunct). It makes it easy to insert badges corresponding to
19624 these stages in your documentation. Usage of deprecated functions are
19625 signalled with increasing levels of non-invasive verbosity.")
19626 (license license:gpl3)))
19628 (define-public r-assertable
19630 (name "r-assertable")
19635 (uri (cran-uri "assertable" version))
19638 "1cciil1nzxd8gbj49w99jiv077lbpb59vx7bmb4p218aj2h5hqq4"))))
19639 (build-system r-build-system)
19641 (list r-data-table))
19644 (home-page "https://cran.r-project.org/web/packages/assertable/")
19645 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
19646 (description "This package provides simple, flexible assertions on
19647 data.frame or data.table objects with verbose output for vetting. While other
19648 assertion packages apply towards more general use-cases, @code{assertable} is
19649 tailored towards tabular data. It includes functions to check variable names
19650 and values, whether the dataset contains all combinations of a given set of
19651 unique identifiers, and whether it is a certain length. In addition,
19652 @code{assertable} includes utility functions to check the existence of target
19653 files and to efficiently import multiple tabular data files into one
19655 (license license:gpl3)))
19657 (define-public r-quadprog
19659 (name "r-quadprog")
19664 (uri (cran-uri "quadprog" version))
19666 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
19667 (build-system r-build-system)
19670 (home-page "https://cran.r-project.org/web/packages/quadprog")
19671 (synopsis "Functions to solve quadratic programming problems")
19673 "This package contains routines and documentation for solving quadratic
19674 programming problems.")
19675 (license license:gpl3+)))
19677 (define-public r-desolve
19684 (uri (cran-uri "deSolve" version))
19686 (base32 "0j7mmg1mimdpql8f4i9dn920ciyyq80a5qnc4fq5xn5lyrx5vxir"))))
19687 (properties `((upstream-name . "deSolve")))
19688 (build-system r-build-system)
19691 (home-page "https://desolve.r-forge.r-project.org/")
19692 (synopsis "Solvers for initial value problems of differential equations")
19693 (description "This package provides functions that solve initial value
19694 problems of a system of first-order @dfn{ordinary differential
19695 equations} (ODE), of @dfn{partial differential equations} (PDE), of
19696 @dfn{differential algebraic equations} (DAE), and of delay differential
19697 equations. The functions provide an interface to the FORTRAN functions
19698 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
19699 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
19700 C-implementation of solvers of the Runge-Kutta family with fixed or variable
19701 time steps. The package contains routines designed for solving ODEs resulting
19702 from 1-D, 2-D and 3-D partial differential equations that have been converted
19703 to ODEs by numerical differencing.")
19704 (license license:gpl2+)))
19706 (define-public r-pracma
19712 (uri (cran-uri "pracma" version))
19714 (base32 "0g5r5ir5k43ba0ngnsanp108k479l2dnsjd5w6idk1d34ivqs7yg"))))
19715 (build-system r-build-system)
19716 (home-page "https://cran.r-project.org/web/packages/pracma/")
19717 (synopsis "Practical numerical math functions")
19718 (description "This package provides functions for numerical analysis and
19719 linear algebra, numerical optimization, differential equations, plus some
19720 special functions. It uses Matlab function names where appropriate to simplify
19722 (license license:gpl3+)))
19724 (define-public r-subplex
19731 (uri (cran-uri "subplex" version))
19734 "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d"))))
19735 (build-system r-build-system)
19738 (home-page "https://cran.r-project.org/web/packages/subplex")
19739 (synopsis "Unconstrained optimization using the subplex algorithm")
19741 "This package implements the Subplex optimization algorithm.
19742 It solves unconstrained optimization problems using a simplex method on
19743 subspaces. The method is well suited for optimizing objective functions that
19744 are noisy or are discontinuous at the solution.")
19745 (license license:gpl3+)))
19747 (define-public r-txtplot
19754 (uri (cran-uri "txtplot" version))
19757 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
19758 (build-system r-build-system)
19759 (home-page "https://cran.r-project.org/web/packages/txtplot/")
19760 (synopsis "Text-based plotting")
19761 (description "This package provides functions to produce rudimentary ASCII
19762 graphics directly in the terminal window. This package provides a basic
19763 plotting function (and equivalents of curve, density, acf and barplot) as well
19764 as a boxplot function.")
19765 (license license:lgpl3+)))
19767 (define-public r-bio3d
19774 (uri (cran-uri "bio3d" version))
19777 "1jvcmpzi9knhxq5jsbhg8slm8hnlx2y8smmwwrbnbyd0rmk5fhci"))))
19778 (properties `((upstream-name . "bio3d")))
19779 (build-system r-build-system)
19780 (inputs (list zlib))
19781 (propagated-inputs (list r-rcpp))
19784 (home-page "http://thegrantlab.org/bio3d/")
19785 (synopsis "Biological structure analysis")
19787 "This package provides utilities to process, organize and explore protein
19788 structure, sequence and dynamics data. Features include the ability to read
19789 and write structure, sequence and dynamic trajectory data, perform sequence
19790 and structure database searches, data summaries, atom selection, alignment,
19791 superposition, rigid core identification, clustering, torsion analysis,
19792 distance matrix analysis, structure and sequence conservation analysis, normal
19793 mode analysis, principal component analysis of heterogeneous structure data,
19794 and correlation network analysis from normal mode and molecular dynamics data.
19795 In addition, various utility functions are provided to enable the statistical
19796 and graphical power of the R environment to work with biological sequence and
19798 (license license:gpl2+)))
19800 (define-public r-bios2cor
19802 (name "r-bios2cor")
19807 (uri (cran-uri "Bios2cor" version))
19810 "1wkj9vr33m9jilidil9jpw5rzr3pf7gkimxdvch22ks4bgkx7l1w"))))
19811 (properties `((upstream-name . "Bios2cor")))
19812 (build-system r-build-system)
19814 (list r-bigmemory r-bio3d r-circular r-igraph))
19815 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
19816 (synopsis "From biological sequences and simulations to correlation analysis")
19818 "This package provides utilities for computation and analysis of
19819 correlation/covariation in multiple sequence alignments and in side chain
19820 motions during molecular dynamics simulations. Features include the
19821 computation of correlation/covariation scores using a variety of scoring
19822 functions between either sequence positions in alignments or side chain
19823 dihedral angles in molecular dynamics simulations and utilities to analyze the
19824 correlation/covariation matrix through a variety of tools including network
19825 representation and principal components analysis. In addition, several
19826 utility functions are based on the R graphical environment to provide friendly
19827 tools for help in data interpretation.")
19828 (license license:gpl2+)))
19830 ;; This package includes minified JavaScript files. When upgrading please
19831 ;; check that there are no new minified JavaScript files.
19832 (define-public r-networkd3
19834 (name "r-networkd3")
19839 (uri (cran-uri "networkD3" version))
19842 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
19845 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
19847 (properties `((upstream-name . "networkD3")))
19848 (build-system r-build-system)
19850 `(#:modules ((guix build utils)
19851 (guix build r-build-system)
19855 (modify-phases %standard-phases
19856 (add-after 'unpack 'process-javascript
19857 (lambda* (#:key inputs #:allow-other-keys)
19858 (with-directory-excursion "inst/htmlwidgets/lib/"
19862 `((,(assoc-ref inputs "d3.v4.js")
19863 "d3-4.5.0/d3.min.js"))))
19864 (lambda (sources targets)
19865 (for-each (lambda (source target)
19866 (format #t "Processing ~a --> ~a~%"
19868 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
19869 (call-with-output-file target
19871 (dump-port minified port)))))
19872 sources targets))))
19875 `(("uglifyjs" ,node-uglify-js)
19876 ;; NOTE: Make sure that this version of d3 is still valid when
19877 ;; upgrading the package.
19881 (uri "https://d3js.org/d3.v4.js")
19884 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
19886 (list r-htmlwidgets r-igraph r-magrittr))
19887 (home-page "https://cran.r-project.org/package=networkD3")
19888 (synopsis "D3 JavaScript network graphs from R")
19890 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
19892 (license license:gpl3+)))
19894 (define-public r-aasea
19901 (uri (cran-uri "aaSEA" version))
19904 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
19905 (properties `((upstream-name . "aaSEA")))
19906 (build-system r-build-system)
19917 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
19918 (synopsis "Amino acid substitution effect analyzer")
19920 "Given a protein multiple sequence alignment, it is a daunting task to
19921 assess the effects of substitutions along sequence length. The aaSEA package
19922 is intended to help researchers to rapidly analyze property changes caused by
19923 single, multiple and correlated amino acid substitutions in proteins.")
19924 (license license:gpl3)))
19926 (define-public r-abacus
19933 (uri (cran-uri "ABACUS" version))
19936 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
19937 (properties `((upstream-name . "ABACUS")))
19938 (build-system r-build-system)
19940 (list r-ggplot2 r-shiny))
19941 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
19942 (synopsis "Apps-based activities for communicating and understanding statistics")
19944 "This package provides a set of Shiny apps for effective communication
19945 and understanding in statistics. The current version includes properties of
19946 normal distribution, properties of sampling distribution, one-sample z and t
19947 tests, two samples independent (unpaired) t test and analysis of variance.")
19948 (license license:gpl3)))
19950 (define-public r-abc-rap
19957 (uri (cran-uri "ABC.RAP" version))
19960 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
19961 (properties `((upstream-name . "ABC.RAP")))
19962 (build-system r-build-system)
19963 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
19964 (synopsis "Array-based CpG region analysis pipeline")
19966 "This package aims to identify candidate genes that are differentially
19967 methylated between cases and controls. It applies Student's t-test and delta
19968 beta analysis to identify candidate genes containing multiple CpG sites.")
19969 (license license:gpl3)))
19971 (define-public r-abcadm
19978 (uri (cran-uri "abcADM" version))
19981 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
19982 (properties `((upstream-name . "abcADM")))
19983 (build-system r-build-system)
19985 (list r-bh r-rcpp))
19986 (home-page "https://cran.r-project.org/web/packages/abcADM/")
19987 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
19989 "This package provides tools to estimate parameters of accumulated
19990 damage (load duration) models based on failure time data under a Bayesian
19991 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
19992 long-term reliability under stochastic load profiles.")
19993 (license license:gpl3)))
19995 (define-public r-rglpk
20002 (uri (cran-uri "Rglpk" version))
20005 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
20006 (properties `((upstream-name . "Rglpk")))
20007 (build-system r-build-system)
20012 (home-page "https://r-forge.r-project.org/projects/rglp/")
20013 (synopsis "R interface to the GNU Linear Programming Kit")
20015 "This package provides an R interface to the GNU Linear Programming Kit,
20016 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
20017 integer linear programming} (MILP) and other related problems.")
20019 (license (list license:gpl2 license:gpl3))))
20021 (define-public r-abcdefba
20023 (name "r-abcdefba")
20028 (uri (cran-uri "abcdeFBA" version))
20031 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
20032 (properties `((upstream-name . "abcdeFBA")))
20033 (build-system r-build-system)
20035 (list r-corrplot r-lattice r-rgl r-rglpk))
20036 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
20037 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
20039 "This package provides functions for Constraint Based Simulation using
20040 Flux Balance Analysis and informative analysis of the data generated during
20042 (license license:gpl2)))
20044 (define-public r-abcrlda
20051 (uri (cran-uri "abcrlda" version))
20054 "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks"))))
20055 (properties `((upstream-name . "abcrlda")))
20056 (build-system r-build-system)
20057 (home-page "https://ieeexplore.ieee.org/document/8720003/")
20058 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
20060 "This package offers methods to perform @dfn{asymptotically
20061 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
20062 cost-sensitive binary classification. The bias-correction is an estimate of
20063 the bias term added to regularized discriminant analysis that minimizes the
20065 (license license:gpl3)))
20067 (define-public r-abemus
20074 (uri (cran-uri "abemus" version))
20077 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
20078 (properties `((upstream-name . "abemus")))
20079 (build-system r-build-system)
20081 (list r-data-table))
20082 (home-page "https://cran.r-project.org/web/packages/abemus/")
20083 (synopsis "Adaptive base error model in ultra-deep sequencing data")
20085 "This package provides an implementation of @dfn{Adaptive Base Error
20086 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
20087 platform-specific genetic knowledge and empirical signal to readily detect and
20088 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
20089 cell free DNA} (cfDNA).")
20090 (license license:gpl3)))
20092 ;; This package includes minified JavaScript files. When upgrading please
20093 ;; check that there are no new minified JavaScript files.
20094 (define-public r-rintrojs
20096 (name "r-rintrojs")
20101 (uri (cran-uri "rintrojs" version))
20104 "00l5mk80gj3xkbf3m1kip566ic98bhd88lh0bg69ybkpk4gifpyw"))
20106 '(delete-file "inst/javascript/introjs/intro.min.js"))))
20107 (properties `((upstream-name . "rintrojs")))
20108 (build-system r-build-system)
20111 (modify-phases %standard-phases
20112 (add-after 'unpack 'process-javascript
20113 (lambda* (#:key inputs #:allow-other-keys)
20114 (with-directory-excursion "inst/javascript/introjs/"
20115 (let ((source (assoc-ref inputs "intro.js"))
20116 (target "intro.min.js"))
20117 (format #true "Processing ~a --> ~a~%"
20119 (invoke "esbuild" source "--minify"
20120 (string-append "--outfile=" target)))))))))
20122 `(("esbuild" ,esbuild)
20126 (uri "https://cdn.jsdelivr.net/npm/intro.js@3.2.1/intro.js")
20129 "0vh5n7hqqyx2pdvlqq6xadfqibcn78h5961rwhpf817kpxfzv8v7"))))))
20131 (list r-jsonlite r-shiny))
20132 (home-page "https://github.com/carlganz/rintrojs")
20133 (synopsis "Wrapper for the Intro.js library")
20135 "This package provides a wrapper for the @url{http://www.introjs.com,
20136 Intro.js} library. This package makes it easy to include step-by-step
20137 introductions, and clickable hints in a Shiny application. It supports both
20138 static introductions in the UI, and programmatic introductions from the
20140 ;; The intro.js library is licensed under Expat.
20141 (license (list license:agpl3+ license:expat))))
20143 (define-public r-sysfonts
20145 (name "r-sysfonts")
20150 (uri (cran-uri "sysfonts" version))
20153 "1fhf0x5sqx3mv72j9d0clkq1qzqiqxbxn1h808f7ccf0mb04v43y"))))
20154 (properties `((upstream-name . "sysfonts")))
20155 (build-system r-build-system)
20157 (list freetype libpng zlib))
20160 (home-page "https://github.com/yixuan/sysfonts")
20161 (synopsis "Loading fonts into R")
20163 "This is a package to simplify loading of system fonts and Google Fonts
20164 into R, in order to support other packages.")
20165 (license license:gpl2)))
20167 (define-public r-showtextdb
20169 (name "r-showtextdb")
20174 (uri (cran-uri "showtextdb" version))
20177 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2"))))
20178 (properties `((upstream-name . "showtextdb")))
20179 (build-system r-build-system)
20182 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
20183 (synopsis "Font files for the 'showtext' package")
20185 "This package provides font files that can be used by the @code{showtext}
20187 (license license:asl2.0)))
20189 (define-public r-showtext
20191 (name "r-showtext")
20196 (uri (cran-uri "showtext" version))
20199 "1gvj32wrs5q31bmg5dy6n85d0igm3jhkldhdv8kscw0pfrk89y36"))))
20200 (properties `((upstream-name . "showtext")))
20201 (build-system r-build-system)
20203 (list freetype libpng zlib))
20205 (list r-showtextdb r-sysfonts))
20207 (list pkg-config r-knitr))
20208 (home-page "https://github.com/yixuan/showtext")
20209 (synopsis "Using fonts more easily in R graphs")
20211 "This package aims to make it easy to use various types of
20212 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
20213 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
20214 will be converted into polygons or raster images, hence after the plot has
20215 been created, it no longer relies on the font files. No external software
20216 such as Ghostscript is needed to use this package.")
20217 (license license:asl2.0)))
20219 (define-public r-emojifont
20221 (name "r-emojifont")
20226 (uri (cran-uri "emojifont" version))
20229 "1hhrwilv36hd9gs1kcl2zsi6519md0h9aixjrm6lfclxvz8r6k1i"))))
20230 (properties `((upstream-name . "emojifont")))
20231 (build-system r-build-system)
20233 (list r-ggplot2 r-proto r-showtext r-sysfonts))
20236 (home-page "https://guangchuangyu.github.io/emojifont")
20237 (synopsis "Emoji and Font Awesome in R graphics")
20239 "This package enables the use of emoji and the Font Awesome glyphs in
20240 both base and ggplot2 graphics.")
20241 (license license:artistic2.0)))
20243 (define-public r-abstractr
20245 (name "r-abstractr")
20250 (uri (cran-uri "abstractr" version))
20253 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
20254 (properties `((upstream-name . "abstractr")))
20255 (build-system r-build-system)
20257 (list r-colourpicker
20264 (home-page "https://matt-kumar.shinyapps.io/portfolio")
20265 (synopsis "R-Shiny application for creating visual abstracts")
20267 "This package provides an R Shiny application to create visual abstracts
20268 for original research. A variety of user defined options and formatting are
20270 (license license:gpl3)))
20272 (define-public r-qgam
20279 (uri (cran-uri "qgam" version))
20282 "0vx2wf3rqc3j8i0870xrwxndkbgza0nnh7f0yxi8h67lfi7gws4s"))))
20283 (properties `((upstream-name . "qgam")))
20284 (build-system r-build-system)
20286 (list r-doparallel r-mgcv r-plyr r-shiny))
20287 (native-inputs (list r-knitr))
20288 (home-page "https://cran.r-project.org/web/packages/qgam/")
20289 (synopsis "Smooth additive quantile regression models")
20291 "This package provides smooth additive quantile regression models, fitted
20292 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
20293 the smoothing parameters are estimated automatically by marginal loss
20294 minimization, while the regression coefficients are estimated using either
20295 PIRLS or Newton algorithm. The learning rate is determined so that the
20296 Bayesian credible intervals of the estimated effects have approximately the
20297 correct coverage. The main function is @code{qgam()} which is similar to
20298 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
20299 regression models.")
20300 (license license:gpl2+)))
20302 (define-public r-abtest
20309 (uri (cran-uri "abtest" version))
20312 "1ak0m4jd1grriwg4pn3aqf1468qma6rjn5kqjh8izx7zl29jd07v"))))
20313 (properties `((upstream-name . "abtest")))
20314 (build-system r-build-system)
20324 (home-page "https://cran.r-project.org/web/packages/abtest/")
20325 (synopsis "Bayesian A/B testing")
20327 "This package provides functions for Bayesian A/B testing including prior
20328 elicitation options based on Kass and Vaidyanathan (1992)
20329 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
20330 (license license:gpl2+)))
20332 (define-public r-reldist
20339 (uri (cran-uri "reldist" version))
20342 "09vips7spcz0fahrpy0bl15hk43zgnq74h189hmygyi41l95aywa"))))
20343 (properties `((upstream-name . "reldist")))
20344 (build-system r-build-system)
20346 (list r-hmisc r-mgcv))
20347 (home-page "http://www.stat.ucla.edu/~handcock/RelDist")
20348 (synopsis "Relative distribution methods")
20350 "This package provides tools for the comparison of distributions. This
20351 includes nonparametric estimation of the relative distribution PDF and CDF and
20352 numerical summaries as described in \"Relative Distribution Methods in the
20353 Social Sciences\" by Mark S. Handcock and Martina Morris, Springer-Verlag,
20354 1999, Springer-Verlag, ISBN 0387987789.")
20355 ;; See also https://cran.r-project.org/web/packages/reldist/LICENSE for
20356 ;; attribution requirements.
20357 (license license:gpl3)))
20359 (define-public r-accept
20366 (uri (cran-uri "accept" version))
20369 "0qn4lm6bk0z2iijwsfbymx1c9y39988fw124ncgmlrgw5kv80b7x"))))
20370 (properties `((upstream-name . "accept")))
20371 (build-system r-build-system)
20373 (list r-dplyr r-reldist))
20374 (home-page "https://cran.r-project.org/web/packages/accept/")
20375 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
20377 "This package allows clinicians to predict the rate and severity of
20378 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
20379 Disease} (COPD) patients, based on the clinical prediction model published in
20380 Adibi et al. (2019) @url{doi:10.1101/651901}.")
20381 (license license:gpl3)))
20383 (define-public r-smpracticals
20385 (name "r-smpracticals")
20390 (uri (cran-uri "SMPracticals" version))
20393 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
20394 (properties `((upstream-name . "SMPracticals")))
20395 (build-system r-build-system)
20397 (list r-ellipse r-mass r-nlme r-survival))
20398 (home-page "http://statwww.epfl.ch/davison/SM/")
20399 (synopsis "Practicals for use with Davison (2003) Statistical Models")
20401 "This package contains the datasets and a few functions for use with the
20402 practicals outlined in Appendix A of the book Statistical Models (Davison,
20403 2003, Cambridge University Press). The practicals themselves can be found at
20404 @url{http://statwww.epfl.ch/davison/SM/}.")
20405 (license license:gpl2+)))
20407 (define-public r-fgui
20414 (uri (cran-uri "fgui" version))
20417 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
20418 (properties `((upstream-name . "fgui")))
20419 (build-system r-build-system)
20421 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
20422 (synopsis "Create GUI for R functions")
20424 "Rapidly create a GUI for a function you created by automatically
20425 creating widgets for arguments of the function. This package automatically
20426 parses help routines for context-sensitive help to these arguments. The
20427 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
20428 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
20429 incorporated into the interface for greater customization for the more
20431 ;; Any version of the GPL.
20432 (license (list license:gpl2+ license:gpl3+))))
20434 (define-public r-tcltk2
20441 (uri (cran-uri "tcltk2" version))
20444 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
20445 (properties `((upstream-name . "tcltk2")))
20446 (build-system r-build-system)
20449 (home-page "https://www.sciviews.org/SciViews-R")
20450 (synopsis "Tcl/Tk additions")
20452 "This package provides a series of additional Tcl commands and Tk widgets
20453 with style and various functions to supplement the tcltk package")
20454 (license license:lgpl3)))
20456 (define-public r-accrual
20463 (uri (cran-uri "accrual" version))
20466 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
20467 (properties `((upstream-name . "accrual")))
20468 (build-system r-build-system)
20470 (list r-fgui r-smpracticals r-tcltk2))
20471 (home-page "https://cran.r-project.org/web/packages/accrual/")
20472 (synopsis "Bayesian accrual prediction")
20474 "Subject recruitment for medical research is challenging. Slow patient
20475 accrual leads to delay in research. Accrual monitoring during the process of
20476 recruitment is critical. Researchers need reliable tools to manage the
20477 accrual rate. This package provides an implementation of a Bayesian method
20478 that integrates researcher's experience on previous trials and data from the
20479 current study, providing reliable prediction on accrual rate for clinical
20480 studies. It provides functions for Bayesian accrual prediction which can be
20481 easily used by statisticians and clinical researchers.")
20482 (license license:gpl2)))
20484 (define-public r-accrued
20491 (uri (cran-uri "accrued" version))
20494 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
20495 (properties `((upstream-name . "accrued")))
20496 (build-system r-build-system)
20497 (home-page "https://cran.r-project.org/web/packages/accrued/")
20498 (synopsis "Data quality visualization tools for partially accruing data")
20500 "This is a package for visualizing data quality of partially accruing
20502 (license license:gpl3)))
20504 (define-public r-mda
20511 (uri (cran-uri "mda" version))
20514 "1hq0zhhz9klmp4zcr1w8hyn7s1h9kfg57d2l2mfm7psx459j0krl"))))
20515 (properties `((upstream-name . "mda")))
20516 (build-system r-build-system)
20517 (propagated-inputs (list r-class))
20518 (native-inputs (list gfortran))
20519 (home-page "https://cran.r-project.org/web/packages/mda/")
20520 (synopsis "Mixture and flexible discriminant analysis")
20522 "This is a package for mixture and flexible discriminant analysis,
20523 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
20524 (license license:gpl2)))
20526 (define-public r-elasticnet
20528 (name "r-elasticnet")
20533 (uri (cran-uri "elasticnet" version))
20536 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8"))))
20537 (properties `((upstream-name . "elasticnet")))
20538 (build-system r-build-system)
20541 (home-page "http://users.stat.umn.edu/~zouxx019/")
20542 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
20544 "This package provides functions for fitting the entire solution path of
20545 the Elastic-Net and also provides functions for estimating sparse Principal
20546 Components. The Lasso solution paths can be computed by the same function.")
20547 (license license:gpl2+)))
20549 (define-public r-sparselda
20551 (name "r-sparselda")
20556 (uri (cran-uri "sparseLDA" version))
20559 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
20560 (properties `((upstream-name . "sparseLDA")))
20561 (build-system r-build-system)
20563 (list r-elasticnet r-mass r-mda))
20564 (home-page "https://www.imm.dtu.dk/~lkhc/")
20565 (synopsis "Sparse discriminant analysis")
20567 "This package performs sparse linear discriminant analysis for Gaussians
20568 and mixture of Gaussian models.")
20569 (license license:gpl2+)))
20571 (define-public r-accsda
20578 (uri (cran-uri "accSDA" version))
20581 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
20582 (properties `((upstream-name . "accSDA")))
20583 (build-system r-build-system)
20591 (home-page "https://github.com/gumeo/accSDA/wiki")
20592 (synopsis "Accelerated sparse discriminant analysis")
20594 "This package provides an implementation of sparse linear discriminant
20595 analysis, which is a supervised classification method for multiple classes.
20596 Various novel optimization approaches to this problem are implemented
20597 including @dfn{alternating direction method of multipliers} (ADMM),
20598 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
20599 Functions for performing cross validation are also supplied along with basic
20600 prediction and plotting functions. @dfn{Sparse zero variance
20601 discriminant} (SZVD) analysis is also included in the package.")
20602 (license license:gpl2+)))
20604 (define-public r-ace2fastq
20606 (name "r-ace2fastq")
20611 (uri (cran-uri "ace2fastq" version))
20614 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
20615 (properties `((upstream-name . "ace2fastq")))
20616 (build-system r-build-system)
20619 (home-page "https://github.com/c5sire/ace2fastq")
20620 (synopsis "ACE file to FASTQ converter")
20622 "The ACE file format is used in genomics to store contigs from sequencing
20623 machines. This tools converts it into FASTQ format. Both formats contain the
20624 sequence characters and their corresponding quality information. Unlike the
20625 FASTQ file, the ACE file stores the quality values numerically. The
20626 conversion algorithm uses the standard Sanger formula. The package
20627 facilitates insertion into pipelines, and content inspection.")
20628 (license license:gpl3)))
20630 (define-public r-rngwell
20637 (uri (cran-uri "rngWELL" version))
20640 "0f1dxxaimfb0fww8ym9ciqf6q760ai46wxldl37m5mfpd57ca00c"))))
20641 (properties `((upstream-name . "rngWELL")))
20642 (build-system r-build-system)
20643 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
20644 (synopsis "Toolbox for WELL random number generators")
20646 "This is a dedicated package to WELL pseudo random generators, which were
20647 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
20648 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
20649 (license license:bsd-3)))
20651 (define-public r-rnmf
20657 (uri (cran-uri "rNMF" version))
20660 "1nz6h0j5ywdh48m0swmhp34hbkycd7n13rclrxaw85qi9wc42597"))))
20661 (build-system r-build-system)
20663 (list r-knitr r-nnls))
20664 (home-page "https://cran.r-project.org/web/packages/rNMF/")
20665 (synopsis "Robust nonnegative matrix factorization")
20667 "This package provides an implementation of robust nonnegative matrix
20668 factorization (rNMF). The rNMF algorithm decomposes a nonnegative high
20669 dimension data matrix into the product of two low rank nonnegative matrices,
20670 while detecting and trimming outliers. The main function is @code{rnmf()}.
20671 The package also includes a visualization tool, @code{see()}, that arranges
20672 and prints vectorized images.")
20673 (license license:gpl2+)))
20675 (define-public r-randtoolbox
20677 (name "r-randtoolbox")
20682 (uri (cran-uri "randtoolbox" version))
20685 "1b9vjzqg014hxp1vfb62m01d7xim5vmpbyxzlbll49bqas0jx69h"))))
20686 (properties `((upstream-name . "randtoolbox")))
20687 (build-system r-build-system)
20692 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
20693 (synopsis "Toolbox for pseudo and quasi random number generation")
20695 "This package provides
20698 @item pseudo random generators, such as general linear
20699 congruential generators, multiple recursive generators and generalized
20700 feedback shift register (SF-Mersenne Twister algorithm and WELL
20703 @item quasi random generators, such as the Torus algorithm, the Sobol
20704 sequence, the Halton sequence (including the Van der Corput sequence), and
20706 @item some generator tests: the gap test, the serial test, the poker test.
20709 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
20710 (license license:bsd-3)))
20712 (define-public r-lhs
20719 (uri (cran-uri "lhs" version))
20722 "1l861h76q5w0nbnbybhgg7hiw7fks677jakyd49n1whwvd48sfz4"))))
20723 (properties `((upstream-name . "lhs")))
20724 (build-system r-build-system)
20725 (propagated-inputs (list r-rcpp))
20728 (home-page "https://github.com/bertcarnell/lhs")
20729 (synopsis "Latin Hypercube Samples")
20731 "This package provides a number of methods for creating and augmenting
20732 Latin Hypercube Samples.")
20733 (license license:gpl3)))
20735 (define-public r-acebayes
20737 (name "r-acebayes")
20742 (uri (cran-uri "acebayes" version))
20745 "11bffz430gdfdaxjx3simig66vhynmx6l1ylac4q2shcmj52nx73"))))
20746 (properties `((upstream-name . "acebayes")))
20747 (build-system r-build-system)
20749 (list r-compare r-lhs r-randtoolbox r-rcpp r-rcpparmadillo))
20750 (home-page "https://cran.r-project.org/web/packages/acebayes/")
20751 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
20753 "Finding an optimal Bayesian experimental design involves maximizing an
20754 objective function given by the expectation of some appropriately chosen
20755 utility function with respect to the joint distribution of unknown
20756 quantities (including responses). This objective function is usually not
20757 available in closed form and the design space can be continuous and of high
20758 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
20759 to maximise an approximation to the expectation of the utility function.")
20760 (license license:gpl2)))
20762 (define-public r-acet
20769 (uri (cran-uri "ACEt" version))
20772 "0b5lfpnppyk0237phr2aybhx29nhm8ngwk2qa1y4lshrvsw97wg4"))))
20773 (properties `((upstream-name . "ACEt")))
20774 (build-system r-build-system)
20776 (list r-bh r-mass r-rcpp r-rcpparmadillo))
20777 (home-page "https://cran.r-project.org/web/packages/ACEt/")
20778 (synopsis "Estimating dynamic heritability and twin model comparison")
20780 "This package supports twin models that are able to estimate the dynamic
20781 behaviour of the variance components in the classical twin models with respect
20782 to age using B-splines and P-splines.")
20783 (license license:gpl2+)))
20785 (define-public r-acfmperiod
20787 (name "r-acfmperiod")
20792 (uri (cran-uri "acfMPeriod" version))
20795 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
20796 (properties `((upstream-name . "acfMPeriod")))
20797 (build-system r-build-system)
20800 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
20801 (synopsis "Estimation of the ACF from the M-periodogram")
20803 "This package support non-robust and robust computations of the sample
20804 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
20805 univariate and multivariate processes. The methodology consists in reversing
20806 the diagonalization procedure involving the periodogram or the
20807 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
20808 ACOVF or the ACF as discussed in Fuller (1995)
20809 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
20810 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
20811 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
20812 (license license:gpl2+)))
20814 (define-public r-gamlss-data
20816 (name "r-gamlss-data")
20821 (uri (cran-uri "gamlss.data" version))
20824 "07mpdl4h9rwmnpl9jmsn6ig8ji11an6pyjfsvg62h2alapwbdcyv"))))
20825 (properties `((upstream-name . "gamlss.data")))
20826 (build-system r-build-system)
20827 (home-page "http://www.gamlss.org/")
20828 (synopsis "GAMLSS data")
20830 "This package provides data used as examples to demonstrate GAMLSS
20832 ;; Either version of the license
20833 (license (list license:gpl2 license:gpl3))))
20835 (define-public r-gamlss
20842 (uri (cran-uri "gamlss" version))
20845 "06mh00jjxnqwknbv777hawjk0zm81ixrp35fg59mrlqz8y3p2w3j"))))
20846 (properties `((upstream-name . "gamlss")))
20847 (build-system r-build-system)
20849 (list r-gamlss-data r-gamlss-dist r-mass r-nlme r-survival))
20850 (home-page "http://www.gamlss.org/")
20851 (synopsis "Generalized additive models for location scale and shape")
20853 "This package provides functions for fitting the generalized additive
20854 models for location scale and shape introduced by Rigby and
20855 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
20856 use a distributional regression approach where all the parameters of the
20857 conditional distribution of the response variable are modelled using
20858 explanatory variables.")
20859 ;; Either version of the license
20860 (license (list license:gpl2 license:gpl3))))
20862 (define-public r-acid
20869 (uri (cran-uri "acid" version))
20872 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
20873 (properties `((upstream-name . "acid")))
20874 (build-system r-build-system)
20876 (list r-gamlss r-gamlss-dist r-hmisc))
20877 (home-page "https://cran.r-project.org/web/packages/acid/")
20878 (synopsis "Analysing conditional income distributions")
20880 "This package provides functions for the analysis of income distributions
20881 for subgroups of the population as defined by a set of variables like age,
20882 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
20883 distribution as well as functions for moments, inequality measures, entropy
20884 measures and polarisation measures of income distributions. This package thus
20885 aides the analysis of income inequality by offering tools for the exploratory
20886 analysis of income distributions at the disaggregated level.")
20887 (license license:gpl3)))
20889 (define-public r-acm4r
20896 (uri (cran-uri "acm4r" version))
20899 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
20900 (properties `((upstream-name . "acm4r")))
20901 (build-system r-build-system)
20902 (propagated-inputs (list r-mass))
20903 (home-page "https://cran.r-project.org/web/packages/acm4r/")
20904 (synopsis "Align-and-count method comparisons of RFLP data")
20906 "This is a package to compare sequence fragment lengths or molecular
20907 weights from pairs of lanes. The number of matching bands in the
20908 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
20909 the align-and-count method.")
20910 ;; Any version of the GPL
20911 (license (list license:gpl2+ license:gpl3+))))
20913 (define-public r-filelock
20915 (name "r-filelock")
20920 (uri (cran-uri "filelock" version))
20923 "00ql5fw1hidpfnm0szaavf43ahmsnvdbi8i5lr1nrcc90yaiaadc"))))
20924 (properties `((upstream-name . "filelock")))
20925 (build-system r-build-system)
20926 (home-page "https://github.com/r-lib/filelock")
20927 (synopsis "Portable file locking")
20929 "This library lets you place an exclusive or shared lock on a file using
20930 the appropriate system call provided by the underlying operating system.")
20931 (license license:expat)))
20933 (define-public r-filematrix
20935 (name "r-filematrix")
20940 (uri (cran-uri "filematrix" version))
20943 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
20944 (properties `((upstream-name . "filematrix")))
20945 (build-system r-build-system)
20946 ;; These inputs are needed for vignettes
20948 (list r-knitr r-rmarkdown))
20949 (home-page "https://github.com/andreyshabalin/filematrix")
20950 (synopsis "File-backed matrix class with convenient read and write access")
20952 "This package provides an interface for working with large matrices
20953 stored in files, not in computer memory. It supports multiple non-character
20954 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
20955 byte real values). Access to parts of the matrix is done by indexing, exactly
20956 as with usual R matrices. It supports very large matrices; the package has
20957 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
20958 columns, ad allows for quick addition of extra columns to a filematrix.")
20959 (license license:lgpl3)))
20961 (define-public r-acmeeqtl
20963 (name "r-acmeeqtl")
20968 (uri (cran-uri "ACMEeqtl" version))
20971 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
20972 (properties `((upstream-name . "ACMEeqtl")))
20973 (build-system r-build-system)
20975 (list r-filematrix))
20976 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
20977 (synopsis "Estimation of interpretable eQTL effect sizes")
20979 "This package provides a non-linear model, termed ACME, that reflects a
20980 parsimonious biological model for allelic contributions of cis-acting eQTLs.
20981 With non-linear least-squares algorithm the maximum likelihood parameters can
20982 be estimated. The ACME model provides interpretable effect size estimates and
20983 p-values with well controlled Type-I error.")
20984 (license license:lgpl3)))
20986 (define-public r-acmer
20993 (uri (cran-uri "acmeR" version))
20996 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
20997 (properties `((upstream-name . "acmeR")))
20998 (build-system r-build-system)
20999 (propagated-inputs (list r-foreign))
21000 (home-page "https://cran.r-project.org/web/packages/acmeR/")
21001 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
21003 "This package provides an implementation of the ACME estimator, described
21004 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
21005 Mortality at Wind Turbines. Unlike most other models, this estimator supports
21006 decreasing-hazard Weibull model for persistence; decreasing search proficiency
21007 as carcasses age; variable bleed-through at successive searches; and interval
21008 mortality estimates. The package provides, based on search data, functions
21009 for estimating the mortality inflation factor in Frequentist and Bayesian
21011 (license license:expat)))
21013 (define-public r-r-huge
21020 (uri (cran-uri "R.huge" version))
21023 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
21024 (properties `((upstream-name . "R.huge")))
21025 (build-system r-build-system)
21027 (list r-r-methodss3 r-r-oo r-r-utils))
21028 (home-page "https://github.com/HenrikBengtsson/R.huge")
21029 (synopsis "Methods for accessing huge amounts of data")
21031 "This is a deprecated package for accessing huge amounts of data.
21032 Cross-platform alternatives are the following packages: bigmemory (CRAN),
21033 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
21034 the @code{aroma.affymetrix} package.")
21035 (license license:lgpl2.1+)))
21037 (define-public r-r-filesets
21039 (name "r-r-filesets")
21044 (uri (cran-uri "R.filesets" version))
21047 "08xv8b3c81nf54viyr3w912al18483k5gfnjpg7bxbdfk70dfzbh"))))
21048 (properties `((upstream-name . "R.filesets")))
21049 (build-system r-build-system)
21052 (modify-phases %standard-phases
21053 (add-after 'unpack 'set-HOME
21054 (lambda _ (setenv "HOME" "/tmp"))))))
21056 (list r-digest r-r-cache r-r-methodss3 r-r-oo r-r-utils))
21057 (home-page "https://github.com/HenrikBengtsson/R.filesets")
21058 (synopsis "Easy handling of and access to files")
21060 "This package provides classes and methods to locate, setup, subset,
21061 navigate and iterate file sets, i.e. sets of files located in one or more
21062 directories on the file system. The API is designed such that these classes
21063 can be extended via inheritance to provide a richer API for special file
21064 formats. Moreover, a specific name format is defined such that filenames and
21065 directories can be considered to have full names which consists of a name
21066 followed by comma-separated tags. This adds additional flexibility to
21067 identify file sets and individual files.")
21068 (license license:lgpl2.1+)))
21070 (define-public r-r-devices
21072 (name "r-r-devices")
21077 (uri (cran-uri "R.devices" version))
21080 "1djz6vm1b7sjvx1q319dl47gbnz9kvipaxcz9i0spyp094lv3m62"))))
21081 (properties `((upstream-name . "R.devices")))
21082 (build-system r-build-system)
21084 (list r-base64enc r-r-methodss3 r-r-oo r-r-utils))
21085 (home-page "https://github.com/HenrikBengtsson/R.devices")
21086 (synopsis "Unified handling of graphics devices")
21088 "This package provides functions for creating plots and image files in a
21089 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
21090 Default device options as well as scales and aspect ratios are controlled in a
21091 uniform way across all device types. Switching output format requires minimal
21092 changes in code. This package is ideal for large-scale batch processing,
21093 because it will never leave open graphics devices or incomplete image files
21094 behind, even on errors or user interrupts.")
21095 (license license:lgpl2.1+)))
21097 (define-public r-acnr
21104 (uri (cran-uri "acnr" version))
21107 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
21108 (properties `((upstream-name . "acnr")))
21109 (build-system r-build-system)
21110 (home-page "https://github.com/mpierrejean/acnr")
21111 (synopsis "Annotated copy-number regions")
21113 "This package provides SNP array data from different types of copy-number
21114 regions. These regions were identified manually by the authors of the package
21115 and may be used to generate realistic data sets with known truth.")
21116 (license license:lgpl2.1+)))
21118 (define-public r-acopula
21125 (uri (cran-uri "acopula" version))
21128 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
21129 (properties `((upstream-name . "acopula")))
21130 (build-system r-build-system)
21131 (home-page "https://cran.r-project.org/web/packages/acopula/")
21132 (synopsis "Modelling dependence with multivariate Archimax copulas")
21134 "Archimax copulas are a mixture of Archimedean and EV copulas. This
21135 package provides definitions of several parametric families of generator and
21136 dependence function, computes CDF and PDF, estimates parameters, tests for
21137 goodness of fit, generates random sample and checks copula properties for
21138 custom constructs. In the 2-dimensional case explicit formulas for density
21139 are used, contrary to higher dimensions when all derivatives are linearly
21140 approximated. Several non-archimax families (normal, FGM, Plackett) are
21141 provided as well.")
21142 (license license:gpl2)))
21144 (define-public r-tuner
21147 (version "1.3.3.1")
21151 (uri (cran-uri "tuneR" version))
21154 "12nixpqrc5gp7p2clr7ia6jwb0jq2i3brlxiwlp00ixmnm5g1jyd"))))
21155 (properties `((upstream-name . "tuneR")))
21156 (build-system r-build-system)
21157 (propagated-inputs (list r-signal))
21158 (home-page "https://cran.r-project.org/web/packages/tuneR/")
21159 (synopsis "Analysis of music and speech")
21161 "This is a package for the analysis of music and speech. Analyze music
21162 and speech, extract features like MFCCs, handle wave files and their
21163 representation in various ways, read MP3, read MIDI, perform steps of a
21164 transcription, ...")
21165 ;; Either of these versions.
21166 (license (list license:gpl2 license:gpl3))))
21168 (define-public r-seewave
21175 (uri (cran-uri "seewave" version))
21178 "1szcvryvl4kb3av2pcvl14bz6whl7xrq4wb1ck6w7lfc4mrlirhh"))))
21179 (properties `((upstream-name . "seewave")))
21180 (build-system r-build-system)
21185 (home-page "http://rug.mnhn.fr/seewave")
21186 (synopsis "Sound analysis and synthesis")
21188 "This package provides functions for analysing, manipulating, displaying,
21189 editing and synthesizing time waves (particularly sound). This package
21190 processes time analysis (oscillograms and envelopes), spectral content,
21191 resonance quality factor, entropy, cross correlation and autocorrelation,
21192 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
21193 and 3D spectrograms and many other analyses.")
21194 (license license:gpl2+)))
21196 (define-public r-acousticndlcoder
21198 (name "r-acousticndlcoder")
21203 (uri (cran-uri "AcousticNDLCodeR" version))
21206 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
21208 `((upstream-name . "AcousticNDLCodeR")))
21209 (build-system r-build-system)
21211 (list r-seewave r-tuner r-zoo))
21212 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
21213 (synopsis "Coding sound files for use with NDL")
21215 "Make acoustic cues to use with the R package @code{ndl}.
21216 The package implements functions used in the PLoS ONE paper \"Words from
21217 spontaneous conversational speech can be recognized with human-like accuracy
21218 by an error-driven learning algorithm that discriminates between meanings
21219 straight from smart acoustic features, bypassing the phoneme as recognition
21220 unit.\" @url{doi:10.1371/journal.pone.0174623}")
21221 (license license:gpl2+)))
21223 (define-public r-acp
21230 (uri (cran-uri "acp" version))
21233 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
21234 (properties `((upstream-name . "acp")))
21235 (build-system r-build-system)
21237 (list r-quantmod r-tseries))
21238 (home-page "https://cran.r-project.org/web/packages/acp/")
21239 (synopsis "Autoregressive conditional Poisson")
21241 "This package supports the analysis of count data exhibiting
21242 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
21243 model (ACP(p,q)) proposed by Heinen (2003).")
21244 (license license:gpl2)))
21246 (define-public r-ada
21253 (uri (cran-uri "ada" version))
21256 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
21257 (properties `((upstream-name . "ada")))
21258 (build-system r-build-system)
21259 (propagated-inputs (list r-rpart))
21260 (home-page "https://cran.r-project.org/web/packages/ada/")
21261 (synopsis "Stochastic boosting")
21263 "This package provides a straightforward, well-documented, and broad
21264 boosting routine for classification, ideally suited for small to
21265 moderate-sized data sets. It performs discrete, real, and gentle boost under
21266 both exponential and logistic loss on a given data set.")
21267 ;; Any version of the GPL.
21268 (license (list license:gpl2+ license:gpl3+))))
21270 (define-public r-genalg
21277 (uri (cran-uri "genalg" version))
21280 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
21281 (properties `((upstream-name . "genalg")))
21282 (build-system r-build-system)
21283 (home-page "https://github.com/egonw/genalg")
21284 (synopsis "R based genetic algorithm")
21286 "This package provides an R based genetic algorithm for binary and
21287 floating point chromosomes.")
21288 (license license:gpl2)))
21290 (define-public r-kernelfactory
21292 (name "r-kernelfactory")
21297 (uri (cran-uri "kernelFactory" version))
21300 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
21301 (properties `((upstream-name . "kernelFactory")))
21302 (build-system r-build-system)
21304 (list r-auc r-genalg r-kernlab r-randomforest))
21305 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
21306 (synopsis "Ensemble of kernel machines")
21308 "Kernel factory is an ensemble method where each base classifier (random
21309 forest) is fit on the kernel matrix of a subset of the training data.")
21310 (license license:gpl2+)))
21312 (define-public r-dummies
21319 (uri (cran-uri "dummies" version))
21322 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
21323 (properties `((upstream-name . "dummies")))
21324 (build-system r-build-system)
21325 (home-page "https://decisionpatterns.com")
21326 (synopsis "Create dummy/indicator variables flexibly and efficiently")
21328 "This package lets you expand factors, characters and other eligible
21329 classes into dummy/indicator variables.")
21330 (license license:gpl2+)))
21332 (define-public r-acrm
21339 (uri (cran-uri "aCRM" version))
21342 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
21343 (properties `((upstream-name . "aCRM")))
21344 (build-system r-build-system)
21346 (list r-ada r-dummies r-kernelfactory r-randomforest))
21347 (home-page "https://cran.r-project.org/web/packages/aCRM/")
21348 (synopsis "Convenience functions for analytical customer relationship management")
21350 "This package provides convenience functions for data preparation and
21351 modeling often used in @dfn{analytical customer relationship
21352 management} (aCRM).")
21353 (license license:gpl2+)))
21355 (define-public r-tree
21361 (uri (cran-uri "tree" version))
21364 "13jwdxx3na16mly176n01zdkaqn4a8x9fc43rq5xx5vx31drkkr1"))))
21365 (build-system r-build-system)
21366 (home-page "https://cran.r-project.org/web/packages/tree/")
21367 (synopsis "Classification and regression trees")
21368 (description "This package provides procedures to work with classification
21369 and regression trees.")
21370 (license license:gpl2+)))
21372 (define-public r-treeclust
21374 (name "r-treeclust")
21379 (uri (cran-uri "treeClust" version))
21382 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
21383 (properties `((upstream-name . "treeClust")))
21384 (build-system r-build-system)
21386 (list r-cluster r-rpart))
21387 (home-page "https://cran.r-project.org/web/packages/treeClust/")
21388 (synopsis "Cluster distances through trees")
21390 "This package provides tools to create a measure of inter-point
21391 dissimilarity useful for clustering mixed data, and, optionally, perform the
21393 (license license:gpl2+)))
21395 (define-public r-acrosstic
21397 (name "r-acrosstic")
21402 (uri (cran-uri "AcrossTic" version))
21405 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
21406 (properties `((upstream-name . "AcrossTic")))
21407 (build-system r-build-system)
21409 (list r-lpsolve r-treeclust))
21410 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
21411 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
21413 "This is a package for constructing minimum-cost regular spanning
21414 subgraph as part of a non-parametric two-sample test for equality of
21416 (license license:gpl2+)))
21418 (define-public r-acrt
21425 (uri (cran-uri "acrt" version))
21428 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
21429 (properties `((upstream-name . "acrt")))
21430 (build-system r-build-system)
21432 (list r-rcpp r-rcppeigen r-sandwich))
21433 (home-page "https://cran.r-project.org/web/packages/acrt/")
21434 (synopsis "Autocorrelation robust testing")
21436 "This package provides functions for testing affine hypotheses on the
21437 regression coefficient vector in regression models with autocorrelated
21439 (license license:gpl2)))
21441 (define-public r-acs
21448 (uri (cran-uri "acs" version))
21451 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
21452 (properties `((upstream-name . "acs")))
21453 (build-system r-build-system)
21455 (list r-httr r-plyr r-rcpp r-stringr r-xml))
21456 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
21457 (synopsis "Work with data from the US Census")
21459 "This package provides a general toolkit for downloading, managing,
21460 analyzing, and presenting data from the
21461 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
21462 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
21463 American Community Survey (ACS). Confidence intervals provided with ACS data
21464 are converted to standard errors to be bundled with estimates in complex
21465 @code{acs} objects. The package provides new methods to conduct standard
21466 operations on @code{acs} objects and present/plot data in statistically
21467 appropriate ways.")
21468 (license license:gpl3)))
21470 (define-public r-acss-data
21472 (name "r-acss-data")
21477 (uri (cran-uri "acss.data" version))
21480 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
21481 (properties `((upstream-name . "acss.data")))
21482 (build-system r-build-system)
21483 (home-page "http://complexitycalculator.com/methodology.html")
21484 (synopsis "Data for algorithmic complexity of short strings")
21486 "This is a data only package providing the algorithmic complexity of
21487 short strings, computed using the coding theorem method. For a given set of
21488 symbols in a string, all possible or a large number of random samples of
21489 Turing machines with a given number of states (e.g., 5) and number of symbols
21490 corresponding to the number of symbols in the strings were simulated until
21491 they reached a halting state or failed to end. This package contains data on
21492 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
21493 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
21494 distribution of the halting states.")
21495 (license license:gpl2+)))
21497 (define-public r-acss
21504 (uri (cran-uri "acss" version))
21507 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
21508 (properties `((upstream-name . "acss")))
21509 (build-system r-build-system)
21511 (list r-acss-data r-zoo))
21512 (home-page "http://complexitycalculator.com/methodology.html")
21513 (synopsis "Algorithmic complexity for short strings")
21515 "The main purpose of this package is to provide the algorithmic
21516 complexity for short strings, an approximation of the Kolmogorov Complexity of
21517 a short string using the coding theorem method. While the database containing
21518 the complexity is provided in the data only package @code{acss.data}, this
21519 package provides functions accessing the data such as @code{prob_random}
21520 returning the posterior probability that a given string was produced by a
21521 random process. In addition, two traditional (but problematic) measures of
21522 complexity are also provided: entropy and change complexity.")
21523 (license license:gpl2+)))
21525 (define-public r-acswr
21532 (uri (cran-uri "ACSWR" version))
21535 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
21536 (properties `((upstream-name . "ACSWR")))
21537 (build-system r-build-system)
21540 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
21541 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
21543 "This is a companion package for the book \"A Course in Statistics with
21544 R\" (ISBN 978-1-119-15272-9.)")
21545 (license license:gpl2)))
21547 (define-public r-alabama
21550 (version "2015.3-1")
21554 (uri (cran-uri "alabama" version))
21557 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
21558 (properties `((upstream-name . "alabama")))
21559 (build-system r-build-system)
21560 (propagated-inputs (list r-numderiv))
21561 (home-page "https://cran.r-project.org/web/packages/alabama/")
21562 (synopsis "Constrained nonlinear optimization")
21564 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
21565 Algorithm; it is used for optimizing smooth nonlinear objective functions with
21566 constraints. Linear or nonlinear equality and inequality constraints are
21568 (license license:gpl2+)))
21570 (define-public r-gdina
21577 (uri (cran-uri "GDINA" version))
21580 "08cdjp4mqn81j3wa770v7n8zkslys9jqqb3d3c09dkfmgdk6hga4"))))
21581 (properties `((upstream-name . "GDINA")))
21582 (build-system r-build-system)
21596 (home-page "https://github.com/Wenchao-Ma/GDINA")
21597 (synopsis "Generalized DINA model framework")
21599 "This package provides a set of psychometric tools for cognitive
21600 diagnosis modeling based on the generalized deterministic inputs, noisy and
21601 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
21602 and its extensions, including the sequential G-DINA model by Ma and de la
21603 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
21604 polytomous G-DINA model by Chen and de la Torre
21605 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
21606 distribution can be independent, saturated, higher-order, loglinear smoothed
21607 or structured. Q-matrix validation, item and model fit statistics, model
21608 comparison at test and item level and differential item functioning can also
21609 be conducted. A graphical user interface is also provided.")
21610 (license license:gpl3)))
21612 (define-public r-actcd
21619 (uri (cran-uri "ACTCD" version))
21622 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
21623 (properties `((upstream-name . "ACTCD")))
21624 (build-system r-build-system)
21626 (list r-gdina r-r-methodss3))
21629 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
21630 (synopsis "Asymptotic classification theory for cognitive diagnosis")
21632 "This is a package supporting cluster analysis for cognitive diagnosis
21633 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
21634 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
21635 sum-scores, cluster analysis techniques can be used to classify examinees into
21636 latent classes based on their attribute patterns. In addition to the
21637 algorithms used to classify data, three labeling approaches are proposed to
21638 label clusters so that examinees' attribute profiles can be obtained.")
21639 (license license:gpl2+)))
21641 (define-public r-ineq
21648 (uri (cran-uri "ineq" version))
21651 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
21652 (properties `((upstream-name . "ineq")))
21653 (build-system r-build-system)
21654 (home-page "https://cran.r-project.org/web/packages/ineq/")
21655 (synopsis "Measuring inequality, concentration, and poverty")
21657 "This package provides tools for measuring inequality, concentration, and
21658 poverty measures. It provides both empirical and theoretical Lorenz curves.")
21659 ;; Either of these two versions.
21660 (license (list license:gpl2 license:gpl3))))
21662 (define-public r-actfrag
21669 (uri (cran-uri "ActFrag" version))
21672 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
21673 (properties `((upstream-name . "ActFrag")))
21674 (build-system r-build-system)
21676 (list r-accelerometry r-dplyr r-ineq r-survival r-tidyr))
21677 (home-page "https://github.com/junruidi/ActFrag")
21678 (synopsis "Activity fragmentation metrics extraction")
21680 "This package provides functions to extract commonly used fragmentation
21681 metrics to quantify time accumulation strategies based on minute level
21682 actigraphy-measured activity counts data.")
21683 (license license:gpl3)))
21685 (define-public r-ash
21692 (uri (cran-uri "ash" version))
21695 "1ay2a2agdmiz7zzvn26mli0x0iwk09g5pp4yy1r23knhkp1pn2lb"))))
21696 (properties `((upstream-name . "ash")))
21697 (build-system r-build-system)
21698 (native-inputs (list gfortran))
21699 (home-page "https://cran.r-project.org/web/packages/ash/")
21700 (synopsis "David Scott's ASH routines")
21702 "This package provides David Scott's ASH routines ported from S-PLUS to
21704 (license license:gpl2+)))
21706 (define-public r-hdrcde
21713 (uri (cran-uri "hdrcde" version))
21716 "16qlk44cjvn2s0vzaf915df65ksdx20dbxhy7fpdqins46hccha3"))))
21717 (properties `((upstream-name . "hdrcde")))
21718 (build-system r-build-system)
21726 (native-inputs (list gfortran))
21727 (home-page "http://pkg.robjhyndman.com/hdrcde")
21728 (synopsis "Highest density regions and conditional density estimation")
21730 "This is a package for the computation of highest density regions in one
21731 and two dimensions, kernel estimation of univariate density functions
21732 conditional on one covariate, and multimodal regression.")
21733 (license license:gpl3)))
21735 (define-public r-rainbow
21742 (uri (cran-uri "rainbow" version))
21745 "11vfcck17d2xjc049ci5i8l1nqv345anmd110gdz7654i1pj9lb3"))))
21746 (properties `((upstream-name . "rainbow")))
21747 (build-system r-build-system)
21755 (home-page "https://cran.r-project.org/web/packages/rainbow/")
21756 (synopsis "Bagplots, boxplots and rainbow plots for functional data")
21758 "This is a package for visualizing functional data and identifying
21759 functional outliers with bagplots, boxplots and rainbow plots.")
21760 (license license:gpl3)))
21762 (define-public r-fds
21769 (uri (cran-uri "fds" version))
21772 "1284vncixrzrz9x6b52gslrbrbia07sd0xac7nwdqhp5f5v5wfi0"))))
21773 (properties `((upstream-name . "fds")))
21774 (build-system r-build-system)
21776 (list r-rainbow r-rcurl))
21777 (home-page "https://cran.r-project.org/web/packages/fds/")
21778 (synopsis "Functional data sets")
21779 (description "This package contains a list of functional time series,
21780 sliced functional time series, and functional data sets. Functional time
21781 series is a special type of functional data observed over time. Sliced
21782 functional time series is a special type of functional time series with a time
21783 variable observed over time.")
21784 (license license:gpl2+)))
21786 (define-public r-fda
21793 (uri (cran-uri "fda" version))
21796 "0fm2vswc8fdi2p1axby0hjwh8m6lc1zrdikrpiamilr6w9m2zanw"))))
21797 (properties `((upstream-name . "fda")))
21798 (build-system r-build-system)
21800 (list r-desolve r-fds r-matrix))
21801 (home-page "https://www.functionaldata.org")
21802 (synopsis "Functional data analysis")
21804 "These functions were developed to support functional data analysis as
21805 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
21806 Analysis. The package includes data sets and script files working many
21808 (license license:gpl2+)))
21810 (define-public r-actigraphy
21812 (name "r-actigraphy")
21817 (uri (cran-uri "Actigraphy" version))
21820 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
21821 (properties `((upstream-name . "Actigraphy")))
21822 (build-system r-build-system)
21825 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
21826 (synopsis "Actigraphy data analysis")
21828 "This package provides tools for functional linear modeling and analysis
21829 of actigraphy data.")
21830 (license license:asl2.0)))
21832 (define-public r-activedriver
21834 (name "r-activedriver")
21839 (uri (cran-uri "ActiveDriver" version))
21842 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
21843 (properties `((upstream-name . "ActiveDriver")))
21844 (build-system r-build-system)
21847 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
21848 (synopsis "Tools for finding cancer driver proteins")
21850 "This package provides a mutation analysis tool that discovers cancer
21851 driver genes with frequent mutations in protein signalling sites such as
21852 post-translational modifications (phosphorylation, ubiquitination, etc). The
21853 Poisson generalized linear regression model identifies genes where cancer
21854 mutations in signalling sites are more frequent than expected from the
21855 sequence of the entire gene. Integration of mutations with signalling
21856 information helps find new driver genes and propose candidate mechanisms to
21858 (license license:gpl2+)))
21860 (define-public r-activitycounts
21862 (name "r-activitycounts")
21867 (uri (cran-uri "activityCounts" version))
21870 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
21872 `((upstream-name . "activityCounts")))
21873 (build-system r-build-system)
21875 (list r-lubridate r-magrittr r-seewave r-signal r-tibble))
21876 (home-page "https://github.com/walkabillylab/activityCounts")
21877 (synopsis "Generate ActiLife counts")
21879 "ActiLife generates activity counts from data collected by Actigraph
21880 accelerometers. Actigraph is one of the most common research-grade
21881 accelerometers. There is considerable research validating and developing
21882 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
21883 counts are proprietary and difficult to implement if researchers use different
21884 accelerometer brands. The code creates ActiLife counts from raw acceleration
21885 data for different accelerometer brands.")
21886 (license license:gpl3)))
21888 (define-public r-activityindex
21890 (name "r-activityindex")
21895 (uri (cran-uri "ActivityIndex" version))
21898 "1zj2b6x31a1kxl80rarmkrlm7ack4154mrkbqs3fpi48zpmjbgd5"))))
21899 (properties `((upstream-name . "ActivityIndex")))
21900 (build-system r-build-system)
21902 (list r-data-table r-matrixstats r-r-utils))
21905 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
21906 (synopsis "Activity Index calculation using raw accelerometry data")
21908 "This is a package to read raw accelerometry from GT3X+ accelerometry
21909 data and plain table data to calculate the Activity Index from Bai et
21910 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
21911 (license license:gpl3)))
21913 (define-public r-activpal
21915 (name "r-activpal")
21920 (uri (cran-uri "activPAL" version))
21923 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
21924 (properties `((upstream-name . "activPAL")))
21925 (build-system r-build-system)
21933 (home-page "https://cran.r-project.org/web/packages/activPAL")
21934 (synopsis "Processing and chart generation from activPAL events files")
21936 "This package contains functions to generate pre-defined summary
21937 statistics from activPAL events files. The package also contains functions to
21938 produce informative graphics that visualize physical activity behaviour and
21939 trends. This includes generating graphs that align physical activity
21940 behaviour with additional time based observations described by other data
21941 sets, such as sleep diaries and continuous glucose monitoring data.")
21942 (license license:gpl3)))
21944 (define-public r-activpalprocessing
21946 (name "r-activpalprocessing")
21951 (uri (cran-uri "activpalProcessing" version))
21954 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
21956 `((upstream-name . "activpalProcessing")))
21957 (build-system r-build-system)
21960 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
21961 (synopsis "Process activPAL events files")
21963 "This package performs estimation of physical activity and sedentary
21964 behavior variables from activPAL events files.")
21965 ;; Either version of the GPL.
21966 (license (list license:gpl2 license:gpl3))))
21968 (define-public r-actogrammr
21970 (name "r-actogrammr")
21975 (uri (cran-uri "actogrammr" version))
21978 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
21979 (properties `((upstream-name . "actogrammr")))
21980 (build-system r-build-system)
21982 (list r-dplyr r-ggplot2 r-lubridate r-readr r-tidyr))
21983 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
21984 (synopsis "Read in activity data and plot actograms")
21986 "Read in activity measurements from standard file formats used by
21987 circadian rhythm researchers, currently only ClockLab format, and process and
21988 plot the data. The central type of plot is the actogram, as first described
21989 in \"Activity and distribution of certain wild mice in relation to biotic
21990 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
21991 (license license:gpl3)))
21993 (define-public r-expint
22000 (uri (cran-uri "expint" version))
22003 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
22004 (properties `((upstream-name . "expint")))
22005 (build-system r-build-system)
22006 (home-page "https://gitlab.com/vigou3/expint")
22007 (synopsis "Exponential integral and incomplete Gamma function")
22009 "This package provides the exponential integrals @code{E_1(x)},
22010 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
22011 function @code{G(a, x)} defined for negative values of its first argument.
22012 The package also gives easy access to the underlying C routines through an
22013 API; see the package vignette for details.")
22014 (license license:gpl2+)))
22016 (define-public r-actuar
22023 (uri (cran-uri "actuar" version))
22026 "015brjjgmkwmjajdjdw8gs02jrd96if425pk9a97d499hzsq3xds"))))
22027 (properties `((upstream-name . "actuar")))
22028 (build-system r-build-system)
22029 (propagated-inputs (list r-expint))
22030 (home-page "https://gitlab.com/vigou3/actuar")
22031 (synopsis "Actuarial functions and heavy tailed distributions")
22033 "This package provides functions and data sets for actuarial science:
22034 modeling of loss distributions; risk theory and ruin theory; simulation of
22035 compound models, discrete mixtures and compound hierarchical models;
22036 credibility theory. It boasts support for many additional probability
22037 distributions to model insurance loss amounts and loss frequency: 19
22038 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
22039 distribution; zero-truncated and zero-modified extensions of the standard
22040 discrete distributions. It also supports phase-type distributions commonly
22041 used to compute ruin probabilities.")
22042 (license license:gpl2+)))
22044 (define-public r-bmp
22051 (uri (cran-uri "bmp" version))
22054 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
22055 (properties `((upstream-name . "bmp")))
22056 (build-system r-build-system)
22057 (home-page "https://cran.r-project.org/web/packages/bmp/")
22058 (synopsis "Read Bitmap (BMP) images")
22060 "This package provides pure R tools to read BMP format images. It is
22061 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
22062 (license license:gpl2+)))
22064 (define-public r-readbitmap
22066 (name "r-readbitmap")
22071 (uri (cran-uri "readbitmap" version))
22074 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
22075 (properties `((upstream-name . "readbitmap")))
22076 (build-system r-build-system)
22078 `(("libjpeg" ,libjpeg-turbo)
22079 ("libpng" ,libpng)))
22081 (list r-bmp r-jpeg r-png r-tiff))
22082 (home-page "https://github.com/jefferis/readbitmap")
22083 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
22085 "This package provides tools to identify and read BMP, JPEG, PNG, and
22086 TIFF format bitmap images. Identification defaults to the use of the magic
22087 number embedded in the file rather than the file extension.")
22088 (license license:gpl2+)))
22090 (define-public r-imager
22093 (version "0.42.11")
22097 (uri (cran-uri "imager" version))
22100 "1a1jhmgrpv1d0fk14axj88qvxgb25bqnj65d60g1k985ipzvgy27"))))
22101 (properties `((upstream-name . "imager")))
22102 (build-system r-build-system)
22104 (list fftw libtiff libx11 zlib))
22116 (list pkg-config r-knitr))
22117 (home-page "https://dahtah.github.io/imager/")
22118 (synopsis "Image processing library")
22120 "This is a package for fast image processing for images in up to 4
22121 dimensions (two spatial dimensions, one time/depth dimension, one color
22122 dimension). It provides most traditional image processing tools (filtering,
22123 morphology, transformations, etc.) as well as various functions for easily
22124 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
22125 simple, modern C++ library for image processing.")
22126 (license license:lgpl3)))
22128 (define-public r-acuityview
22130 (name "r-acuityview")
22135 (uri (cran-uri "AcuityView" version))
22138 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
22139 (properties `((upstream-name . "AcuityView")))
22140 (build-system r-build-system)
22142 (list r-fftwtools r-imager r-plotrix))
22143 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
22144 (synopsis "Display scenes as seen by an animal with less acute vision")
22146 "This package provides a simple method for representing a visual scene as
22147 it may be seen by an animal with less acute vision.")
22148 (license license:gpl2+)))
22150 (define-public r-caret
22157 (uri (cran-uri "caret" version))
22160 "1g36m06hp2fxxwv155bwbqlf97xhcia1lmg3axg6d74kgpns8lg8"))))
22161 (build-system r-build-system)
22176 (home-page "https://github.com/topepo/caret")
22177 (synopsis "Classification and regression training")
22179 "This package provides miscellaneous functions for training and plotting
22180 classification and regression models.")
22181 (license license:gpl2+)))
22183 (define-public r-adabag
22190 (uri (cran-uri "adabag" version))
22193 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
22194 (properties `((upstream-name . "adabag")))
22195 (build-system r-build-system)
22197 (list r-caret r-doparallel r-foreach r-rpart))
22198 (home-page "https://cran.r-project.org/web/packages/adabag/")
22199 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
22201 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
22202 Breiman's Bagging algorithm using classification trees as individual
22203 classifiers. Once these classifiers have been trained, they can be used to
22204 predict on new data. Also, cross validation estimation of the error can be
22206 (license license:gpl2+)))
22208 (define-public r-adagio
22215 (uri (cran-uri "adagio" version))
22218 "0ihv05402iq003m0338f85pnqnlnrmx0pf1mg8cz9sgi5h98mbnl"))))
22219 (properties `((upstream-name . "adagio")))
22220 (build-system r-build-system)
22223 (home-page "https://cran.r-project.org/web/packages/adagio/")
22224 (synopsis "Discrete and global optimization routines")
22226 "This package provides methods and algorithms for discrete optimization,
22227 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
22228 Hooke-Jeeves minimization, and some (evolutionary) global optimization
22230 (license license:gpl3+)))
22232 (define-public r-univoutl
22234 (name "r-univoutl")
22239 (uri (cran-uri "univOutl" version))
22242 "1hhpxrpmp2wbrynx9xjndnp2sccirgky2x6ksd6yk6phmk0rbzjp"))))
22243 (properties `((upstream-name . "univOutl")))
22244 (build-system r-build-system)
22246 (list r-hmisc r-robustbase))
22247 (home-page "https://github.com/marcellodo/univOutl")
22248 (synopsis "Detection of univariate outliers")
22250 "This package provides well-known outlier detection techniques in the
22251 univariate case. Methods to deal with skewed distribution are included too.
22252 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
22253 historical data is implemented as well. When available, survey weights can be
22254 used in outliers detection.")
22255 (license license:gpl2+)))
22257 (define-public r-tolerance
22259 (name "r-tolerance")
22264 (uri (cran-uri "tolerance" version))
22267 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
22268 (properties `((upstream-name . "tolerance")))
22269 (build-system r-build-system)
22271 (list r-mass r-rgl))
22272 (home-page "https://cran.r-project.org/web/packages/tolerance/")
22273 (synopsis "Statistical tolerance intervals and regions")
22275 "This package provides functions for estimating tolerance
22276 limits (intervals) for various univariate distributions (binomial, Cauchy,
22277 discrete Pareto, exponential, two-parameter exponential, extreme value,
22278 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
22279 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
22280 Bayesian normal tolerance limits, multivariate normal tolerance regions,
22281 nonparametric tolerance intervals, tolerance bands for regression
22282 settings (linear regression, nonlinear regression, nonparametric regression,
22283 and multivariate regression), and analysis of variance tolerance intervals.
22284 Visualizations are also available for most of these settings.")
22285 (license license:gpl2+)))
22287 (define-public r-additivitytests
22289 (name "r-additivitytests")
22294 (uri (cran-uri "additivityTests" version))
22297 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
22299 `((upstream-name . "additivityTests")))
22300 (build-system r-build-system)
22301 (home-page "https://github.com/simecek/additivityTests")
22302 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
22304 "This package provides an implementation of the Tukey, Mandel,
22305 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
22306 (license license:gpl3)))
22308 (define-public r-flexclust
22310 (name "r-flexclust")
22315 (uri (cran-uri "flexclust" version))
22318 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
22319 (properties `((upstream-name . "flexclust")))
22320 (build-system r-build-system)
22322 (list r-class r-lattice r-modeltools))
22323 (home-page "https://cran.r-project.org/web/packages/flexclust/")
22324 (synopsis "Flexible cluster algorithms")
22326 "The main function @code{kcca} implements a general framework for
22327 k-centroids cluster analysis supporting arbitrary distance measures and
22328 centroid computation. Further cluster methods include hard competitive
22329 learning, neural gas, and QT clustering. There are numerous visualization
22330 methods for cluster results (neighborhood graphs, convex cluster hulls,
22331 barcharts of centroids, ...), and bootstrap methods for the analysis of
22332 cluster stability.")
22333 (license license:gpl2)))
22335 (define-public r-biclust
22342 (uri (cran-uri "biclust" version))
22345 "0lgyc2f04dhr65cwga78pradxsdzgjrpp8vphchqn60ab1z95dlp"))))
22346 (properties `((upstream-name . "biclust")))
22347 (build-system r-build-system)
22349 (list r-additivitytests
22356 (home-page "https://cran.r-project.org/web/packages/biclust/")
22357 (synopsis "BiCluster algorithms")
22359 "The main function @code{biclust()} provides several algorithms to find
22360 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
22361 In addition, the package provides methods for data
22362 preprocessing (normalization and discretization), visualization, and
22363 validation of bicluster solutions.")
22364 (license license:gpl3)))
22366 (define-public r-icge
22373 (uri (cran-uri "ICGE" version))
22376 "0w6hbi3h98q6gsxqbb43p95v6xykgrasxcjivwm8hw9fly4avxyi"))))
22377 (properties `((upstream-name . "ICGE")))
22378 (build-system r-build-system)
22380 (list r-cluster r-fastcluster r-mass))
22381 (home-page "https://cran.r-project.org/web/packages/ICGE/")
22382 (synopsis "Cluster estimation and identification of atypical units")
22384 "ICGE is a package that helps to estimate the number of real clusters in
22385 data as well as to identify atypical units. The underlying methods are based
22386 on distances rather than on unit x variables.")
22387 (license license:gpl2+)))
22389 (define-public r-depth
22392 (version "2.1-1.1")
22396 (uri (cran-uri "depth" version))
22399 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
22400 (properties `((upstream-name . "depth")))
22401 (build-system r-build-system)
22403 (list r-abind r-circular r-rgl))
22406 (home-page "https://cran.r-project.org/web/packages/depth/")
22407 (synopsis "Nonparametric depth functions for multivariate analysis")
22409 "This package provides tools for depth functions methodology applied to
22410 multivariate analysis. Besides allowing calculation of depth values and
22411 depth-based location estimators, the package includes functions or drawing
22412 contour plots and perspective plots of depth functions. Euclidean and
22413 spherical depths are supported.")
22414 (license license:gpl2)))
22416 (define-public r-archetypes
22418 (name "r-archetypes")
22419 (version "2.2-0.1")
22423 (uri (cran-uri "archetypes" version))
22426 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
22427 (properties `((upstream-name . "archetypes")))
22428 (build-system r-build-system)
22430 (list r-modeltools r-nnls))
22431 (home-page "https://cran.r-project.org/web/packages/archetypes")
22432 (synopsis "Archetypal analysis")
22434 "The main function @code{archetypes} implements a framework for
22435 archetypal analysis supporting arbitrary problem solving mechanisms for the
22436 different conceptual parts of the algorithm.")
22437 (license license:gpl2+)))
22439 (define-public r-shapes
22446 (uri (cran-uri "shapes" version))
22449 "1p9fr95zk3q2v277c5ksb0nh26mcpzwjzjb2lmag51z6hck8cb66"))))
22450 (properties `((upstream-name . "shapes")))
22451 (build-system r-build-system)
22453 (list r-mass r-minpack-lm r-rgl r-scatterplot3d))
22454 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
22455 (synopsis "Statistical shape analysis")
22457 "This package provides routines for the statistical analysis of landmark
22458 shapes, including Procrustes analysis, graphical displays, principal
22459 components analysis, permutation and bootstrap tests, thin-plate spline
22460 transformation grids and comparing covariance matrices. See Dryden, I.L. and
22461 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
22462 Edition), John Wiley and Sons.")
22463 (license license:gpl2)))
22465 (define-public r-anthropometry
22467 (name "r-anthropometry")
22472 (uri (cran-uri "Anthropometry" version))
22475 "0iqlmp9vig4qdavs37kislqxwhk0c0pgsn1kwz3mm75nylxmpbp0"))))
22476 (properties `((upstream-name . "Anthropometry")))
22477 (build-system r-build-system)
22490 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
22491 (synopsis "Statistical methods for anthropometric data")
22493 "This package provides statistical methods especially developed to
22494 analyze anthropometric data. These methods are aimed at providing effective
22495 solutions to some commons problems related to Ergonomics and Anthropometry.
22496 They are based on clustering, the statistical concept of data depth,
22497 statistical shape analysis and archetypal analysis.")
22498 (license license:gpl2+)))
22500 (define-public r-adamethods
22502 (name "r-adamethods")
22507 (uri (cran-uri "adamethods" version))
22510 "150awbd3skb1mqca18bqjykhyycqw8crviw66s6qrcnmcsbk77pj"))))
22511 (properties `((upstream-name . "adamethods")))
22512 (build-system r-build-system)
22514 (list r-anthropometry
22521 (home-page "https://cran.r-project.org/web/packages/adamethods/")
22522 (synopsis "Archetypoid algorithms and anomaly detection")
22524 "This package is a collection of several algorithms to obtain
22525 archetypoids with small and large databases and with both classical
22526 multivariate data and functional data (univariate and multivariate). Some of
22527 these algorithms also detect anomalies (outliers).")
22528 (license license:gpl2+)))
22530 (define-public r-idpmisc
22537 (uri (cran-uri "IDPmisc" version))
22540 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
22541 (properties `((upstream-name . "IDPmisc")))
22542 (build-system r-build-system)
22545 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
22546 (synopsis "Functions for data analyses and visualization")
22548 "This package provides different high-level graphics functions for
22549 displaying large datasets, displaying circular data in a very flexible way,
22550 finding local maxima, brewing color ramps, drawing nice arrows, zooming
22551 2D-plots, creating figures with differently colored margin and plot region.
22552 In addition, the package contains auxiliary functions for data manipulation
22553 like omitting observations with irregular values or selecting data by logical
22554 vectors, which include NAs. Other functions are especially useful in
22555 spectroscopy and analyses of environmental data: robust baseline fitting,
22556 finding peaks in spectra, converting humidity measures.")
22557 (license license:gpl3+)))
22559 (define-public r-qqman
22566 (uri (cran-uri "qqman" version))
22569 "1a6qp5wv9bvwjchfw8x4jh48hkynlnfr21a8vqgnswldvwbq7njq"))))
22570 (properties `((upstream-name . "qqman")))
22571 (build-system r-build-system)
22573 (list r-calibrate))
22576 (home-page "https://cran.r-project.org/web/packages/qqman/")
22577 (synopsis "Q-Q and Manhattan plots for GWAS data")
22579 "This package allows you to create Q-Q and Manhattan plots for GWAS data
22580 from PLINK results.")
22581 (license license:gpl3)))
22583 (define-public r-ggplot-multistats
22585 (name "r-ggplot-multistats")
22590 (uri (cran-uri "ggplot.multistats" version))
22593 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
22595 `((upstream-name . "ggplot.multistats")))
22596 (build-system r-build-system)
22598 (list r-ggplot2 r-hexbin r-rlang r-scales))
22599 (home-page "https://github.com/flying-sheep/ggplot.multistats")
22600 (synopsis "Multiple summary statistics for binned stats/geometries")
22602 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
22603 which functions similar to its singular form, but allows the use of multiple
22604 statistics per bin. Those statistics can be mapped to multiple bin
22606 (license license:gpl3)))
22608 (define-public r-knn-covertree
22610 (name "r-knn-covertree")
22615 (uri (cran-uri "knn.covertree" version))
22618 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
22619 (properties `((upstream-name . "knn.covertree")))
22620 (build-system r-build-system)
22622 (list r-matrix r-rcpp r-rcppeigen))
22623 (home-page "https://github.com/flying-sheep/knn.covertree")
22624 (synopsis "Accurate kNN Implementation with multiple distance measures")
22626 "Similarly to the FNN package, this package allows calculation of the k
22627 nearest neighbors (kNN) of a data matrix. The implementation is based on
22628 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
22629 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
22630 (license license:agpl3+)))
22632 (define-public r-poibin
22639 (uri (cran-uri "poibin" version))
22642 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
22643 (properties `((upstream-name . "poibin")))
22644 (build-system r-build-system)
22645 (home-page "https://cran.r-project.org/web/packages/poibin/")
22646 (synopsis "Poisson binomial distribution")
22648 "This package provides an implementation of both the exact and
22649 approximation methods for computing the @dfn{cumulative distribution
22650 function} (CDF) of the Poisson binomial distribution. It also provides the
22651 @dfn{probability mass function} (PMF), quantile function, and random number
22652 generation for the Poisson binomial distribution.")
22653 (license license:gpl2)))
22655 (define-public r-diagram
22662 (uri (cran-uri "diagram" version))
22665 "1r3lyl0h7mk9cfg8smr3jydfkjdawaphnxibkxfjqa7029vkxh79"))))
22666 (properties `((upstream-name . "diagram")))
22667 (build-system r-build-system)
22670 (home-page "https://cran.r-project.org/web/packages/diagram/")
22671 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
22673 "This package provides tools to visualize simple graphs (networks) based
22674 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
22675 electrical networks, etc. It also includes supporting material for the book
22676 \"A practical guide to ecological modelling - using R as a simulation
22677 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
22678 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
22679 Francesca Mazzia (2012).")
22680 (license license:gpl2+)))
22682 (define-public r-lim
22689 (uri (cran-uri "LIM" version))
22692 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
22693 (properties `((upstream-name . "LIM")))
22694 (build-system r-build-system)
22696 (list r-diagram r-limsolve))
22697 (home-page "https://cran.r-project.org/web/packages/LIM/")
22698 (synopsis "Linear inverse model examples and solution methods")
22700 "This package provides functions that read and solve linear inverse
22701 problems (food web problems, linear programming problems).")
22702 (license license:gpl2+)))
22704 (define-public r-shinycssloaders
22706 (name "r-shinycssloaders")
22711 (uri (cran-uri "shinycssloaders" version))
22714 "0r3xm273lhdhzbs2mkgw1m2kwb7z1dh1pzya8yxy5vacda1l2ikl"))))
22716 `((upstream-name . "shinycssloaders")))
22717 (build-system r-build-system)
22719 (list r-digest r-glue r-shiny))
22720 (home-page "https://github.com/andrewsali/shinycssloaders")
22721 (synopsis "Add CSS loading animations to Shiny outputs")
22723 "This package provides tools to create a lightweight Shiny wrapper for
22724 the css-loaders created by Luke Hass
22725 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
22726 automatically show a loader when the output is (re)calculating.")
22727 (license license:gpl3)))
22729 (define-public r-rsvg
22736 (uri (cran-uri "rsvg" version))
22739 "10p6aps2rsvhf4xgngl9x20cf2wqbzhlpjds8biyihvj58c1q8nn"))))
22740 (properties `((upstream-name . "rsvg")))
22741 (build-system r-build-system)
22743 (list librsvg zlib))
22745 (list pkg-config r-knitr))
22746 (home-page "https://github.com/jeroen/rsvg#readme")
22747 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
22749 "This package allows you to render vector-based SVG images into
22750 high-quality custom-size bitmap arrays using the librsvg2 library. The
22751 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
22752 addition, the package can convert images directly to various formats such as
22753 PDF or PostScript.")
22754 (license license:expat)))
22756 (define-public r-influencer
22758 (name "r-influencer")
22759 (version "0.1.0.1")
22763 (uri (cran-uri "influenceR" version))
22766 "0rj7rm236vn3v8302nwl12s0kvpv6xpdbm3q3gxk7vgwfl8nzi33"))))
22767 (properties `((upstream-name . "influenceR")))
22768 (build-system r-build-system)
22770 (list r-igraph r-matrix))
22771 (home-page "https://github.com/rcc-uchicago/influenceR")
22772 (synopsis "Tools to quantify structural importance of nodes in a network")
22774 "This package provides functionality to compute various node centrality
22775 measures on networks. Included are functions to compute betweenness
22776 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
22777 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
22778 algorithm to identify key players, and Valente's bridging metric. The
22779 betweenness, Key Players, and bridging implementations are parallelized with
22781 (license license:gpl2)))
22783 (define-public r-emplik
22790 (uri (cran-uri "emplik" version))
22793 "1kw8g8j075bsicdvgkjf4870rfv5c30gvmw6qkkaz3ki22x74w77"))))
22794 (properties `((upstream-name . "emplik")))
22795 (build-system r-build-system)
22798 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
22799 (synopsis "Empirical likelihood ratio for censored/truncated data")
22801 "This package provides empirical likelihood ratio tests for
22802 means/quantiles/hazards from possibly censored and/or truncated data. It also
22804 (license license:gpl2+)))
22806 (define-public r-imputeyn
22808 (name "r-imputeyn")
22813 (uri (cran-uri "imputeYn" version))
22816 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
22817 (properties `((upstream-name . "imputeYn")))
22818 (build-system r-build-system)
22820 (list r-boot r-emplik r-mvtnorm r-quadprog r-survival))
22821 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
22822 (synopsis "Impute last largest censored observation under weighted least squares")
22824 "This package allows for the imputation of the last largest censored
22825 observantions. This method brings less bias and more efficient estimates for
22827 (license license:gpl2)))
22829 (define-public r-adapenetclass
22831 (name "r-adapenetclass")
22836 (uri (cran-uri "AdapEnetClass" version))
22839 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
22840 (properties `((upstream-name . "AdapEnetClass")))
22841 (build-system r-build-system)
22843 (list r-glmnet r-imputeyn r-lars r-quadprog))
22844 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
22845 (synopsis "Class of adaptive elastic net methods for censored data")
22847 "This package provides methods for variable selection for AFT models.")
22848 (license license:gpl2)))
22850 (define-public r-flock
22857 (uri (cran-uri "flock" version))
22860 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
22861 (properties `((upstream-name . "flock")))
22862 (build-system r-build-system)
22863 (propagated-inputs (list r-rcpp))
22864 (home-page "https://cran.r-project.org/web/packages/flock/")
22865 (synopsis "Process synchronization using file locks")
22867 "This package implements synchronization between R processes (spawned by
22868 using the @code{parallel} package for instance) using file locks. It supports
22869 both exclusive and shared locking.")
22870 (license license:asl2.0)))
22872 (define-public r-archivist
22874 (name "r-archivist")
22879 (uri (cran-uri "archivist" version))
22882 "0q1qysack30xzxdbvvi56rk7r85hsj4ghls9r70ki7bl3rqwr4c9"))))
22883 (properties `((upstream-name . "archivist")))
22884 (build-system r-build-system)
22896 (home-page "https://pbiecek.github.io/archivist/")
22897 (synopsis "Tools for storing, restoring and searching for R objects")
22899 "Data exploration and modelling is a process in which a lot of data
22900 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
22901 statistical models, different versions of data sets and different versions of
22902 results. Archivist helps to store and manage artifacts created in R. It
22903 allows you to store selected artifacts as binary files together with their
22904 metadata and relations. Archivist allows sharing artifacts with others. It
22905 can look for already created artifacts by using its class, name, date of the
22906 creation or other properties. It also makes it easy to restore such
22908 (license license:gpl2)))
22910 (define-public r-versions
22912 (name "r-versions")
22917 (uri (cran-uri "versions" version))
22920 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
22921 (properties `((upstream-name . "versions")))
22922 (build-system r-build-system)
22923 (home-page "https://cran.r-project.org/web/packages/versions/")
22924 (synopsis "Query and install specific versions of CRAN packages")
22926 "This package allows you to install specified versions of R packages
22927 hosted on CRAN and provides functions to list available versions and the
22928 versions of currently installed packages.")
22929 (license license:bsd-3)))
22931 (define-public r-adapr
22938 (uri (cran-uri "adapr" version))
22941 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
22942 (properties `((upstream-name . "adapr")))
22943 (build-system r-build-system)
22960 (home-page "https://cran.r-project.org/web/packages/adapr/")
22961 (synopsis "Implementation of an accountable data analysis process")
22963 "This package tracks reading and writing within R scripts that are
22964 organized into a directed acyclic graph. It contains an interactive Shiny
22965 application @code{adaprApp()}. It uses Git and file hashes to track version
22966 histories of inputs and outputs.")
22967 (license license:lgpl2.0)))
22969 (define-public r-adapsamp
22971 (name "r-adapsamp")
22976 (uri (cran-uri "AdapSamp" version))
22979 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
22980 (properties `((upstream-name . "AdapSamp")))
22981 (build-system r-build-system)
22982 (propagated-inputs (list r-pracma))
22983 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
22984 (synopsis "Adaptive sampling algorithms")
22986 "For distributions whose probability density functions are log-concave,
22987 the adaptive rejection sampling algorithm can be used to build envelope
22988 functions for sampling. For others, the modified adaptive rejection sampling
22989 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
22990 adaptive slice sampling algorithm can be used. This R package mainly includes
22991 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
22992 @code{rASS()}. These functions can realize sampling based on the algorithms
22994 (license license:gpl2)))
22996 (define-public r-adaptalint
22998 (name "r-adaptalint")
23003 (uri (cran-uri "adaptalint" version))
23006 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
23007 (properties `((upstream-name . "adaptalint")))
23008 (build-system r-build-system)
23010 (list r-dplyr r-lintr r-purrr))
23011 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
23012 (synopsis "Check R code style")
23014 "This package provides tools to infer the code style (which style rules
23015 are followed and which ones are not) from one package and use it to check
23016 another. This makes it easier to find and correct the most important problems
23018 (license license:gpl3)))
23020 (define-public r-fracdiff
23022 (name "r-fracdiff")
23027 (uri (cran-uri "fracdiff" version))
23030 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
23031 (properties `((upstream-name . "fracdiff")))
23032 (build-system r-build-system)
23033 (home-page "https://github.com/mmaechler/fracdiff")
23035 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
23037 "This package provides tools for the maximum likelihood estimation of the
23038 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
23039 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
23040 (license license:gpl2+)))
23042 (define-public r-forecast
23044 (name "r-forecast")
23049 (uri (cran-uri "forecast" version))
23052 "0x4ij55sb45qnwba3bybs50vsvv82q3j8p47xmbv959h13nsnfn7"))))
23053 (properties `((upstream-name . "forecast")))
23054 (build-system r-build-system)
23069 (list r-knitr)) ; needed for vignettes
23070 (home-page "https://pkg.robjhyndman.com/forecast/")
23071 (synopsis "Forecasting functions for time series and linear models")
23073 "This package provides methods and tools for displaying and analysing
23074 univariate time series forecasts including exponential smoothing via state
23075 space models and automatic ARIMA modelling.")
23076 (license license:gpl3)))
23078 (define-public r-formattable
23080 (name "r-formattable")
23085 (uri (cran-uri "formattable" version))
23087 (base32 "1vdxi0xmg019qyzjrp8bkjxciz245jcxsrkhfzd44ynqcwi4s3ag"))))
23088 (properties `((upstream-name . "formattable")))
23089 (build-system r-build-system)
23091 (list r-htmltools r-htmlwidgets r-lifecycle r-rmarkdown))
23094 (home-page "https://github.com/renkun-ken/formattable")
23095 (synopsis "Print vectors and data frames with text fromatting")
23097 "This R package provides functions to create formattable vectors and data
23098 frames. @emph{Formattable} vectors are printed with text formatting, and
23099 formattable data frames are printed with multiple types of formatting in HTML
23100 to improve the readability of data presented in tabular form rendered in web
23102 (license license:expat)))
23104 (define-public r-xmisc
23111 (uri (cran-uri "Xmisc" version))
23114 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
23115 (properties `((upstream-name . "Xmisc")))
23116 (build-system r-build-system)
23117 (home-page "https://cran.r-project.org/package=Xmisc")
23119 "Xiaobei's miscellaneous classes and functions")
23121 "This package provides Xiaobei's miscellaneous classes and functions,
23122 which are useful when developing R packages for @dfn{object oriented
23123 programming} (OOP) using R Reference Class.")
23124 (license license:gpl2+)))
23126 (define-public r-proxyc
23133 (uri (cran-uri "proxyC" version))
23136 "1g90d82rp82dkidlfykankprzpp94d7394s2b2qjlyiia3k0hlb3"))))
23137 (properties `((upstream-name . "proxyC")))
23138 (build-system r-build-system)
23140 (list r-matrix r-rcpp r-rcpparmadillo r-rcppparallel))
23141 (home-page "https://cran.r-project.org/package=proxyC")
23142 (synopsis "Compute proximity in large sparse matrices")
23144 "This package provides efficient tools to compute the proximity between
23145 rows or columns of large matrices. Functions are optimised for large sparse
23146 matrices using the Armadillo and Intel TBB libraries. Among several built-in
23147 similarity/distance measures, computation of correlation, cosine similarity
23148 and Euclidean distance is particularly fast.")
23149 (license license:gpl3)))
23151 (define-public r-isocodes
23153 (name "r-isocodes")
23154 (version "2021.02.24")
23158 (uri (cran-uri "ISOcodes" version))
23161 "19irnn2yi1bzhf03g666la84kj8040f5913kfrmd16dfnjy6j9qm"))))
23162 (properties `((upstream-name . "ISOcodes")))
23163 (build-system r-build-system)
23164 (home-page "https://cran.r-project.org/package=ISOcodes")
23165 (synopsis "Selected ISO codes")
23167 "This package provides ISO language, territory, currency, script and
23168 character codes. It provides ISO 639 language codes, ISO 3166 territory
23169 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
23170 character codes as well as the UN M.49 area codes.")
23171 (license license:gpl2)))
23173 (define-public r-stopwords
23175 (name "r-stopwords")
23180 (uri (cran-uri "stopwords" version))
23183 "1ci1cgxrcvlhhplximsfv0plvjdbcd5kv0nphxnpildsn5m1rv65"))))
23184 (properties `((upstream-name . "stopwords")))
23185 (build-system r-build-system)
23188 (home-page "https://github.com/quanteda/stopwords")
23189 (synopsis "Multilingual stopword lists")
23191 "This package provides multiple sources of stopwords, for use in text
23192 analysis and natural language processing.")
23193 (license license:expat)))
23195 (define-public r-spacyr
23202 (uri (cran-uri "spacyr" version))
23205 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
23206 (properties `((upstream-name . "spacyr")))
23207 (build-system r-build-system)
23209 (list r-data-table r-reticulate))
23210 (home-page "https://spacyr.quanteda.io")
23211 (synopsis "R wrapper for the spaCy NLP library")
23213 "This package provides an R wrapper to the Python @dfn{natural language
23214 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
23215 (license license:gpl3)))
23217 (define-public r-snowballc
23219 (name "r-snowballc")
23224 (uri (cran-uri "SnowballC" version))
23227 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
23228 (properties `((upstream-name . "SnowballC")))
23229 (build-system r-build-system)
23230 (home-page "https://r-forge.r-project.org/projects/r-temis/")
23231 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
23233 "This package provides an R interface to the C @code{libstemmer} library
23234 that implements Porter's word stemming algorithm for collapsing words to a
23235 common root to aid comparison of vocabulary. Currently supported languages
23236 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
23237 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
23238 (license license:bsd-3)))
23240 (define-public r-quanteda
23242 (name "r-quanteda")
23247 (uri (cran-uri "quanteda" version))
23250 "0gafbb73gcxx2gq9q7bg88alyhymkr471lp394m5ydij6mdm4hb9"))))
23251 (properties `((upstream-name . "quanteda")))
23252 (build-system r-build-system)
23267 (home-page "https://quanteda.io")
23268 (synopsis "Quantitative analysis of textual data")
23270 "This package provides a fast, flexible, and comprehensive framework for
23271 quantitative text analysis in R. It provides functionality for corpus
23272 management, creating and manipulating tokens and ngrams, exploring keywords in
23273 context, forming and manipulating sparse matrices of documents by features and
23274 feature co-occurrences, analyzing keywords, computing feature similarities and
23275 distances, applying content dictionaries, applying supervised and unsupervised
23276 machine learning, visually representing text and text analyses, and more.")
23277 (license license:gpl3)))
23279 (define-public r-topicmodels
23281 (name "r-topicmodels")
23286 (uri (cran-uri "topicmodels" version))
23289 "1d6iizmn042b59q2y6qc82z19wq3xm0zvgkf8iqf8fdzh51kmn5g"))))
23290 (properties `((upstream-name . "topicmodels")))
23291 (build-system r-build-system)
23295 (list r-modeltools r-slam r-tm))
23296 (home-page "https://cran.r-project.org/package=topicmodels")
23297 (synopsis "Topic models")
23299 "This package provides an interface to the C code for @dfn{Latent
23300 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
23301 David M. Blei and co-authors and the C++ code for fitting LDA models using
23302 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
23303 (license license:gpl2)))
23305 (define-public r-stm
23312 (uri (cran-uri "stm" version))
23315 "0qwq4nin2n9fjd06852r8k7arvcgh46kcfb3lm21swgx6j8bgrhb"))))
23316 (properties `((upstream-name . "stm")))
23317 (build-system r-build-system)
23330 (home-page "http://www.structuraltopicmodel.com/")
23331 (synopsis "Estimation of the Structural Topic Model")
23333 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
23334 topic models with document-level covariates. The package also includes tools
23335 for model selection, visualization, and estimation of topic-covariate
23337 (license license:expat)))
23339 (define-public r-polycor
23346 (uri (cran-uri "polycor" version))
23349 "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna"))))
23350 (properties `((upstream-name . "polycor")))
23351 (build-system r-build-system)
23353 (list r-matrix r-mvtnorm))
23354 (home-page "https://r-forge.r-project.org/projects/polycor/")
23355 (synopsis "Polychoric and polyserial correlations")
23357 "This package provides tools to compute polychoric and polyserial
23358 correlations by quick \"two-step\" methods or ML, optionally with standard
23359 errors; tetrachoric and biserial correlations are special cases.")
23360 (license license:gpl2+)))
23362 (define-public r-msm
23369 (uri (cran-uri "msm" version))
23372 "08vhazswyxr3y1zb9y60mbg3bappzlizxml8s08p65mh82xxkz5f"))))
23373 (properties `((upstream-name . "msm")))
23374 (build-system r-build-system)
23376 (list r-expm r-mvtnorm r-survival))
23377 (home-page "https://github.com/chjackson/msm")
23378 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
23380 "This package provides functions for fitting continuous-time Markov and
23381 hidden Markov multi-state models to longitudinal data. It was designed for
23382 processes observed at arbitrary times in continuous time (panel data) but some
23383 other observation schemes are supported. Both Markov transition rates and the
23384 hidden Markov output process can be modelled in terms of covariates, which may
23385 be constant or piecewise-constant in time.")
23386 (license license:gpl2+)))
23388 (define-public r-ltm
23395 (uri (cran-uri "ltm" version))
23398 "1qrgzwx5l58qf5rfp1knxc84r0g943q5sdr3ky74zzwpnmrf2vf7"))))
23399 (properties `((upstream-name . "ltm")))
23400 (build-system r-build-system)
23402 (list r-mass r-msm r-polycor))
23403 (home-page "https://github.com/drizopoulos/ltm")
23404 (synopsis "Latent trait models under IRT")
23406 "This is a package supporting the analysis of multivariate dichotomous
23407 and polytomous data using latent trait models under the Item Response Theory
23408 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
23409 Three-Parameter, the Graded Response, and the Generalized Partial Credit
23411 (license license:gpl2+)))
23413 (define-public r-mi
23420 (uri (cran-uri "mi" version))
23423 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
23424 (properties `((upstream-name . "mi")))
23425 (build-system r-build-system)
23427 (list r-arm r-matrix))
23428 (home-page "http://www.stat.columbia.edu/~gelman/")
23429 (synopsis "Missing data imputation and model checking")
23431 "This package provides functions for data manipulation, imputing missing
23432 values in an approximate Bayesian framework, diagnostics of the models used to
23433 generate the imputations, confidence-building mechanisms to validate some of
23434 the assumptions of the imputation algorithm, and functions to analyze multiply
23435 imputed data sets with the appropriate degree of sampling uncertainty.")
23436 (license license:gpl2+)))
23438 (define-public r-matrixcalc
23440 (name "r-matrixcalc")
23445 (uri (cran-uri "matrixcalc" version))
23448 "1jkgl1v1q7cqpl1rf49qahdr9y0f33f0ldsbgby8xhfv0vpy21jr"))))
23449 (properties `((upstream-name . "matrixcalc")))
23450 (build-system r-build-system)
23451 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
23452 (synopsis "Collection of functions for matrix calculations")
23454 "This package provides a collection of functions to support matrix
23455 calculations for probability, econometric and numerical analysis. There are
23456 additional functions that are comparable to APL functions which are useful for
23457 actuarial models such as pension mathematics.")
23458 (license license:gpl2+)))
23460 (define-public r-sem
23467 (uri (cran-uri "sem" version))
23470 "0r9g4j0w6q4qy9jl9gkjkihml4109ymg3y6zmhyg806q19qryx07"))))
23471 (properties `((upstream-name . "sem")))
23472 (build-system r-build-system)
23474 (list r-boot r-mass r-mi))
23475 (home-page "https://cran.r-project.org/package=sem")
23476 (synopsis "Structural equation models")
23478 "This package provides functions for fitting general linear structural
23479 equation models (with observed and latent variables) using the RAM approach,
23480 and for fitting structural equations in observed-variable models by two-stage
23482 (license license:gpl2+)))
23484 (define-public r-semtools
23486 (name "r-semtools")
23491 (uri (cran-uri "semTools" version))
23494 "1dpsn43ifvfy5v8w2fqdy54yclmy0d3qlzix67lflr2r7isq7y6x"))))
23495 (properties `((upstream-name . "semTools")))
23496 (build-system r-build-system)
23498 (list r-lavaan r-pbivnorm))
23499 (home-page "https://github.com/simsem/semTools/wiki")
23500 (synopsis "Useful tools for structural equation modeling")
23502 "This package provides useful tools for structural equation modeling.")
23503 (license license:gpl2+)))
23505 (define-public r-regsem
23512 (uri (cran-uri "regsem" version))
23515 "1v33wkrsawcvaa06cijp8ybwi82a0x34y59hdknwdbywplnirzr8"))))
23516 (properties `((upstream-name . "regsem")))
23517 (build-system r-build-system)
23519 (list r-lavaan r-rcpp r-rcpparmadillo r-rsolnp))
23522 (home-page "https://cran.r-project.org/package=regsem")
23523 (synopsis "Regularized structural equation modeling")
23525 "This package uses both ridge and lasso penalties (and extensions) to
23526 penalize specific parameters in structural equation models. The package
23527 offers additional cost functions, cross validation, and other extensions
23528 beyond traditional structural equation models. It also contains a function to
23529 perform @dfn{exploratory mediation} (XMed).")
23530 (license license:gpl2+)))
23532 (define-public r-stanheaders
23534 (name "r-stanheaders")
23535 (version "2.21.0-7")
23539 (uri (cran-uri "StanHeaders" version))
23542 "0srkyawyiykn3p5lw1z3zf18s4ax4iasv1ci3l1px40f9w36wm17"))))
23543 (properties `((upstream-name . "StanHeaders")))
23544 (build-system r-build-system)
23545 (inputs (list pandoc))
23547 (list r-rcppeigen r-rcppparallel))
23549 (list gfortran r-knitr)) ; for vignettes
23550 (home-page "https://mc-stan.org/")
23551 (synopsis "C++ header files for Stan")
23553 "The C++ header files of the Stan project are provided by this package.
23554 There is a shared object containing part of the @code{CVODES} library, but it
23555 is not accessible from R. @code{r-stanheaders} is only useful for developers
23556 who want to utilize the @code{LinkingTo} directive of their package's
23557 DESCRIPTION file to build on the Stan library without incurring unnecessary
23560 The Stan project develops a probabilistic programming language that implements
23561 full or approximate Bayesian statistical inference via Markov Chain Monte
23562 Carlo or variational methods and implements (optionally penalized) maximum
23563 likelihood estimation via optimization. The Stan library includes an advanced
23564 automatic differentiation scheme, templated statistical and linear algebra
23565 functions that can handle the automatically differentiable scalar types (and
23566 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
23567 package provides user-facing R functions to parse, compile, test, estimate,
23568 and analyze Stan models.")
23569 (license license:bsd-3)))
23571 (define-public r-rpf
23578 (uri (cran-uri "rpf" version))
23581 "1yr1i7kswq57mcxv05lh7bvbicz1djqxcl6f13dlgsf3ww56gzg1"))))
23582 (properties `((upstream-name . "rpf")))
23583 (build-system r-build-system)
23585 (list r-lifecycle r-mvtnorm r-rcpp r-rcppeigen))
23588 (home-page "https://github.com/jpritikin/rpf")
23589 (synopsis "Response probability functions")
23591 "The purpose of this package is to factor out logic and math common to
23592 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
23593 core support code suitable for more specialized IRT packages to build upon.
23594 Complete access to optimized C functions is made available with
23595 @code{R_RegisterCCallable()}.")
23596 (license license:gpl3+)))
23598 (define-public r-openmx
23605 (uri (cran-uri "OpenMx" version))
23608 "0q37mwxqhgdi05rwdfwfapgazfp541xsvw3yskf21lv11y2yjjyb"))))
23609 (properties `((upstream-name . "OpenMx")))
23610 (build-system r-build-system)
23622 (native-inputs (list gfortran))
23623 (home-page "http://openmx.ssri.psu.edu")
23624 (synopsis "Extended structural equation modelling")
23626 "This package allows for the estimation of a wide variety of advanced
23627 multivariate statistical models. It consists of a library of functions and
23628 optimizers that allow you to quickly and flexibly define an SEM model and
23629 estimate parameters given observed data.")
23630 (license license:asl2.0)))
23632 (define-public r-kutils
23639 (uri (cran-uri "kutils" version))
23642 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
23643 (properties `((upstream-name . "kutils")))
23644 (build-system r-build-system)
23646 (list r-foreign r-openxlsx r-plyr r-runit r-xtable))
23647 (home-page "https://cran.r-project.org/package=kutils")
23648 (synopsis "Project management tools")
23650 "This package provides tools for data importation, recoding, and
23651 inspection. There are functions to create new project folders, R code
23652 templates, create uniquely named output directories, and to quickly obtain a
23653 visual summary for each variable in a data frame. The main feature here is
23654 the systematic implementation of the \"variable key\" framework for data
23655 importation and recoding.")
23656 (license license:gpl2)))
23658 (define-public r-rockchalk
23660 (name "r-rockchalk")
23661 (version "1.8.144")
23665 (uri (cran-uri "rockchalk" version))
23668 "07dp1n155b9gfvk8l30h6bhjbhbylsjxfzns08mryn4mxj3nqpnb"))))
23669 (properties `((upstream-name . "rockchalk")))
23670 (build-system r-build-system)
23672 (list r-cardata r-kutils r-lme4 r-mass))
23673 (home-page "https://cran.r-project.org/package=rockchalk")
23674 (synopsis "Regression estimation and presentation")
23676 "This package provides a collection of functions for interpretation and
23677 presentation of regression analysis. These functions are used to produce the
23678 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
23679 includes regression diagnostics, regression tables, and plots of interactions
23680 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
23681 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
23682 fairly comprehensive overview.")
23683 (license license:gpl3+)))
23685 (define-public r-lisreltor
23687 (name "r-lisreltor")
23692 (uri (cran-uri "lisrelToR" version))
23695 "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
23696 (properties `((upstream-name . "lisrelToR")))
23697 (build-system r-build-system)
23698 (home-page "https://cran.r-project.org/package=lisrelToR")
23699 (synopsis "Import output from LISREL into R")
23701 "This is an unofficial package aimed at automating the import of LISREL
23703 (license license:gpl2)))
23705 (define-public r-bdgraph
23712 (uri (cran-uri "BDgraph" version))
23715 "0pnzbw09c7amsvj8l4p1jnmss4rkbr1dsmagiygh8lj5fbrklgr4"))))
23716 (properties `((upstream-name . "BDgraph")))
23717 (build-system r-build-system)
23720 (home-page "https://www.uva.nl/profile/a.mohammadi")
23721 (synopsis "Bayesian structure learning in graphical models")
23723 "This package provides statistical tools for Bayesian structure learning
23724 in undirected graphical models for continuous, discrete, and mixed data. It
23725 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
23726 on a continuous-time birth-death process.")
23727 (license license:gpl2+)))
23729 (define-public r-d3network
23731 (name "r-d3network")
23732 (version "0.5.2.1")
23736 (uri (cran-uri "d3Network" version))
23739 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
23740 (properties `((upstream-name . "d3Network")))
23741 (build-system r-build-system)
23743 (list r-plyr r-rjson r-whisker))
23744 (home-page "http://christophergandrud.github.io/d3Network/")
23745 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
23747 "This package is intended to make it easy to create D3 JavaScript
23748 network, tree, dendrogram, and Sankey graphs from R using data frames.")
23749 (license license:gpl3+)))
23751 (define-public r-qgraph
23758 (uri (cran-uri "qgraph" version))
23761 "1ahhzp64jdgki5p2wga5mn8a2n1x2zldgpilrpf7hy5l9nf4imz1"))))
23762 (properties `((upstream-name . "qgraph")))
23763 (build-system r-build-system)
23783 (home-page "http://sachaepskamp.com/qgraph/")
23784 (synopsis "Weighted network visualization and analysis")
23786 "This package implements tools for weighted network visualization and
23787 analysis, as well as Gaussian graphical model computation. It contains graph
23788 plotting methods, and tools for psychometric data visualization and graphical
23789 model estimation. See Epskamp et al. (2012)
23790 @url{doi:10.18637/jss.v048.i04}.")
23791 (license license:gpl2)))
23793 (define-public r-semplot
23800 (uri (cran-uri "semPlot" version))
23803 "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr"))))
23804 (properties `((upstream-name . "semPlot")))
23805 (build-system r-build-system)
23819 (home-page "https://github.com/SachaEpskamp/semPlot")
23820 (synopsis "Unified visualizations of structural equation models")
23822 "Structural equation modeling (SEM) has a long history of representing
23823 models graphically as path diagrams. The semPlot package for R fills the gap
23824 between advanced, but time-consuming, graphical software and the limited
23825 graphics produced automatically by SEM software. In addition, semPlot offers
23826 more functionality than drawing path diagrams: it can act as a common ground
23827 for importing SEM results into R. Any result usable as input to semPlot can
23828 also be represented in any of the three popular SEM frame-works, as well as
23829 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
23830 (license license:gpl2)))
23832 (define-public r-cdm
23839 (uri (cran-uri "CDM" version))
23842 "159ny2dz0rf1r3k1mqlfwambffc8rx425sggf5bn51nybpzanq3l"))))
23843 (properties `((upstream-name . "CDM")))
23844 (build-system r-build-system)
23846 (list r-mvtnorm r-polycor r-rcpp r-rcpparmadillo))
23848 "https://github.com/alexanderrobitzsch/CDM")
23849 (synopsis "Cognitive diagnosis modeling")
23851 "This package provides functions for cognitive diagnosis modeling and
23852 multidimensional item response modeling for dichotomous and polytomous item
23853 responses. It enables the estimation of the DINA and DINO model, the multiple
23854 group (polytomous) GDINA model, the multiple choice DINA model, the general
23855 diagnostic model (GDM), the structured latent class model (SLCA), and
23856 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
23857 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
23858 estimation and the package structure. For tutorials on how to use the CDM
23859 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
23860 well as Ravand and Robitzsch (2015).")
23861 (license license:gpl2+)))
23863 (define-public r-tam
23870 (uri (cran-uri "TAM" version))
23873 "1969xm1f7s183h0xnd4g1bxhjp80rl7kad29zwcig0fmw6bs2mpd"))))
23874 (properties `((upstream-name . "TAM")))
23875 (build-system r-build-system)
23877 (list r-cdm r-rcpp r-rcpparmadillo))
23878 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
23879 (synopsis "Test analysis modules")
23881 "This package includes tools for marginal maximum likelihood estimation
23882 and joint maximum likelihood estimation for unidimensional and
23883 multidimensional item response models. The package functionality covers the
23884 Rasch model, 2PL model, 3PL model, generalized partial credit model,
23885 multi-faceted Rasch model, nominal item response model, structured latent
23886 class model, mixture distribution IRT models, and located latent class models.
23887 Latent regression models and plausible value imputation are also supported.")
23888 (license license:gpl2+)))
23890 (define-public r-erm
23897 (uri (cran-uri "eRm" version))
23900 "0smym010kswc5vx90qr3x1vl16xj1x1i54rvrj006dc4agc1vmlk"))))
23901 (properties `((upstream-name . "eRm")))
23902 (build-system r-build-system)
23904 (list r-colorspace r-lattice r-mass r-matrix r-psych))
23905 (native-inputs (list gfortran))
23906 (home-page "https://cran.r-project.org/package=eRm")
23907 (synopsis "Extended Rasch modeling")
23909 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
23910 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
23911 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
23912 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
23913 data matrix. Additional features are the ML estimation of the person
23914 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
23915 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
23916 infit and outfit measures, ICC and other plots, automated stepwise item
23917 elimination, and a simulation module for various binary data matrices.")
23918 (license license:gpl3)))
23920 (define-public r-irtoys
23927 (uri (cran-uri "irtoys" version))
23930 "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
23931 (properties `((upstream-name . "irtoys")))
23932 (build-system r-build-system)
23935 (home-page "https://cran.r-project.org/package=irtoys")
23936 (synopsis "Collection of functions related to Item Response Theory (IRT)")
23938 "This package provides a collection of functions useful in learning and
23939 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
23940 programs. It provides basic CTT analysis, a simple common interface to the
23941 estimation of item parameters in IRT models for binary responses with three
23942 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
23943 EAP, WLE, plausible values), item and person fit statistics, scaling
23944 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
23945 array of parametric and non-parametric (kernel) plots. It estimates and plots
23946 Haberman's interaction model when all items are dichotomously scored.")
23947 (license license:gpl2+)))
23949 (define-public r-iheatmapr
23951 (name "r-iheatmapr")
23956 (uri (cran-uri "iheatmapr" version))
23959 "1pwkwh7ljlpr6zyz6j8knpz3iw60xzkw8amc98x4pc2mw148jvzx"))))
23960 (properties `((upstream-name . "iheatmapr")))
23961 (build-system r-build-system)
23963 (list r-fastcluster
23973 (home-page "https://docs.ropensci.org/iheatmapr")
23974 (synopsis "Interactive, Complex Heatmaps")
23976 "iheatmapr is an R package for building complex, interactive heatmaps
23977 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
23978 subplots along the rows or columns of the main heatmap add more information
23979 about each row or column. For example, a one column additional heatmap may
23980 indicate what group a particular row or column belongs to. Complex heatmaps
23981 may also include multiple side by side heatmaps which show different types of
23982 data for the same conditions. Interactivity can improve complex heatmaps by
23983 providing tooltips with information about each cell and enabling zooming into
23984 interesting features. iheatmapr uses the plotly library for interactivity.")
23985 (license license:expat)))
23987 (define-public r-packrat
23994 (uri (cran-uri "packrat" version))
23997 "1hnwhdgqljqs3m7c4rjlyndyc0k85jpa4rbfymxkm3zjg3yy3g78"))))
23998 (properties `((upstream-name . "packrat")))
23999 (build-system r-build-system)
24000 (home-page "https://github.com/rstudio/packrat/")
24001 (synopsis "Dependency management R projects")
24003 "This package provides a dependency manager for R projects that allows
24004 you to manage the R packages your project depends on in an isolated, portable,
24005 and reproducible way.")
24006 (license license:gpl2)))
24008 (define-public r-rsconnect
24010 (name "r-rsconnect")
24015 (uri (cran-uri "rsconnect" version))
24018 "1kyr4v7vds2yw3xmkk2yr56ylz1h95944brylwvwmwj5yxvm419w"))))
24019 (properties `((upstream-name . "rsconnect")))
24020 (build-system r-build-system)
24029 (home-page "https://github.com/rstudio/rsconnect")
24030 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
24032 "This package provides a programmatic deployment interface for RPubs,
24033 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
24034 documents, Shiny applications, Plumber APIs, plots, and static web content.")
24035 (license license:gpl2)))
24037 ;; This package includes minified JavaScript files. When upgrading please
24038 ;; check that there are no new minified JavaScript files.
24039 (define-public r-dygraphs
24041 (name "r-dygraphs")
24042 (version "1.1.1.6")
24046 (uri (cran-uri "dygraphs" version))
24049 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
24050 (properties `((upstream-name . "dygraphs")))
24051 (build-system r-build-system)
24053 `(#:modules ((guix build utils)
24054 (guix build r-build-system)
24058 (modify-phases %standard-phases
24059 (add-after 'unpack 'process-javascript
24060 (lambda* (#:key inputs #:allow-other-keys)
24061 (with-directory-excursion "inst/htmlwidgets/lib/"
24065 `(("dygraphs/dygraph-combined-dev.js"
24066 "dygraph-combined.js")
24067 (,(assoc-ref inputs "js-jquery")
24068 "jquery/jquery.min.js")
24069 (,(assoc-ref inputs "js-fquarter")
24070 "fquarter/moment-fquarter.min.js"))))
24071 (lambda (sources targets)
24072 (for-each (lambda (source target)
24073 (format #t "Processing ~a --> ~a~%"
24075 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
24076 (call-with-output-file target
24078 (dump-port minified port)))))
24079 sources targets))))
24082 `(("uglifyjs" ,node-uglify-js)
24083 ;; They actually use version 1.11.1, but this more recent version
24084 ;; should be just fine.
24088 (uri "https://code.jquery.com/jquery-1.12.4.js")
24091 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
24095 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
24096 "moment-fquarter/1.0.1/moment-fquarter.js"))
24099 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
24101 (list r-htmltools r-htmlwidgets r-magrittr r-xts r-zoo))
24102 (home-page "https://github.com/rstudio/dygraphs")
24103 (synopsis "Interface to Dygraphs interactive time series charting library")
24105 "This package provides an R interface to the dygraphs JavaScript charting
24106 library (a copy of which is included in the package). It provides rich
24107 facilities for charting time-series data in R, including highly configurable
24108 series- and axis-display and interactive features like zoom/pan and
24109 series/point highlighting.")
24110 (license license:expat)))
24112 (define-public r-shinystan
24114 (name "r-shinystan")
24119 (uri (cran-uri "shinystan" version))
24122 "18alf5kiqw7y2l6m5nxxizwc2znsf9frxfsqhvgcad8hld9cbya5"))))
24123 (properties `((upstream-name . "shinystan")))
24124 (build-system r-build-system)
24143 (home-page "https://mc-stan.org/")
24144 (synopsis "Interactive visual and numerical analysis for Bayesian models")
24146 "This package provides a graphical user interface for interactive
24147 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
24148 for analyzing a posterior sample. The interface is powered by the Shiny web
24149 application framework and works with the output of MCMC programs written in
24150 any programming language (and has extended functionality for Stan models fit
24151 using the @code{rstan} and @code{rstanarm} packages).")
24152 (license license:gpl3+)))
24154 (define-public r-rstantools
24156 (name "r-rstantools")
24161 (uri (cran-uri "rstantools" version))
24164 "0b9x8rzj3dr4m7yjx476nn42z22xd1xnw85m9frfwxy5ivg1any9"))))
24165 (properties `((upstream-name . "rstantools")))
24166 (build-system r-build-system)
24167 (inputs (list pandoc))
24169 (list r-desc r-rcpp r-rcppparallel))
24172 (home-page "https://mc-stan.org/rstantools/")
24173 (synopsis "Tools for developing R packages interfacing with Stan")
24175 "This package provides various tools for developers of R packages
24176 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
24177 up the required package structure, S3 generics and default methods to unify
24178 function naming across Stan-based R packages, and vignettes with
24179 recommendations for developers.")
24180 (license license:gpl3+)))
24182 (define-public r-loo
24189 (uri (cran-uri "loo" version))
24191 (base32 "0l2v8zpashqbnck3qx5lp1gqjcfphzky8mxyw5gfk9wk99mzn8dw"))))
24192 (properties `((upstream-name . "loo")))
24193 (build-system r-build-system)
24197 (list r-checkmate r-matrixstats))
24200 (home-page "https://mc-stan.org/loo/")
24201 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
24203 "This package provides an implementation of efficient approximate
24204 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
24205 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
24206 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
24207 procedure for regularizing importance weights. As a byproduct of the
24208 calculations, we also obtain approximate standard errors for estimated
24209 predictive errors and for the comparison of predictive errors between models.
24210 The package also provides methods for using stacking and other model weighting
24211 techniques to average Bayesian predictive distributions.")
24212 (license license:gpl3+)))
24214 (define-public r-rstan
24221 (uri (cran-uri "rstan" version))
24224 "0jh58qfrksd2j9w2zy4bajryivgp36m3xdb9mjrjqbk1ib9h83p3"))))
24225 (properties `((upstream-name . "rstan")))
24226 (build-system r-build-system)
24229 (modify-phases %standard-phases
24230 (add-before 'install 'set-timezone
24231 ;; This package is picky about timezones.
24232 (lambda* (#:key inputs #:allow-other-keys)
24233 (setenv "TZ" "UTC+1")
24235 (search-input-directory inputs
24236 "share/zoneinfo")))))))
24238 (list tzdata-for-tests pandoc r-knitr))
24252 (home-page "https://discourse.mc-stan.org/")
24253 (synopsis "R interface to Stan")
24255 "User-facing R functions are provided to parse, compile, test, estimate,
24256 and analyze Stan models by accessing the header-only Stan library provided by
24257 the StanHeaders package. The Stan project develops a probabilistic
24258 programming language that implements full Bayesian statistical inference via
24259 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
24260 approximation, and (optionally penalized) maximum likelihood estimation via
24261 optimization. In all three cases, automatic differentiation is used to
24262 quickly and accurately evaluate gradients without burdening the user with the
24263 need to derive the partial derivatives.")
24264 (license license:gpl3+)))
24266 (define-public r-rstanarm
24268 (name "r-rstanarm")
24273 (uri (cran-uri "rstanarm" version))
24276 "04ggzak3f7jaxza3dxyrmxp5b48qcgyspy22ykbhr03g4hzp7jk8"))))
24277 (properties `((upstream-name . "rstanarm")))
24278 (build-system r-build-system)
24299 (home-page "https://mc-stan.org/rstanarm/")
24300 (synopsis "Bayesian applied regression modeling via Stan")
24302 "This package estimates previously compiled regression models using the
24303 @code{rstan} package, which provides the R interface to the Stan C++ library
24304 for Bayesian estimation. Users specify models via the customary R syntax with
24305 a formula and @code{data.frame} plus some additional arguments for priors.")
24306 (license license:gpl3+)))
24308 (define-public r-kendall
24315 (uri (cran-uri "Kendall" version))
24318 "0z2yr3x2nvdm81w2imb61hxwcbmg14kfb2bxgh3wmkmv3wfjwkwn"))))
24319 (properties `((upstream-name . "Kendall")))
24320 (build-system r-build-system)
24325 (home-page "https://cran.r-project.org/web/packages/Kendall/")
24326 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
24328 "This package computes the Kendall rank correlation and Mann-Kendall
24330 (license license:gpl2+)))
24332 (define-public r-keyring
24339 (uri (cran-uri "keyring" version))
24342 "1rqz29ycsmfqixhnzhhfd89j9ivnmp7x2z3vxdla622zmakbcy4c"))))
24343 (properties `((upstream-name . "keyring")))
24344 (build-system r-build-system)
24354 (native-inputs (list pkg-config))
24355 (home-page "https://github.com/r-lib/keyring")
24356 (synopsis "Access the system credential store from R")
24358 "This package provides a platform-independent API to access the operating
24359 system's credential store. It currently supports Keychain on macOS,
24360 Credential Store on Windows, the Secret Service API on GNU/Linux, and a
24361 simple, platform independent store implemented with environment variables.
24362 Additional storage back-ends can be added easily.")
24363 (license license:expat)))
24365 (define-public r-zyp
24368 (version "0.10-1.1")
24372 (uri (cran-uri "zyp" version))
24375 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
24376 (properties `((upstream-name . "zyp")))
24377 (build-system r-build-system)
24380 (home-page "https://cran.r-project.org/web/packages/zyp/")
24381 (synopsis "Zhang + Yue-Pilon Trends Package")
24383 "This package contains an efficient implementation of Sen's slope
24384 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
24385 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
24387 (license license:lgpl2.1)))
24389 (define-public r-rlinsolve
24391 (name "r-rlinsolve")
24396 (uri (cran-uri "Rlinsolve" version))
24399 "1xv500n1480qyakw0isanw1s5ywykhc207hqja4804s5s2m8zfjw"))))
24400 (properties `((upstream-name . "Rlinsolve")))
24401 (build-system r-build-system)
24403 (list r-matrix r-rcpp r-rcpparmadillo r-rdpack))
24404 (home-page "https://cran.r-project.org/web/packages/Rlinsolve/")
24405 (synopsis "Iterative solvers for (sparse) linear system of equations")
24407 "Solving a system of linear equations is one of the most fundamental
24408 computational problems for many fields of mathematical studies, such as
24409 regression problems from statistics or numerical partial differential
24410 equations. This package provides basic stationary iterative solvers such as
24411 Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods.
24412 Nonstationary, also known as Krylov subspace methods are also provided.
24413 Sparse matrix computation is also supported in that solving large and sparse
24414 linear systems can be manageable using the @code{Matrix} package along with
24415 @code{RcppArmadillo}.")
24416 (license license:gpl3+)))
24418 (define-public r-zvcv
24425 (uri (cran-uri "ZVCV" version))
24428 "0gc76j9i8fkm2v638nyzzb1qxl4zmapbspkkaffb8gi5qyjja448"))))
24429 (properties `((upstream-name . "ZVCV")))
24430 (build-system r-build-system)
24441 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
24442 (synopsis "Zero-Variance Control Variates")
24444 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
24445 to reduce the variance of Monte Carlo estimators of expectations using the
24446 derivatives of the log target. Once the derivatives are available, the only
24447 additional computational effort is in solving a linear regression problem.
24448 This method has been extended to higher dimensions using regularisation. This
24449 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
24450 samples, derivatives and function evaluations are available. Additional
24451 functions for applying ZV-CV to two estimators for the normalising constant of
24452 the posterior distribution in Bayesian statistics are also supplied.")
24453 (license license:gpl2+)))
24455 (define-public r-ztype
24462 (uri (cran-uri "ztype" version))
24465 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
24466 (properties `((upstream-name . "ztype")))
24467 (build-system r-build-system)
24476 (home-page "https://cran.r-project.org/web/packages/ztype/")
24477 (synopsis "Run a Ztype game loaded with R functions")
24479 "How fast can you type R functions on your keyboard? Find out by running
24480 a @code{zty.pe} game: export R functions as instructions to type to destroy
24481 opponents' vessels.")
24482 (license license:gpl3)))
24484 (define-public r-zseq
24491 (uri (cran-uri "Zseq" version))
24494 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
24495 (properties `((upstream-name . "Zseq")))
24496 (build-system r-build-system)
24499 (home-page "https://cran.r-project.org/web/packages/Zseq/")
24500 (synopsis "Integer sequence generator")
24502 "This package generates well-known integer sequences. The @code{gmp}
24503 package is adopted for computing with arbitrarily large numbers. Every
24504 function has a hyperlink to its corresponding item in the @dfn{On-Line
24505 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
24506 (license license:gpl3+)))
24508 (define-public r-isoband
24515 (uri (cran-uri "isoband" version))
24518 "19bbi0n0kz33xdgmdprcmc6raphd1hcm1w1brc16z5phcsh3zxa6"))))
24519 (properties `((upstream-name . "isoband")))
24520 (build-system r-build-system)
24523 (home-page "https://github.com/wilkelab/isoband")
24524 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
24526 "This package provides a fast C++ implementation to generate contour
24527 lines (isolines) and contour polygons (isobands) from regularly spaced grids
24528 containing elevation data.")
24529 (license license:expat)))
24531 (define-public r-ppcor
24538 (uri (cran-uri "ppcor" version))
24541 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
24542 (properties `((upstream-name . "ppcor")))
24543 (build-system r-build-system)
24546 (home-page "https://cran.r-project.org/web/packages/ppcor/")
24547 (synopsis "Partial and semi-partial correlation")
24549 "This package provides users not only with a function to readily
24550 calculate the higher-order partial and semi-partial correlations but also with
24551 statistics and p-values of the correlation coefficients.")
24552 (license license:gpl2)))
24554 (define-public r-hrbrthemes
24556 (name "r-hrbrthemes")
24561 (uri (cran-uri "hrbrthemes" version))
24563 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
24564 (properties `((upstream-name . "hrbrthemes")))
24565 (build-system r-build-system)
24577 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
24578 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
24580 "This package provides a compilation of extra @code{ggplot2} themes,
24581 scales and utilities, including a spell check function for plot label fields
24582 and an overall emphasis on typography.")
24583 (license license:expat)))
24585 (define-public r-crochet
24592 (uri (cran-uri "crochet" version))
24595 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq"))))
24596 (build-system r-build-system)
24599 (home-page "https://github.com/agrueneberg/crochet")
24600 (synopsis "Implementation Helper for Matrix-Like Types")
24602 "Functions to help implement the extraction / subsetting / indexing
24603 function @code{[} and replacement function @code{[<-} of custom matrix-like
24604 types (based on S3, S4, etc.), modeled as closely to the base matrix class
24605 as possible (with tests to prove it).")
24606 (license license:expat)))
24608 (define-public r-boa
24611 (version "1.1.8-2")
24615 (uri (cran-uri "boa" version))
24618 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
24619 (properties `((upstream-name . "boa")))
24620 (build-system r-build-system)
24621 (home-page "https://www.jstatsoft.org/v21/i11")
24622 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
24624 "This package provides a menu-driven program and library of functions for
24625 carrying out convergence diagnostics and statistical and graphical analysis of
24626 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
24627 (license license:gpl2+)))
24629 (define-public r-httpcode
24631 (name "r-httpcode")
24635 (uri (cran-uri "httpcode" version))
24638 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
24639 (build-system r-build-system)
24640 (home-page "https://github.com/sckott/httpcode")
24641 (synopsis "HTTP status code helper")
24642 (description "@code{httpcode} provides functionality for finding and
24643 explaining the meaning of @code{HTTP} status codes. Functions are included for
24644 searching for codes by full or partial number, by message, and to get
24645 appropriate dog and cat images for many status codes.")
24646 (license license:expat)))
24648 (define-public r-latex2exp
24650 (name "r-latex2exp")
24654 (uri (cran-uri "latex2exp" version))
24657 "0qknpw7zwwbzsbry94j8fn48mq7kq5rc5448g9hybbisain3wfvg"))))
24658 (build-system r-build-system)
24660 (list r-stringr r-magrittr))
24663 (home-page "https://github.com/stefano-meschiari/latex2exp/")
24664 (synopsis "Use LaTeX expressions in plots")
24665 (description "@code{latex2exp} parses and converts LaTeX math formulas to
24666 R's plotmath expressions, used to enter mathematical formulas and symbols to be
24667 rendered as text, axis labels, etc. throughout R's plotting system.")
24668 (license license:expat)))
24670 (define-public r-oai
24676 (uri (cran-uri "oai" version))
24679 "1zcbcxhw692s0y6izvwazyzhgx0iwsxsbcan2nk0mb7n11p7bypb"))))
24680 (build-system r-build-system)
24682 (list r-xml2 r-httr r-plyr r-stringr r-tibble))
24685 (home-page "https://github.com/ropensci/oai/")
24686 (synopsis "General purpose OAI-PMH services client")
24687 (description "@code{oai} provides a general purpose client to work with
24688 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
24689 service. Functions are provided to work with the OAI-PMH verbs:
24690 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
24691 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
24692 (license license:expat)))
24694 (define-public r-argon2
24701 (uri (cran-uri "argon2" version))
24704 "09hzl0wz0lw2v7g64rdv0lij2hq36zl37a6rmxwvinmjdzijcsyw"))))
24705 (properties `((upstream-name . "argon2")))
24706 (build-system r-build-system)
24707 (home-page "https://github.com/wrathematics/argon2")
24708 (synopsis "Secure password hashing based on the argon2 algorithm")
24710 "This package provides utilities for secure password hashing via the
24711 argon2 algorithm.")
24712 (license license:bsd-2)))
24714 (define-public r-getpass
24721 (uri (cran-uri "getPass" version))
24724 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
24725 (properties `((upstream-name . "getPass")))
24726 (build-system r-build-system)
24728 (list r-rstudioapi))
24729 (home-page "https://github.com/wrathematics/getPass")
24730 (synopsis "Masked user input")
24732 "This package provides a micro-package for reading \"passwords\", i.e.
24733 reading user input with masking, so that the input is not displayed as it is
24734 typed. Currently, RStudio, the command line (every OS), and any platform
24735 where tcltk is present are supported.")
24736 (license license:bsd-2)))
24738 (define-public r-remoter
24745 (uri (cran-uri "remoter" version))
24748 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
24749 (properties `((upstream-name . "remoter")))
24750 (build-system r-build-system)
24752 (list r-argon2 r-getpass r-pbdzmq r-png))
24753 (home-page "https://github.com/RBigData/remoter")
24754 (synopsis "Control a remote R session from a local one")
24756 "This package provides a set of utilities for client/server computing
24757 with R, controlling a remote R session (the server) from a local one (the
24759 (license license:bsd-2)))
24761 (define-public r-asd
24768 (uri (cran-uri "asd" version))
24771 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
24772 (properties `((upstream-name . "asd")))
24773 (build-system r-build-system)
24776 (home-page "https://cran.r-project.org/web/packages/asd")
24777 (synopsis "Simulations for Adaptive Seamless Designs")
24779 "This package provdes means to run simulations for adaptive seamless
24780 designs with and without early outcomes for treatment selection and
24781 subpopulation type designs.")
24782 (license license:gpl3)))
24784 (define-public r-nbconvertr
24786 (name "r-nbconvertr")
24791 (uri (cran-uri "nbconvertR" version))
24794 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
24795 (properties `((upstream-name . "nbconvertR")))
24796 (build-system r-build-system)
24798 `(("jupyter" ,python-nbconvert)
24799 ("pandoc" ,pandoc)))
24800 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
24801 (synopsis "Vignette engine wrapping Jupyter notebooks")
24803 "This package calls the Jupyter script @code{nbconvert} to create
24804 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
24805 containing rich text, code, and its output. Code cells can be edited and
24806 evaluated interactively.")
24807 (license license:gpl3)))
24809 (define-public r-bridgesampling
24811 (name "r-bridgesampling")
24816 (uri (cran-uri "bridgesampling" version))
24819 "0sry1xwiv4y52k44hq6z8y2kysp5kxgl4dix3m94svg3ladd7v2l"))))
24821 `((upstream-name . "bridgesampling")))
24822 (build-system r-build-system)
24824 (list r-brobdingnag
24832 (home-page "https://github.com/quentingronau/bridgesampling")
24833 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
24835 "This package provides functions for estimating marginal likelihoods,
24836 Bayes factors, posterior model probabilities, and normalizing constants in
24837 general, via different versions of bridge sampling.")
24838 (license license:gpl2+)))
24840 (define-public r-tea
24847 (uri (cran-uri "tea" version))
24850 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
24852 `((upstream-name . "tea")))
24853 (build-system r-build-system)
24856 (home-page "https://cran.r-project.org/web/packages/tea/")
24857 (synopsis "Threshold estimation approaches")
24859 "This package provides different approaches for selecting the threshold
24860 in generalized Pareto distributions. Most of them are based on minimizing the
24861 AMSE-criterion or at least by reducing the bias of the assumed GPD-model.
24862 Others are heuristically motivated by searching for stable sample paths, i.e.
24863 a nearly constant region of the tail index estimator with respect to k, which
24864 is the number of data in the tail. The third class is motivated by graphical
24865 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
24866 is also implemented here.")
24867 (license license:gpl3)))
24869 (define-public r-awsmethods
24871 (name "r-awsmethods")
24876 (uri (cran-uri "awsMethods" version))
24879 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
24881 `((upstream-name . "awsMethods")))
24882 (build-system r-build-system)
24883 (home-page "http://www.wias-berlin.de/software/imaging/")
24884 (synopsis "Class and methods definitions")
24886 "This package defines the generic method @code{extract} and provides
24887 @code{openMP} support as needed in several packages like
24888 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
24889 (license license:gpl2+)))
24891 (define-public r-aws
24898 (uri (cran-uri "aws" version))
24901 "1fhm87iax6bkvd4vszvjbcqw3b2drs11rjxr7zf2w4sgc72svaz8"))))
24903 `((upstream-name . "aws")))
24904 (build-system r-build-system)
24906 (list r-awsmethods r-gsl))
24909 (home-page "https://cran.r-project.org/web/packages/aws/")
24910 (synopsis "Adaptive weights smoothing")
24912 "This package provides a collection of R-functions implementing adaptive
24913 smoothing procedures in 1D, 2D and 3D. This includes the
24914 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
24915 Confidence Intervals} (ICI), variational approaches, and a non-local means
24917 (license license:gpl2+)))
24919 (define-public r-sgloptim
24921 (name "r-sgloptim")
24926 (uri (cran-uri "sglOptim" version))
24929 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
24931 `((upstream-name . "sglOptim")))
24932 (build-system r-build-system)
24943 (home-page "https://github.com/nielsrhansen/sglOptim")
24944 (synopsis "Generic sparse group Lasso solver")
24946 "This package provides a fast generic solver for sparse group lasso
24947 optimization problems. The loss (objective) function must be defined in a C++
24948 module. The optimization problem is solved using a coordinate gradient
24949 descent algorithm. Convergence of the algorithm is established and the
24950 algorithm is applicable to a broad class of loss functions. Use of parallel
24951 computing for cross validation and subsampling is supported through the
24952 @code{foreach} and @code{doParallel} packages.")
24953 (license license:gpl2+)))
24955 (define-public r-grouped
24962 (uri (cran-uri "grouped" version))
24965 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
24967 `((upstream-name . "grouped")))
24968 (build-system r-build-system)
24971 (home-page "https://cran.r-project.org/web/packages/grouped/")
24972 (synopsis "Regression analysis of grouped and coarse data")
24974 "This package provides regression models for grouped and coarse data,
24975 under the coarsened at random assumption.")
24976 (license license:gpl2+)))
24978 (define-public r-stam
24985 (uri (cran-uri "stam" version))
24988 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
24990 `((upstream-name . "stam")))
24991 (build-system r-build-system)
24994 (home-page "https://cran.r-project.org/web/packages/stam")
24995 (synopsis "Spatio-temporal analysis and modelling")
24997 "This package provides various methods to conduct Spatio-Temporal
24998 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
24999 Inferred Spatio-Temporal Modelling.")
25000 (license license:gpl2+)))
25002 (define-public r-dcv
25009 (uri (cran-uri "dcv" version))
25012 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
25014 `((upstream-name . "dcv")))
25015 (build-system r-build-system)
25018 (home-page "https://cran.r-project.org/web/packages/dcv/")
25019 (synopsis "Conventional cross-validation statistics for climate-growth model")
25021 "This package performs several conventional cross-validation statistical
25022 methods for climate-growth model in the climate reconstruction from tree
25023 rings, including Sign Test statistic, Reduction of Error statistic, Product
25024 Mean Test, Durbin-Watson statistic etc.")
25025 (license license:gpl2)))
25027 (define-public r-rcdd
25034 (uri (cran-uri "rcdd" version))
25037 "0zxx0qvv26ba30jkm8mvca4h59rqklay4jwazpcw7h9dzp4189jr"))))
25039 `((upstream-name . "rcdd")))
25040 (build-system r-build-system)
25043 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
25044 (synopsis "Computational geometry")
25046 "This package converts back and forth between two representations of a
25047 convex polytope: as solution of a set of linear equalities and inequalities
25048 and as convex hull of set of points and rays. Also does linear programming
25049 and redundant generator elimination. All functions can use exact
25050 infinite-precision rational arithmetic.")
25051 (license license:gpl2)))
25053 (define-public r-rxnat
25060 (uri (cran-uri "Rxnat" version))
25063 "0siylypjd8cgcmr2c443w8krg8sgr5gz4zapbinanp8vsfzivdv2"))))
25065 `((upstream-name . "Rxnat")))
25066 (build-system r-build-system)
25068 (list r-httr r-rcurl r-tibble))
25071 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
25072 (synopsis "Queries and extracts images from neuroimaging datasets")
25074 "This package allows communication with the Extensible Neuroimaging
25075 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
25077 (license license:gpl2)))
25079 (define-public r-rserve
25086 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
25087 version ".tar.gz"))
25090 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
25091 (build-system r-build-system)
25094 (modify-phases %standard-phases
25095 (add-before 'install 'install-server-binary
25096 ;; Makevars tries to install to R's store directory.
25097 (lambda* (#:key outputs #:allow-other-keys)
25098 (let* ((out (assoc-ref outputs "out"))
25099 (bin (string-append out "/bin")))
25100 (substitute* "src/Makevars.in"
25101 (("\\$\\(R_HOME\\)") out))
25102 (mkdir-p bin)))))))
25112 (list openssl zlib))
25113 (home-page "https://github.com/s-u/Rserve")
25115 "Server providing access to R from many languages and systems")
25117 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
25118 binary requests to be sent to R. Every connection has a separate workspace
25119 and working directory. Client-side implementations are available for popular
25120 languages such as C/C++ and Java, allowing any application to use facilities
25121 of R without the need of linking to R code. Rserve supports remote
25122 connection, user authentication and file transfer. A simple R client is
25123 included in this package as well.")
25124 (license license:gpl2)))
25126 (define-public r-gamm4
25133 (uri (cran-uri "gamm4" version))
25136 "128c725y9s07c1m9cvd9hgi9hldrymcs5divd8pw7bdjh9jvdiap"))))
25137 (properties `((upstream-name . "gamm4")))
25138 (build-system r-build-system)
25140 (list r-lme4 r-matrix r-mgcv))
25141 (home-page "https://cran.r-project.org/web/packages/gamm4/")
25142 (synopsis "Generalized additive mixed models using mgcv and lme4")
25144 "Estimate generalized additive mixed models via a version of function
25145 @code{gamm} from the @code{mgcv} package, using the @code{lme4} packagefor
25147 (license license:gpl2+)))
25149 (define-public r-optimx
25152 (version "2021-10.12")
25156 (uri (cran-uri "optimx" version))
25159 "0hvrpfya767vp3anmb8ih516v4zz1sv4h193rn93kyjydf2lqf1r"))))
25160 (properties `((upstream-name . "optimx")))
25161 (build-system r-build-system)
25162 (propagated-inputs (list r-numderiv))
25163 (native-inputs (list r-knitr))
25164 (home-page "https://cran.r-project.org/web/packages/optimx/")
25165 (synopsis "Expanded replacement and extension of the optim function")
25167 "This package provides a replacement and extension of the @code{optim}
25168 function to call to several function minimization codes in R in a single
25169 statement. These methods handle smooth, possibly box constrained functions of
25170 several or many parameters. Note that the function @code{optimr} was prepared
25171 to simplify the incorporation of minimization codes going forward. This
25172 package also implements some utility codes and some extra solvers, including
25173 safeguarded Newton methods. Many methods previously separate are now included
25175 (license license:gpl2)))
25177 (define-public r-projpred
25179 (name "r-projpred")
25184 (uri (cran-uri "projpred" version))
25187 "0nx514mrfh3gv854pr71w5x3zgdnn0kinf5nh7z90q3h7ysry2mg"))))
25188 (properties `((upstream-name . "projpred")))
25189 (build-system r-build-system)
25205 (native-inputs (list r-knitr))
25206 (home-page "https://mc-stan.org/projpred/")
25207 (synopsis "Projection predictive feature selection")
25209 "This package performs projection predictive feature selection for
25210 generalized linear models and generalized linear and additive multilevel
25211 models. The package is compatible with the @code{rstanarm} and @code{brms}
25212 packages, but other reference models can also be used. See the package
25213 vignette for more information and examples.")
25214 (license license:gpl3)))
25216 (define-public r-distributional
25218 (name "r-distributional")
25223 (uri (cran-uri "distributional" version))
25226 "0ps30ijlf0xwranxkq1z29d76d3zgy8drwxpnxp6ffmyma8mm3h2"))))
25228 `((upstream-name . "distributional")))
25229 (build-system r-build-system)
25241 (home-page "https://pkg.mitchelloharawild.com/distributional/")
25242 (synopsis "Vectorized probability distributions")
25244 "This package provides vectorized distribution objects with tools for
25245 manipulating, visualizing, and using probability distributions. It was
25246 designed to allow model prediction outputs to return distributions rather than
25247 their parameters, allowing users to directly interact with predictive
25248 distributions in a data-oriented workflow. In addition to providing generic
25249 replacements for p/d/q/r functions, other useful statistics can be computed
25250 including means, variances, intervals, and highest density regions.")
25251 (license license:gpl3)))
25253 (define-public r-posterior
25255 (name "r-posterior")
25260 (uri (cran-uri "posterior" version))
25263 "1lpldkkkxv94dr30q5wb5qr61qrgp9shqnskgwriigy1phnjdxpg"))))
25264 (properties `((upstream-name . "posterior")))
25265 (build-system r-build-system)
25278 (home-page "https://mc-stan.org/posterior/")
25279 (synopsis "Tools for working with posterior distributions")
25281 "This package provides useful tools for both users and developers of
25282 packages for fitting Bayesian models or working with output from Bayesian
25283 models. The primary goals of the package are to:
25286 @item Efficiently convert between many different useful formats of
25287 draws (samples) from posterior or prior distributions.
25289 @item Provide consistent methods for operations commonly performed on draws,
25290 for example, subsetting, binding, or mutating draws.
25292 @item Provide various summaries of draws in convenient formats.
25294 @item Provide lightweight implementations of state of the art posterior
25295 inference diagnostics.
25298 (license license:bsd-3)))
25300 (define-public r-brms
25307 (uri (cran-uri "brms" version))
25310 "1i0vkkfziac29vncw4igja5m7a6rhw9rqwifrw3y47q6zgczp7kl"))))
25311 (properties `((upstream-name . "brms")))
25312 (build-system r-build-system)
25334 (native-inputs (list r-knitr))
25336 "https://github.com/paul-buerkner/brms")
25338 "Bayesian Regression Models using 'Stan'")
25340 "Fit Bayesian generalized (non-)linear multivariate multilevel models
25341 using 'Stan' for full Bayesian inference. A wide range of distributions and
25342 link functions are supported, allowing users to fit -- among others -- linear,
25343 robust linear, count data, survival, response times, ordinal, zero-inflated,
25344 hurdle, and even self-defined mixture models all in a multilevel context.
25345 Further modeling options include non-linear and smooth terms, auto-correlation
25346 structures, censored data, meta-analytic standard errors, and quite a few
25347 more. In addition, all parameters of the response distribution can be
25348 predicted in order to perform distributional regression. Prior specifications
25349 are flexible and explicitly encourage users to apply prior distributions that
25350 actually reflect their beliefs. Model fit can easily be assessed and compared
25351 with posterior predictive checks and leave-one-out cross-validation.")
25352 (license license:gpl2)))
25354 (define-public r-mstate
25361 (uri (cran-uri "mstate" version))
25364 "054dzrd5b0xjjjl7862q3aq1jwgrxbkqz7zpvbdirqsld3zksirw"))))
25365 (properties `((upstream-name . "mstate")))
25366 (build-system r-build-system)
25377 "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/")
25379 "Data Preparation, Estimation and Prediction in Multi-State Models")
25381 "Contains functions for data preparation, descriptives, hazard estimation
25382 and prediction with Aalen-Johansen or simulation in competing risks and
25383 multi-state models.")
25384 (license license:gpl2+)))
25386 (define-public r-scatterpie
25388 (name "r-scatterpie")
25393 (uri (cran-uri "scatterpie" version))
25396 "1pmspv8a7k20zyd5xvmav2k9mnjrkfhdij3rr9k504zyki8hfy1z"))))
25397 (properties `((upstream-name . "scatterpie")))
25398 (build-system r-build-system)
25400 (list r-ggforce r-ggfun r-ggplot2 r-rlang r-tidyr))
25403 (home-page "https://cran.r-project.org/web/packages/scatterpie/")
25404 (synopsis "Scatter pie plot")
25406 "This package creates scatterpie plots, especially useful for plotting
25408 (license license:artistic2.0)))
25410 (define-public r-scrypt
25417 (uri (cran-uri "scrypt" version))
25420 "14iblgbp9v2by8fjbrpsd59iknp5babcz7j3yv1yxxzcwyb6wrrm"))))
25421 (properties `((upstream-name . "scrypt")))
25422 (build-system r-build-system)
25425 (home-page "https://github.com/rstudio/rscrypt")
25426 (synopsis "Key derivation functions for R based on Scrypt")
25428 "This package provides functions for working with the scrypt key
25429 derivation functions. Scrypt is a password-based key derivation function
25430 created by Colin Percival. The algorithm was specifically designed to make it
25431 costly to perform large-scale custom hardware attacks by requiring large
25432 amounts of memory.")
25433 (license license:bsd-2)))
25435 (define-public r-boruta
25442 (uri (cran-uri "Boruta" version))
25445 "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg"))))
25446 (properties `((upstream-name . "Boruta")))
25447 (build-system r-build-system)
25448 (propagated-inputs (list r-ranger))
25449 (home-page "https://gitlab.com/mbq/Boruta/")
25450 (synopsis "Wrapper algorithm for all relevant feature selection")
25452 "This package provides an all relevant feature selection wrapper
25453 algorithm. It finds relevant features by comparing original attributes'
25454 importance with importance achievable at random, estimated using their
25455 permuted copies (shadows).")
25456 (license license:gpl2+)))
25458 (define-public r-directlabels
25460 (name "r-directlabels")
25461 (version "2021.1.13")
25465 (uri (cran-uri "directlabels" version))
25468 "0415kh9k2qzdwi8zb32fh2icl5wf5335kyj11cyfdmfxji39zv2w"))))
25469 (build-system r-build-system)
25474 (home-page "http://directlabels.r-forge.r-project.org/")
25475 (synopsis "Direct labels for multicolor plots")
25477 "This package provides an extensible framework for automatically placing
25478 direct labels onto multicolor plots. Label positions are described using
25479 positioning methods that can be re-used across several different plots. There
25480 are heuristics for examining @code{trellis} and @code{ggplot} objects and
25481 inferring an appropriate positioning method.")
25482 (license license:gpl3)))
25484 (define-public r-lsd
25491 (uri (cran-uri "LSD" version))
25493 (base32 "17pbdlcbhzf3v7l42mjikln1ga5xjp5r78gjg6a88iahk0lwwlvm"))))
25494 (properties `((upstream-name . "LSD")))
25495 (build-system r-build-system)
25496 (home-page "https://cran.r-project.org/web/packages/LSD/")
25497 (synopsis "Lots of superior depictions tool creates colorful plots")
25499 "This package creates lots of colorful plots in a multitude of variations.
25500 Try a demo of the LSD by running @code{demotour()}.")
25502 (license (list license:gpl2 license:gpl3))))
25504 (define-public r-phylogram
25506 (name "r-phylogram")
25511 (uri (cran-uri "phylogram" version))
25513 (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v"))))
25514 (properties `((upstream-name . "phylogram")))
25515 (build-system r-build-system)
25516 (propagated-inputs (list r-ape))
25517 (home-page "https://github.com/ropensci/phylogram/")
25518 (synopsis "Dendrograms for evolutionary analysis")
25520 "The @code{r-phylogram} package is a tool for for developing phylogenetic
25521 trees as deeply-nested lists known as \"dendrogram\" objects. It provides
25522 functions for conversion between \"dendrogram\" and \"phylo\" class objects,
25523 as well as several tools for command-line tree manipulation and import/export
25524 via Newick parenthetic text. This improves accessibility to the comprehensive
25525 range of object-specific analytical and tree-visualization functions found
25526 across a wide array of bioinformatic R packages.")
25527 (license license:gpl3)))
25529 (define-public r-kmer
25536 (uri (cran-uri "kmer" version))
25538 (base32 "0jimn9r0abglwxdl1zqz0lxa99cmj6haydkxjzqfbpx9by80wnww"))))
25539 (properties `((upstream-name . "kmer")))
25540 (build-system r-build-system)
25542 (list r-openssl r-phylogram r-rcpp))
25543 (home-page "https://github.com/shaunpwilkinson/kmer/")
25544 (synopsis "Fast K-Mer counting and clustering for biological sequence analysis")
25546 "@code{r-kmer} is an R package for rapidly computing distance matrices
25547 and clustering large sequence datasets using fast alignment-free k-mer
25548 counting and recursive k-means partitioning.")
25549 (license license:gpl3)))
25551 (define-public r-hardhat
25558 (uri (cran-uri "hardhat" version))
25561 "07mx8c24gy0xfmip9hb5w29gp10sfnpnilzc1pi0hjadnrqz8mks"))))
25562 (properties `((upstream-name . "hardhat")))
25563 (build-system r-build-system)
25565 (list r-glue r-rlang r-tibble r-vctrs))
25568 (home-page "https://github.com/tidymodels/hardhat")
25569 (synopsis "Construct modeling packages")
25571 "Building modeling packages is hard. A large amount of effort generally
25572 goes into providing an implementation for a new method that is efficient,
25573 fast, and correct, but often less emphasis is put on the user interface. A
25574 good interface requires specialized knowledge about S3 methods and formulas,
25575 which the average package developer might not have. The goal of
25576 @code{hardhat} is to reduce the burden around building new modeling packages
25577 by providing functionality for preprocessing, predicting, and validating
25579 (license license:expat)))
25581 (define-public r-lightgbm
25583 (name "r-lightgbm")
25588 (uri (cran-uri "lightgbm" version))
25591 "0hvpwirskzcd7ww47f9gllgl3wjvpghnwj8a41glpppwwaaxa0z4"))))
25592 (properties `((upstream-name . "lightgbm")))
25593 (build-system r-build-system)
25595 (list r-data-table r-jsonlite r-matrix r-r6))
25596 (home-page "https://github.com/Microsoft/LightGBM")
25597 (synopsis "Light gradient boosting machine")
25599 "Tree based algorithms can be improved by introducing boosting
25600 frameworks. LightGBM is one such framework, based on Ke, Guolin et
25601 al. (2017). This package offers an R interface to work with it. It is
25602 designed to be distributed and efficient with the following goals:
25605 @item Faster training speed and higher efficiency;
25606 @item lower memory usage;
25607 @item better accuracy;
25608 @item parallel learning supported; and
25609 @item capable of handling large-scale data.
25612 (license license:expat)))
25614 (define-public r-shapforxgboost
25616 (name "r-shapforxgboost")
25621 (uri (cran-uri "SHAPforxgboost" version))
25624 "106nsf02b1w3yshb55lwnyw1rl1a60162v2wk8znjz3b4ln3mqj5"))))
25626 `((upstream-name . "SHAPforxgboost")))
25627 (build-system r-build-system)
25639 (home-page "https://github.com/liuyanguu/SHAPforxgboost")
25640 (synopsis "SHAP Plots for XGBoost")
25642 "The aim of @code{SHAPforxgboost} is to aid in visual data investigations
25643 using @dfn{SHAP} (Shapley additive explanation) visualization plots for
25644 @code{XGBoost}. It provides summary plot, dependence plot, interaction plot,
25645 and force plot. It relies on the @code{XGBoost} package to produce SHAP
25647 (license license:expat)))
25649 (define-public r-rismed
25656 (uri (cran-uri "RISmed" version))
25659 "0vpi88gzi9r85v6nhjz9jbw671zkrmyazwna2z881346wfyr3l8b"))))
25660 (properties `((upstream-name . "RISmed")))
25661 (build-system r-build-system)
25663 (list r-httr r-xml2))
25664 (home-page "https://cran.r-project.org/web/packages/RISmed")
25665 (synopsis "Download content from NCBI databases")
25667 "This package provides a set of tools to extract bibliographic
25668 content from the National Center for Biotechnology Information (NCBI)
25669 databases, including PubMed. The name RISmed is a portmanteau of
25670 RIS (for Research Information Systems, a common tag format for
25671 bibliographic data) and PubMed.")
25672 (license license:gpl2+)))
25674 (define-public r-semver
25681 (uri (cran-uri "semver" version))
25684 "10wpkyms2cix3bsin2q0qhkbl445pwwpa5gm2s4jjw1989namkxy"))))
25685 (properties `((upstream-name . "semver")))
25686 (build-system r-build-system)
25688 (list r-assertthat r-rcpp))
25689 (native-inputs (list r-knitr))
25690 (home-page "https://github.com/johndharrison/semver")
25691 (synopsis "Parser for Semantic Versioning 2.0.0")
25693 "This package provides tools and functions for parsing, rendering and
25694 operating on semantic version strings. Semantic versioning is a simple set of
25695 rules and requirements that dictate how version numbers are assigned and
25696 incremented as outlined at @url{http://semver.org}.")
25697 (license license:expat)))
25699 (define-public r-binman
25706 (uri (cran-uri "binman" version))
25709 "00l7m98h41r67gf0qxqis3vx63j7wylnk9vlgcyk41szkrz8ikkc"))))
25710 (properties `((upstream-name . "binman")))
25711 (build-system r-build-system)
25720 (native-inputs (list r-knitr))
25721 (home-page "https://github.com/ropensci/binman")
25722 (synopsis "Binary download manager")
25724 "This package provides tools and functions for managing the download of
25725 binary files. Binary repositories are defined in the YAML format. Defining
25726 new pre-download, download and post-download templates allow additional
25727 repositories to be added.")
25728 (license license:expat)))
25730 (define-public r-wdman
25737 (uri (cran-uri "wdman" version))
25740 "1yf41lsrr9dbf5n4f5hv9mlmzl736fhnp9gxkm2g9apws6gsig02"))))
25741 (properties `((upstream-name . "wdman")))
25742 (build-system r-build-system)
25744 (list r-assertthat r-binman r-processx r-semver r-yaml))
25745 (native-inputs (list r-knitr))
25746 (home-page "https://docs.ropensci.org/wdman/")
25747 (synopsis "Webdriver/Selenium binary manager")
25749 "There are a number of binary files associated with the
25750 Webdriver/Selenium project (see @url{http://www.seleniumhq.org/download/},
25751 @url{https://sites.google.com/a/chromium.org/chromedriver/},
25752 @url{https://github.com/mozilla/geckodriver},
25753 @url{http://phantomjs.org/download.html}, and
25754 @url{https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver} for
25755 more information). This package provides functions to download these binaries
25756 and to manage processes involving them.")
25757 (license license:expat)))
25759 (define-public r-rselenium
25761 (name "r-rselenium")
25766 (uri (cran-uri "RSelenium" version))
25769 "1xn5fdbzmq7b1f5fc9ls23g177bmnd8bn4p4d8aafr6z3jwkmfir"))))
25770 (properties `((upstream-name . "RSelenium")))
25771 (build-system r-build-system)
25779 (native-inputs (list r-knitr))
25780 (home-page "https://docs.ropensci.org/RSelenium/")
25781 (synopsis "R bindings for Selenium WebDriver")
25783 "This package provides a set of R bindings for the Selenium 2.0
25784 WebDriver (see @url{https://selenium.dev/documentation/en/} for more
25785 information) using the @code{JsonWireProtocol} (see
25786 @url{https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol} for more
25787 information). Selenium 2.0 WebDriver allows driving a web browser natively as
25788 a user would either locally or on a remote machine using the Selenium server
25789 it marks a leap forward in terms of web browser automation. Selenium
25790 automates web browsers (commonly referred to as browsers). Using RSelenium
25791 you can automate browsers locally or remotely.")
25792 (license license:agpl3+)))
25794 (define-public r-conquer
25801 (uri (cran-uri "conquer" version))
25804 "0i9g27f52zl2kb2392g0y614drf6s87dqz12aphj889ajq7zjm0k"))))
25805 (properties `((upstream-name . "conquer")))
25806 (build-system r-build-system)
25808 (list r-caret r-matrix r-matrixstats r-rcpp r-rcpparmadillo))
25809 (home-page "https://github.com/XiaoouPan/conquer")
25810 (synopsis "Convolution-type smoothed quantile regression")
25812 "This package provides fast and accurate convolution-type smoothed
25813 quantile regression, implemented using Barzilai-Borwein gradient descent with
25814 a Huber regression warm start. Confidence intervals for regression
25815 coefficients are constructed using multiplier bootstrap.")
25816 (license license:gpl3)))
25818 (define-public r-fastshap
25820 (name "r-fastshap")
25825 (uri (cran-uri "fastshap" version))
25828 "08f25ib5mry6h8lvj0g3clc9kfl5g2wdd8x8bw455wwmbcm6x5vg"))))
25829 (properties `((upstream-name . "fastshap")))
25830 (build-system r-build-system)
25840 (home-page "https://github.com/bgreenwell/fastshap")
25841 (synopsis "Fast approximate Shapley values")
25843 "This package computes fast (relative to other implementations)
25844 approximate Shapley values for any supervised learning model. Shapley values
25845 help to explain the predictions from any black box model using ideas from game
25846 theory; see @url{Strumbel and Kononenko (2014),
25847 doi.org/10.1007/s10115-013-0679-x} for details.")
25848 (license license:gpl2+)))
25850 (define-public r-memuse
25856 (uri (cran-uri "memuse" version))
25859 "1wvwnjaaiv2647561z2b55dss35033ildx4kk8hzxfzgsjmdpsgm"))))
25860 (properties `((upstream-name . "memuse")))
25861 (build-system r-build-system)
25862 (home-page "https://github.com/shinra-dev/memuse")
25863 (synopsis "Memory Estimation Utilities")
25865 "This package provides procedures to answer the following questions:
25866 How much ram do you need to store a 100,000 by 100,000 matrix? How much ram is
25867 your current R session using? How much ram do you even have?")
25868 (license license:bsd-2)))
25870 (define-public r-metrics
25877 (uri (cran-uri "Metrics" version))
25880 "0fh8qbjlwzagh272lgwr4bxcqcjb1qpz53mgs8rzlvncax6nk5bk"))))
25881 (properties `((upstream-name . "Metrics")))
25882 (build-system r-build-system)
25883 (home-page "https://github.com/mfrasco/Metrics")
25884 (synopsis "Evaluation metrics for machine learning")
25886 "This package provides an implementation of evaluation metrics in R that
25887 are commonly used in supervised machine learning. It implements metrics for
25888 regression, time series, binary classification, classification, and
25889 information retrieval problems. It has zero dependencies and a consistent,
25890 simple interface for all functions.")
25891 (license license:bsd-3)))
25893 (define-public r-iml
25900 (uri (cran-uri "iml" version))
25903 "1wz6xqhvqkzj723nw7qrlwb1171wvvpxhv3pa8cq7vcbkiflq37r"))))
25904 (properties `((upstream-name . "iml")))
25905 (build-system r-build-system)
25917 (native-inputs (list r-knitr))
25918 (home-page "https://github.com/christophM/iml")
25919 (synopsis "Interpretable machine learning")
25921 "This package provides interpretability methods to analyze the behavior
25922 and predictions of any machine learning model. Implemented methods are:
25925 @item Feature importance described by Fisher et al. (2018),
25926 @item accumulated local effects plots described by Apley (2018),
25927 @item partial dependence plots described by Friedman (2001),
25928 @item individual conditional expectation ('ice') plots described by Goldstein
25929 et al. (2013) @url{https://doi.org/10.1080/10618600.2014.907095},
25930 @item local models (variant of 'lime') described by Ribeiro et. al (2016),
25931 @item the Shapley Value described by Strumbelj et. al (2014)
25932 @url{https://doi.org/10.1007/s10115-013-0679-x},
25933 @item feature interactions described by Friedman et. al
25934 @url{https://doi.org/10.1214/07-AOAS148} and tree surrogate models.
25937 (license license:expat)))
25939 (define-public r-goftest
25946 (uri (cran-uri "goftest" version))
25949 "06bz6k7smr4jbvzmb73qc5fkf4my59w5gbl18wlmpkkymsv78prs"))))
25950 (properties `((upstream-name . "goftest")))
25951 (build-system r-build-system)
25952 (home-page "https://github.com/baddstats/goftest")
25953 (synopsis "Classical Goodness-of-Fit tests for univariate distributions")
25955 "This package provides Cramer-Von Mises and Anderson-Darling tests of
25956 goodness-of-fit for continuous univariate distributions, using efficient
25958 (license license:gpl2+)))
25960 (define-public r-tensor
25967 (uri (cran-uri "tensor" version))
25970 "19mfsgr6vz4lgwidm80i4yw0y1dr3n8i6qz7g4n2xa0k74zc5pp1"))))
25971 (properties `((upstream-name . "tensor")))
25972 (build-system r-build-system)
25973 (home-page "https://cran.r-project.org/web/packages/tensor/")
25974 (synopsis "Tensor product of arrays")
25976 "The tensor product of two arrays is notionally an outer product of the
25977 arrays collapsed in specific extents by summing along the appropriate
25978 diagonals. This package allows you to compute the tensor product of arrays.")
25979 (license license:gpl2+)))
25981 (define-public r-spatstat-utils
25983 (name "r-spatstat-utils")
25988 (uri (cran-uri "spatstat.utils" version))
25991 "1aypccpv0zavxwmqzvlka8981n9km7ml3jbmxz21sql58997xn2s"))))
25993 `((upstream-name . "spatstat.utils")))
25994 (build-system r-build-system)
25995 (home-page "http://www.spatstat.org")
25996 (synopsis "Utility functions for spatstat")
25998 "This package contains utility functions for the @code{spatstat} package
25999 which may also be useful for other purposes.")
26000 (license license:gpl2+)))
26002 (define-public r-spatstat-sparse
26004 (name "r-spatstat-sparse")
26009 (uri (cran-uri "spatstat.sparse" version))
26012 "1iqrpazb88s4w208adf2qgm4ajwz3kwqck65k9g5l28zw9jcxyr7"))))
26014 `((upstream-name . "spatstat.sparse")))
26015 (build-system r-build-system)
26017 (list r-abind r-matrix r-spatstat-utils r-tensor))
26018 (home-page "http://spatstat.org/")
26019 (synopsis "Sparse three-dimensional arrays and linear algebra utilities")
26021 "This package defines sparse three-dimensional arrays and supports
26022 standard operations on them. The package also includes utility functions for
26023 matrix calculations that are common in statistics, such as quadratic forms.")
26024 (license license:gpl2+)))
26026 (define-public r-spatstat-data
26028 (name "r-spatstat-data")
26033 (uri (cran-uri "spatstat.data" version))
26036 "0csmz5vjaxnznkbsfah8qd3v8p0y56jvis01ialxzvf71snl160v"))))
26037 (properties `((upstream-name . "spatstat.data")))
26038 (build-system r-build-system)
26040 (list r-matrix r-spatstat-utils))
26041 (home-page "http://www.spatstat.org")
26042 (synopsis "Datasets for spatstat")
26044 "This package contains all the datasets for the @code{spatstat}
26046 (license license:gpl2+)))
26048 (define-public r-spatstat-geom
26050 (name "r-spatstat-geom")
26055 (uri (cran-uri "spatstat.geom" version))
26058 "1iz9zi45nli5lf96ng6bqqbl4ix3zxzlfclkg4cdb9h98nj4c5vv"))))
26059 (properties `((upstream-name . "spatstat.geom")))
26060 (build-system r-build-system)
26062 (list r-deldir r-polyclip r-spatstat-data r-spatstat-utils))
26063 (home-page "http://spatstat.org/")
26064 (synopsis "Geometrical functionality of the spatstat package")
26066 "This is a subset of the original spatstat package, containing the
26067 user-level code from spatstat which performs geometrical operations, except
26068 for the geometry of linear networks.")
26069 (license license:gpl2+)))
26071 (define-public r-spatstat-core
26073 (name "r-spatstat-core")
26078 (uri (cran-uri "spatstat.core" version))
26081 "1fq6ynds66d836drf758syqhfz0341fxif0r5hbf5lfkwp3a2wfk"))))
26082 (properties `((upstream-name . "spatstat.core")))
26083 (build-system r-build-system)
26096 (home-page "http://spatstat.org/")
26097 (synopsis "Core functionality of the spatstat package")
26099 "This is a subset of the original spatstat package, containing all of the
26100 user-level code from spatstat, except for the code for linear networks.")
26101 (license license:gpl2+)))
26103 (define-public r-spatstat-linnet
26105 (name "r-spatstat-linnet")
26110 (uri (cran-uri "spatstat.linnet" version))
26113 "1yd2z629f7908xw9kyqiahk3qn9ajpl6qffbkv887zmq3p28kh7h"))))
26115 `((upstream-name . "spatstat.linnet")))
26116 (build-system r-build-system)
26124 (home-page "http://spatstat.org/")
26125 (synopsis "Linear networks functionality of the spatstat package")
26127 "This is a subset of the spatstat package, containing its functionality
26128 for spatial data on a linear network.")
26129 (license license:gpl2+)))
26131 (define-public r-spatstat
26133 (name "r-spatstat")
26138 (uri (cran-uri "spatstat" version))
26141 "0lz3sidn05xjswxaxhagal6jj5hra6aya0azxybjw7mgspl903wg"))))
26142 (properties `((upstream-name . "spatstat")))
26143 (build-system r-build-system)
26145 (list r-spatstat-core r-spatstat-data r-spatstat-geom
26146 r-spatstat-linnet r-spatstat-utils))
26147 (home-page "http://www.spatstat.org")
26148 (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests")
26150 "This package provides a comprehensive toolbox for analysing Spatial
26151 Point Patterns. It is focused mainly on two-dimensional point patterns,
26152 including multitype/marked points, in any spatial region. It also supports
26153 three-dimensional point patterns, space-time point patterns in any number of
26154 dimensions, point patterns on a linear network, and patterns of other
26155 geometrical objects. It supports spatial covariate data such as pixel images
26156 and contains over 2000 functions for plotting spatial data, exploratory data
26157 analysis, model-fitting, simulation, spatial sampling, model diagnostics, and
26158 formal inference.")
26159 (license license:gpl2+)))
26161 (define-public r-gaston
26168 (uri (cran-uri "gaston" version))
26171 "14z94dpln4dvgrv2w7w9ik7h6rpvbf02qhq1hqzx8c2cndzxr21i"))))
26172 (properties `((upstream-name . "gaston")))
26173 (build-system r-build-system)
26174 (inputs (list zlib))
26176 (list r-rcpp r-rcppeigen r-rcppparallel))
26177 (native-inputs (list r-knitr))
26178 (home-page "https://cran.r-project.org/web/packages/gaston/")
26179 (synopsis "Genetic data handling (QC, GRM, LD, PCA) and linear mixed models")
26181 "This is a package for the manipulation of genetic data (SNPs).
26182 Computation of @dfn{genetic relationship matrix} (GRM) and dominance matrix,
26183 @dfn{linkage disequilibrium} (LD), and heritability with efficient algorithms
26184 for linear mixed models (AIREML).")
26185 (license license:gpl3)))
26187 (define-public r-cpp11
26194 (uri (cran-uri "cpp11" version))
26197 "1nk47xkab7i17h7917l4cfyfvnxf782dfq67wwxa6n0r4jqqxzz9"))))
26198 (properties `((upstream-name . "cpp11")))
26199 (build-system r-build-system)
26200 (native-inputs (list r-knitr))
26201 (home-page "https://github.com/r-lib/cpp11")
26202 (synopsis "C++11 Interface for R's C Interface")
26204 "This package provides a header only, C++11 interface to R's C interface.
26205 Compared to other approaches @code{cpp11} strives to be safe against long
26206 jumps from the C API as well as C++ exceptions, conform to normal R function
26207 semantics and supports interaction with @code{ALTREP} vectors.")
26208 (license license:expat)))
26210 (define-public r-rcppziggurat
26212 (name "r-rcppziggurat")
26217 (uri (cran-uri "RcppZiggurat" version))
26220 "0wgd1v2p7zajnbrjf3hfi56p3pk3ld6iwkanbb04bjbnlif2ay4w"))))
26221 (properties `((upstream-name . "RcppZiggurat")))
26222 (build-system r-build-system)
26224 (list r-rcpp r-rcppgsl))
26225 (native-inputs (list r-knitr))
26226 (home-page "https://cran.r-project.org/web/packages/RcppZiggurat/")
26227 (synopsis "Rcpp integration of different \"Ziggurat\" normal RNG implementations")
26229 "The Ziggurat generator for normally distributed random numbers,
26230 originally proposed by Marsaglia and Tsang (2000,
26231 @url{https://doi.org/10.18637/jss.v005.i08}) has been improved upon a few
26232 times starting with Leong et al (2005,
26233 @url{https://doi.org/10.18637/jss.v012.i07}). This package provides an
26234 aggregation for comparing different implementations in order to provide a
26235 'faster but good enough' alternative for use with R and C++ code.")
26236 (license license:gpl2+)))
26238 (define-public r-rfast
26245 (uri (cran-uri "Rfast" version))
26248 "1bmhmli6q4kg8321595k0yy91w9cblk14s6qbc9wf8f05108rg15"))))
26249 (properties `((upstream-name . "Rfast")))
26250 (build-system r-build-system)
26252 (list r-rcpp r-rcpparmadillo r-rcppziggurat))
26253 (home-page "https://github.com/RfastOfficial/Rfast")
26254 (synopsis "Collection of efficient and fast R functions")
26256 "This package provides a collection of fast (utility) functions for data
26257 analysis. Column- and row- wise means, medians, variances, minimums,
26258 maximums, many t, F and G-square tests, many regressions (normal, logistic,
26259 Poisson), are some of the many fast functions.")
26260 (license license:gpl2+)))
26262 (define-public r-rffc
26268 (uri (string-append
26269 "https://download.r-forge.r-project.org/src/contrib/"
26270 "rfFC_" version ".tar.gz"))
26273 "05x9wgzsmx4vb12lmcspymgmpb2xw8bwryb8ysg7vzg2nkh0ma3g"))))
26274 (build-system r-build-system)
26276 (list r-randomforest))
26277 (home-page "https://r-forge.r-project.org/projects/rffc/")
26278 (synopsis "Random Forest Feature Contributions")
26279 (description "This package provides functions for extracting feature
26280 contributions from a random forest model from package @code{randomForest}.
26281 Feature contributions provide detailed information about the relationship
26282 between data variables and the predicted value returned by random forest
26284 (license license:gpl2)))
26286 (define-public r-clusterr
26288 (name "r-clusterr")
26293 (uri (cran-uri "ClusterR" version))
26296 "1fsb9pzs1paw1cbyr5a56lfh8h2d50232p6isk0xg5sl110ql7kx"))))
26297 (properties `((upstream-name . "ClusterR")))
26298 (build-system r-build-system)
26300 (list r-ggplot2 r-gmp r-gtools r-rcpp r-rcpparmadillo))
26301 (native-inputs (list r-knitr))
26302 (home-page "https://github.com/mlampros/ClusterR")
26303 (synopsis "Clustering")
26305 "This package provides Gaussian mixture models, k-means,
26306 mini-batch-kmeans, k-medoids and affinity propagation clustering with the
26307 option to plot, validate, predict (new data) and estimate the optimal number
26308 of clusters. The package takes advantage of @code{RcppArmadillo} to speed up
26309 the computationally intensive parts of the functions. For more information,
26313 @item \"Clustering in an Object-Oriented Environment\" by Anja Struyf, Mia
26314 Hubert, Peter Rousseeuw (1997), Journal of Statistical Software,
26315 @url{https://doi.org/10.18637/jss.v001.i04};
26316 @item \"Web-scale k-means clustering\" by D. Sculley (2010), ACM Digital
26317 Library, @url{https://doi.org/10.1145/1772690.1772862};
26318 @item \"Armadillo: a template-based C++ library
26319 for linear algebra\" by Sanderson et al (2016), The Journal of Open Source
26320 Software, @url{https://doi.org/10.21105/joss.00026};
26321 @item \"Clustering by Passing Messages Between Data Points\" by Brendan
26322 J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814,
26323 pp. 972-976, @url{https://doi.org/10.1126/science.1136800}.
26326 (license license:gpl3)))
26328 (define-public r-spectrum
26330 (name "r-spectrum")
26335 (uri (cran-uri "Spectrum" version))
26338 "0n38d360azkck6vvhr771zsh0gbvd9qsf9ygg5r18vhz0pb1xcfw"))))
26339 (properties `((upstream-name . "Spectrum")))
26340 (build-system r-build-system)
26342 (list r-clusterr r-diptest r-ggplot2 r-rfast))
26343 (native-inputs (list r-knitr))
26344 (home-page "https://cran.r-project.org/web/packages/Spectrum/")
26345 (synopsis "Fast adaptive spectral clustering for single and multi-view data")
26347 "This package provides a self-tuning spectral clustering method for
26348 single or multi-view data. Spectrum uses a new type of adaptive density aware
26349 kernel that strengthens connections in the graph based on common nearest
26350 neighbours. It uses a tensor product graph data integration and diffusion
26351 procedure to integrate different data sources and reduce noise. Spectrum uses
26352 either the eigengap or multimodality gap heuristics to determine the number of
26353 clusters. The method is sufficiently flexible so that a wide range of
26354 Gaussian and non-Gaussian structures can be clustered with automatic selection
26356 (license license:agpl3+)))
26358 (define-public r-nabor
26365 (uri (cran-uri "nabor" version))
26368 "1nj39cdfwrmhgsi3cq8imxv3n6xzc1v6dzdb2cf2hybjk368v4s7"))))
26369 (properties `((upstream-name . "nabor")))
26370 (build-system r-build-system)
26372 (list r-bh r-rcpp r-rcppeigen))
26373 (home-page "https://cran.r-project.org/web/packages/nabor/")
26374 (synopsis "Wrapper for K nearest neighbour library for low dimensions")
26376 "This package provides an R wrapper for libnabo, an exact or approximate
26377 k nearest neighbour library which is optimised for low dimensional
26378 spaces (e.g. 3D). @code{nabor} includes a @code{knn} function that is
26379 designed as a drop-in replacement for the RANN function @code{nn2}. In
26380 addition, objects which include the k-d tree search structure can be returned
26381 to speed up repeated queries of the same set of target points.")
26382 (license license:bsd-3)))
26384 (define-public r-naturalsort
26386 (name "r-naturalsort")
26390 (uri (cran-uri "naturalsort" version))
26393 "0mz801y9mzld9ypp3xmsjw2d8l9q97sdnv09wrci9xi3yg2sjf6d"))))
26394 (build-system r-build-system)
26395 (home-page "https://cran.r-project.org/web/packages/naturalsort/")
26396 (synopsis "Natural ordering")
26397 (description "This package provides functions related to human natural
26398 ordering. It handles adjacent digits in a character sequence as a number
26399 so that natural sort function arranges a character vector by their numbers,
26400 not digit characters.")
26401 (license license:bsd-3)))
26403 (define-public r-visdat
26409 (uri (cran-uri "visdat" version))
26412 "1ikqp29nncbw1xlwyb9dqqgcdk9q0bs3wxhnhnjpb11vcjv7cz2j"))))
26413 (build-system r-build-system)
26425 (home-page "https://visdat.njtierney.com/")
26426 (synopsis "Preliminary Visualisation of Data")
26427 (description "This package provides procedures to create preliminary exploratory
26428 data visualisations of an entire dataset to identify problems or unexpected features
26429 using @code{ggplot2}.")
26430 (license license:expat)))
26432 (define-public r-muhaz
26435 (version "1.2.6.4")
26439 (uri (cran-uri "muhaz" version))
26442 "1ddy8ayr4rdhzcipdvxdwd7z5g9hfp0ppacl7xf6f2612cn1185g"))))
26443 (properties `((upstream-name . "muhaz")))
26444 (build-system r-build-system)
26449 (home-page "https://cran.r-project.org/web/packages/muhaz/")
26450 (synopsis "Hazard function estimation in survival analysis")
26452 "This package produces a smooth estimate of the hazard function for
26454 ;; Any version of the GPL.
26455 (license license:gpl3+)))
26457 (define-public r-flexsurv
26459 (name "r-flexsurv")
26464 (uri (cran-uri "flexsurv" version))
26467 "0kwij9nkdvnsn1kn12fj3hjkd2qpgw7bdda4qad7basq5p6divlp"))))
26468 (properties `((upstream-name . "flexsurv")))
26469 (build-system r-build-system)
26492 (home-page "https://github.com/chjackson/flexsurv-dev")
26493 (synopsis "Flexible parametric survival and multi-state models")
26495 "This package provides flexible parametric models for time-to-event data,
26496 including the Royston-Parmar spline model, generalized gamma and generalized F
26497 distributions. Any user-defined parametric distribution can be fitted, given
26498 at least an R function defining the probability density or hazard. There are
26499 also tools for fitting and predicting from fully parametric multi-state
26501 (license license:gpl2+)))
26503 (define-public r-transphylo
26505 (name "r-transphylo")
26510 (uri (cran-uri "TransPhylo" version))
26513 "0g92kwi1nlmpc8m4pc9kv9xhczryr2kn9icfr3js7da7vy8g50xy"))))
26514 (properties `((upstream-name . "TransPhylo")))
26515 (build-system r-build-system)
26517 (list r-ape r-rcpp))
26520 (home-page "https://cran.r-project.org/web/packages/TransPhylo/")
26521 (synopsis "Inference of transmission tree from a dated phylogeny")
26523 "This is a package to infer transmission trees from a dated phylogeny.
26524 It includes methods to simulate and analyze outbreaks. The methodology is
26525 described in @url{https://doi.org/10.1093/molbev/msu121,Didelot et al. (2014)}
26526 and @url{https://doi.org/10.1093/molbev/msw275,Didelot et al. (2017)}.")
26527 (license license:gpl2+)))
26529 (define-public r-km-ci
26536 (uri (cran-uri "km.ci" version))
26539 "1l6kw8jppaa1802yc5pbfwwgac56nhwc9p076ivylhms4w7cdf8v"))))
26540 (properties `((upstream-name . "km.ci")))
26541 (build-system r-build-system)
26544 (home-page "https://cran.r-project.org/web/packages/km.ci/")
26545 (synopsis "Confidence intervals for the Kaplan-Meier estimator")
26547 "This package computes various @dfn{confidence intervals} (CI) for the
26548 Kaplan-Meier estimator, namely: Petos CI, Rothman CI, CIs based on Greenwoods
26549 variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by
26550 Nair and Hall and Wellner.")
26551 (license license:gpl2+)))
26553 (define-public r-kmsurv
26560 (uri (cran-uri "KMsurv" version))
26563 "0hi5vvk584rl70gbrr75w9hc775xmbxnaig0dd6hlpi4071pnqjm"))))
26564 (properties `((upstream-name . "KMsurv")))
26565 (build-system r-build-system)
26566 (home-page "https://cran.r-project.org/web/packages/KMsurv/")
26567 (synopsis "Data sets from Klein and Moeschberger (1997), Survival Analysis")
26569 "This package provides data sets and functions for Klein and Moeschberger
26570 (1997), \"Survival Analysis, Techniques for Censored and Truncated Data\",
26572 (license license:gpl3+)))
26574 (define-public r-survmisc
26576 (name "r-survmisc")
26581 (uri (cran-uri "survMisc" version))
26584 "00nvvl8gz4477ab24rd0xvfksm8msv8h021b9ld5c9cizc41n2bm"))))
26585 (properties `((upstream-name . "survMisc")))
26586 (build-system r-build-system)
26599 (home-page "https://cran.r-project.org/web/packages/survMisc/")
26600 (synopsis "Miscellaneous functions for survival data")
26602 "This package provides a collection of functions to help in the analysis
26603 of right-censored survival data. These extend the methods available in
26604 the @code{survival} package.")
26605 (license license:gpl2)))
26607 (define-public r-exactranktests
26609 (name "r-exactranktests")
26614 (uri (cran-uri "exactRankTests" version))
26617 "1i4mwz61mjlh1ai3dww2pjkicx9ww8c4mljnr8xlawh91479lva9"))))
26619 `((upstream-name . "exactRankTests")))
26620 (build-system r-build-system)
26621 (home-page "https://cran.r-project.org/web/packages/exactRankTests/")
26622 (synopsis "Exact distributions for rank and permutation tests")
26624 "This package computes exact conditional p-values and quantiles using an
26625 implementation of the Shift-Algorithm by Streitberg & Roehmel.")
26626 (license license:gpl2+)))
26628 (define-public r-maxstat
26635 (uri (cran-uri "maxstat" version))
26638 "114z1rwxwvk05ijjhdppzm148n1h192fp0w12ky10zkrhf6kphbg"))))
26639 (properties `((upstream-name . "maxstat")))
26640 (build-system r-build-system)
26642 (list r-exactranktests r-mvtnorm))
26643 (home-page "https://cran.r-project.org/web/packages/maxstat/")
26644 (synopsis "Maximally selected rank statistics")
26646 "This package provides maximally selected rank statistics with several
26647 p-value approximations.")
26648 (license license:gpl2+)))
26650 (define-public r-survminer
26652 (name "r-survminer")
26657 (uri (cran-uri "survminer" version))
26660 "0byh0wxdbjfwdrzsnqv4xlmnik6lj0vkkzfxy7lssk8dv5zmj7nz"))))
26661 (properties `((upstream-name . "survminer")))
26662 (build-system r-build-system)
26681 (home-page "https://rpkgs.datanovia.com/survminer/index.html")
26682 (synopsis "Drawing survival curves using ggplot2")
26684 "This package contains the function @code{ggsurvplot()} for easily
26685 drawing beautiful and 'ready-to-publish' survival curves with the 'number at
26686 risk' table and 'censoring count plot'. Other functions are also available to
26687 plot adjusted curves for Cox model and to visually examine Cox model
26689 (license license:gpl2)))
26691 (define-public r-forge
26698 (uri (cran-uri "forge" version))
26701 "0pjfzsc35agkh0zfw2czwajkbsyn6liys5irl5bhz5r1vim3jmwa"))))
26702 (properties `((upstream-name . "forge")))
26703 (build-system r-build-system)
26705 (list r-magrittr r-rlang))
26706 (home-page "https://cran.r-project.org/web/packages/forge/")
26707 (synopsis "Cast values into shape")
26709 "This package provides helper functions with a consistent interface to
26710 coerce and verify the types and shapes of values for input checking.")
26711 (license license:asl2.0)))
26713 (define-public r-config
26720 (uri (cran-uri "config" version))
26723 "0l2zp7v6qaz72dclcbjrlis633zlwp8rsi5azr7iw127iyz7i26l"))))
26724 (properties `((upstream-name . "config")))
26725 (build-system r-build-system)
26730 (home-page "https://github.com/rstudio/config")
26731 (synopsis "Manage environment specific configuration values")
26733 "This package lets you manage configuration values across multiple
26734 environments (e.g. development, test, production). It reads values using a
26735 function that determines the current environment and returns the appropriate
26737 (license license:gpl3)))
26739 (define-public r-adaptivesparsity
26741 (name "r-adaptivesparsity")
26745 (uri (cran-uri "AdaptiveSparsity" version))
26748 "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
26750 `((upstream-name . "AdaptiveSparsity")))
26751 (build-system r-build-system)
26754 (modify-phases %standard-phases
26755 (add-after 'unpack 'link-against-armadillo
26757 (substitute* "src/Makevars"
26758 (("PKG_LIBS=" prefix)
26759 (string-append prefix "-larmadillo")))
26762 (list r-mass r-matrix r-rcpp r-rcpparmadillo))
26765 (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
26766 (synopsis "Adaptive sparsity models")
26768 "This package implements the Figueiredo machine learning algorithm for
26769 adaptive sparsity and the Wong algorithm for adaptively sparse Gaussian
26770 geometric models.")
26771 (license license:lgpl3+)))
26773 (define-public r-diffusionmap
26775 (name "r-diffusionmap")
26780 (uri (cran-uri "diffusionMap" version))
26783 "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))
26784 (properties `((upstream-name . "diffusionMap")))
26785 (build-system r-build-system)
26787 (list r-igraph r-matrix r-scatterplot3d))
26788 (home-page "https://www.r-project.org")
26789 (synopsis "Diffusion map")
26790 (description "This package implements the diffusion map method of data
26791 parametrization, including creation and visualization of diffusion maps,
26792 clustering with diffusion K-means and regression using the adaptive regression
26794 (license license:gpl2)))
26796 (define-public r-igraph
26803 (uri (cran-uri "igraph" version))
26806 "01hvphaf5mx9xvwiazcw39kp6gc1lafqrbjwczy6f7hr145dn1pl"))))
26807 (build-system r-build-system)
26811 (list gmp glpk libxml2 zlib))
26813 (list r-magrittr r-matrix r-pkgconfig))
26814 (home-page "https://igraph.org")
26815 (synopsis "Network analysis and visualization")
26817 "This package provides routines for simple graphs and network analysis.
26818 It can handle large graphs very well and provides functions for generating
26819 random and regular graphs, graph visualization, centrality methods and much
26821 (license license:gpl2+)))
26823 (define-public r-workflows
26825 (name "r-workflows")
26830 (uri (cran-uri "workflows" version))
26833 "1sxrgza922p137z41jcj2iwk19lxzwh6kp4kz7h9kw0b8rvfqwab"))))
26834 (properties `((upstream-name . "workflows")))
26835 (build-system r-build-system)
26849 (home-page "https://github.com/tidymodels/workflows")
26850 (synopsis "Modeling workflows")
26852 "A workflow is an object that can bundle together your pre-processing,
26853 modeling, and post-processing requests. For example, if you have a
26854 @code{recipe} and @code{parsnip} model, these can be combined into a
26855 workflow. The advantages are:
26858 @item You don’t have to keep track of separate objects in your workspace.
26859 @item The recipe prepping and model fitting can be executed using a single
26860 call to @code{fit()}.
26861 @item If you have custom tuning parameter settings, these can be defined using
26862 a simpler interface when combined with @code{tune}.
26863 @item In the future, workflows will be able to add post-processing operations,
26864 such as modifying the probability cutoff for two-class models.
26867 (license license:expat)))
26869 (define-public r-lobstr
26876 (uri (cran-uri "lobstr" version))
26879 "0vkif17825x33cz8r89j0qph4wj5l8fzfgl8nh2g7m2v140cxjdq"))))
26880 (properties `((upstream-name . "lobstr")))
26881 (build-system r-build-system)
26883 (list r-crayon r-rcpp r-rlang))
26884 (home-page "https://github.com/r-lib/lobstr")
26885 (synopsis "Visualize R data structures with trees")
26887 "This package provides a set of tools for inspecting and understanding R
26888 data structures inspired by @code{str}. It includes @code{ast} for
26889 visualizing abstract syntax trees, @code{ref} for showing shared references,
26890 @code{cst} for showing call stack trees, and @code{obj_size} for computing
26892 (license license:gpl3)))
26894 (define-public r-gpfit
26901 (uri (cran-uri "GPfit" version))
26904 "05mpiyi2vxv0wqp422n1mnxa8msc4daq40cwpnpngbcwqhlgqkby"))))
26905 (properties `((upstream-name . "GPfit")))
26906 (build-system r-build-system)
26908 (list r-lattice r-lhs))
26909 (home-page "https://cran.r-project.org/web/packages/GPfit/")
26910 (synopsis "Gaussian Processes modeling")
26912 "This package provides a computationally stable approach of fitting a
26913 @dfn{Gaussian Process} (GP) model to a deterministic simulator.")
26914 (license license:gpl2)))
26916 (define-public r-yardstick
26918 (name "r-yardstick")
26923 (uri (cran-uri "yardstick" version))
26926 "13b0lyj2k0r568mwlyz9yvp9156rzlj4jqnjazaffh9vwqh4whir"))))
26927 (properties `((upstream-name . "yardstick")))
26928 (build-system r-build-system)
26938 (home-page "https://github.com/tidymodels/yardstick")
26939 (synopsis "Tidy characterizations of model performance")
26941 "This package provides tidy tools for quantifying how well a model fits
26942 to a data set such as confusion matrices, class probability curve summaries,
26943 and regression metrics (e.g., RMSE).")
26944 (license license:gpl2)))
26946 (define-public r-warp
26953 (uri (cran-uri "warp" version))
26956 "0s0acddc5h14245hi1faycxp0fyvw6nlgaz2df7da4fpyd2f638f"))))
26957 (properties `((upstream-name . "warp")))
26958 (build-system r-build-system)
26959 (native-inputs (list r-knitr))
26960 (home-page "https://github.com/DavisVaughan/warp")
26961 (synopsis "Group dates")
26963 "This package provides tooling to group dates by a variety of periods
26964 including: yearly, monthly, by second, by week of the month, and more. The
26965 groups are defined in such a way that they also represent the distance between
26966 dates in terms of the period. This extracts valuable information that can be
26967 used in further calculations that rely on a specific temporal spacing between
26969 (license license:expat)))
26971 (define-public r-slider
26978 (uri (cran-uri "slider" version))
26981 "1vxk2bc33svwcki2j8zr5jcxswh27i0fqgzjw2a5a1pp9dh3fmd3"))))
26982 (properties `((upstream-name . "slider")))
26983 (build-system r-build-system)
26985 (list r-ellipsis r-glue r-rlang r-vctrs r-warp))
26986 (native-inputs (list r-knitr))
26987 (home-page "https://github.com/DavisVaughan/slider")
26988 (synopsis "Sliding window functions")
26990 "This package provides type-stable rolling window functions over any R
26991 data type. Cumulative and expanding windows are also supported. For more
26992 advanced usage, an index can be used as a secondary vector that defines how
26993 sliding windows are to be created.")
26994 (license license:expat)))
26996 (define-public r-rsample
27003 (uri (cran-uri "rsample" version))
27006 "01xwhj4zfvxbv9cjb6mbz3aphxqc3cnjjx1xy2yx2wd94fbka42z"))))
27007 (properties `((upstream-name . "rsample")))
27008 (build-system r-build-system)
27024 (home-page "https://rsample.tidymodels.org")
27025 (synopsis "General resampling infrastructure")
27027 "This package provides classes and functions to create and summarize
27028 different types of resampling objects (e.g. bootstrap, cross-validation).")
27029 (license license:gpl2)))
27031 (define-public r-dicedesign
27033 (name "r-dicedesign")
27038 (uri (cran-uri "DiceDesign" version))
27041 "1a8ixa65xgyfri03cviic8qi2plbhdyz8m02bwif8w94w0q3ghlk"))))
27042 (properties `((upstream-name . "DiceDesign")))
27043 (build-system r-build-system)
27044 (home-page "http://dice.emse.fr/")
27045 (synopsis "Designs of computer experiments")
27047 "This package provides tools to create some specific @code{Space-Filling
27048 Design} (SFD) and to test their quality.")
27049 (license license:gpl3)))
27051 (define-public r-dials
27058 (uri (cran-uri "dials" version))
27061 "1vhqcfwgic01pkw0i3000fvqq9yxfzsv26c0psfjhxkkdcz8h2px"))))
27062 (properties `((upstream-name . "dials")))
27063 (build-system r-build-system)
27074 (native-inputs (list r-knitr))
27075 (home-page "https://dials.tidymodels.org/")
27076 (synopsis "Tools for creating tuning parameter values")
27078 "Many models contain tuning parameters (i.e. parameters that cannot be
27079 directly estimated from the data). These tools can be used to define objects
27080 for creating, simulating, or validating values for such parameters.")
27081 (license license:gpl2)))
27083 (define-public r-tune
27090 (uri (cran-uri "tune" version))
27093 "1356w98ljiay8fwa7narr7j5hfbvi69gy03gr7kqiwnfglyksrza"))))
27094 (properties `((upstream-name . "tune")))
27095 (build-system r-build-system)
27118 (home-page "https://github.com/tidymodels/tune")
27119 (synopsis "Tidy tuning tools")
27121 "The ability to tune models is important. @code{tune} contains functions
27122 and classes to be used in conjunction with other @code{tidymodels} packages
27123 for finding reasonable values of hyper-parameters in models, pre-processing
27124 methods, and post-processing steps.")
27125 (license license:expat)))
27127 (define-public r-workflowsets
27129 (name "r-workflowsets")
27134 (uri (cran-uri "workflowsets" version))
27137 "0596hb17mshpag3vjy2wl6fi2mdw54i9gc5za10vzy8vpkigb9jy"))))
27138 (properties `((upstream-name . "workflowsets")))
27139 (build-system r-build-system)
27159 (home-page "https://github.com/tidymodels/workflowsets")
27160 (synopsis "Create a collection of tidymodels workflows")
27162 "A workflow is a combination of a model and preprocessors (e.g, a
27163 formula, recipe, etc.). In order to try different combinations of these, an
27164 object can be created that contains many workflows. There are functions to
27165 create workflows en masse as well as training them and visualizing the
27167 (license license:expat)))
27169 (define-public r-tidyposterior
27171 (name "r-tidyposterior")
27176 (uri (cran-uri "tidyposterior" version))
27179 "1h1664sjrg6akph6nrk8ynn2kjiswv6gshy35gamam1h4axf6wah"))))
27180 (properties `((upstream-name . "tidyposterior")))
27181 (build-system r-build-system)
27197 (home-page "https://tidyposterior.tidymodels.org")
27198 (synopsis "Bayesian analysis to compare models using resampling statistics")
27200 "This package can be used to conduct post hoc analyses of resampling
27201 results generated by models. For example, if two models are evaluated with
27202 the @dfn{root mean squared error} (RMSE) using 10-fold cross-validation, there
27203 are 10 paired statistics. These can be used to make comparisons between
27204 models without involving a test set.")
27205 (license license:gpl2)))
27207 (define-public r-tidypredict
27209 (name "r-tidypredict")
27214 (uri (cran-uri "tidypredict" version))
27217 "0fff349pkksss8h1k2qza78l81ha6avx63pxziv6dfa8h62qmrdy"))))
27218 (properties `((upstream-name . "tidypredict")))
27219 (build-system r-build-system)
27231 (home-page "https://tidypredict.tidymodels.org")
27232 (synopsis "Run predictions inside the database")
27234 "This package parses a fitted R model object, and returns a formula in
27235 Tidy Eval code that calculates the predictions. It works with several
27236 database backends because it leverages @code{dplyr} and @code{dbplyr} for the
27237 final SQL translation of the algorithm. It currently supports @code{lm()},
27238 @code{glm()}, @code{randomForest()}, @code{ranger()}, @code{earth()},
27239 @code{xgb.Booster.complete()}, @code{cubist()}, and @code{ctree()} models.")
27240 (license license:gpl3)))
27242 (define-public r-janeaustenr
27244 (name "r-janeaustenr")
27249 (uri (cran-uri "janeaustenr" version))
27252 "1wyn4qc28a3sval8shmyi2d7s4nl3jh96s8pzq871brxcmrncbwr"))))
27253 (properties `((upstream-name . "janeaustenr")))
27254 (build-system r-build-system)
27255 (home-page "https://github.com/juliasilge/janeaustenr")
27256 (synopsis "Jane Austen's complete novels")
27258 "This package provides the full texts for Jane Austen's six completed
27259 novels, ready for text analysis. These novels are \"Sense and Sensibility\",
27260 \"Pride and Prejudice\", \"Mansfield Park\", \"Emma\", \"Northanger Abbey\",
27261 and \"Persuasion\".")
27262 (license license:expat)))
27264 (define-public r-tokenizers
27266 (name "r-tokenizers")
27271 (uri (cran-uri "tokenizers" version))
27274 "006xf1vdrmp9skhpss9ldhmk4cwqk512cjp1pxm2gxfybpf7qq98"))))
27275 (properties `((upstream-name . "tokenizers")))
27276 (build-system r-build-system)
27278 (list r-rcpp r-snowballc r-stringi))
27281 (home-page "https://lincolnmullen.com/software/tokenizers/")
27282 (synopsis "Fast, consistent tokenization of natural language text")
27284 "This is a package for converting natural language text into tokens.
27285 It includes tokenizers for shingled n-grams, skip n-grams, words, word stems,
27286 sentences, paragraphs, characters, shingled characters, lines, tweets, Penn
27287 Treebank, regular expressions, as well as functions for counting characters,
27288 words, and sentences, and a function for splitting longer texts into separate
27289 documents, each with the same number of words. The tokenizers have a
27290 consistent interface, and the package is built on the @code{stringi} and
27291 @code{Rcpp} packages for fast yet correct tokenization in UTF-8 encoding.")
27292 (license license:expat)))
27294 (define-public r-hunspell
27296 (name "r-hunspell")
27301 (uri (cran-uri "hunspell" version))
27304 "0ql6y05d4xxpm468rslb0wxdp1x9l3flxzmb5w6pjg617f8vpv8z"))))
27305 (properties `((upstream-name . "hunspell")))
27306 (build-system r-build-system)
27308 (list r-digest r-rcpp))
27311 (home-page "https://github.com/ropensci/hunspell#readme")
27312 (synopsis "High-performance stemmer, tokenizer, and spell checker")
27314 "This package provides a low-level spell checker and morphological
27315 analyzer based on the famous @code{hunspell} library. The package can analyze
27316 or check individual words as well as parse text, LaTeX, HTML or XML documents.
27317 For a more user-friendly interface use the @code{spelling} package which
27318 builds on this package to automate checking of files, documentation and
27319 vignettes in all common formats.")
27320 ;; The hunspell library itself is available under one of GPL2, LGPL2.1, or
27321 ;; MPL; in addition to these licenses the rest of the R wrapper is also
27322 ;; available under the Expat license.
27323 (license (list license:gpl2
27328 (define-public r-tidytext
27330 (name "r-tidytext")
27335 (uri (cran-uri "tidytext" version))
27338 "0as7lscjl6ywk85almmb4f71vxmgkfds46g52ryggkg2isksvq3g"))))
27339 (properties `((upstream-name . "tidytext")))
27340 (build-system r-build-system)
27356 (home-page "https://github.com/juliasilge/tidytext")
27357 (synopsis "Text mining using dplyr, ggplot2, and other Tidy tools")
27359 "This is a package for text mining for word processing and sentiment
27360 analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.")
27361 (license license:expat)))
27363 (define-public r-parsnip
27370 (uri (cran-uri "parsnip" version))
27373 "12chngdzplwkk1c9k8y7cwaqlyy72yamlknp7ksg7g9p3b58f1fb"))))
27374 (properties `((upstream-name . "parsnip")))
27375 (build-system r-build-system)
27392 (home-page "https://parsnip.tidymodels.org")
27393 (synopsis "Common API to modeling and analysis functions")
27395 "This package provides a common interface to allow users to specify a
27396 model without having to remember the different argument names across different
27397 functions or computational engines (e.g. R, Spark, Stan, etc).")
27398 (license license:gpl2)))
27400 (define-public r-infer
27407 (uri (cran-uri "infer" version))
27410 "1qbpcn7jqbvgwnpiyylj021j8m33p58a204yd1pfkpzd3x2lbsm6"))))
27411 (properties `((upstream-name . "infer")))
27412 (build-system r-build-system)
27427 (home-page "https://github.com/tidymodels/infer")
27428 (synopsis "Tidy statistical inference")
27430 "The objective of this package is to perform inference using an
27431 expressive statistical grammar that coheres with the Tidy design framework.")
27432 (license license:cc0)))
27434 (define-public r-modeldata
27436 (name "r-modeldata")
27441 (uri (cran-uri "modeldata" version))
27444 "0jgrwf9k8p9j3ywg3yv2wzwsx3snlwm3dd9vfqwhlr7j63jg3cm4"))))
27445 (properties `((upstream-name . "modeldata")))
27446 (build-system r-build-system)
27447 (home-page "https://modeldata.tidymodels.org")
27448 (synopsis "Data sets useful for modeling packages")
27450 "This package provides data sets used for demonstrating or testing
27451 model-related packages.")
27452 (license license:expat)))
27454 (define-public r-conflicted
27456 (name "r-conflicted")
27461 (uri (cran-uri "conflicted" version))
27464 "0xp04cdvmp3b1phazhmjqn0vmax1b2218xsb5854ffv43m7qvrra"))))
27465 (properties `((upstream-name . "conflicted")))
27466 (build-system r-build-system)
27468 (list r-memoise r-rlang))
27469 (home-page "https://github.com/r-lib/conflicted")
27470 (synopsis "Alternative conflict resolution strategy")
27472 "R's default conflict management system gives the most recently loaded
27473 package precedence. This can make it hard to detect conflicts, particularly
27474 when they arise because a package update creates ambiguity that did not
27475 previously exist. The @code{conflicted} package takes a different approach,
27476 making every conflict an error and forcing you to choose which function to
27478 (license license:gpl3)))
27480 (define-public r-tidymodels
27482 (name "r-tidymodels")
27487 (uri (cran-uri "tidymodels" version))
27490 "18krycdn0h1i8swrq6bgj8qnb200rr0pqhr6maq3h1jc66x0y7nd"))))
27491 (properties `((upstream-name . "tidymodels")))
27492 (build-system r-build-system)
27516 (list r-knitr r-rmarkdown pandoc))
27517 (home-page "https://github.com/tidymodels/tidymodels")
27518 (synopsis "Tidy collection for modeling and statistical analysis")
27520 "The tidy modeling \"verse\" is a collection of packages for modeling and
27521 statistical analysis that share the underlying design philosophy, grammar, and
27522 data structures of the tidyverse.")
27523 (license license:gpl3)))
27525 (define-public r-lsa
27532 (uri (cran-uri "lsa" version))
27535 "1a33irqa6qvbc02z12rgbgv8kxq2gmahy7j5bg8b23lvvaxif06b"))))
27536 (properties `((upstream-name . "lsa")))
27537 (build-system r-build-system)
27539 (list r-snowballc))
27540 (home-page "https://cran.r-project.org/package=lsa")
27541 (synopsis "Latent semantic analysis")
27543 "The basic idea of latent semantic analysis (LSA) is, that text do have a
27544 higher order (=latent semantic) structure which, however, is obscured by word
27545 usage (e.g. through the use of synonyms or polysemy). By using conceptual
27546 indices that are derived statistically via a truncated singular value
27547 decomposition (a two-mode factor analysis) over a given document-term matrix,
27548 this variability problem can be overcome.")
27549 (license license:gpl2+)))
27551 (define-public r-mlecens
27558 (uri (cran-uri "MLEcens" version))
27561 "0zlmrcjraypscgs2v0w4s4hm7qccsmaz4hjsgqpn0058vx622945"))))
27562 (properties `((upstream-name . "MLEcens")))
27563 (build-system r-build-system)
27564 (home-page "http://stat.ethz.ch/~maathuis/")
27565 (synopsis "Computation of the MLE for bivariate (interval) censored data")
27567 "This package contains functions to compute the nonparametric
27568 @dfn{maximum likelihood estimator} (MLE) for the bivariate distribution of
27569 @code{(X,Y)}, when realizations of @code{(X,Y)} cannot be observed directly.
27570 To be more precise, we consider the situation where we observe a set of
27571 rectangles that are known to contain the unobservable realizations of (X,Y).
27572 We compute the MLE based on such a set of rectangles. The methods can also be
27573 used for univariate censored data (see data set @code{cosmesis}), and for
27574 censored data with competing risks (see data set @code{menopause}). The
27575 package also provides functions to visualize the observed data and the MLE.")
27576 (license license:gpl2+)))
27578 (define-public r-metafor
27585 (uri (cran-uri "metafor" version))
27588 "1b599fxk7s0brkchmx698fr5k4g1kzkia2rnlvhg349ffs5nfjmn"))))
27589 (properties `((upstream-name . "metafor")))
27590 (build-system r-build-system)
27592 (list r-matrix r-nlme))
27593 (home-page "https://cran.r-project.org/web/packages/metafor/")
27594 (synopsis "Meta-analysis package for R")
27596 "This package provides a comprehensive collection of functions for
27597 conducting meta-analyses in R. The package includes functions to calculate
27598 various effect sizes or outcome measures, fit fixed-, random-, and
27599 mixed-effects models to such data, carry out moderator and meta-regression
27600 analyses, and create various types of meta-analytical plots (e.g., forest,
27601 funnel, radial, L'Abbe, Baujat, GOSH plots). For meta-analyses of binomial
27602 and person-time data, the package also provides functions that implement
27603 specialized methods, including the Mantel-Haenszel method, Peto's method, and
27604 a variety of suitable generalized linear (mixed-effects) models (i.e.
27605 mixed-effects logistic and Poisson regression models). Finally, the package
27606 provides functionality for fitting meta-analytic multivariate/multilevel
27607 models that account for non-independent sampling errors and/or true
27608 effects (e.g. due to the inclusion of multiple treatment studies, multiple
27609 endpoints, or other forms of clustering). Network meta-analyses and
27610 meta-analyses accounting for known correlation structures (e.g. due to
27611 phylogenetic relatedness) can also be conducted.")
27612 (license license:gpl2+)))
27614 (define-public r-altmeta
27621 (uri (cran-uri "altmeta" version))
27624 "1xq12hnzxh7kgv2i36xprg4lkvqfmxwz3sq4a1jlq2d5g3narvcm"))))
27625 (properties `((upstream-name . "altmeta")))
27626 (build-system r-build-system)
27628 (list r-coda r-lme4 r-matrix r-metafor r-rjags))
27629 (home-page "https://cran.r-project.org/web/packages/altmeta/")
27630 (synopsis "Alternative meta-analysis methods")
27632 "This package provides alternative statistical methods for meta-analysis,
27636 @item bivariate generalized linear mixed models for synthesizing odds ratios,
27637 relative risks, and risk differences
27638 @item heterogeneity tests and measures that are robust to outliers;
27639 @item measures, tests, and visualization tools for publication bias or
27640 small-study effects;
27641 @item meta-analysis of diagnostic tests for synthesizing sensitivities,
27642 specificities, etc.;
27643 @item meta-analysis methods for synthesizing proportions;
27644 @item models for multivariate meta-analysis.
27647 (license license:gpl2+)))
27649 (define-public r-perm
27652 (version "1.0-0.2")
27656 (uri (cran-uri "perm" version))
27659 "182ac1y91yzb34zwdcmx5fdfr5z0cha0gx2bgk36gwxhgfc994kj"))))
27660 (properties `((upstream-name . "perm")))
27661 (build-system r-build-system)
27662 (home-page "https://cran.r-project.org/web/packages/perm/")
27663 (synopsis "Exact or asymptotic permutation tests")
27665 "This package provides several methods for performing permutation tests.
27666 It has three main functions, to perform linear permutation tests. These tests
27667 are tests where the test statistic is the sum of the product of a
27668 covariate (usually group indicator) and the scores.")
27669 ;; Any version of the GPL
27670 (license license:gpl2+)))
27672 (define-public r-qtl
27679 (uri (cran-uri "qtl" version))
27682 "1mcy9wlp5lj5f3z4mf3n5li7x32vj67rmhjnzsp8fhfw0ipnaf1d"))))
27683 (build-system r-build-system)
27684 (home-page "https://rqtl.org/")
27685 (synopsis "R package for analyzing QTL experiments in genetics")
27686 (description "R/qtl is an extension library for the R statistics system.
27687 It is used to analyze experimental crosses for identifying genes contributing
27688 to variation in quantitative traits (so-called quantitative trait loci, QTLs).
27690 Using a hidden Markov model, R/qtl estimates genetic maps, to identify
27691 genotyping errors, and to perform single-QTL and two-QTL, two-dimensional
27693 (license license:gpl3)))
27695 (define-public r-qtl2
27701 (uri (cran-uri "qtl2" version))
27703 (base32 "0ppc6dzlq77mppxc6bczai9gi40jrbxd1466y2cn2s8a4ah1jg9y"))))
27704 (build-system r-build-system)
27712 (home-page "https://kbroman.org/qtl2/")
27713 (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
27715 "This package provides a set of tools to perform @dfn{Quantitative Trait
27716 Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the
27717 @code{R/qtl} package to better handle high-dimensional data and complex cross
27718 designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
27719 (license license:gpl3)))
27721 (define-public r-seqminer
27723 (name "r-seqminer")
27728 (uri (cran-uri "seqminer" version))
27731 "097313x72jr2q6dp8ma33w8kyp3gfw71snf1qx2maxbwwnysk085"))))
27732 (build-system r-build-system)
27735 (home-page "http://seqminer.genomic.codes")
27736 (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
27738 "This package provides tools to integrate nucleotide sequencing
27739 data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
27740 ;; Any version of the GPL is acceptable
27741 (license (list license:gpl2+ license:gpl3+))))
27743 (define-public r-maldiquant
27745 (name "r-maldiquant")
27750 (uri (cran-uri "MALDIquant" version))
27753 "1h9i158czlzwbn5zakkqd2ggc9g90r73vdspmp6kgfcmy9frvwzz"))))
27754 (properties `((upstream-name . "MALDIquant")))
27755 (build-system r-build-system)
27758 (home-page "https://cran.r-project.org/web/packages/MALDIquant")
27759 (synopsis "Quantitative analysis of mass spectrometry data")
27761 "This package provides a complete analysis pipeline for matrix-assisted
27762 laser desorption/ionization-time-of-flight (MALDI-TOF) and other
27763 two-dimensional mass spectrometry data. In addition to commonly used plotting
27764 and processing methods it includes distinctive features, namely baseline
27765 subtraction methods such as morphological filters (TopHat) or the
27766 statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
27767 alignment using warping functions, handling of replicated measurements as well
27768 as allowing spectra with different resolutions.")
27769 (license license:gpl3+)))
27771 (define-public r-scattermore
27773 (name "r-scattermore")
27778 (uri (cran-uri "scattermore" version))
27781 "18nzlprmphkvjg946h10h2qq0wbkmv2526p8di6k2xl4gccq0qpk"))))
27782 (properties `((upstream-name . "scattermore")))
27783 (build-system r-build-system)
27785 (list r-ggplot2 r-scales))
27786 (home-page "https://github.com/exaexa/scattermore")
27787 (synopsis "Scatterplots with more points")
27789 "This package provides C-based tools for converting large scatterplot
27790 data to rasters. It speeds up plotting of data with millions of points.")
27791 (license license:gpl3+)))
27793 (define-public r-seuratobject
27795 (name "r-seuratobject")
27800 (uri (cran-uri "SeuratObject" version))
27803 "06gch6416hmwpfxa7bidw5izfp4yvkdka7mvxp6grmldnj5iqm6g"))))
27804 (properties `((upstream-name . "SeuratObject")))
27805 (build-system r-build-system)
27807 (list r-matrix r-rcpp r-rcppeigen r-rlang))
27808 (home-page "https://satijalab.org/seurat")
27809 (synopsis "Data structures for single cell data")
27811 "This package defines S4 classes for single-cell genomic data and
27812 associated information, such as dimensionality reduction embeddings,
27813 nearest-neighbor graphs, and spatially-resolved coordinates. It provides data
27814 access methods and R-native hooks to ensure the Seurat object is familiar to
27816 (license license:gpl3)))
27818 (define-public r-seurat
27824 (uri (cran-uri "Seurat" version))
27827 "18svlpfbgs5vdzw2jyg99kj0jacag6dwwhjdg1zpmrh0fm0praxg"))))
27828 (properties `((upstream-name . "Seurat")))
27829 (build-system r-build-system)
27874 (home-page "http://www.satijalab.org/seurat")
27875 (synopsis "Seurat is an R toolkit for single cell genomics")
27877 "This package is an R package designed for QC, analysis, and
27878 exploration of single cell RNA-seq data. It easily enables widely-used
27879 analytical techniques, including the identification of highly variable genes,
27880 dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
27881 algorithms; density clustering, hierarchical clustering, k-means, and the
27882 discovery of differentially expressed genes and markers.")
27883 (license license:gpl3)))
27885 (define-public r-seuratdisk
27886 (let ((commit "163f1aade5bac38ed1e9e9c912283a7e74781610")
27889 (name "r-seuratdisk")
27890 (version (git-version "0.0.0.9019" revision commit))
27894 (uri (git-reference
27895 (url "https://github.com/mojaveazure/seurat-disk")
27897 (file-name (git-file-name name version))
27899 (base32 "1d1v8qi6kknzy5fj6bl8akwy74h5h143i00lyidsnqjbwp9n4qnw"))))
27900 (properties `((upstream-name . "SeuratDisk")))
27901 (build-system r-build-system)
27915 (home-page "https://github.com/mojaveazure/seurat-disk")
27916 (synopsis "Interfaces for HDF5-based single cell file formats")
27918 "The h5Seurat file format is specifically designed for the storage and
27919 analysis of multi-modal single-cell and spatially-resolved expression
27920 experiments, for example, from CITE-seq or 10X Visium technologies. It holds
27921 all molecular information and associated metadata, including (for example)
27922 nearest-neighbor graphs, dimensional reduction information, spatial
27923 coordinates and image data, and cluster labels. This package also supports
27924 rapid and on-disk conversion between h5Seurat and AnnData objects, with the
27925 goal of enhancing interoperability between Seurat and Scanpy.")
27926 (license license:gpl3))))
27928 (define-public r-seuratdata
27929 (let ((commit "b59556b24d7d6728a5744c9c715dd5f7f32ed7a5")
27932 (name "r-seuratdata")
27933 (version (git-version "0.2.1" revision commit))
27937 (uri (git-reference
27938 (url "https://github.com/satijalab/seurat-data")
27940 (file-name (git-file-name name version))
27942 (base32 "1xfdmdmgn4r0z6w4cxa98ic6xk8i6qz054r215dvqbjs1vydsbf9"))))
27943 (properties `((upstream-name . "SeuratData")))
27944 (build-system r-build-system)
27947 (modify-phases %standard-phases
27948 ;; When there is no HOME directory, this package will fail to load
27949 ;; the included list of packages.
27950 (add-after 'unpack 'set-HOME
27951 (lambda _ (setenv "HOME" "/tmp"))))))
27953 (list r-cli r-crayon r-rappdirs))
27954 (home-page "https://github.com/satijalab/seurat-data")
27955 (synopsis "Install and manage Seurat datasets")
27957 "Single cell RNA sequencing datasets can be large, consisting of
27958 matrices that contain expression data for several thousand features across
27959 several thousand cells. This package is designed to easily install, manage,
27960 and learn about various single-cell datasets, provided Seurat objects and
27961 distributed as independent packages.")
27962 (license license:gpl3))))
27964 (define-public r-phangorn
27966 (name "r-phangorn")
27971 (uri (cran-uri "phangorn" version))
27974 "1pg5lfc5m4ccphswbfbihj91ppmqhf4084kbjlmfsrqxylsyy8ch"))))
27975 (build-system r-build-system)
27985 (home-page "https://github.com/KlausVigo/phangorn")
27986 (synopsis "Phylogenetic analysis in R")
27988 "Phangorn is a package for phylogenetic analysis in R. It supports
27989 estimation of phylogenetic trees and networks using Maximum Likelihood,
27990 Maximum Parsimony, distance methods and Hadamard conjugation.")
27991 (license license:gpl2+)))
27993 (define-public r-diversitree
27995 (name "r-diversitree")
28000 (uri (cran-uri "diversitree" version))
28003 "0rzrk7xsn4gy271pbcw3azndhx0c06bmsgrg6libjmlfnmq6j8sc"))))
28004 (build-system r-build-system)
28007 (inputs (list fftw gsl))
28009 (list r-ape r-desolve r-rcpp r-subplex))
28010 (home-page "https://www.zoology.ubc.ca/prog/diversitree")
28011 (synopsis "Comparative 'phylogenetic' analyses of diversification")
28012 (description "This package contains a number of comparative \"phylogenetic\"
28013 methods, mostly focusing on analysing diversification and character evolution.
28014 Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
28015 and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
28016 Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
28017 include Markov models of discrete and continuous trait evolution and constant
28018 rate speciation and extinction.")
28019 (license license:gpl2+)))
28021 (define-public r-calculus
28023 (name "r-calculus")
28028 (uri (cran-uri "calculus" version))
28031 "0m9cjc3bqv88vrrj51kd7c7xnczka5w9q0ln4l4nk514gvlr79bn"))))
28032 (properties `((upstream-name . "calculus")))
28033 (build-system r-build-system)
28038 (home-page "https://github.com/eguidotti/calculus")
28039 (synopsis "High dimensional numerical and symbolic calculus")
28041 "Efficient C++ optimized functions for numerical and symbolic calculus.
28042 It includes basic symbolic arithmetic, tensor calculus, Einstein summing
28043 convention, fast computation of the Levi-Civita symbol and generalized
28044 Kronecker delta, Taylor series expansion, multivariate Hermite polynomials,
28045 accurate high-order derivatives, differential operators (Gradient, Jacobian,
28046 Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary
28047 orthogonal coordinate systems: cartesian, polar, spherical, cylindrical,
28048 parabolic or user defined by custom scale factors.")
28049 (license license:gpl3)))
28051 (define-public r-decon
28058 (uri (cran-uri "decon" version))
28061 "036cv56wf42q2p3d5h15hbrp5rc29xxy20qwv4k1qzhkq6hmw0qs"))))
28062 (properties `((upstream-name . "decon")))
28063 (build-system r-build-system)
28067 "https://cran.r-project.org/web/packages/decon/")
28068 (synopsis "Deconvolution Estimation in Measurement Error Models")
28070 "This package contains a collection of functions to deal with
28071 nonparametric measurement error problems using deconvolution
28072 kernel methods. We focus two measurement error models in the
28073 package: (1) an additive measurement error model, where the
28074 goal is to estimate the density or distribution function from
28075 contaminated data; (2) nonparametric regression model with
28076 errors-in-variables. The R functions allow the measurement errors
28077 to be either homoscedastic or heteroscedastic. To make the
28078 deconvolution estimators computationally more efficient in R,
28079 we adapt the \"Fast Fourier Transform\" (FFT) algorithm for
28080 density estimation with error-free data to the deconvolution
28081 kernel estimation. Several methods for the selection of the
28082 data-driven smoothing parameter are also provided in the package.
28083 See details in: Wang, X.F. and Wang, B. (2011). Deconvolution
28084 estimation in measurement error models: The R package decon.
28085 Journal of Statistical Software, 39(10), 1-24.")
28086 (license license:gpl3+)))
28088 (define-public r-locpol
28095 (uri (cran-uri "locpol" version))
28098 "1p915n0l09kbwkly627074jslxl01yssp1rf0c7sygvsw6sgy5lm"))))
28099 (properties `((upstream-name . "locpol")))
28100 (build-system r-build-system)
28102 "https://cran.r-project.org/web/packages/locpol/")
28103 (synopsis "Kernel Local Polynomial Regression")
28105 "Computes local polynomial estimators for the regression and
28106 also density. It comprises several different utilities to handle
28107 kernel estimators.")
28108 (license license:gpl2+)))
28110 (define-public r-lpme
28117 (uri (cran-uri "lpme" version))
28120 "1b0w5ji8hjayni1sh5id193cmanf6n11p16fijkxln4sv4lks4aw"))))
28121 (properties `((upstream-name . "lpme")))
28122 (build-system r-build-system)
28124 (list r-decon r-flexmix r-locpol r-rcpp r-rcpparmadillo))
28126 "https://cran.r-project.org/web/packages/lpme/")
28127 (synopsis "Nonparametric Estimation of Measurement Error Models")
28129 "Provide nonparametric methods for mean regression model,
28130 modal regression and conditional density estimation in the
28131 presence/absence of measurement error. Bandwidth selection is
28132 also provided for each method.")
28133 (license license:gpl2+)))
28135 (define-public r-aws-signature
28137 (name "r-aws-signature")
28142 (uri (cran-uri "aws.signature" version))
28145 "15llpcnrdq4y6jsn7079yjmgbr5d1wgy2ymsm3jj3gkrd5l4zzpp"))))
28146 (properties `((upstream-name . "aws.signature")))
28147 (build-system r-build-system)
28149 (list r-base64enc r-digest))
28150 (home-page "https://github.com/cloudyr/aws.signature")
28151 (synopsis "Amazon Web Services Request Signatures")
28153 "This package generates version 2 and 4 request signatures for Amazon Web
28154 Services (AWS) and provides a mechanism for retrieving credentials from
28155 environment variables, AWS credentials files, and EC2 instance metadata. For
28156 use on EC2 instances, the package 'aws.ec2metadata' is suggested.")
28157 (license license:gpl2+)))
28159 (define-public r-aws-s3
28166 (uri (cran-uri "aws.s3" version))
28169 "132cczq0ml7lpp2yl6l4p99dn1zihrncnpa6wyad4m9mnr50a8dx"))))
28170 (properties `((upstream-name . "aws.s3")))
28171 (build-system r-build-system)
28173 (list r-aws-signature
28179 (home-page "https://github.com/cloudyr/aws.s3")
28180 (synopsis "AWS S3 Client Package")
28182 "This package provides a simple client package for the Amazon Web
28183 Services (AWS) Simple Storage Service (S3) REST API.")
28184 (license license:gpl2+)))
28186 (define-public r-lgr
28192 (uri (cran-uri "lgr" version))
28195 "18s92qyakhvp336kk2777ydypwfrfwfz6a1gqkq812zy3kcb4mcc"))))
28196 (build-system r-build-system)
28201 (home-page "https://s-fleck.github.io/lgr/")
28202 (synopsis "Fully featured logging framework")
28203 (description "This package offers a flexible, feature-rich yet
28204 light-weight logging framework based on @code{R6} classes. It supports
28205 hierarchical loggers, custom log levels, arbitrary data fields in log events,
28206 logging to plaintext, JSON, (rotating) files, memory buffers, and databases, as
28207 well as email and push notifications.")
28208 (license license:expat)))
28210 (define-public r-mhg
28217 (uri (cran-uri "mHG" version))
28220 "1rz5ncrvvv9h9grls15apa63v2nh9j87fmp4mwjjil37jx6a5zki"))))
28221 (properties `((upstream-name . "mHG")))
28222 (build-system r-build-system)
28223 (home-page "https://cran.r-project.org/package=mHG")
28224 (synopsis "Minimum-hypergeometric test")
28226 "This package runs a minimum-hypergeometric (mHG) test as described in
28227 \"Discovering Motifs in Ranked Lists of DNA Sequences\" by Eran Eden.")
28228 (license license:gpl2)))
28230 (define-public r-mlr3measures
28232 (name "r-mlr3measures")
28236 (uri (cran-uri "mlr3measures" version))
28239 "1qlqfan5akz42zwkcz3ncln6rd9c302dy4cyp7nx0jcafr5i459f"))))
28240 (build-system r-build-system)
28242 (list r-checkmate r-prroc))
28243 (home-page "https://mlr3measures.mlr-org.com/")
28244 (synopsis "Performance measures for mlr3")
28245 (description "This package implements multiple performance measures for
28246 supervised learning. It includes over 40 measures for regression and
28247 classification. Additionally, meta information about the performance measures
28248 can be queried, e.g. what the best and worst possible performances scores
28250 (license license:lgpl3)))
28252 (define-public r-mlr3misc
28254 (name "r-mlr3misc")
28258 (uri (cran-uri "mlr3misc" version))
28261 "1ax1mvnm8xjcskq12x63jkal766v1zwilpgrkdv6yawd7yrww4q9"))))
28262 (build-system r-build-system)
28264 (list r-backports r-checkmate r-data-table r-digest r-r6))
28265 (home-page "https://mlr3misc.mlr-org.com/")
28266 (synopsis "Helper functions for mlr3")
28267 (description "@code{mlr3misc} provides frequently used helper functions
28268 and assertions used in @code{mlr3} and its companion packages. It comes with
28269 helper functions for functional programming, for printing, to work with
28270 @code{data.table}, as well as some generally useful @code{R6} classes. This
28271 package also supersedes the package @code{BBmisc}.")
28272 (license license:lgpl3)))
28274 (define-public r-paradox
28280 (uri (cran-uri "paradox" version))
28283 "1difp0bzsfxcmbm1snahh3i6417k1a2w4mnjx65p20n2yiclmrgs"))))
28284 (build-system r-build-system)
28286 (list r-backports r-checkmate r-data-table r-mlr3misc r-r6))
28287 (home-page "https://paradox.mlr-org.com/")
28288 (synopsis "Define and work with parameter spaces for complex algorithms")
28289 (description "With this package it is possible to define parameter spaces,
28290 constraints and dependencies for arbitrary algorithms, and to program on such
28291 spaces. It also includes statistical designs and random samplers. Objects are
28292 implemented as @code{R6} classes.")
28293 (license license:lgpl3)))
28295 (define-public r-mlr3
28301 (uri (cran-uri "mlr3" version))
28304 "1729wbdp62cjjk775qxrahyskp191s9qqnmqbxncfjrpdxphxk34"))))
28305 (build-system r-build-system)
28321 (home-page "https://mlr3.mlr-org.com/")
28322 (synopsis "Machine Learning in R - Next Generation")
28323 (description "@code{mlr3} enables efficient, object-oriented programming
28324 on the building blocks of machine learning. It provides @code{R6} objects for
28325 tasks, learners, resamplings, and measures. The package is geared towards
28326 scalability and larger datasets by supporting parallelization and out-of-memory
28327 data-backends like databases. While @code{mlr3} focuses on the core
28328 computational operations, add-on packages provide additional functionality.")
28329 (license license:lgpl3)))
28331 (define-public r-mlr3learners
28333 (name "r-mlr3learners")
28337 (uri (cran-uri "mlr3learners" version))
28340 "1yc3mrk1b9h1k342wnw7sm4zmcw7w31l5ybh558g88f5hmibdl98"))))
28341 (build-system r-build-system)
28349 (home-page "https://mlr3learners.mlr-org.com/")
28350 (synopsis "Recommended Learners for @code{mlr3}")
28351 (description "@code{mlr3learners} extends @code{mlr3} and @code{mlr3proba}
28352 with interfaces to essential machine learning packages on CRAN. This includes,
28353 but is not limited to: (penalized) linear and logistic regression, linear and
28354 quadratic discriminant analysis, k-nearest neighbors, naive Bayes, support
28355 vector machines, and gradient boosting.")
28356 (license license:lgpl3)))
28358 (define-public r-bbotk
28365 (uri (cran-uri "bbotk" version))
28368 "09cw6z397laszsg5wsgpjh7jda74amqrcl2p25bgjg33ina2nvg7"))))
28369 (properties `((upstream-name . "bbotk")))
28370 (build-system r-build-system)
28380 (home-page "https://bbotk.mlr-org.com")
28381 (synopsis "Black-Box Optimization Toolkit")
28382 (description "This package provides a common framework for optimization of
28383 black-box functions for other packages, e.g. @code{mlr3}. It offers various
28384 optimization methods e.g. grid search, random search and generalized simulated
28386 (license license:lgpl3)))
28388 (define-public r-mlr3tuning
28390 (name "r-mlr3tuning")
28394 (uri (cran-uri "mlr3tuning" version))
28397 "0i428kdbak81j1wlwmdf9y40hqi63azhyny802ms2z04wl8lwnvs"))))
28398 (build-system r-build-system)
28409 (home-page "https://mlr3tuning.mlr-org.com/")
28410 (synopsis "Tuning for @code{mlr3}")
28411 (description "@code{mlr3tuning} implements methods for hyperparameter
28412 tuning, e.g. Grid Search, Random Search, or Simulated Annealing. Various
28413 termination criteria can be set and combined. The class @code{AutoTuner} provides a
28414 convenient way to perform nested resampling in combination with @code{mlr3}.")
28415 (license license:lgpl3)))
28417 (define-public r-fontliberation
28419 (name "r-fontliberation")
28424 (uri (cran-uri "fontLiberation" version))
28427 "1w1rl0g4ayyp8lwppmz9yzj9cizg7i50g07216jkm1q5w0is9pmc"))))
28429 `((upstream-name . "fontLiberation")))
28430 (build-system r-build-system)
28431 (home-page "https://cran.r-project.org/package=fontLiberation")
28432 (synopsis "Liberation fonts")
28434 "This package provides a placeholder for the Liberation fontset intended
28435 for the fontquiver package. This fontset covers the 12 combinations of
28436 families (sans, serif, mono) and faces (plain, bold, italic, bold italic)
28437 supported in R graphics devices.")
28438 (license license:silofl1.1)))
28440 (define-public r-fontbitstreamvera
28442 (name "r-fontbitstreamvera")
28447 (uri (cran-uri "fontBitstreamVera" version))
28450 "0nipdlmhjv1wr3aidcl97nk6mppdkd65krgwqnhdsnv0jpfv761j"))))
28452 `((upstream-name . "fontBitstreamVera")))
28453 (build-system r-build-system)
28454 (home-page "https://cran.r-project.org/package=fontBitstreamVera")
28455 (synopsis "Fonts for fontquiver")
28457 "This package is a placeholder for the Bitstream Vera font. It is
28458 intended for the fontquiver package.")
28460 (license:fsdg-compatible
28461 "https://www.gnome.org/fonts/#Final_Bitstream_Vera_Fonts"
28462 "The Font Software may be sold as part of a larger software package but
28463 no copy of one or more of the Font Software typefaces may be sold by
28466 (define-public r-fontquiver
28468 (name "r-fontquiver")
28473 (uri (cran-uri "fontquiver" version))
28476 "0qv3i9hch7cygl9983s3w68wfh5qvym2jkm52pp06p6mq8a1i1wm"))))
28477 (properties `((upstream-name . "fontquiver")))
28478 (build-system r-build-system)
28480 (list r-fontbitstreamvera r-fontliberation))
28481 (home-page "https://cran.r-project.org/package=fontquiver")
28482 (synopsis "Set of installed fonts")
28484 "This package provides a set of fonts. This is useful when you want to
28485 avoid system fonts to make sure your outputs are reproducible.")
28486 (license license:gpl3)))
28488 (define-public r-freetypeharfbuzz
28490 (name "r-freetypeharfbuzz")
28495 (uri (cran-uri "freetypeharfbuzz" version))
28498 "0r3icgnq3jk4fm6z92cmhzdmflbk5df8zsmjg0dzpc4y48xafnk7"))))
28500 `((upstream-name . "freetypeharfbuzz")))
28501 (build-system r-build-system)
28504 (modify-phases %standard-phases
28505 (add-after 'unpack 'prepare-static-libraries
28506 (lambda* (#:key inputs #:allow-other-keys)
28507 (mkdir-p "src/target/include")
28508 (let ((freetype (assoc-ref inputs "static-freetype"))
28509 (harfbuzz (assoc-ref inputs "static-harfbuzz")))
28510 (substitute* "src/Makevars.in"
28511 (("include @MK_FILE@") "") ; do not build static libs
28512 (("^HB_STATIC_LIB =.*")
28513 (string-append "HB_STATIC_LIB = " harfbuzz "/lib/libharfbuzz.a\n"))
28514 (("^FT_STATIC_LIB =.*")
28515 (string-append "FT_STATIC_LIB = " freetype "/lib/libfreetype.a\n")))
28516 (copy-recursively (string-append freetype "/include")
28517 "src/target/include")
28518 (copy-recursively (string-append harfbuzz "/include")
28519 "src/target/include")))))))
28521 (list r-fontquiver))
28522 ;; This may defeat the purpose of this package as our versions of freetype
28523 ;; and harfbuzz obviously differ from the tarballs offered by this
28524 ;; project. On the other hand, Guix arguably does a better job at
28525 ;; "ensur[ing] deterministic computation".
28527 `(("static-freetype"
28529 (inherit (static-package freetype))
28531 `(#:configure-flags
28532 (list "--enable-static=yes"
28537 "--without-harfbuzz")))))
28540 (inherit (static-package harfbuzz))
28542 `(#:tests? #false ; fail because shared library is disabled
28544 (list "--enable-static=yes"
28545 "--enable-shared=no"
28547 "--with-freetype=yes"
28550 "--without-fontconfig"
28551 "--without-glib")))))))
28554 (home-page "https://cran.r-project.org/package=freetypeharfbuzz")
28555 (synopsis "Deterministic computation of text box metrics")
28557 "Unlike other tools that dynamically link to the Cairo stack,
28558 freetypeharfbuzz is statically linked to specific versions of the FreeType and
28559 harfbuzz libraries. This ensures deterministic computation of text box
28560 extents for situations where reproducible results are crucial (for instance
28561 unit tests of graphics).")
28562 (license license:gpl3)))
28564 (define-public r-vdiffr
28571 (uri (cran-uri "vdiffr" version))
28574 "1zjwjw8lqqnx7cxj2aik5rn1g67zsyf0bq08yfwwmsi7v2x6ly3x"))))
28575 (properties `((upstream-name . "vdiffr")))
28576 (build-system r-build-system)
28578 (list libpng zlib))
28588 (home-page "https://github.com/r-lib/vdiffr")
28589 (synopsis "Visual regression testing and graphical diffing")
28591 "This package is an extension to the testthat package that makes it easy
28592 to add graphical unit tests. It provides a Shiny application to manage the
28594 (license license:gpl3)))
28596 (define-public r-highlight
28598 (name "r-highlight")
28603 (uri (cran-uri "highlight" version))
28606 "1shar4y07wyixg0ichdrn2xhgwkl3mv2pxkalqzisc69w605b3hf"))))
28607 (properties `((upstream-name . "highlight")))
28608 (build-system r-build-system)
28609 (home-page "https://github.com/hadley/highlight")
28610 (synopsis "Syntax highlighter for R code")
28612 "This package provides a syntax highlighter for R code based on the
28613 results of the R parser. It supports rendering in HTML and LaTeX markup. It
28614 includes a custom Sweave driver performing syntax highlighting of R code
28616 (license license:gpl3+)))
28618 (define-public r-clustree
28620 (name "r-clustree")
28625 (uri (cran-uri "clustree" version))
28628 "0vwmicajl7c0rmjdmf4f857fii0xrxz25vjkn888svlsikw00qbs"))))
28629 (properties `((upstream-name . "clustree")))
28630 (build-system r-build-system)
28643 (home-page "https://github.com/lazappi/clustree")
28644 (synopsis "Visualize clusterings at different resolutions")
28646 "Deciding what resolution to use can be a difficult question when
28647 approaching a clustering analysis. One way to approach this problem is to
28648 look at how samples move as the number of clusters increases. This package
28649 allows you to produce clustering trees, a visualization for interrogating
28650 clusterings as resolution increases.")
28651 (license license:gpl3)))
28653 (define-public r-textshaping
28655 (name "r-textshaping")
28660 (uri (cran-uri "textshaping" version))
28663 "1niaj1dh09rqrg9hrh98ddnc0f2nkyq9iizv24lcwm9gjs3w1ql0"))))
28664 (properties `((upstream-name . "textshaping")))
28665 (build-system r-build-system)
28667 (list freetype fribidi harfbuzz zlib))
28669 (list r-cpp11 r-systemfonts))
28671 (list pkg-config r-knitr))
28672 (home-page "https://github.com/r-lib/textshaping")
28673 (synopsis "Bindings to the HarfBuzz and Fribidi libraries for text shaping")
28675 "This package provides access to the text shaping functionality in the
28676 HarfBuzz library and the bidirectional algorithm in the Fribidi library. This
28677 is a low-level utility package mainly for graphic devices that expands upon
28678 the font tool-set provided by the @code{systemfonts} package.")
28679 (license license:expat)))
28681 (define-public r-ragg
28688 (uri (cran-uri "ragg" version))
28691 "1wbk7vny8435ii3aak586imd0dgh4ri55kqypx5b10x6ygp32avb"))))
28692 (properties `((upstream-name . "ragg")))
28693 (build-system r-build-system)
28695 `(("freetype" ,freetype)
28696 ("libjpeg" ,libjpeg-turbo)
28698 ("libtiff" ,libtiff)
28701 (list r-systemfonts r-textshaping))
28704 (home-page "https://ragg.r-lib.org")
28705 (synopsis "Graphic devices based on AGG")
28707 "Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D
28708 drawing library. The ragg package provides a set of graphic devices based on
28709 AGG to use as alternative to the raster devices provided through the
28710 @code{grDevices} package.")
28711 (license license:expat)))
28713 (define-public r-downlit
28720 (uri (cran-uri "downlit" version))
28723 "10zvrqdpwavdy97h3q26bqh3k63z61fmc04w9vwsnvmnv8hnh3vl"))))
28724 (properties `((upstream-name . "downlit")))
28725 (build-system r-build-system)
28736 (home-page "https://downlit.r-lib.org/")
28737 (synopsis "Syntax highlighting and automatic linking")
28739 "This package provides syntax highlighting of R code, specifically
28740 designed for the needs of RMarkdown packages like @code{pkgdown},
28741 @code{hugodown}, and @code{bookdown}. It includes linking of function calls
28742 to their documentation on the web, and automatic translation of ANSI escapes
28743 in output to the equivalent HTML.")
28744 (license license:expat)))
28746 (define-public r-pkgdown
28753 (uri (cran-uri "pkgdown" version))
28756 "1k31biyvxkv3xjc1yy3nzb9wfza3vbx97fv17nly5a6vlv7zqbs4"))))
28757 (properties `((upstream-name . "pkgdown")))
28758 (build-system r-build-system)
28759 (inputs (list pandoc))
28783 (home-page "https://pkgdown.r-lib.org")
28784 (synopsis "Make static HTML documentation for an R package")
28786 "The goal of this package is to generate an attractive and useful website
28787 from a source package. @code{pkgdown} converts your documentation, vignettes,
28788 README file, and more to HTML making it easy to share information about your
28790 (license license:expat)))
28792 (define-public r-prereg
28799 (uri (cran-uri "prereg" version))
28802 "0bck13iiaxwpqh0rd45mp1s5d8z62ggg0wa7rmyi8a65aywiypsi"))))
28803 (properties `((upstream-name . "prereg")))
28804 (build-system r-build-system)
28806 (list r-rmarkdown))
28807 (home-page "https://github.com/crsh/prereg")
28809 "R Markdown Templates to preregister Scientific Studies")
28811 "This package provides a collection of templates to author
28812 preregistration documents for scientific studies in PDF format.")
28813 (license license:gpl3)))
28815 (define-public r-ez
28822 (uri (cran-uri "ez" version))
28825 "0a58s94x576dfz7wcbivrr2hmdh5x1vy16zwkqp9fmdzqx38pagq"))))
28826 (properties `((upstream-name . "ez")))
28827 (build-system r-build-system)
28839 (home-page "https://github.com/mike-lawrence/ez")
28840 (synopsis "Easy Analysis and Visualization of Factorial Experiments")
28842 "Facilitates easy analysis of factorial experiments, including purely
28843 within-Ss designs (a.k.a. \"repeated measures\"), purely between-Ss designs,
28844 and mixed within-and-between-Ss designs. The functions in this package aim to
28845 provide simple, intuitive and consistent specification of data analysis and
28846 visualization. Visualization functions also include design visualization for
28847 pre-analysis data auditing, and correlation matrix visualization. Finally,
28848 this package includes functions for non-parametric analysis, including
28849 permutation tests and bootstrap resampling. The bootstrap function obtains
28850 predictions either by cell means or by more advanced/powerful mixed effects
28851 models, yielding predictions and confidence intervals that may be easily
28852 visualized at any level of the experiment's design.")
28853 (license license:gpl2+)))
28855 (define-public r-qdapregex
28857 (name "r-qdapregex")
28862 (uri (cran-uri "qdapRegex" version))
28865 "1xa8q1way3gjadrjh3mv3xr4c6b4h16nd2c6lgl969difplpfz9p"))))
28866 (properties `((upstream-name . "qdapRegex")))
28867 (build-system r-build-system)
28868 (propagated-inputs (list r-stringi))
28870 "https://trinker.github.com/qdapRegex/")
28872 "Regular Expression Removal, Extraction, and Replacement Tools")
28874 "This package provides a collection of regular expression tools
28875 associated with the @code{qdap} package that may be useful outside of the
28876 context of discourse analysis. Tools include removal/extraction/replacement of
28877 abbreviations, dates, dollar amounts, email addresses, hash tags, numbers,
28878 percentages, citations, person tags, phone numbers, times, and zip codes.")
28879 (license license:gpl2)))
28881 (define-public r-mgsub
28888 (uri (cran-uri "mgsub" version))
28891 "1mci6x65h94qiz9cwikx2inbrwkykv43zbs8abfbx416zrh2bbn9"))))
28892 (properties `((upstream-name . "mgsub")))
28893 (build-system r-build-system)
28894 (native-inputs (list r-knitr))
28896 "https://cran.r-project.org/package=mgsub")
28898 "Safe, Multiple, Simultaneous String Substitution")
28900 "Designed to enable simultaneous substitution in strings in a safe
28901 fashion. Safe means it does not rely on placeholders (which can cause errors
28902 in same length matches).")
28903 (license license:expat)))
28905 (define-public r-textshape
28907 (name "r-textshape")
28912 (uri (cran-uri "textshape" version))
28915 "0k9injxykgj2qprc7dygd7gafvcbh3r9x84qzaa1al21pk0dz7ds"))))
28916 (properties `((upstream-name . "textshape")))
28917 (build-system r-build-system)
28919 (list r-data-table r-slam r-stringi))
28920 (home-page "https://github.com/trinker/textshape")
28921 (synopsis "Tools for Reshaping Text")
28923 "Tools that can be used to reshape and restructure text data.")
28924 (license license:gpl2)))
28926 (define-public r-syuzhet
28933 (uri (cran-uri "syuzhet" version))
28936 "16iccqdbw02iw82nah6kwz3gwfghi864j2y698n4b9dyc386ijzv"))))
28937 (properties `((upstream-name . "syuzhet")))
28938 (build-system r-build-system)
28947 (native-inputs (list r-knitr))
28948 (home-page "https://github.com/mjockers/syuzhet")
28950 "Extracts Sentiment and Sentiment-Derived Plot Arcs from Text")
28952 "Extracts sentiment and sentiment-derived plot arcs from text using a
28953 variety of sentiment dictionaries conveniently packaged for consumption by R
28954 users. Implemented dictionaries include @dfn{syuzhet} (default) developed in the
28955 Nebraska Literary Lab, @dfn{afinn} developed by Finn Arup Nielsen, @dfn{bing}
28956 developed by Minqing Hu and Bing Liu, and @dfn{nrc} developed by Mohammad, Saif
28957 M. and Turney, Peter D. Applicable references are available in
28958 @file{README.md} and in the documentation for the @code{get_sentiment}
28959 function. The package also provides a hack for implementing Stanford's coreNLP
28960 sentiment parser. The package provides several methods for plot arc
28962 (license license:gpl3)))
28964 (define-public r-lexicon
28971 (uri (cran-uri "lexicon" version))
28974 "0x7rscsh6par2lj11sby7bmz41cxn63iiw51lgh29z09cg8j606c"))))
28975 (properties `((upstream-name . "lexicon")))
28976 (build-system r-build-system)
28978 (list r-data-table r-syuzhet))
28979 (home-page "https://github.com/trinker/lexicon")
28980 (synopsis "Lexicons for Text Analysis")
28982 "This package provides a collection of lexical hash tables, dictionaries,
28984 (license license:gpl3)))
28986 (define-public r-english
28993 (uri (cran-uri "english" version))
28996 "1g3nmy5p8wj3ix1vp1qmkmy3dyqisrw0md8cjrx4klqkp0wqlms9"))))
28997 (properties `((upstream-name . "english")))
28998 (build-system r-build-system)
28999 (native-inputs (list r-knitr))
29001 "https://cran.r-project.org/package=english")
29002 (synopsis "Translate Integers into English")
29004 "Allow numbers to be presented in an English language version, one, two,
29005 three, ... Ordinals are also available, first, second, third, ... and
29006 indefinite article choice, \"a\" or \"an\".")
29007 (license license:gpl2)))
29009 (define-public r-textclean
29011 (name "r-textclean")
29016 (uri (cran-uri "textclean" version))
29019 "0kgjh6c4f14qkjc4fds7q7rpf4nkma3p0igm54fplmm3p853nvrz"))))
29020 (properties `((upstream-name . "textclean")))
29021 (build-system r-build-system)
29032 "https://github.com/trinker/textclean")
29033 (synopsis "Text Cleaning Tools")
29035 "Tools to clean and process text. Tools are geared at checking for
29036 substrings that are not optimal for analysis and replacing or removing them
29037 (normalizing) with more analysis friendly substrings (see Sproat, Black, Chen,
29038 Kumar, Ostendorf, & Richards (2001) @url{doi:10.1006/csla.2001.0169}) or
29039 extracting them into new variables. For example, emoticons are often used in
29040 text but not always easily handled by analysis algorithms. The
29041 @code{replace_emoticon()} function replaces emoticons with word equivalents.")
29042 (license license:gpl2)))
29044 (define-public r-striprtf
29046 (name "r-striprtf")
29051 (uri (cran-uri "striprtf" version))
29054 "0dqcsh3fb8j0mmmxvxjl77rryhmrjm7a3scqvk2xkgxk4xq6q316"))))
29055 (properties `((upstream-name . "striprtf")))
29056 (build-system r-build-system)
29058 (list r-magrittr r-rcpp r-stringr))
29059 (home-page "https://github.com/kota7/striprtf")
29060 (synopsis "Extract Text from RTF File")
29062 "Extracts plain text from @dfn{Rich Text Format} (RTF) file.")
29063 (license license:expat)))
29065 (define-public r-ndjson
29072 (uri (cran-uri "ndjson" version))
29075 "0lvzbgfi1sg4kya1mvv67z14qk3vz9q57x22qh57xq8ampdkg812"))
29076 (modules '((guix build utils)))
29079 ;; unvendor gzstream
29080 (for-each delete-file '("src/gzstream.cpp" "src/gzstream.h"))
29082 (properties `((upstream-name . "ndjson")))
29083 (build-system r-build-system)
29086 (modify-phases %standard-phases
29087 (add-after 'unpack 'use-system-gzstream
29088 (lambda* (#:key inputs #:allow-other-keys)
29089 (substitute* "src/Makevars"
29090 (("PKG_LIBS = " all)
29091 (string-append all "-lgzstream ")))
29093 (inputs (list zlib gzstream))
29095 (list r-data-table r-rcpp r-tibble))
29096 (home-page "https://gitlab.com/hrbrmstr/ndjson")
29098 "Wicked-Fast @dfn{Streaming JSON} (ndjson) Reader")
29100 "@dfn{Streaming JSON} (ndjson) has one JSON record per-line and many
29101 modern ndjson files contain large numbers of records. These constructs may not
29102 be columnar in nature, but it is often useful to read in these files and
29103 \"flatten\" the structure out to enable working with the data in an R
29104 @code{data.frame}-like context. Functions are provided that make it possible
29105 to read in plain ndjson files or compressed (@code{gz}) ndjson files and either
29106 validate the format of the records or create \"flat\" @code{data.table}
29107 structures from them.")
29108 (license license:expat)))
29110 (define-public r-streamr
29117 (uri (cran-uri "streamR" version))
29120 "1clx3b0j2515r1nmnl6ki7qw5n54q3x2jvqv3zrc00kq71mlj7ix"))))
29121 (properties `((upstream-name . "streamR")))
29122 (build-system r-build-system)
29124 (list r-ndjson r-rcurl r-rjson))
29126 "https://cran.r-project.org/package=streamR")
29128 "Access to Twitter Streaming API via R")
29130 "This package provides functions to access Twitter's filter, sample, and
29131 user streams, and to parse the output into data frames.")
29132 (license license:gpl2)))
29134 (define-public r-readods
29141 (uri (cran-uri "readODS" version))
29144 "1hi217ab7hp15jsbzi5ak57cqf8jn2rv78bnn74q72gn9mrfra7n"))))
29145 (properties `((upstream-name . "readODS")))
29146 (build-system r-build-system)
29148 (list r-cellranger r-readr r-stringi r-xml2))
29149 (native-inputs (list r-knitr))
29151 "https://cran.r-project.org/package=readODS")
29152 (synopsis "Read and Write ODS Files")
29154 "Import @dfn{OpenDocument Spreadsheet} (ODS) into R as a data frame.
29155 Also support writing data frame into ODS file.")
29156 (license license:gpl3)))
29158 (define-public r-qpdf
29165 (uri (cran-uri "qpdf" version))
29168 "03lnfncw8qd1fwfyqh1mjvnsjr3b63wxbah0wp5g7z7gba90dwbi"))
29169 (modules '((guix build utils)))
29172 ;; unvendor libqpdf
29173 (delete-file-recursively "src/libqpdf")
29174 (delete-file-recursively "src/include/qpdf")
29176 (properties `((upstream-name . "qpdf")))
29177 (build-system r-build-system)
29180 (modify-phases %standard-phases
29181 (add-after 'unpack 'configure
29183 (setenv "EXTERNAL_QPDF" "1")
29188 (list r-askpass r-curl r-rcpp))
29189 (native-inputs (list pkg-config))
29190 (home-page "https://github.com/ropensci/qpdf")
29192 "Split, Combine and Compress PDF Files")
29194 "Content-preserving transformations transformations of PDF files such as
29195 split, combine, and compress. This package interfaces directly to the
29196 @code{qpdf} C++ API and does not require any command line utilities. Note that
29197 @code{qpdf} does not read actual content from PDF files: to extract text and
29198 data you need the @code{pdftools} package.")
29199 (license license:asl2.0)))
29201 (define-public r-pdftools
29203 (name "r-pdftools")
29208 (uri (cran-uri "pdftools" version))
29211 "1dcbs5n5y8zi7bbyx491m9ik8kkmjr301x8ms85fmwdfb5a97m8k"))))
29212 (properties `((upstream-name . "pdftools")))
29213 (build-system r-build-system)
29215 (list zlib poppler))
29217 (list r-qpdf r-rcpp))
29218 (native-inputs (list pkg-config))
29220 "https://docs.ropensci.org/pdftools/")
29222 "Text Extraction, Rendering and Converting of PDF Documents")
29224 "Utilities based on @code{libpoppler} for extracting text, fonts,
29225 attachments and metadata from a PDF file. Also supports high quality rendering
29226 of PDF documents into PNG, JPEG, TIFF format, or into raw bitmap vectors for
29227 further processing in R.")
29228 (license license:expat)))
29230 (define-public r-antiword
29232 (name "r-antiword")
29237 (uri (cran-uri "antiword" version))
29240 "034znb0g9wwb8gi1r3z75v3sbb4mh83qrc4y8mbfx5lbgh8zhj6j"))
29241 (modules '((guix build utils)))
29244 ;; unvendor libantiword
29245 (delete-file-recursively "src")
29247 (properties `((upstream-name . "antiword")))
29248 (build-system r-build-system)
29251 (modify-phases %standard-phases
29252 (add-after 'unpack 'use-system-antiword
29253 (lambda* (#:key inputs #:allow-other-keys)
29254 (substitute* "R/antiword.R"
29255 (("system.file\\(\"bin\", package = \"antiword\"\\)")
29256 (string-append "\"" (assoc-ref inputs "antiword") "/bin\"")))
29258 (inputs (list antiword))
29259 (propagated-inputs (list r-sys))
29261 "https://github.com/ropensci/antiword#readme")
29263 "Extract Text from Microsoft Word Documents")
29265 "Wraps the @code{AntiWord} utility to extract text from Microsoft Word
29266 documents. The utility only supports the old @code{doc} format, not the new
29267 xml based @code{docx} format. Use the @code{xml2} package to read the
29269 (license license:gpl2)))
29271 (define-public r-readtext
29273 (name "r-readtext")
29278 (uri (cran-uri "readtext" version))
29281 "0k782h5hns5v5h8a6qyfqck2hc15nq0awg8bsp196q4zviv5jw3c"))))
29282 (properties `((upstream-name . "readtext")))
29283 (build-system r-build-system)
29298 (native-inputs (list r-knitr))
29300 "https://github.com/quanteda/readtext")
29302 "Import and Handling for Plain and Formatted Text Files")
29304 "This package provides functions for importing and handling text files
29305 and formatted text files with additional meta-data, such including @code{.csv},
29306 @code{.tab}, @code{.json}, @code{.xml}, @code{.html}, @code{.pdf}, @code{.doc},
29307 @code{.docx}, @code{.rtf}, @code{.xls}, @code{.xlsx}, and others.")
29308 (license license:gpl3)))
29310 (define-public r-packcircles
29312 (name "r-packcircles")
29317 (uri (cran-uri "packcircles" version))
29320 "05pv5c4k4njkr0xw6i6ksiy34hcyx2lbiqpv5gxw81yrkm0rxfyk"))))
29321 (properties `((upstream-name . "packcircles")))
29322 (build-system r-build-system)
29323 (propagated-inputs (list r-rcpp))
29324 (native-inputs (list r-knitr))
29326 "https://github.com/mbedward/packcircles")
29327 (synopsis "Circle Packing")
29329 "Algorithms to find arrangements of non-overlapping circles.")
29330 (license license:expat)))
29332 ;; Cannot unbundle liblwgeom, because PostGIS does not support building it on
29334 (define-public r-lwgeom
29341 (uri (cran-uri "lwgeom" version))
29344 "0d4b1djwrzla91mmyya2m1250mb44fzmq3d36w5mk81d4bg952pl"))))
29345 (properties `((upstream-name . "lwgeom")))
29346 (build-system r-build-system)
29348 (list geos proj sqlite zlib))
29350 (list r-rcpp r-sf r-units))
29351 (native-inputs (list pkg-config))
29352 (home-page "https://github.com/r-spatial/lwgeom/")
29353 (synopsis "Bindings to Selected 'liblwgeom' Functions for Simple Features")
29355 "Access to selected functions found in
29356 @url{https://github.com/postgis/postgis/tree/master/liblwgeom,liblwgeom}, the
29357 light-weight geometry library used by @url{http://postgis.net/,PostGIS}.")
29358 (license license:gpl2)))
29360 (define-public r-stars
29367 (uri (cran-uri "stars" version))
29370 "1h5fway2fk637mkglw0h3ajiyyx8saqcapg42xzsiwbk8lnaf9f4"))))
29371 (properties `((upstream-name . "stars")))
29372 (build-system r-build-system)
29380 (native-inputs (list r-knitr))
29381 (home-page "https://r-spatial.github.io/stars/")
29383 "Spatiotemporal Arrays, Raster and Vector Data Cubes")
29385 "Reading, manipulating, writing and plotting spatiotemporal arrays
29386 (raster and vector data cubes) in @code{R}, using @code{GDAL} bindings provided
29387 by @code{sf}, and @code{NetCDF} bindings by @code{ncmeta} and @code{RNetCDF}.")
29388 (license license:asl2.0)))
29390 (define-public r-tmaptools
29392 (name "r-tmaptools")
29397 (uri (cran-uri "tmaptools" version))
29400 "0bal3czrdr93qig8s5cf5szld5vjbbks67rismfhlkmlgw6wp2gx"))))
29401 (properties `((upstream-name . "tmaptools")))
29402 (build-system r-build-system)
29414 "https://github.com/mtennekes/tmaptools")
29415 (synopsis "Thematic Map Tools")
29417 "Set of tools for reading and processing spatial data. The aim is to
29418 supply the workflow to create thematic maps. This package also facilitates
29419 @code{tmap}, the package for visualizing thematic maps.")
29420 (license license:gpl3)))
29422 (define-public r-rworldmap
29424 (name "r-rworldmap")
29429 (uri (cran-uri "rworldmap" version))
29432 "1q1h0n9qr0m5pdx10swrh9ddsvdj8kv5nqngrf3lnx9rg9iwivjk"))))
29433 (properties `((upstream-name . "rworldmap")))
29434 (build-system r-build-system)
29436 (list r-fields r-maptools r-sp))
29438 "https://github.com/AndySouth/rworldmap/")
29439 (synopsis "Mapping Global Data")
29441 "Enables mapping of country level and gridded user datasets.")
29442 (license license:gpl2+)))
29444 (define-public r-rtweet
29451 (uri (cran-uri "rtweet" version))
29454 "05pbvxm2vmf6935b9s6663k3aifnkr3m52wh2jvnplmrwyrfpn9n"))))
29455 (properties `((upstream-name . "rtweet")))
29456 (build-system r-build-system)
29465 (native-inputs (list r-knitr))
29467 "https://docs.ropensci.org/rtweet/")
29468 (synopsis "Collecting Twitter Data")
29470 "An implementation of calls designed to collect and organize Twitter data
29471 via @url{https://developer.twitter.com/en/docs,Twitter's REST and stream
29472 Application Program Interfaces (API)}.")
29473 (license license:expat)))
29475 (define-public r-intervals
29477 (name "r-intervals")
29482 (uri (cran-uri "intervals" version))
29485 "0mvwfwc03ifb30a3dzbmkv9adwqb8ajxhcw24d8xip8px063plhb"))))
29486 (properties `((upstream-name . "intervals")))
29487 (build-system r-build-system)
29488 (home-page "https://github.com/edzer/intervals")
29490 "Tools for Working with Points and Intervals")
29492 "Tools for working with and comparing sets of points and intervals.")
29493 (license license:artistic2.0)))
29495 (define-public r-eyelinker
29497 (name "r-eyelinker")
29502 (uri (cran-uri "eyelinker" version))
29505 "0wijd45p6j2qal6wnj7zywks8p9v3m9cmyp7axmk44mrjdjx2i71"))))
29506 (properties `((upstream-name . "eyelinker")))
29507 (build-system r-build-system)
29509 (list r-intervals r-readr r-stringi r-stringr r-tibble))
29510 (native-inputs (list r-knitr))
29512 "https://github.com/a-hurst/eyelinker")
29514 "Import ASC Files from EyeLink Eye Trackers")
29516 "Imports plain-text ASC data files from EyeLink eye trackers into
29517 (relatively) tidy data frames for analysis and visualization.")
29518 (license license:gpl3)))
29520 (define-public r-btm
29527 (uri (cran-uri "BTM" version))
29530 "0ab0wr8nbwn1w1j9hpwfz52lm1sw0qk93713y9k0hpm3pw9dq4jr"))))
29531 (properties `((upstream-name . "BTM")))
29532 (build-system r-build-system)
29533 (propagated-inputs (list r-rcpp))
29534 (home-page "https://github.com/bnosac/BTM")
29535 (synopsis "Biterm Topic Models for Short Text")
29537 "Biterm Topic Models find topics in collections of short texts. It is a
29538 word co-occurrence based topic model that learns topics by modeling word-word
29539 co-occurrences patterns which are called biterms. This in contrast to
29540 traditional topic models like Latent Dirichlet Allocation and Probabilistic
29541 Latent Semantic Analysis which are word-document co-occurrence topic models. A
29542 biterm consists of two words co-occurring in the same short text window. This
29543 context window can for example be a twitter message, a short answer on a
29544 survey, a sentence of a text or a document identifier. The techniques are
29545 explained in detail in the paper 'A Biterm Topic Model For Short Text' by
29546 Xiaohui Yan, Jiafeng Guo, Yanyan Lan, Xueqi Cheng (2013)
29547 @url{https://github.com/xiaohuiyan/xiaohuiyan.github.io/blob/master/paper/\
29549 (license license:asl2.0)))
29551 (define-public r-delaporte
29553 (name "r-delaporte")
29558 (uri (cran-uri "Delaporte" version))
29561 "0ijhmwclpg5czs2sl2vykcw8qj2pxy26xf6knh62rqq6p6sm43f4"))))
29562 (properties `((upstream-name . "Delaporte")))
29563 (build-system r-build-system)
29564 (native-inputs (list gfortran))
29565 (home-page "https://github.com/aadler/Delaporte")
29566 (synopsis "Statistical functions for the Delaporte distribution")
29568 "This package provides probability mass, distribution, quantile,
29569 random-variate generation, and method-of-moments parameter-estimation
29570 functions for the Delaporte distribution with parameterization based on
29571 Vose (2008). The Delaporte is a discrete probability distribution which can
29572 be considered the convolution of a negative binomial distribution with a
29573 Poisson distribution. Alternatively, it can be considered a counting
29574 distribution with both Poisson and negative binomial components. It has been
29575 studied in actuarial science as a frequency distribution which has more
29576 variability than the Poisson, but less than the negative binomial.")
29577 (license license:bsd-2)))
29579 (define-public r-rjsonio
29582 (version "1.3-1.6")
29586 (uri (cran-uri "RJSONIO" version))
29589 "17x0ayk7daprbc8w2hvb2jl9mfnw4dic9yc3sr5adcjqfzmcklc2"))))
29590 (properties `((upstream-name . "RJSONIO")))
29591 (build-system r-build-system)
29592 (home-page "https://cran.r-project.org/package=RJSONIO")
29593 (synopsis "Serialize R objects to JSON")
29595 "This is a package that allows conversion to and from data in JavaScript
29596 Object Notation (JSON) format. This allows R objects to be inserted into
29597 Javascript/ECMAScript/ActionScript code and allows R programmers to read and
29598 convert JSON content to R objects. This is an alternative to the @code{rjson}
29600 (license license:bsd-3)))
29602 (define-public r-revgeo
29609 (uri (cran-uri "revgeo" version))
29612 "1ns7d1817475lriss6wwgvdm6lj760p40yxqaifla13c2xb73a55"))))
29613 (properties `((upstream-name . "revgeo")))
29614 (build-system r-build-system)
29616 (list r-rcurl r-rjsonio))
29617 (home-page "https://cran.r-project.org/package=revgeo")
29618 (synopsis "Reverse geocoding")
29620 "The @code{revgeo} procedure allows you to use the Photon geocoder for
29621 OpenStreetMap, Google Maps, and Bing to reverse geocode coordinate pairs with
29623 (license license:gpl3+)))
29625 (define-public r-qpcr
29632 (uri (cran-uri "qpcR" version))
29635 "1r01q7jv3w59yx1gc0qw91rq7rvdhqsi8y57sqqkmwyqfw2x2vsv"))))
29636 (properties `((upstream-name . "qpcR")))
29637 (build-system r-build-system)
29639 (list r-mass r-matrix r-minpack-lm r-rgl r-robustbase))
29640 (home-page "https://cran.r-project.org/package=qpcR")
29641 (synopsis "Modelling and analysis of real-time PCR data")
29643 "This is a package for model fitting, optimal model selection and
29644 calculation of various features that are essential in the analysis of
29645 quantitative real-time polymerase chain reaction (qPCR).")
29646 (license license:gpl2+)))
29648 (define-public r-textplot
29650 (name "r-textplot")
29655 (uri (cran-uri "textplot" version))
29658 "10nxh9axhy6kyp6f3rz7smq08yl35ydx9jx47bs7i0bmcl2kwxvl"))))
29659 (properties `((upstream-name . "textplot")))
29660 (build-system r-build-system)
29662 (list r-data-table r-lattice r-matrix))
29663 (native-inputs (list r-knitr))
29664 (home-page "https://github.com/bnosac/textplot")
29665 (synopsis "Text Plots")
29667 "Visualise complex relations in texts. This is done by providing
29668 functionalities for displaying text co-occurrence networks, text correlation
29669 networks, dependency relationships as well as text clustering. Feel free to
29670 join the effort of providing interesting text visualisations.")
29671 (license license:gpl2)))
29673 (define-public r-gsa
29680 (uri (cran-uri "GSA" version))
29683 "05x9wspah1cdznjpncqam1iawsxdiigyl8v2anyhss2k7wwd94p1"))))
29684 (properties `((upstream-name . "GSA")))
29685 (build-system r-build-system)
29686 (home-page "https://statweb.stanford.edu/~tibs/GSA/")
29687 (synopsis "Gene set analysis")
29688 (description "This package lets you determine the significance of
29689 pre-defined sets of genes with respect to an outcome variable, such as a group
29690 indicator, a quantitative variable or a survival time.")
29691 ;; Any version of the LGPL
29692 (license license:lgpl3+)))
29694 (define-public r-randomforestsrc
29696 (name "r-randomforestsrc")
29701 (uri (cran-uri "randomForestSRC" version))
29704 "05ifvj49jv0n5p6k46milpgj9r10sc5aw23fypyyibdgwpwvwixw"))))
29706 `((upstream-name . "randomForestSRC")))
29707 (build-system r-build-system)
29708 (home-page "https://cran.r-project.org/web/packages/randomForestSRC/")
29709 (synopsis "Random forests for survival, regression, and classification")
29711 "This package implements fast OpenMP parallel computing of Breiman's
29712 random forests for survival, competing risks, regression and classification
29713 based on Ishwaran and Kogalur's popular random survival forests (RSF) package.
29714 It handles missing data and now includes multivariate, unsupervised forests,
29715 quantile regression and solutions for class imbalanced data. It provides a
29716 fast interface using subsampling and confidence regions for variable
29718 (license license:gpl3+)))
29720 (define-public r-contfrac
29722 (name "r-contfrac")
29727 (uri (cran-uri "contfrac" version))
29730 "0sq5c7ny235yrkv2xc4insgxby6rvzc1qsj8h301cd2if3lwbgwm"))))
29731 (properties `((upstream-name . "contfrac")))
29732 (build-system r-build-system)
29734 "https://github.com/RobinHankin/contfrac")
29735 (synopsis "Continued Fractions")
29737 "Various utilities for evaluating continued fractions.")
29738 (license license:gpl2)))
29740 (define-public r-elliptic
29742 (name "r-elliptic")
29747 (uri (cran-uri "elliptic" version))
29750 "1dhba0yfxjd5rlqsxp5a7s2hclfkla9wigsr39dlma67l6qjjmxn"))))
29751 (properties `((upstream-name . "elliptic")))
29752 (build-system r-build-system)
29753 (inputs (list pari-gp))
29754 (propagated-inputs (list r-mass))
29756 "https://github.com/RobinHankin/elliptic")
29758 "Weierstrass and Jacobi Elliptic Functions")
29760 "A suite of elliptic and related functions including Weierstrass and
29761 Jacobi forms. Also includes various tools for manipulating and visualizing
29762 complex functions.")
29763 (license license:gpl2)))
29765 (define-public r-hypergeo
29767 (name "r-hypergeo")
29772 (uri (cran-uri "hypergeo" version))
29775 "13jdiy216znwhr91iqnh03mvkmyscw439syb3h4i67dd78sphnvd"))))
29776 (properties `((upstream-name . "hypergeo")))
29777 (build-system r-build-system)
29779 (list r-contfrac r-desolve r-elliptic))
29781 "https://cran.r-project.org/web/packages/hypergeo/")
29782 (synopsis "The Gauss Hypergeometric Function")
29784 "The Gaussian hypergeometric function for complex numbers.")
29785 (license license:gpl2)))
29787 (define-public r-gganimate
29789 (name "r-gganimate")
29794 (uri (cran-uri "gganimate" version))
29797 "046v6j92xxgaghsnh88dy5h8x040qsfa8csvhp4dmsfmrrf0dz0f"))))
29798 (properties `((upstream-name . "gganimate")))
29799 (build-system r-build-system)
29802 (modify-phases %standard-phases
29803 (add-after 'unpack 'absolute-paths
29804 (lambda* (#:key inputs #:allow-other-keys)
29805 (substitute* "R/renderers.R"
29807 (string-append "'" (assoc-ref inputs "ffmpeg") "/bin/ffmpeg'"))))))))
29809 ;; For video output.
29820 ;; For GIF/SVG output. gifski is faster, but depends on Rust.
29822 ;; For HTML output.
29825 (native-inputs (list r-knitr))
29826 (home-page "https://gganimate.com")
29827 (synopsis "Grammar of Animated Graphics")
29829 "This package extends the grammar of graphics as implemented by
29830 @code{ggplot2} to include the description of animation. It does this by
29831 providing a range of new grammar classes that can be added to the plot object
29832 in order to customise how it should change with time.")
29833 (license license:expat)))
29835 ;; This library bundles ‘date’ from (gnu packages calendar). We cannot unbundle
29836 ;; it, because its C++ libtz.so is built with different compiler flags than
29838 (define-public r-tzdb
29845 (uri (cran-uri "tzdb" version))
29848 "1afmav7s29fb5cd920h6vrzg9cvc4jsidfalxpvhlh1b8mfr0df3"))))
29849 (properties `((upstream-name . "tzdb")))
29850 (build-system r-build-system)
29851 (propagated-inputs (list r-cpp11))
29852 (home-page "https://github.com/r-lib/tzdb")
29853 (synopsis "Time Zone Database Information")
29855 "This package provides an up-to-date copy of the Internet Assigned
29856 Numbers Authority (IANA) Time Zone Database. It is updated periodically to
29857 reflect changes made by political bodies to time zone boundaries, UTC offsets,
29858 and daylight saving time rules. Additionally, this package provides a C++
29859 interface for working with the @code{date} library. @code{date} provides
29860 comprehensive support for working with dates and date-times, which this package
29861 exposes to make it easier for other R packages to utilize. Headers are
29862 provided for calendar specific calculations, along with a limited interface for
29863 time zone manipulations.")
29864 (license license:expat)))
29866 (define-public r-vroom
29873 (uri (cran-uri "vroom" version))
29876 "0b1lbi20gadwjwinw1v0az4g0y79vlcqfqyblphls601h3nnmn3p"))))
29877 (properties `((upstream-name . "vroom")))
29878 (build-system r-build-system)
29894 (native-inputs (list r-knitr))
29895 (home-page "https://vroom.r-lib.org")
29897 "Read and Write Rectangular Text Data")
29899 "This package reads and writes data files like @acronym{CSV},
29900 @acronym{TSV} and @acronym{FWF}. When reading it uses a quick initial indexing
29901 step, then reads the values lazily, so only the data you actually use needs to
29902 be read. The writer formats the data in parallel and writes to disk
29903 asynchronously from formatting.")
29904 (license license:expat)))
29906 (define-public r-rmisc
29912 (uri (cran-uri "Rmisc" version))
29915 "1ijjhfy3v91fspid77rrkc5dkcb2lav37wc3f4k5lwrn24wzy5y8"))))
29916 (build-system r-build-system)
29918 (list r-plyr r-rcpp r-lattice))
29919 (home-page "https://cran.r-project.org/web/packages/Rmisc/")
29920 (synopsis "Ryan Miscellaneous")
29921 (description "The Rmisc library contains functions for data analysis and
29922 utility operations.")
29923 (license license:gpl3)))
29925 (define-public r-webutils
29927 (name "r-webutils")
29932 (uri (cran-uri "webutils" version))
29934 (base32 "16a6ds0fnb6y8i1r9ba1hf1ydb53am57s070b3hi5jmrs84b9qik"))))
29935 (properties `((upstream-name . "webutils")))
29936 (build-system r-build-system)
29938 (list r-curl r-jsonlite))
29939 (home-page "https://github.com/jeroen/webutils")
29940 (synopsis "Utility functions for developing web applications")
29942 "This package parses HTTP request data in @code{application/json},
29943 @code{multipart/form-data}, or @code{application/x-www-form-urlencoded}
29944 format. It includes an example of hosting and parsing HTML form data in R
29945 using either @code{httpuv} or @code{Rhttpd}.")
29946 (license license:expat)))
29948 (define-public r-protolite
29950 (name "r-protolite")
29955 (uri (cran-uri "protolite" version))
29957 (base32 "0g1r3lzmvx1w44qzqzdvxfn21zmz11srlp6cr76kd7pd5wzjv82p"))))
29958 (properties `((upstream-name . "protolite")))
29959 (build-system r-build-system)
29963 (list r-jsonlite r-rcpp))
29965 (list protobuf pkg-config))
29966 (home-page "https://github.com/jeroen/protolite")
29967 (synopsis "Highly optimized protocol buffer serializers")
29969 "This package provides pure C++ implementations for reading and writing
29970 several common data formats based on Google protocol-buffers. It currently
29971 supports @code{rexp.proto} for serialized R objects, @code{geobuf.proto} for
29972 binary geojson, and @code{mvt.proto} for vector tiles. This package uses the
29973 auto-generated C++ code by protobuf-compiler, hence the entire serialization
29974 is optimized at compile time. The @code{RProtoBuf} package on the other hand
29975 uses the protobuf runtime library to provide a general-purpose toolkit for
29976 reading and writing arbitrary protocol-buffer data in R.")
29977 (license license:expat)))
29979 (define-public r-opencpu
29986 (uri (cran-uri "opencpu" version))
29988 (base32 "1qlwx8iq30qfy2sh0v31pxg955bj4zs0r7v8yklbdwb3qw7kv30g"))))
29989 (properties `((upstream-name . "opencpu")))
29990 (build-system r-build-system)
30010 (home-page "https://www.opencpu.org")
30011 (synopsis "API for embedded scientific computing")
30013 "This package provides a system for embedded scientific computing and
30014 reproducible research with R. The OpenCPU server exposes a simple but
30015 powerful HTTP API for RPC and data interchange with R. This provides a
30016 reliable and scalable foundation for statistical services or building R web
30017 applications. The OpenCPU server runs either as a single-user development
30018 server within the interactive R session, or as a multi-user stack based on
30020 (license license:asl2.0)))
30022 (define-public r-exactextractr
30024 (name "r-exactextractr")
30029 (uri (cran-uri "exactextractr" version))
30032 "1gc1p9pgazhblk8jgykxxjpblylbaq5r9hdlw3ilz5g45yjjwcnc"))))
30033 (properties `((upstream-name . "exactextractr")))
30034 (build-system r-build-system)
30035 (inputs (list geos))
30037 (list r-raster r-rcpp r-sf))
30040 (home-page "https://isciences.gitlab.io/exactextractr/")
30041 (synopsis "Fast extraction from raster datasets using polygons")
30043 "This package provides a replacement for the @code{extract} function from
30044 the @code{raster} package that is suitable for extracting raster values using
30045 @code{sf} polygons.")
30046 (license license:asl2.0)))
30048 (define-public r-stringfish
30050 (name "r-stringfish")
30055 (uri (cran-uri "stringfish" version))
30058 "1n67y9vgv8vb8qd091d1wm5sgbalcm2avh2fz0hd3mmglpkr83wf"))))
30059 (properties `((upstream-name . "stringfish")))
30060 (build-system r-build-system)
30062 (list r-rcpp r-rcppparallel))
30064 (list pkg-config r-knitr))
30065 (home-page "https://github.com/traversc/stringfish")
30066 (synopsis "Alternative string implementation")
30068 "This package provides an extendable, performant and multithreaded
30069 @code{alt-string} implementation backed by C++ vectors and strings.")
30070 (license license:gpl3)))
30072 (define-public r-rapiserialize
30074 (name "r-rapiserialize")
30079 (uri (cran-uri "RApiSerialize" version))
30082 "0gm2j8kh40imhncwwx1sx9kmraaxcxycvgwls53lcyy2ap344k9j"))))
30083 (properties `((upstream-name . "RApiSerialize")))
30084 (build-system r-build-system)
30086 "https://cran.r-project.org/package=RApiSerialize")
30087 (synopsis "R API serialization")
30089 "This package provides other packages with access to the internal R
30090 serialization code. Access to this code is provided at the C function level
30091 by using the registration of native function mechanism. Client packages
30092 simply include a single header file RApiSerializeAPI.h provided by this
30094 (license license:gpl2+)))
30096 (define-public r-qs
30099 (version "0.25.1.1")
30103 (uri (cran-uri "qs" version))
30106 "077i181vh0izvsdy2d4366yir0ajg531g6d1s7ab044ssbphg38x"))))
30107 (properties `((upstream-name . "qs")))
30108 (build-system r-build-system)
30109 (inputs (list zlib))
30111 (list r-rapiserialize r-rcpp r-stringfish))
30113 (list pkg-config r-knitr))
30114 (home-page "https://github.com/traversc/qs")
30115 (synopsis "Quick serialization of R objects")
30117 "This package provides functions for quickly writing and reading any R
30118 object to and from disk.")
30119 (license license:gpl3)))
30121 (define-public r-rgeos
30128 (uri (cran-uri "rgeos" version))
30131 "05539shf38slvq38pf92h9q57vmzn2vfqbirl3pbbvvc2j957cqd"))))
30132 (properties `((upstream-name . "rgeos")))
30133 (build-system r-build-system)
30138 (home-page "https://cran.r-project.org/package=rgeos")
30139 (synopsis "Interface to Geometry Engine (GEOS)")
30141 "This package provides an R interface to Geometry Engine (GEOS) using the
30142 C API for topology operations on geometries.")
30143 (license license:gpl2+)))
30145 (define-public r-tfruns
30152 (uri (cran-uri "tfruns" version))
30155 "04lfckg1if3kfwcl4s4fcc9aw04crwk4m1qr55ag22j2x2jlb2l9"))))
30156 (properties `((upstream-name . "tfruns")))
30157 (build-system r-build-system)
30169 (native-inputs (list r-knitr))
30170 (home-page "https://github.com/rstudio/tfruns")
30171 (synopsis "Training run tools for TensorFlow")
30173 "Create and manage unique directories for each TensorFlow training run.
30174 This package provides a unique, time stamped directory for each run along with
30175 functions to retrieve the directory of the latest run or latest several
30177 (license license:asl2.0)))
30179 (define-public r-tfautograph
30181 (name "r-tfautograph")
30186 (uri (cran-uri "tfautograph" version))
30189 "0fmaq1ggjyxgf2ss7qb8jk74sfwc3s1vc123pd5glclxcy1ib0j2"))))
30190 (properties `((upstream-name . "tfautograph")))
30191 (build-system r-build-system)
30192 (inputs (list tensorflow))
30194 (list r-backports r-reticulate))
30195 (home-page "https://t-kalinowski.github.io/tfautograph/")
30196 (synopsis "Autograph R for Tensorflow")
30198 "This package lets you translate R control flow expressions into
30199 Tensorflow graphs.")
30200 (license license:gpl3)))
30202 (define-public r-tensorflow
30204 (name "r-tensorflow")
30209 (uri (cran-uri "tensorflow" version))
30212 "0xgm8jb1hl8564vviqys3aqwzvfbh0d43m154cj07j9spdz306ng"))))
30213 (properties `((upstream-name . "tensorflow")))
30214 (build-system r-build-system)
30215 (inputs (list tensorflow))
30224 (home-page "https://github.com/rstudio/tensorflow")
30225 (synopsis "R interface to TensorFlow")
30227 "R interface to TensorFlow a library for numerical computation using data
30228 flow graphs. Nodes in the graph represent mathematical operations, while the
30229 graph edges represent the multidimensional data arrays (tensors) communicated
30231 (license license:asl2.0)))
30233 (define-public r-keras
30240 (uri (cran-uri "keras" version))
30243 "004z9aajc0b7lw7g68ri7ndabdwbylmnlyvmziljmm29z6fzk8y5"))))
30244 (properties `((upstream-name . "keras")))
30245 (build-system r-build-system)
30257 (native-inputs (list r-knitr))
30258 (home-page "https://keras.rstudio.com")
30259 (synopsis "R Interface to 'Keras'")
30261 "This package provides an interface to Keras, a high-level neural
30262 networks API. Keras was developed with a focus on enabling fast
30263 experimentation, supports both convolution based networks and recurrent
30264 networks (as well as combinations of the two), and runs seamlessly on both CPU
30266 (license license:expat)))
30268 (define-public r-zzlite
30275 (uri (cran-uri "zzlite" version))
30278 "0vi1slx2s4r5zf82lazqv0c3m12xq73wlgsbz6af4y00h0bkr3ps"))))
30279 (properties `((upstream-name . "zzlite")))
30280 (build-system r-build-system)
30282 (list r-httr r-jsonlite))
30285 (home-page "https://cran.r-project.org/package=zzlite")
30286 (synopsis "Wrapper for the Zamzar file conversion API")
30288 "This package provides a minor collection of HTTP wrappers for the Zamzar
30289 file conversion API. The wrappers makes it easy to utilize the API and thus
30290 convert between more than 100 different file formats (ranging from audio
30291 files, images, movie formats, etc., etc.) through an R session.")
30292 (license license:gpl3)))
30294 (define-public r-ztree
30301 (uri (cran-uri "zTree" version))
30304 "005zk6wpchpss6865ki35yawgf668pn70163ah97rnfkhfaswm6y"))))
30305 (properties `((upstream-name . "zTree")))
30306 (build-system r-build-system)
30309 (home-page "https://cran.r-project.org/package=zTree")
30310 (synopsis "Functions to import data from z-Tree into R")
30312 "This package provides tools for reading @code{.xls} and @code{.sbj}
30313 files which are written by the proprietary program z-Tree for developing and
30314 carrying out economic experiments.")
30315 (license license:gpl3)))
30317 (define-public r-distributionutils
30319 (name "r-distributionutils")
30324 (uri (cran-uri "DistributionUtils" version))
30327 "08vq54pyqxlqsj6q6gsg5ikqa0z3x842j52ld5dxaq272p6xchvl"))))
30329 `((upstream-name . "DistributionUtils")))
30330 (build-system r-build-system)
30333 (home-page "https://cran.r-project.org/package=DistributionUtils")
30334 (synopsis "Distribution utilities")
30336 "This package provides utilities for dealing with distributions.
30337 Functionality includes sample skewness and kurtosis, log-histogram, tail
30338 plots, moments by integration, changing the point about which a moment is
30339 calculated, functions for testing distributions using inversion tests and the
30340 Massart inequality. Also included is an implementation of the incomplete
30341 Bessel K function.")
30342 (license license:gpl2+)))
30344 (define-public r-ztpln
30351 (uri (cran-uri "ztpln" version))
30354 "1b22m72a8117yrgq5k1gzsrbx6yrsrj7bpd49lh7x3vbaz56c0wr"))))
30355 (properties `((upstream-name . "ztpln")))
30356 (build-system r-build-system)
30358 (list r-distributionutils r-mixtools r-rcpp r-rcppeigen
30362 (home-page "https://github.com/mattocci27/ztpln")
30363 (synopsis "Zero-truncated Poisson lognormal distribution")
30365 "This package provides functions for obtaining the density, random
30366 variates and maximum likelihood estimates of the Zero-truncated Poisson
30367 lognormal distribution and their mixture distribution.")
30368 (license license:expat)))
30370 (define-public r-zscorer
30377 (uri (cran-uri "zscorer" version))
30380 "0aijhs0fyird5gq68x4dxchb02mxa7ijk10k9zjhngghxbjj7iqn"))))
30381 (properties `((upstream-name . "zscorer")))
30382 (build-system r-build-system)
30387 (home-page "https://github.com/nutriverse/zscorer")
30388 (synopsis "Child Anthropometry z-Score Calculator")
30390 "This package provides a tool for calculating z-scores and centiles for
30391 weight-for-age, length/height-for-age, weight-for-length/height, BMI-for-age,
30392 head circumference-for-age, age circumference-for-age, subscapular
30393 skinfold-for-age, triceps skinfold-for-age based on the WHO Child Growth
30395 (license license:agpl3+)))
30397 (define-public r-zra
30404 (uri (cran-uri "ZRA" version))
30407 "1sx1q5yf68hhlb5j1hicpj594rmgajqr25llg7ax416j0m2rnagi"))))
30408 (properties `((upstream-name . "ZRA")))
30409 (build-system r-build-system)
30411 (list r-dygraphs r-forecast))
30412 (home-page "https://cran.r-project.org/package=ZRA")
30413 (synopsis "Dynamic plots for time series forecasting")
30415 "This package combines a forecast of a time series, using the function @code{forecast},
30416 with the dynamic plots from @code{dygraphs}.")
30417 (license license:gpl2+)))
30419 (define-public r-rfigshare
30421 (name "r-rfigshare")
30426 (uri (cran-uri "rfigshare" version))
30429 "1qgzn0mpjy4czy0pnbi395fxxx84arkg8r7rk8aidmd34584gjiq"))))
30430 (properties `((upstream-name . "rfigshare")))
30431 (build-system r-build-system)
30440 (home-page "https://github.com/ropensci/rfigshare")
30441 (synopsis "R Interface to figshare")
30443 "This package provides an interface to figshare, a scientific repository
30444 to archive and assign DOIs to data, software, figures, and more.")
30445 (license license:cc0)))
30447 (define-public r-dismo
30454 (uri (cran-uri "dismo" version))
30457 "1rqf6h4imbqvs7hjd1k4my6154wg0qnmnp5byan403rcshr1jbl1"))))
30458 (properties `((upstream-name . "dismo")))
30459 (build-system r-build-system)
30461 (list r-raster r-rcpp r-sp r-terra))
30462 (home-page "https://rspatial.org/raster/sdm/")
30463 (synopsis "Species distribution modeling")
30465 "This package provides methods for species distribution modeling, i.e.,
30466 predicting the environmental similarity of any site to that of the locations
30467 of known occurrences of a species.")
30468 (license license:gpl3+)))
30470 (define-public r-zoon
30477 (uri (cran-uri "zoon" version))
30480 "02y29vr2yn8al69km8faiqrwjrc1r3hsvw3dg8lwjr65cxw1krip"))))
30481 (properties `((upstream-name . "zoon")))
30482 (build-system r-build-system)
30497 (home-page "https://github.com/zoonproject/zoon")
30498 (synopsis "Reproducible, accessible and shareable species distribution modelling")
30500 "This package reads user submitted modules from an online repository,
30501 runs full species distribution modelling workflows and returns output that is
30502 fully reproducible.")
30503 (license license:bsd-3)))
30505 (define-public r-paws-common
30507 (name "r-paws-common")
30512 (uri (cran-uri "paws.common" version))
30515 "013yiki3bjx0np577wy17ikfxdr2hiv6sd10anv281r108kldm1x"))))
30516 (properties `((upstream-name . "paws.common")))
30517 (build-system r-build-system)
30519 (list r-base64enc r-digest r-httr r-jsonlite r-xml2))
30520 (home-page "https://cran.r-project.org/package=paws.common")
30521 (synopsis "Paws low-level Amazon Web Services API")
30523 "This package provides functions for making low-level API requests to
30524 Amazon Web Services. The functions handle building, signing, and sending
30525 requests, and receiving responses. They are designed to help build
30526 higher-level interfaces to individual services, such as Simple Storage
30528 (license license:asl2.0)))
30530 (define-public r-paws-customer-engagement
30532 (name "r-paws-customer-engagement")
30537 (uri (cran-uri "paws.customer.engagement" version))
30540 "0ac6hzn4ilfjhzdmc9x80999fl18cz16mky31qd3y09m93w2xkdj"))))
30542 `((upstream-name . "paws.customer.engagement")))
30543 (build-system r-build-system)
30545 (list r-paws-common))
30546 (home-page "https://github.com/paws-r/paws")
30547 (synopsis "Amazon Web Services customer engagement services")
30549 "This package provides an interface to Amazon Web Services customer
30550 engagement services, including Simple Email Service, Connect contact center
30551 service, and more.")
30552 (license license:asl2.0)))
30554 (define-public r-paws-cost-management
30556 (name "r-paws-cost-management")
30561 (uri (cran-uri "paws.cost.management" version))
30564 "0in4f8ygw5g2v6vl3lz2y0v51llglh8b1ymbd04d54xxlgn83knh"))))
30566 `((upstream-name . "paws.cost.management")))
30567 (build-system r-build-system)
30569 (list r-paws-common))
30570 (home-page "https://github.com/paws-r/paws")
30571 (synopsis "Amazon Web Services cost management services")
30573 "This package provides an interface to Amazon Web Services cost
30574 management services, including cost and usage reports, budgets, pricing, and
30576 (license license:asl2.0)))
30578 (define-public r-paws-developer-tools
30580 (name "r-paws-developer-tools")
30585 (uri (cran-uri "paws.developer.tools" version))
30587 (base32 "16gb8g8s67al7qdd95fbigxqkih9a9p7slkyf3cga42wb6miiby2"))))
30588 (properties `((upstream-name . "paws.developer.tools")))
30589 (build-system r-build-system)
30591 (list r-paws-common))
30592 (home-page "https://github.com/paws-r/paws")
30593 (synopsis "Amazon Web Services developer tools services")
30595 "This package provides an interface to Amazon Web Services developer
30596 tools services, including version control, continuous integration and
30597 deployment, and more.")
30598 (license license:asl2.0)))
30600 (define-public r-paws-end-user-computing
30602 (name "r-paws-end-user-computing")
30607 (uri (cran-uri "paws.end.user.computing" version))
30609 (base32 "1xxsz86nx128sizym9np8vldzkbym0p3i6vcy94kq1y0cylaicv3"))))
30610 (properties `((upstream-name . "paws.end.user.computing")))
30611 (build-system r-build-system)
30613 (list r-paws-common))
30614 (home-page "https://github.com/paws-r/paws")
30615 (synopsis "Amazon Web Services end user computing services")
30617 "This package provides an interface to Amazon Web Services end user
30618 computing services, including collaborative document editing, mobile intranet,
30620 (license license:asl2.0)))
30622 (define-public r-paws-application-integration
30624 (name "r-paws-application-integration")
30629 (uri (cran-uri "paws.application.integration" version))
30632 "0llyd9hc679pad1ih0rcc38q5xxpzinhwrl8cvrkgsjgbc3agq42"))))
30634 `((upstream-name . "paws.application.integration")))
30635 (build-system r-build-system)
30637 (list r-paws-common))
30638 (home-page "https://github.com/paws-r/paws")
30639 (synopsis "Amazon Web Services application integration services")
30641 "This package provides an interface to Amazon Web Services application
30642 integration services, including Simple Queue Service (SQS) message queue,
30643 Simple Notification Service (SNS) publish/subscribe messaging, and more.")
30644 (license license:asl2.0)))
30646 (define-public r-paws-security-identity
30648 (name "r-paws-security-identity")
30653 (uri (cran-uri "paws.security.identity" version))
30656 "092lz2ipn5iqr593x7ra8c0bj64yf6315mdc3llgwrjyb4vfxif9"))))
30658 `((upstream-name . "paws.security.identity")))
30659 (build-system r-build-system)
30661 (list r-paws-common))
30662 (home-page "https://github.com/paws-r/paws")
30663 (synopsis "Amazon Web Services security, identity, and compliance services")
30665 "This package provides an interface to Amazon Web Services security,
30666 identity, and compliance services, including the Identity and Access
30667 Management (IAM) service for managing access to services and resources, and
30669 (license license:asl2.0)))
30671 (define-public r-paws-analytics
30673 (name "r-paws-analytics")
30678 (uri (cran-uri "paws.analytics" version))
30681 "04gnaxmj21l312xkrsd9bisi0bz9h6h5fyhwlqylcxi077z1yb2g"))))
30683 `((upstream-name . "paws.analytics")))
30684 (build-system r-build-system)
30686 (list r-paws-common))
30687 (home-page "https://github.com/paws-r/paws")
30688 (synopsis "Amazon Web Services analytics services")
30690 "This package provides an interface to Amazon Web Services analytics
30691 services, including Elastic MapReduce Hadoop and Spark big data service,
30692 Elasticsearch search engine, and more.")
30693 (license license:asl2.0)))
30695 (define-public r-paws-machine-learning
30697 (name "r-paws-machine-learning")
30702 (uri (cran-uri "paws.machine.learning" version))
30705 "01w2y5952pk50xjbzby2pc51xrkrzjpfxbmii1b10cl2xgzfkxsa"))))
30707 `((upstream-name . "paws.machine.learning")))
30708 (build-system r-build-system)
30710 (list r-paws-common))
30711 (home-page "https://github.com/paws-r/paws")
30712 (synopsis "Amazon Web Services machine learning services")
30714 "This package provides an interface to Amazon Web Services machine
30715 learning services, including SageMaker managed machine learning service,
30716 natural language processing, speech recognition, translation, and more.")
30717 (license license:asl2.0)))
30719 (define-public r-paws-management
30721 (name "r-paws-management")
30726 (uri (cran-uri "paws.management" version))
30729 "09k7wg0jlj40zs2yb3vldffpkdcjg7ap98n7c5lxr5plpca08swg"))))
30731 `((upstream-name . "paws.management")))
30732 (build-system r-build-system)
30734 (list r-paws-common))
30735 (home-page "https://github.com/paws-r/paws")
30736 (synopsis "Amazon Web Services management and governance services")
30738 "This package provides an interface to Amazon Web Services management and
30739 governance services, including CloudWatch application and infrastructure
30740 monitoring, Auto Scaling for automatically scaling resources, and more.")
30741 (license license:asl2.0)))
30743 (define-public r-paws-networking
30745 (name "r-paws-networking")
30750 (uri (cran-uri "paws.networking" version))
30753 "02hxaa5nlj70mdggh379ij3fn09xm8h5ldzsyf45c342prpl6zwj"))))
30755 `((upstream-name . "paws.networking")))
30756 (build-system r-build-system)
30758 (list r-paws-common))
30759 (home-page "https://github.com/paws-r/paws")
30760 (synopsis "Amazon Web Services networking and content delivery services")
30762 "This package provides an interface to Amazon Web Services networking and
30763 content delivery services, including Route 53 Domain Name System service,
30764 CloudFront content delivery, load balancing, and more.")
30765 (license license:asl2.0)))
30767 (define-public r-paws-database
30769 (name "r-paws-database")
30774 (uri (cran-uri "paws.database" version))
30777 "08jpwz95fw3f68j0wxh2lg57nn60khflldab0ryhkkbcw1iy0qyz"))))
30778 (properties `((upstream-name . "paws.database")))
30779 (build-system r-build-system)
30781 (list r-paws-common))
30782 (home-page "https://github.com/paws-r/paws")
30784 "Amazon Web Services Database Services")
30786 "This package provides an interface to Amazon Web Services database
30787 services, including Relational Database Service (RDS), DynamoDB NoSQL
30788 database, and more.")
30789 (license license:asl2.0)))
30791 (define-public r-paws-storage
30793 (name "r-paws-storage")
30798 (uri (cran-uri "paws.storage" version))
30801 "06m887vpqp5d6k3zxdlga599dsv8v3rladk7xqaxqnld1f17am04"))))
30802 (properties `((upstream-name . "paws.storage")))
30803 (build-system r-build-system)
30805 (list r-paws-common))
30806 (home-page "https://github.com/paws-r/paws")
30807 (synopsis "Amazon Web Services storage services")
30809 "This package provides an interface to Amazon Web Services storage
30810 services, including Simple Storage Service (S3).")
30811 (license license:asl2.0)))
30813 (define-public r-paws-compute
30815 (name "r-paws-compute")
30820 (uri (cran-uri "paws.compute" version))
30823 "1km6fng6il5fcjlrbbndahsw2dr2ql83hwac9wlpd67zm3wy9lky"))))
30824 (properties `((upstream-name . "paws.compute")))
30825 (build-system r-build-system)
30827 (list r-paws-common))
30828 (home-page "https://github.com/paws-r/paws")
30829 (synopsis "Amazon Web Services compute services")
30831 "This package provides an interface to Amazon Web Services compute
30832 services, including Elastic Compute Cloud (EC2), Lambda
30833 functions-as-a-service, containers, batch processing, and more.")
30834 (license license:asl2.0)))
30836 (define-public r-paws
30843 (uri (cran-uri "paws" version))
30846 "0kn1z045r106fwqcaz52hb02bhrcblh479cajfjiq480s1iljcw6"))))
30847 (properties `((upstream-name . "paws")))
30848 (build-system r-build-system)
30850 (list r-paws-analytics
30851 r-paws-application-integration
30853 r-paws-cost-management
30854 r-paws-customer-engagement
30856 r-paws-developer-tools
30857 r-paws-end-user-computing
30858 r-paws-machine-learning
30861 r-paws-security-identity
30863 (home-page "https://github.com/paws-r/paws")
30864 (synopsis "Amazon Web Services software development kit")
30866 "This package provides an interface to Amazon Web Services, including
30867 storage, database, and compute services, such as Simple Storage Service (S3),
30868 DynamoDB NoSQL database, and Lambda functions-as-a-service.")
30869 (license license:asl2.0)))
30871 (define-public r-zoomgroupstats
30873 (name "r-zoomgroupstats")
30878 (uri (cran-uri "zoomGroupStats" version))
30881 "0gndiq92cy6gi7f833hdjvqii3cn83wz5rjvygcvjl3dw4pwv966"))))
30883 `((upstream-name . "zoomGroupStats")))
30884 (build-system r-build-system)
30895 (native-inputs (list r-knitr))
30896 (home-page "http://zoomgroupstats.org")
30897 (synopsis "Analyze text, audio, and video from Zoom meetings")
30899 "This package provides utilities for processing and analyzing the files
30900 that are exported from a recorded Zoom meeting. This includes analyzing data
30901 captured through video cameras and microphones, the text-based chat, and
30902 meta-data. You can analyze aspects of the conversation among meeting
30903 participants and their emotional expressions throughout the meeting.")
30904 (license license:expat)))
30906 (define-public r-zoom
30913 (uri (cran-uri "zoom" version))
30916 "03f5rxfr6ncf1j6vpn7pip21q7ylj4bx0a5xphqb6x6i33lxf1g5"))))
30917 (properties `((upstream-name . "zoom")))
30918 (build-system r-build-system)
30919 (home-page "https://github.com/cbarbu/R-package-zoom")
30920 (synopsis "Spatial data visualization tool")
30922 "This package provides @code{zm}, a utility that allows you to
30923 zoom/navigate any plot when called with any active plot.")
30924 (license license:gpl3+)))
30926 (define-public r-zoolog
30933 (uri (cran-uri "zoolog" version))
30936 "1wxxxscw4ji4p4599vdw6vcrkqm0g75x1gh13m4758lb51wav9ks"))))
30937 (properties `((upstream-name . "zoolog")))
30938 (build-system r-build-system)
30940 (list r-rdpack r-stringi))
30943 (home-page "https://josempozo.github.io/zoolog/")
30944 (synopsis "Zooarchaeological analysis with log-ratios")
30946 "This package includes functions and reference data to generate and
30947 manipulate log-ratios (also known as @dfn{log size index} (LSI) values) from
30948 measurements obtained on zooarchaeological material. Log ratios are used to
30949 compare the relative (rather than the absolute) dimensions of animals from
30950 archaeological contexts. The zoolog package is also able to seamlessly
30951 integrate data and references with heterogeneous nomenclature, which is
30952 internally managed by a zoolog thesaurus.")
30953 (license license:gpl3)))
30955 (define-public r-filehash
30957 (name "r-filehash")
30962 (uri (cran-uri "filehash" version))
30965 "14zv7h5195dmfksgk8qvjgc2qq8253vga6267aa1bqs5bpvmdl5n"))))
30966 (properties `((upstream-name . "filehash")))
30967 (build-system r-build-system)
30968 (home-page "http://github.com/rdpeng/filehash")
30969 (synopsis "Simple key-value database")
30971 "This package implements a simple key-value style database where
30972 character string keys are associated with data values that are stored on the
30973 disk. A simple interface is provided for inserting, retrieving, and deleting
30974 data from the database. Utilities are provided that allow filehash databases
30975 to be treated much like environments and lists are already used in R. These
30976 utilities are provided to encourage interactive and exploratory analysis on
30978 (license license:gpl2+)))
30980 (define-public r-mlearning
30982 (name "r-mlearning")
30987 (uri (cran-uri "mlearning" version))
30990 "0r8xfaxw83s2r27b8x5qd0k4r5ayxpkafzn9b1a0jvsr87i6520r"))))
30991 (properties `((upstream-name . "mlearning")))
30992 (build-system r-build-system)
31000 (home-page "http://www.sciviews.org/zooimage")
31001 (synopsis "Machine learning algorithms with unified interface")
31003 "This package provides a unified interface to various machine learning
31004 algorithms. Confusion matrices are provided too.")
31005 (license license:gpl2+)))
31007 (define-public r-zooimage
31009 (name "r-zooimage")
31014 (uri (cran-uri "zooimage" version))
31017 "0ck8w0zb9l1n9xvjwqshq9q9l8pigy3yslq2hnfbgcwk17kk9mp8"))))
31018 (properties `((upstream-name . "zooimage")))
31019 (build-system r-build-system)
31033 (home-page "http://www.sciviews.org/zooimage")
31034 (synopsis "Analysis of numerical plankton images")
31036 "This package provides a solution for analyzing digital images of
31037 plankton. In combination with ImageJ, an image analysis system, it processes
31038 digital images, measures individuals, trains for automatic classification of
31039 taxa, and finally, measures plankton samples (abundances, total and partial
31040 size spectra or biomasses, etc.).")
31041 (license license:gpl2+)))
31043 (define-public r-zooarch
31050 (uri (cran-uri "zooaRch" version))
31053 "0grc378xppv0303sf4flfqz5002vq5a23nzbq4bsff41rww7dihc"))))
31054 (properties `((upstream-name . "zooaRch")))
31055 (build-system r-build-system)
31056 (propagated-inputs (list r-ggplot2))
31057 (native-inputs (list r-knitr))
31059 "https://cran.r-project.org/package=zooaRch")
31061 "Analytical Tools for Zooarchaeological Data")
31063 "The analysis and inference of faunal remains recovered from
31064 archaeological sites concerns the field of zooarchaeology. The zooaRch
31065 package provides analytical tools to make inferences on zooarchaeological
31066 data. Functions in this package allow users to read, manipulate, visualize,
31067 and analyze zooarchaeological data.")
31068 (license license:gpl2+)))
31070 (define-public r-zonebuilder
31072 (name "r-zonebuilder")
31077 (uri (cran-uri "zonebuilder" version))
31080 "0mxf3dz0d6bi5wwjilqivdxhy5ypnq5svky8zygha0clv45l4dmn"))))
31081 (properties `((upstream-name . "zonebuilder")))
31082 (build-system r-build-system)
31084 (list r-rcolorbrewer r-sf))
31087 (home-page "https://github.com/zonebuilders/zonebuilder")
31088 (synopsis "Create and explore geographic zoning systems")
31090 "This package provides functions, documentation and example data to help
31091 divide geographic space into discrete polygons (zones). The functions are
31092 motivated by research into the merits of different zoning systems. A flexible
31093 @code{ClockBoard} zoning system is provided, which breaks-up space by
31094 concentric rings and radial lines emanating from a central point.")
31095 (license license:gpl3)))
31097 (define-public r-zonator
31104 (uri (cran-uri "zonator" version))
31107 "1plxchpd4ypp36phl13pi9yvlrqi3lk83lv5rldrhdqynhcgfw2k"))))
31108 (properties `((upstream-name . "zonator")))
31109 (build-system r-build-system)
31111 (list r-ggplot2 r-raster r-rcolorbrewer r-reshape2 r-rgdal))
31112 (native-inputs (list r-knitr))
31113 (home-page "https://cbig.github.io/zonator/")
31114 (synopsis "Utilities for Zonation spatial conservation prioritization")
31116 "Create new analysis setups and deal with results of Zonation
31117 conservation prioritization software.")
31118 (license license:bsd-2)))
31120 (define-public r-mmwrweek
31122 (name "r-mmwrweek")
31127 (uri (cran-uri "MMWRweek" version))
31130 "1l1ks44v52iggw9nhs56lfj6804yab5b17k8fzrc6h1kvj3vda0s"))))
31131 (properties `((upstream-name . "MMWRweek")))
31132 (build-system r-build-system)
31133 (home-page "http://wwwn.cdc.gov/nndss/document/MMWR_Week_overview.pdf")
31134 (synopsis "Convert dates to MMWR day, week, and year")
31136 "The first day of any MMWR week is Sunday. MMWR week numbering is
31137 sequential beginning with 1 and incrementing with each week to a maximum of 52
31138 or 53. MMWR week #1 of an MMWR year is the first week of the year that has at
31139 least four days in the calendar year. This package provides functionality to
31140 convert dates to MMWR day, week, and year and the reverse.")
31141 (license license:gpl2+)))
31143 (define-public r-crul
31150 (uri (cran-uri "crul" version))
31153 "133g0skz4lifl8hm8pqdryd2m2drbrm6mdfzbbsrw8fg46di86my"))))
31154 (properties `((upstream-name . "crul")))
31155 (build-system r-build-system)
31163 (native-inputs (list r-knitr))
31164 (home-page "https://github.com/ropensci/crul")
31165 (synopsis "HTTP client")
31167 "This package provides a simple HTTP client, with tools for making HTTP
31168 requests, and mocking HTTP requests. The package is built on R6, and takes
31169 inspiration from Ruby's @code{faraday} gem.")
31170 (license license:expat)))
31172 (define-public r-gistr
31179 (uri (cran-uri "gistr" version))
31182 "0ac9ikrdg6i8xvlma0gizvsdva46408lk7hvsgkqirhy2ljy02hp"))))
31183 (properties `((upstream-name . "gistr")))
31184 (build-system r-build-system)
31194 (native-inputs (list r-knitr))
31195 (home-page "https://github.com/ropensci/gistr")
31196 (synopsis "Work with Gists in browser")
31198 "This package allows the user to create new Github gists, update gists
31199 with new files, rename files, delete files, get and delete gists, star and
31200 un-star them, fork them, open a gist in your default browser, get an embed
31201 code for a gist, list gist commits, and get rate limit information when
31203 (license license:expat)))
31205 (define-public r-rbokeh
31212 (uri (cran-uri "rbokeh" version))
31215 "1h2fpzqf17pw9d09r1g1iyxsj5qma4fsk8vnar7f1z4fjyypvi6q"))
31217 '(for-each delete-file '("inst/htmlwidgets/lib/bokehjs/bokeh-widgets.min.js"
31218 "inst/htmlwidgets/lib/bokehjs/bokeh.min.js")))))
31219 (properties `((upstream-name . "rbokeh")))
31220 (build-system r-build-system)
31223 (modify-phases %standard-phases
31224 (add-after 'unpack 'process-javascript
31225 (lambda* (#:key inputs #:allow-other-keys)
31226 (with-directory-excursion "inst/htmlwidgets/lib/bokehjs"
31228 `((,(assoc-ref inputs "js-bokeh-widgets")
31229 . "bokeh-widgets.min.js")
31230 (,(assoc-ref inputs "js-bokeh")
31231 . "bokeh.min.js"))))
31232 (for-each (lambda (source target)
31233 (format #true "Processing ~a --> ~a~%"
31235 (invoke "esbuild" source "--minify"
31236 (string-append "--outfile=" target)))
31238 (map cdr mapping)))))))))
31250 ;; Version 0.12.15 is mentioned in lib/htmlwidgets/rbokeh.yaml.
31252 `(("esbuild" ,esbuild)
31253 ("js-bokeh-widgets"
31256 (uri "https://unpkg.com/bokehjs@0.12.15/build/js/bokeh-widgets.js")
31259 "07v9lrkfcbdznpb10qqwi4m660zp65g85vlnfw7kn83zmkxkhhxy"))))
31263 (uri "https://unpkg.com/bokehjs@0.12.15/build/js/bokeh.js")
31266 "1pq0059aad7d2jv50nv9449p3w0gbkxkl0mhblc76m5d9qjqav2q"))))
31267 ("r-knitr" ,r-knitr)))
31268 (home-page "https://cran.r-project.org/web/packages/rbokeh/")
31269 (synopsis "R interface for the Bokeh visualization library")
31271 "This package provides a native R plotting library that provides a
31272 flexible declarative interface for creating interactive web-based graphics,
31273 backed by the @url{https://bokeh.pydata.org/, Bokeh visualization library}.")
31274 (license license:expat)))
31276 (define-public r-fauxpas
31283 (uri (cran-uri "fauxpas" version))
31286 "129fzqb7wsskbn50s8x0marr4wm8jrns6hiycqcsk166k3dnyyy8"))))
31287 (properties `((upstream-name . "fauxpas")))
31288 (build-system r-build-system)
31290 (list r-httpcode r-r6 r-whisker))
31293 (home-page "https://docs.ropensci.org/fauxpas")
31294 (synopsis "HTTP error helpers")
31296 "This package provides HTTP error helpers. Methods are included for
31297 general purpose HTTP error handling, as well as individual methods for every
31298 HTTP status code, both via status code numbers as well as their descriptive
31299 names. It supports the ability to adjust behavior to stop, message or
31300 warning. It includes the ability to use a custom whisker template to have any
31301 configuration of status code, short description, and verbose message.")
31302 (license license:expat)))
31304 (define-public r-webmockr
31306 (name "r-webmockr")
31311 (uri (cran-uri "webmockr" version))
31314 "0j40srwi0yasmllb9wsww4m6zkiyzqd549cis4dxd7c7p24hak8j"))))
31315 (properties `((upstream-name . "webmockr")))
31316 (build-system r-build-system)
31326 (home-page "https://github.com/ropensci/webmockr")
31327 (synopsis "Stubbing and setting expectations on HTTP Requests")
31329 "This is a package for stubbing and setting expectations on HTTP
31330 requests. It includes tools for stubbing HTTP requests, including expected
31331 request conditions and response conditions. You can match on HTTP method,
31332 query parameters, request body, headers and more. It can be used for unit
31333 tests or outside of a testing context.")
31334 (license license:expat)))
31336 (define-public r-mockery
31343 (uri (cran-uri "mockery" version))
31346 "16zayzi2qdmiy513hvlci9f4p8jwry24006yfzrgmrvf6sf293lq"))))
31347 (properties `((upstream-name . "mockery")))
31348 (build-system r-build-system)
31353 (home-page "https://github.com/jfiksel/mockery")
31354 (synopsis "Mocking library for R")
31356 "The two main functionalities of this package are creating mock
31357 objects (functions) and selectively intercepting calls to a given function
31358 that originate in some other function. It can be used with any testing
31359 framework available for R. Mock objects can be injected with either this
31360 package's own @code{stub} function or a similar @code{with_mock} facility
31361 present in the @code{testthat} package.")
31362 (license license:expat)))
31364 (define-public r-zoltr
31371 (uri (cran-uri "zoltr" version))
31374 "12zh7y3pwidclscgvd0b0iaqq9j5y8mc8xd6pz4vs0jy5qs3ahar"))))
31375 (properties `((upstream-name . "zoltr")))
31376 (build-system r-build-system)
31388 (native-inputs (list r-knitr))
31389 (home-page "https://github.com/reichlab/zoltr")
31390 (synopsis "Interface to the Zoltar forecast repository API")
31392 "Zoltar is a website that provides a repository of model forecast results
31393 in a standardized format and a central location. It supports storing,
31394 retrieving, comparing, and analyzing time series forecasts for prediction
31395 challenges of interest to the modeling community. This package provides
31396 functions for working with the Zoltar API, including connecting and
31397 authenticating, getting information about projects, models, and forecasts,
31398 deleting and uploading forecast data, and downloading scores.")
31399 (license license:gpl3)))
31401 (define-public r-zoib
31408 (uri (cran-uri "zoib" version))
31411 "0inm7f2pc68ksqxvq12xp9jc99vj7ydylvs24ip12nksbj5k1n8f"))))
31412 (properties `((upstream-name . "zoib")))
31413 (build-system r-build-system)
31415 (list r-abind r-coda r-formula r-rjags))
31416 (home-page "https://www.r-project.org")
31417 (synopsis "Bayesian inference for beta regression")
31419 "This package lets you fit beta regression and zero-or-one inflated beta
31420 regression and obtain Bayesian inference of the model via the Markov Chain
31421 Monte Carlo approach implemented in JAGS.")
31422 (license license:gpl3+)))
31424 (define-public r-logger
31431 (uri (cran-uri "logger" version))
31433 (base32 "08kym5i5fvbf5xhh9qdszp4jdgyc7j7zpnwzy68wabqz73aff6sg"))))
31434 (properties `((upstream-name . "logger")))
31435 (build-system r-build-system)
31436 (native-inputs (list r-knitr))
31437 (home-page "https://daroczig.github.io/logger/")
31438 (synopsis "Lightweight and flexible logging utility")
31440 "Inspired by the the @code{futile.logger} R package and @code{logging}
31441 Python module, this utility provides a flexible and extensible way of
31442 formatting and delivering log messages with low overhead.")
31443 (license license:agpl3+)))
31445 (define-public r-fasterize
31447 (name "r-fasterize")
31452 (uri (cran-uri "fasterize" version))
31454 (base32 "10bzl77c1b9jhcn1xp467qzp2n8c7s3wpxn53qjh1nwvbri5kd32"))))
31455 (properties `((upstream-name . "fasterize")))
31456 (build-system r-build-system)
31458 (list r-raster r-rcpp r-rcpparmadillo r-sp))
31459 (native-inputs (list r-knitr))
31460 (home-page "https://github.com/ecohealthalliance/fasterize")
31461 (synopsis "Fast Polygon to Raster Conversion")
31463 "This package provides a drop-in replacement for @code{rasterize} from
31464 the @code{raster} package that takes sf-type objects, and is much faster.
31465 There is support for the main options provided by the @code{rasterize}
31466 function, including setting the field used and background value, and
31467 options for aggregating multi-layer rasters.")
31468 (license license:expat)))
31470 (define-public r-bien
31477 (uri (cran-uri "BIEN" version))
31479 (base32 "1dagrs54ciagm2mgqrvxl6k2akahr0qk63ifxqnks7iljm0x1gw6"))))
31480 (properties `((upstream-name . "BIEN")))
31481 (build-system r-build-system)
31483 (list r-knitr r-testthat))
31496 (home-page "https://cran.r-project.org/package=BIEN")
31497 (synopsis "Tools for accessing the BIEN database")
31499 "This package provides tools for accessing the Botanical Information and
31500 Ecology Network (BIEN) database. The BIEN database contains cleaned and
31501 standardized botanical data including occurrence, trait, plot and taxonomic
31502 data. This package provides functions that query the BIEN database by
31503 constructing and executing optimized SQL queries.")
31504 (license license:expat)))
31506 (define-public r-ggh4x
31513 (uri (cran-uri "ggh4x" version))
31516 "0gv9ckkdqbcjknzsv8h3955wnikawdfypr279v74hvwyq86af29r"))))
31517 (properties `((upstream-name . "ggh4x")))
31518 (build-system r-build-system)
31520 (list r-ggplot2 r-gtable r-rlang r-scales r-vctrs))
31523 (home-page "https://github.com/teunbrand/ggh4x")
31524 (synopsis "Extension for ggplot2")
31525 (description "This package is a @code{ggplot2} extension. It provides some
31526 utility functions that do not entirely fit within the grammar of graphics
31527 concept. The package extends @code{ggpplots} facets through customisation, by
31528 setting individual scales per panel, resizing panels and providing nested
31529 facets. It also allows multiple colour, fill scales per plot and hosts a
31530 smaller collection of stats, geoms and axis guides.")
31531 (license license:expat)))