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gnu: Add r-pairwiseadonis.

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* gnu/packages/bioinformatics.scm (r-pairwiseadonis): New variable.

Change-Id: Idf7ad9efa3625bb60663f421ec79d0a69170e4dd
Signed-off-by: Andreas Enge <andreas@enge.fr>
This commit is contained in:
Mădălin Ionel Patrașcu 2024-09-04 13:37:40 +02:00 committed by Andreas Enge
parent 6c137dcf84
commit 2fb4ce5110
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1 changed files with 49 additions and 1 deletions
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gnu/packages/bioinformatics.scm
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@ -11,7 +11,7 @@
;;; Copyright © 2017, 2021, 2022, 2024 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
;;; Copyright © 2018-2023 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
;;; Copyright © 2018-2024 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
;;; Copyright © 2019, 2020, 2021, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com>
;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
@ -13155,6 +13155,54 @@ (define-public r-pairadise
(propagated-inputs (list r-doparallel r-foreach r-iterators r-nloptr))
(license license:expat)))
(define-public r-pairwiseadonis
;; There is no tag for version 0.4.1, nor is there a release archive.
(let ((commit "cb190f7668a0c82c0b0853927db239e7b9ec3e83")
(revision "1"))
(package
(name "r-pairwiseadonis")
;; The versioning scheme of this package is inconsistent, with versions
;; progressing from 0.21 to 0.3 and then to 0.4.1, which does not follow
;; a standard numerical order or convention (e.g., semantic versioning).
(version (git-version "0.4.1" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/pmartinezarbizu/pairwiseAdonis")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "11hl6qqmr5vns476921802y0qmb46i1jf0rf7xfkyswlh6xkcl99"))))
(properties `((upstream-name . "pairwiseAdonis")))
(build-system r-build-system)
(arguments
(list
#:phases
;; Move into the subdirectory containing the R package files
'(modify-phases %standard-phases
(add-after 'unpack 'move-to-subdir
(lambda _ (chdir "pairwiseAdonis"))))))
(propagated-inputs
(list r-cluster
r-permute
r-vegan))
(synopsis "Pairwise multilevel comparison using adonis")
(description
"This package implements two functions:
@itemize
@item @code{pairwise.adonis} is a wrapper function for multilevel pairwise
comparison using adonis2 from package vegan. The function returns adjusted
p-values using @code{p.adjust()}. It does not accept interaction between factors
neither strata.
@item @code{pairwise.adonis2} accepts a model formula like in adonis from vegan.
You can use interactions between factors and define strata to constrain
permutations. For pairwise comparison a list of unique pairwise combination of
factors is produced.
@end itemize")
(home-page "https://github.com/pmartinezarbizu/pairwiseAdonis")
(license license:gpl2+))))
(define-public pardre
(package
(name "pardre")