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Change-Id: Idf7ad9efa3625bb60663f421ec79d0a69170e4dd --- gnu/packages/bioinformatics.scm | 50 ++++++++++++++++++++++++++++++++- 1 file changed, 49 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4653360792..0206ebe1a3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11,7 +11,7 @@ ;;; Copyright © 2017, 2021, 2022, 2024 Arun Isaac ;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; Copyright © 2018 Gábor Boskovits -;;; Copyright © 2018-2023 Mădălin Ionel Patrașcu +;;; Copyright © 2018-2024 Mădălin Ionel Patrașcu ;;; Copyright © 2019, 2020, 2021, 2023 Maxim Cournoyer ;;; Copyright © 2019 Brian Leung ;;; Copyright © 2019 Brett Gilio @@ -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") base-commit: 7fa9df431e9423e2b79c8c520de1d0ef7aed910d -- 2.45.2