Mădălin Ionel Patrașcu wrote 6 months ago
(address . guix-patches@gnu.org)
c3895546de04902d8ea4379f2e07943479fde420.1725449860.git.madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioinformatics.scm (r-pairwiseadonis): New variable.
Change-Id: Idf7ad9efa3625bb60663f421ec79d0a69170e4dd
---
gnu/packages/bioinformatics.scm | 50 ++++++++++++++++++++++++++++++++-
1 file changed, 49 insertions(+), 1 deletion(-)
Toggle diff (72 lines)
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 <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")
base-commit: 7fa9df431e9423e2b79c8c520de1d0ef7aed910d
--
2.45.2