aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorLeo Famulari <leo@famulari.name>2018-02-17 17:06:26 -0500
committerLeo Famulari <leo@famulari.name>2018-03-15 10:57:51 -0400
commit32cbbac11a8d8d656ed795865d88a6eeb3877dbe (patch)
tree4ce92d65b43caa64a97dbf71affbe85ef4854faf
parent799ad71bfc05f084d595ee11b608745a9c56eb10 (diff)
downloadgnu-guix-32cbbac11a8d8d656ed795865d88a6eeb3877dbe.tar
gnu-guix-32cbbac11a8d8d656ed795865d88a6eeb3877dbe.tar.gz
gnu: Add Diversitree.
* gnu/packages/bioinformatics.scm (r-diversitree): New variable.
-rw-r--r--gnu/packages/bioinformatics.scm32
1 files changed, 32 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 567dd2c24b..3d754bfbfa 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9,6 +9,7 @@
;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com>
;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -12855,3 +12856,34 @@ data of bisulfite experiments; it produces reports on aggregate methylation
and coverage and can be used to produce information on differential
methylation and segmentation.")
(license license:gpl3+)))
+
+(define-public r-diversitree
+ (package
+ (name "r-diversitree")
+ (version "0.9-10")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "diversitree" version))
+ (sha256
+ (base32
+ "0gh4rcrp0an3jh8915i1fsxlgyfk7njywgbd5ln5r2jhr085kpz7"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))
+ (propagated-inputs
+ `(("r-ape" ,r-ape)
+ ("r-desolve" ,r-desolve)
+ ("r-rcpp" ,r-rcpp)
+ ("r-suplex" ,r-subplex)))
+ (home-page "https://www.zoology.ubc.ca/prog/diversitree")
+ (synopsis "Comparative 'phylogenetic' analyses of diversification")
+ (description "This package contains a number of comparative \"phylogenetic\"
+methods, mostly focusing on analysing diversification and character evolution.
+Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
+and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
+Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
+include Markov models of discrete and continuous trait evolution and constant
+rate speciation and extinction.")
+ (license license:gpl2+)))