Subject: [bug#30570] [PATCH 09/16] gnu: Add Diversitree.

From: Leo Famulari <[email-masked]>
Date: Wed, 21 Feb 2018 14:35:13 -0500

* gnu/packages/bioinformatics.scm (r-diversitree): New variable.
---
 gnu/packages/bioinformatics.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 820bd84d6..3353565cf 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9,6 +9,7 @@
 ;;; Copyright © 2016, 2018 Raoul Bonnal <[email-masked]>
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <[email-masked]>
 ;;; Copyright © 2017 Arun Isaac <[email-masked]>
+;;; Copyright © 2018 Joshua Sierles, Nextjournal <[email-masked]>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -11886,3 +11887,34 @@ variable number of row and column annotations.  Loom also supports sparse
 graphs.  This library makes it easy to work with @file{.loom} files for
 single-cell RNA-seq data.")
     (license license:bsd-3)))
+
+(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+)))
-- 
2.16.1