From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:4830:134:3::10]:37447) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1eoaCW-0005N6-HX for guix-patches@gnu.org; Wed, 21 Feb 2018 14:38:23 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1eoaBS-0007lW-Eq for guix-patches@gnu.org; Wed, 21 Feb 2018 14:37:12 -0500 Received: from debbugs.gnu.org ([208.118.235.43]:47009) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1eoaBS-0007kz-3g for guix-patches@gnu.org; Wed, 21 Feb 2018 14:36:06 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1eoaBR-0008Sx-SV for guix-patches@gnu.org; Wed, 21 Feb 2018 14:36:05 -0500 Subject: [bug#30570] [PATCH 09/16] gnu: Add Diversitree. Resent-Message-ID: From: Leo Famulari Date: Wed, 21 Feb 2018 14:35:13 -0500 Message-Id: In-Reply-To: <7597f2a5e819b04be0bd24566b4fcd7950abb5c1.1519241713.git.leo@famulari.name> References: <7597f2a5e819b04be0bd24566b4fcd7950abb5c1.1519241713.git.leo@famulari.name> MIME-Version: 1.0 In-Reply-To: <7597f2a5e819b04be0bd24566b4fcd7950abb5c1.1519241713.git.leo@famulari.name> References: <7597f2a5e819b04be0bd24566b4fcd7950abb5c1.1519241713.git.leo@famulari.name> Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+kyle=kyleam.com@gnu.org Sender: "Guix-patches" To: 30570@debbugs.gnu.org * 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 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice ;;; Copyright © 2017 Arun Isaac +;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; ;;; 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