# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)

from spack import *


class RCorhmm(RPackage):
    """Hidden Markov Models of Character Evolution.

    Fits hidden Markov models of discrete character evolution which allow
    different transition rate classes on different portions of a phylogeny.
    Beaulieu et al (2013) <doi:10.1093/sysbio/syt034>."""

    cran = "corHMM"

    version('2.7', sha256='0d54ba0f6b3f884343bcc26919d8febc05efb0b739cb962d3072ca0bc0ce270a')
    version('2.6', sha256='726de9707ede8ef447915171a3abe1003a0e42fe8e17eb440442cac9adf8cdcf')
    version('1.22', sha256='d262fa1183eab32087afb70f1789fabae6fb49bec01d627974c54a088a48b10d')

    depends_on('r-ape', type=('build', 'run'))
    depends_on('r-nloptr', type=('build', 'run'))
    depends_on('r-gensa', type=('build', 'run'))
    depends_on('r-expm', type=('build', 'run'))
    depends_on('r-numderiv', type=('build', 'run'))
    depends_on('r-corpcor', type=('build', 'run'))
    depends_on('r-mass', type=('build', 'run'), when='@2.6:')
    depends_on('r-nnet', type=('build', 'run'))
    depends_on('r-phangorn', type=('build', 'run'))
    depends_on('r-viridis', type=('build', 'run'), when='@2.6:')
    depends_on('r-rmpfr', type=('build', 'run'))
    depends_on('r-igraph', type=('build', 'run'), when='@2.6:')
    depends_on('r-phytools', type=('build', 'run'), when='@2.6:')
