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# Copyright 2013-2024 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.package 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("2.8", sha256="d6e46641f5b2b15720c8bb6c51d715220519dd8a6ba44171d13ef75bfa2eb6df")
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:")
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