56 lines
3.0 KiB
Python
56 lines
3.0 KiB
Python
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack import *
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class RPhytools(RPackage):
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"""Phylogenetic Tools for Comparative Biology (and Other Things)
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A wide range of functions for phylogenetic analysis. Functionality is
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concentrated in phylogenetic comparative biology, but also includes
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numerous methods for visualizing, manipulating, reading or writing, and
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even inferring phylogenetic trees and data. Included among the functions in
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phylogenetic comparative biology are various for ancestral state
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reconstruction, model-fitting, simulation of phylogenies and data, and
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multivariate analysis. There are a broad range of plotting methods for
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phylogenies and comparative data which include, but are not restricted to,
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methods for mapping trait evolution on trees, for projecting trees into
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phenotypic space or a geographic map, and for visualizing correlated
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speciation between trees. Finally, there are a number of functions for
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reading, writing, analyzing, inferring, simulating, and manipulating
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phylogenetic trees and comparative data not covered by other packages. For
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instance, there are functions for randomly or non-randomly attaching
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species or clades to a phylogeny, for estimating supertrees or consensus
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phylogenies from a set, for simulating trees and phylogenetic data under a
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range of models, and for a wide variety of other manipulations and analyses
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that phylogenetic biologists might find useful in their research."""
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homepage = "http://github.com/liamrevell/phytools"
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url = "https://cloud.r-project.org/src/contrib/phytools_0.6-60.tar.gz"
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list_url = "https://cloud.r-project.org/src/contrib/Archive/phytools/"
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version('0.7-70', sha256='e3432c3b006e5cc6f1292bebd81ebc20044edf1f56c3d27a3497f738eb99f0d3')
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version('0.6-99', sha256='2ef532cba77c5f73803bd34582bef05709705311a0b50e42316e69944567390f')
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version('0.6-60', sha256='55cad759510d247ebbf03a53a46caddadd3bf87584ccf7fcd6dd06d44516b377')
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depends_on('r@3.2.0:', type=('build', 'run'))
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depends_on('r@3.5.0:', when='@0.7-70:', type=('build', 'run'))
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depends_on('r-ape@4.0:', type=('build', 'run'))
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depends_on('r-maps', type=('build', 'run'))
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depends_on('r-clustergeneration', type=('build', 'run'))
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depends_on('r-coda', type=('build', 'run'))
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depends_on('r-combinat', type=('build', 'run'))
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depends_on('r-expm', type=('build', 'run'))
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depends_on('r-gtools', when='@0.6-99:', type=('build', 'run'))
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depends_on('r-mass', type=('build', 'run'))
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depends_on('r-mnormt', type=('build', 'run'))
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depends_on('r-nlme', type=('build', 'run'))
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depends_on('r-numderiv', type=('build', 'run'))
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depends_on('r-phangorn@2.3.1:', type=('build', 'run'))
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depends_on('r-plotrix', type=('build', 'run'))
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depends_on('r-scatterplot3d', type=('build', 'run'))
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depends_on('r-animation', when='@:0.6-99', type=('build', 'run'))
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