59 lines
3.2 KiB
Python
59 lines
3.2 KiB
Python
# Copyright 2013-2023 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.package 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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cran = "phytools"
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version("1.2-0", sha256="ba3c684118c0eaab4601b21988c553ce7ee019df1714d2ac8d4451075f843b86")
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version("1.0-3", sha256="bfe2aec6aae8235264c1494eee42be494fed81a676c6de9e39c57a6e3682b37d")
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version("1.0-1", sha256="b7bf5d35ec4205115112481f6761de3e276e6b086a3e5249621ad63aa23a1ac8")
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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:", type=("build", "run"), when="@0.7-70:")
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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-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-optimparallel", type=("build", "run"), when="@1.2-0:")
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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", type=("build", "run"), when="@:0.6-99")
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depends_on("r-gtools", type=("build", "run"), when="@0.6-99:0.7-70")
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