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# Copyright 2013-2023 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 RAdegenet(RPackage):
"""Exploratory Analysis of Genetic and Genomic Data.
Toolset for the exploration of genetic and genomic data. Adegenet provides
formal (S4) classes for storing and handling various genetic data,
including genetic markers with varying ploidy and hierarchical population
structure ('genind' class), alleles counts by populations ('genpop'), and
genome-wide SNP data ('genlight'). It also implements original multivariate
methods (DAPC, sPCA), graphics, statistical tests, simulation tools,
distance and similarity measures, and several spatial methods. A range of
both empirical and simulated datasets is also provided to illustrate
various methods."""
cran = "adegenet"
license("GPL-2.0-or-later")
version("2.1.10", sha256="ab62780ac1dd575d01f3e0869b34728a74b2ca2eaeeccb2f520007e9a578b163")
version("2.1.8", sha256="80d72c3eefe077723dec91c98b7d46815b9659ab7196581d18b6e9d6c27f5025")
version("2.1.6", sha256="7823de4933634cb887481fe4b12cf2faacbaa1b4b66939584d10fcb7ce2da26b")
version("2.1.5", sha256="e4eee8c41dae6cb0841db74ec6f9adb2580873f3e313471f37df58324c1857f2")
version("2.1.3", sha256="0790114ecb22642683b5be1f4b3a6a49856e06dc2f9e21b9cba4390c2257f6c6")
version("2.1.1", sha256="3043fe5d731a38ff0e266f090dcda448640c3d0fd61934c76da32d082e5dce7a")
version("2.1.0", sha256="7ee44061002b41164bbc09256307ab02e536f4f2ac03f36c7dc8f85f6af4639a")
version("2.0.1", sha256="7eddf46e64f680d54d034b68c50900d9bd5bc2e08309d062e230121b7460bb10")
depends_on("r@2.14:", type=("build", "run"))
depends_on("r-ade4", type=("build", "run"))
depends_on("r-mass", type=("build", "run"))
depends_on("r-igraph", type=("build", "run"))
depends_on("r-ape", type=("build", "run"))
depends_on("r-shiny", type=("build", "run"))
depends_on("r-ggplot2", type=("build", "run"))
depends_on("r-seqinr", type=("build", "run"))
depends_on("r-boot", type=("build", "run"))
depends_on("r-reshape2", type=("build", "run"))
depends_on("r-dplyr@0.4.1:", type=("build", "run"))
depends_on("r-vegan", type=("build", "run"))
depends_on("r-spdep", type=("build", "run"), when="@:2.1.3")
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