graph4lg: Build Graphs for Landscape Genetics Analysis

Build graphs for landscape genetics analysis. This set of functions can be used to import and convert spatial and genetic data initially in different formats, import landscape graphs created with 'GRAPHAB' software (Foltete et al., 2012) <doi:10.1016/j.envsoft.2012.07.002>, make diagnosis plots of isolation by distance relationships in order to choose how to build genetic graphs, create graphs with a large range of pruning methods, weight their links with several genetic distances, plot and analyse graphs, compare them with other graphs. It uses functions from other packages such as 'adegenet' (Jombart, 2008) <doi:10.1093/bioinformatics/btn129> and 'igraph' (Csardi et Nepusz, 2006) <https://igraph.org/>. It also implements methods commonly used in landscape genetics to create graphs, described by Dyer et Nason (2004) <doi:10.1111/j.1365-294X.2004.02177.x> and Greenbaum et Fefferman (2017) <doi:10.1111/mec.14059>, and to analyse distance data (van Strien et al., 2015) <doi:10.1038/hdy.2014.62>.

Version: 1.8.0
Depends: R (≥ 3.1.0)
Imports: adegenet, ggplot2, stringr, igraph, stats, spatstat.geom, spatstat.linnet, Matrix, vegan, utils, methods, pegas, MASS, tidyr, sp, sf, hierfstat, rappdirs, gdistance, raster, foreign, ecodist, Rdpack
Suggests: knitr, rmarkdown
Published: 2023-01-30
DOI: 10.32614/CRAN.package.graph4lg
Author: Paul Savary ORCID iD [aut, cre], Gilles Vuidel ORCID iD [ctb], Tyler Rudolph [ctb], Alexandrine Daniel [ctb]
Maintainer: Paul Savary <psavary at protonmail.com>
License: GPL-2
NeedsCompilation: no
Citation: graph4lg citation info
Materials: README NEWS
CRAN checks: graph4lg results

Documentation:

Reference manual: graph4lg.pdf
Vignettes: 2 - Genetic graph construction and analysis with 'graph4lg'
4 - Landscape and genetic graph comparison with 'graph4lg'
1 - Landscape and genetic data processing with 'graph4lg'
3 - Landscape graph construction and analysis with Graphab and 'graph4lg'

Downloads:

Package source: graph4lg_1.8.0.tar.gz
Windows binaries: r-devel: graph4lg_1.8.0.zip, r-release: graph4lg_1.8.0.zip, r-oldrel: graph4lg_1.8.0.zip
macOS binaries: r-release (arm64): graph4lg_1.8.0.tgz, r-oldrel (arm64): graph4lg_1.8.0.tgz, r-release (x86_64): graph4lg_1.8.0.tgz, r-oldrel (x86_64): graph4lg_1.8.0.tgz
Old sources: graph4lg archive

Linking:

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