graph4lg
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., 2021) <doi:10.1016/j.simpa.2021.100065>, 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' (Csardiet 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>. Recent updates introducemultiple habitat graph functionalities (as described by Savary et al., 2024)<doi:10.1007/s10980-024-01947-4>.
- adegenet: a R package for the multivariate analysis of genetic markers
- Application of network methods for understanding evolutionary dynamics in discrete habitats
- Graphab: An application for modeling and managing ecological habitat networks
- Isolation-by-distance in landscapes: considerations for landscape genetics
- Multiple habitat graphs: how connectivity brings forth landscape ecological processes
- Population Graphs: the graph theoretic shape of genetic structure
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