Build Graphs for Landscape Genetics Analysis
Add attributes to the nodes of a graph
Check whether the option 'nomerge' was used when building the landscap...
Compare two correlation coefficients obtained from different sample si...
Compute modules from a graph by maximising modularity
Compute graph-theoretic metrics from a graph at the node level
Fit a model to convert cost-distances into Euclidean distances
Convert degrees to radians
Convert an edge-list data.frame into a pairwise matrix
Calculate the Great-Circle distance between two points using the Harve...
Calculate the Great-Circle distance between two points using the Spher...
Calculate the Great-Circle distance between two points using the Vince...
Compute the Great Circle distance between two points
Compute the distance at which the correlation between genetic distance...
Prune a graph using the 'percolation threshold' method
Create an independence graph of genetic differentiation from genetic d...
Create a graph of genetic differentiation using a link weight threshol...
Create a graph of genetic differentiation with a specific topology
Convert a GENEPOP file into a genind object
Convert a genind object into a GENEPOP file
Convert a genind object into a STRUCTURE file
Download Graphab if not present on the user's machine
Get linkset computed in the Graphab project
Get cost values associated with a linkset in a Graphab project
Get metrics computed at the node in the Graphab project
Get unique raster codes from a Graphab project
Compute Gini coefficient from a numeric vector
Compare the partition into modules of two graphs
Compare the local properties of the nodes from two graphs
Create a graph with a minimum planar graph topology
Visualize the topological differences between two spatial graphs on a ...
Convert a graph into a edge list data.frame
Export a spatial graph to shapefile layers
Compute an index comparing graph topologies
Computes custom capacities of patches in the Graphab project
Computes corridors from least-cost paths already computed in the Graph...
Create a graph in the Graphab project
Creates a raster with interpolated connectivity metric values from met...
Create a link set in the Graphab project
Compute connectivity metrics from a graph in the Graphab project
Create modules from a graph in the Graphab project
Add a point set to the Graphab project
Create a Graphab project
Describe the objects of a Graphab project
Create landscape graphs from Graphab link set
Convert a file from gstudio or popgraph into a genind object
Compute the harmonic mean of a numeric vector
Compute dispersal kernel parameters
Compare two link sets created in a Graphab project
Convert a loci object into a genind object
Compute cost distances between points on a raster
Compute a pairwise matrix of genetic distances between populations
Compute Euclidean geographic distances between points
Compute a pairwise genetic distance matrix between populations using B...
Compute a pairwise FST matrix between populations
Vector of custom colors
Extract patch areas from a categorical raster
Plot graphs
Plot histograms of link weights
Compute population-level genetic indices
Compute population-level rarefied genetic indices with ADZE software
Convert a pairwise matrix into an edge-list data.frame
Reorder the rows and columns of a symmetric matrix
Sample points or patches on a categorical raster layer
Scaling function
Plot scatterplots of genetic distance vs landscape distance
Plot scatterplots of distances to visualize the graph pruning intensit...
Convert a file in STRUCTURE format into a genind object
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>.