Build Graphs for Landscape Genetics Analysis

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Documentation for package ‘graph4lg’ version 1.8.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

add_nodes_attr	Add attributes to the nodes of a graph
compute_graph_modul	Compute modules from a graph by maximising modularity
compute_node_metric	Compute graph-theoretic metrics from a graph at the node level
convert_cd	Fit a model to convert cost-distances into Euclidean distances
data_ex_genind	data_ex_genind genetic dataset
data_ex_gstud	data_ex_gstud genetic dataset
data_ex_loci	data_ex_loci genetic dataset
data_simul_genind	data_simul_genind genetic dataset
data_tuto	data_tuto : data used to generate the vignette
df_to_pw_mat	Convert an edge-list data.frame into a pairwise matrix
dist_max_corr	Compute the distance at which the correlation between genetic distance and landscape distance is maximal
genepop_to_genind	Convert a GENEPOP file into a genind object
genind_to_genepop	Convert a genind object into a GENEPOP file
gen_graph_indep	Create an independence graph of genetic differentiation from genetic data of class genind
gen_graph_thr	Create a graph of genetic differentiation using a link weight threshold
gen_graph_topo	Create a graph of genetic differentiation with a specific topology
get_graphab	Download Graphab if not present on the user's machine
get_graphab_linkset	Get linkset computed in the Graphab project
get_graphab_linkset_cost	Get cost values associated with a linkset in a Graphab project
get_graphab_metric	Get metrics computed at the node in the Graphab project
get_graphab_raster_codes	Get unique raster codes from a Graphab project
graphab_capacity	Computes custom capacities of patches in the Graphab project
graphab_corridor	Computes corridors from least-cost paths already computed in the Graphab project
graphab_graph	Create a graph in the Graphab project
graphab_interpol	Creates a raster with interpolated connectivity metric values from metrics already computed in the Graphab project
graphab_link	Create a link set in the Graphab project
graphab_metric	Compute connectivity metrics from a graph in the Graphab project
graphab_modul	Create modules from a graph in the Graphab project
graphab_pointset	Add a point set to the Graphab project
graphab_project	Create a Graphab project
graphab_project_desc	Describe the objects of a Graphab project
graphab_to_igraph	Create landscape graphs from Graphab link set
graph_modul_compar	Compare the partition into modules of two graphs
graph_node_compar	Compare the local properties of the nodes from two graphs
graph_plan	Create a graph with a minimum planar graph topology
graph_plot_compar	Visualize the topological differences between two spatial graphs on a map
graph_topo_compar	Compute an index comparing graph topologies
graph_to_df	Convert a graph into a edge list data.frame
graph_to_shp	Export a spatial graph to shapefile layers
gstud_to_genind	Convert a file from 'gstudio' or 'popgraph' into a genind object
g_percol	Prune a graph using the 'percolation threshold' method
kernel_param	Compute dispersal kernel parameters
loci_to_genind	Convert a loci object into a genind object
mat_cost_dist	Compute cost distances between points on a raster
mat_gen_dist	Compute a pairwise matrix of genetic distances between populations
mat_geo_dist	Compute Euclidean geographic distances between points
plot_graph_lg	Plot graphs
plot_w_hist	Plot histograms of link weights
pop_gen_index	Compute population-level genetic indices
pts_pop_ex	pts_pop_ex : details on simulated populations
pts_pop_simul	pts_pop_simul : details on simulated populations
pw_mat_to_df	Convert a pairwise matrix into an edge-list data.frame
reorder_mat	Reorder the rows and columns of a symmetric matrix
scatter_dist	Plot scatterplots of genetic distance vs landscape distance
scatter_dist_g	Plot scatterplots of distances to visualize the graph pruning intensity
structure_to_genind	Convert a file in STRUCTURE format into a genind object