# Build Graphs for Landscape Genetics Analysis

## Documentation for package ‘graph4lg’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## 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_metric | Get metrics computed at the node in the Graphab project
graphab_graph | Create a graph 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_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