Build Graphs for Landscape Genetics Analysis


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Documentation for package ‘graph4lg’ version 0.3.0

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add_nodes_attr Add attributes to the nodes of a graph
compar_r_fisher Compare two correlation coefficients obtained from different sample sizes
convert_cd Fit a model to convert cost-distances into Euclidean distances
data_pc_genind data_pc_genind genetic dataset
data_pc_gpop data_pc_gpop genetic dataset
data_pc_gstud data_pc_gstud genetic dataset
data_pc_loci data_pc_loci genetic dataset
data_pc_str data_pc_str 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
graphab_to_igraph Import landscape graphs from GRAPHAB software
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_gen_dist Compute a pairwise matrix of genetic distances between populations
mat_geo_dist Compute Euclidean geographic distances between points
mat_pw_dps Compute a pairwise genetic distance matrix between populations using Bowcock et al. (1994) formula
mat_pw_d_j Compute a pairwise Jost's D matrix between populations
mat_pw_fst Compute a pairwise FST matrix between populations
mat_pw_gst Compute a pairwise G'ST matrix between populations
plot_graph_lg Plot graphs
plot_graph_modul Plot the graphs making visible their partition into modules
plot_w_hist Plot histograms of link weights
pop_gen_index Compute population-level genetic indices
pts_pop_pc pts_pop_pc : details on Setophaga plumbea 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