View source: R/gen_graph_topo.R
gen_graph_topo  R Documentation 
The function constructs a genetic graph with a specific topology from genetic and/or geographical distance matrices
gen_graph_topo(mat_w, mat_topo = NULL, topo = "gabriel", k = NULL)
mat_w 
A symmetric (pairwise) 
mat_topo 
(optional) A symmetric (pairwise) distance 
topo 
Which topology does the created graph have?

k 
(if 'topo = 'knn”) An integer which indicates the number of nearest neighbors considered to create the Knearest neighbor graph. k must be lower than the total number of nodes minus 1. 
If 'mat_topo' is not defined, 'mat_w' is used for the pruning. Matrices 'mat_w' and 'mat_topo' must have the same dimensions and the same rows' and columns' names. Values in 'mat_topo' matrix must be positive. Negative values from 'mat_w' are transformed into zeros. The function works only for undirected graphs. Note that the topology 'knn' works best when 'mat_topo' contains distance values from a continuous value range, thereby avoiding equal distances between a node and the others. are more than k nodes located at distances in the kth smallest distances If dist objects are specified, it is assumed that colnames and row.names of mat_w and mat_topo refer to the same populations/locations.
A graph object of class igraph
P. Savary
gabriel1969newgraph4lg
mat_w < mat_gen_dist(x = data_ex_genind, dist = 'DPS') suppressWarnings(mat_topo < mat_geo_dist(pts_pop_ex, ID = "ID", x = "x", y = "y")) mat_topo < mat_topo[row.names(mat_w), colnames(mat_w)] graph < gen_graph_topo(mat_w, mat_topo, topo = "mst")
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