Calculates a similarity (distance) matrix for individuals on the proportion of shared alleles

This script calculates an individual based distance matrix. It uses an C++ implementation, so package Rcpp needs to be installed and it is therefore really fast (once it has compiled the function after the first run).

Usage

gl.propShared(x)

Arguments

x

Name of the genlight containing the SNP genotypes [required].

Author

Bernd Gruber (Post to https://groups.google.com/d/forum/dartr)

Examples

#takes some time at the first run of the function...
if (FALSE) {
res <- gl.propShared(bandicoot.gl)
res[1:5,1:7] #show only a small part of the matrix
}