diss.dist: Calculate a distance matrix based on relative dissimilarity
Description
diss.dist uses the same discrete dissimilarity matrix utilized by the index
of association (see ia for details). By default, it returns a
distance reflecting the number of allelic differences between two
individuals. When percent = TRUE, it returns a ratio of the number of
observed differences by the number of possible differences. Eg. two
individuals who share half of the same alleles will have a distance of 0.5.
This function can analyze distances for any marker system.
logical. Should the distance be represented as a
percent? If set to FALSE (default), the distance will be reflected
as the number of alleles differing between to individuals. When set to
TRUE, These will be divide
mat
logical. Return a matrix object. Default set to
FALSE, returning a dist object. TRUE returns a matrix object.
Value
Pairwise distances between individuals present in the genind object.
Details
The distance calculated here is quite simple and goes by many names,
depending on its application. The most familiar name might be the Hamming
distance, or the number of differences between two strings.
# A simple example. Let's analyze the mean distance among populations of A.# euteiches.
data(Aeut)
mean(diss.dist(popsub(Aeut, 1)))
mean(diss.dist(popsub(Aeut, 2)))
mean(diss.dist(Aeut))