dist.codom: Calculate distance between individual for co-dominant locus
Description
This function calculates the distance between individuals in a genind
object based on their genotypes.
Specifically, the simple metric of Kosman and Leonard (2005) in which
distance is calculated as a propotion of shared alleles at each locus.
Usage
dist.codom(x, matrix = TRUE, global = TRUE, na.rm = TRUE)
Arguments
x
genind object (from package adegenet)
matrix
boolean: if TRUE return matrix (dist object if FALSE)
global
boolean: if TRUE, return a single global estimate based on all
loci. If FALSE return a list of matrices for each locus.
if FALSE
na.rm
boolean: if TRUE remove individuals with NAs
Value
either a list of distance matrices, one for each locus or a single
matrix containing the mean distance between individuals across all lociDropped for each distance matrix and object of class "na.action"
containing indices to those indivudals in the genind object which where
omitted due to having NAs
References
Kosman E., Leonard, K.J. Similarity coefficients for molecular markers in studies of genetic relationships between individuals for haploid
diploid, and polyploid species. Molecular Ecology. 14: 415-424