divSimCo: Similarity coefficients for co-dominant diploid genenotype...

In kkeenan02/diveRsity: A Comprehensive, General Purpose Population Genetics Analysis Package

Description

Calculation of similarity coefficients for co-dominant genotype data, following Kosman and Leonard, (2005).

Usage

divSimCo(infile = NULL, loci = FALSE, boots = 0)

Arguments

infile	Specifying the name of the ‘genepop’ (Rousset, 2008) file from which the statistics are to be calculated This file can be in either the 3 digit of 2 digit format. See http://genepop.curtin.edu.au/help_input.html for detail on the genepop file format.
loci	A logical argument, specifying whether similarity matrices for each locus should be calculated. If FALSE, only a global similarity matrix is given.
boots	An integer, specifying the number of bootstrapped matrices to generate. Loci are resampled with replacement.

Details

Similarity coefficients are calculated according to Kosman and Leonard, (2005). Multi-locus values are calculated from all loci without missing data.

Value

A list containing either one (global) if loci = FALSE, or two elements (global and loci) if loci = TRUE.

global	A pairwise matrix of multilocus similarity coefficients.
loci	A list of pairwise matrices of locus similarity coefficients.

Author(s)

Kevin Keenan

References

Kosman E, Leonard K (2005) Similarity coefficients for molecular markers in studies of genetic relationships between individuals for haploid, diploid, and polyploid species. Molecular ecology, 14, 415-424.

kkeenan02/diveRsity documentation built on May 20, 2019, 10:43 a.m.