STRUCTURE.popgen: Calculate population genetics parameters

In nicholasjclark/STRUCTURE.popgen: Population genetics calculations using STRUCTURE assignment probabilities

Description

This function randomly assigns individuals to clusters using STRUCTURE assignment probabilities provided in the qmatrix. The qmatrix must have column 'ind', which stores individual ids.

Usage

STRUCTURE.popgen(qmatrix = NULL, allele.dat, nclusters, stat, NA.symbol,
  samp.snps, nsamp)

Arguments

qmatrix	Dataframe. The STRUCTURE qmatrix, with individuals in column 'ind'
allele.dat	Dataframe. Raw allele data (sep = '/')
nclusters	Integer. The number of clusters identified by STRUCTURE
stat	The population genetics statistic to return. Must be one of the following: 'ind.dist', 'summary', 'allele.freqs', 'heterozygosity', 'richness','fis','fst'. Note that statistics 'ind.dist','summary' and 'heterozygosity' do not require a qmatrix, while statistics 'allele.freqs', 'richness','fis' and 'fst' must have a supplied qmatrix.
NA.symbol	The code used to represent missing allele data
samp.snps	Logical. If TRUE, a specified number SNPs will be randomly sampled in each iteration to account for uncertainty and speed computations. Default is FALSE
nsamp	(optional) Integer of SNPs to sample during each iteration

Value

Summaries based on the chosen population genetic statistic

nicholasjclark/STRUCTURE.popgen documentation built on May 25, 2019, 10:38 p.m.