richness.STRUCTURE.popgen: Estimate allelic richness for STRUCTURE clusters

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. It then uses resampling to generate distributions of rarefied allelic richness for each locus in each cluster.

Usage

richness.STRUCTURE.popgen(qmatrix, allele.dat, nclusters, nreps, NA.symbol,
  samp.snps, nsamp, ncores)

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
nreps	Integer. The number of times to repeat estimations. Default is 100
NA.symbol	The code used to represent missing allele data
samp.snps	Logical. If TRUE, a specified number of SNPs will be randomly sampled in each iteration to account for uncertainty and speed computations. Default is FALSE
nsamp	(optional) Integer. Number of SNPs to sample during each iteration. If samp.snps = TRUE and nsamp is not provided, default is to sample 50 (i.e. ncol(allele.dat)/2) in each iteration
ncores	(optional) Integer. Number of cores to split job across for parallel computing. Default is 1 (no parallelisation)

Value

Matrix of repeated estimates of allelic richness for each locus in each cluster

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