poppr (version 2.1.1)

genotype_curve: Produce a genotype accumulation curve

Description

GA curves are useful for determining the minimum number of loci necessary to discriminate between individuals in a population. This function will randomly sample loci without replacement and count the number of multilocus genotypes observed.

Usage

genotype_curve(gen, sample = 100, maxloci = 0L, quiet = FALSE,
  thresh = 1)

Arguments

gen

a genclone or genind object.

sample

an integer defining the number of times loci will be resampled without replacement.

maxloci

the maximum number of loci to sample. By default, maxloci = 0, which indicates that n - 1 loci are to be used. Note that this will always take min(n - 1, maxloci)

quiet

if FALSE (default), Progress of the iterations will be displayed. If TRUE, nothing is printed to screen as the function runs.

thresh

a number from 0 to 1. This will draw a line at that fraction of multilocus genotypes, rounded. Defaults to 1, which will draw a line at the maximum number of observable genotypes.

Value

• (invisibly) a matrix of integers showing the results of each randomization. Columns represent the number of loci sampled and rows represent an independent sample.

Examples

data(nancycats)
nan_geno <- genotype_curve(nancycats)
# With AFLP data, it is often necessary to include more markers for resolution
data(Aeut)
Ageno <- genotype_curve(Aeut)

# Many microsatellite data sets have hypervariable markers
data(microbov)
mgeno <- geotype_curve(microbov)

# This data set has been pre filtered
data(monpop)
mongeno <- genotype_curve(monpop)