gl.sample {dartR.base}

Samples individuals from populations

Description

A function to subsample individuals in a genlight object

Usage

gl.sample(
  x,
  nsample = min(table(pop(x))),
  replace = TRUE,
  onepop = FALSE,
  verbose = NULL
)

Arguments

x

genlight object containing SNP/silicodart genotypes

nsample

the number of individuals that should be sampled

replace

a switch to sample by replacement (default).

onepop

switch to ignore population settings of the genlight object and sample from all individuals disregarding the population definition. [default FALSE].

verbose

set verbosity

Details

This is convenience function to facilitate a bootstrap approach

This function is often used to support a bootstrap approach in dartR. For a bootstrap approach it is often desirable to sample a defined number of individuals for each of the populations in a genlight object and then calculate a certain quantity for that subset (redo a 1000 times)

Value

returns a genlight object with nsample samples from each populations.

Author(s)

Bernd Gruber (Post to https://groups.google.com/d/forum/dartr)

See Also

Other data manipulation: gl.define.pop(), gl.drop.ind(), gl.drop.loc(), gl.drop.pop(), gl.edit.recode.pop(), gl.impute(), gl.join(), gl.keep.ind(), gl.keep.loc(), gl.keep.pop(), gl.make.recode.ind(), gl.merge.pop(), gl.reassign.pop(), gl.recode.ind(), gl.recode.pop(), gl.rename.pop(), gl.sim.genotypes(), gl.sort(), gl.subsample.ind(), gl.subsample.loc()

Examples

#bootstrap for 2 possums populations to check effect of sample size on fixed alleles
gl.set.verbosity(0)
pp <- possums.gl[c(1:30,91:120),]
nrep <- 1:10
nss <- seq(1,10,2)
res <- expand.grid(nrep=nrep, nss=nss)
for (i in 1:nrow(res)) {
dummy <- gl.sample(pp, nsample=res$nss[i], replace=TRUE)
dummy <- gl.compliance.check(dummy)
pas <- gl.report.pa(dummy, plot.display= FALSE)
res$fixed[i] <- pas$fixed[1]
}
boxplot(fixed ~ nss, data=res)