Samples individuals from populations

This is a convenience function to prepare 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)

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

Value

returns a genlight object with nsample samples from each populations.

Details

This is convenience function to facilitate a bootstrap approach

Author

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

Examples

if (FALSE) { # \dontrun{
#bootstrap for 2 possums populations to check effect of sample size on fixed alleles
gl.set.verbosity(0)
pp <- possums.gl[1:60,]
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$nss[i], replace=TRUE)
pas <- gl.report.pa(dummy, plot.out = F)
res$fixed[i] <- pas$fixed[1]
}
boxplot(fixed ~ nss, data=res)
} # }