gl.sample: Samples individuals from populations

In dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Samples individuals from populations

Description

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

Details

This is convenience function to facilitate a bootstrap approach

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 base dartR: gl.sort()

Examples

## Not run: 
#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)

## End(Not run)

dartR documentation built on June 8, 2023, 6:48 a.m.