[R-sig-genetics] Bootstrapping of genind objects

[Bhuller, Ravneet]

Dear Members,

I have done the following to estimate mean allelic richness for each of the sampled genind objects:


# Subset the genind object by population

obj<- seppop(niger.data.genind)


# Sample and repool the populations to create a list of genind objects

repooled <- lapply(seq(2, nPop(niger.data.genind), by=1), function(n) repool(obj[sample(nPop(niger.data.genind), n, replace= FALSE)]))


# Calculate mean(allel.rich(e)$mean.richness for each genind object 

lapply(repooled, function(e) mean(allel.rich(e)$mean.richness, na.rm = TRUE))


But, I also want to estimate variances and confidence intervals by bootstrapping the above samples with 10,000 repetitions. I have tried my best to solve it with chao_bootstrap() and replicate() but it is not working. Please if someone can guide me how to bootstrap the above samples with 10,000 repetitions.

Many thanks for your help.

Kind regards,

Rav