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## The function to get allele diversity (q=1,2,3)
qD = function(x, q, ncode) {
# q=1,2,3
diveRsity::readGenepop
gp = ncode
file = readGenepop(x, gp, bootstrap = FALSE)
outfile = file$allele_freq
npops = file$npops
nloci = file$nloci
D = as.data.frame(matrix(data = 0, ncol = npops, nrow = nloci))
#requireNamespace("entropart")
entropart::Diversity
for (i in 1:nloci) {
for (j in 1:npops) {
D[i, j] = Diversity(outfile[[i]][, j], q, CheckArguments=FALSE) # n is the number of files, and i is loci, j is pops
}
}
rownames(D) = file$loci_names
colnames(D) = file$pop_names
return(D)
}
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