R/qD.R

In xinghuq/HierD: R package for calculating hierarchical diversity across metrixs and scales, from genes to ecosystem

## The function to get allele diversity (q=1,2,3)

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