R/AitTrans.R

In Pstat: Assessing Pst Statistics

AitTrans <-
function(data,Rp=0,Ri=0){
nb.var=dim(data)[2]-1;

# function removing unwanted individuals or populations 

dat.rem.ind.pop<-function(data,ind=0,pop=0){
data=as.data.frame(data);
# function removing unwanted individuals
dat.rem.ind<-function(dat,ind){
nb.rem.ind=length(ind);
nb.ind=dim(dat)[1];
for(i in 1:nb.rem.ind) dat=dat[row.names(dat)[1:(nb.ind-i+1)]!=ind[i],];
return(dat)};
# function removing unwanted populations
dat.rem.pop<-function(dat,pop){
nb.rem.pop=length(pop);
for(i in 1:nb.rem.pop) dat=dat[dat[,1]!=pop[i],]; 
return(dat);}
if (ind[1]!=0) data=dat.rem.ind(data,ind);
if (pop[1]!=0) data=dat.rem.pop(data,pop);
return(data);}

# function returning the number of values different from Na in a selected row 

nonNa.row<-function(data,row){
nb.na=0;
for (i in 1:nb.var) if (is.na(data[row,i+1])) nb.na=nb.na+1;
return(nb.var-nb.na);}

data=dat.rem.ind.pop(data,ind=Ri,pop=Rp);
nb.ind=dim(data)[1];
cor.val=rep(0,nb.ind);
for (i in 1:nb.ind) 
{cor.val[i]=1/(nonNa.row(data,i))*sum(log(data[i,-1],base=10),na.rm=TRUE);
for (j in 1:nb.var) data[i,(j+1)]=log(data[i,(j+1)],base=10)-cor.val[i];}
return(data);}