R/ReistTrans.R

In Pstat: Assessing Pst Statistics

ReistTrans <-
function(data,reg,Rp=0,Ri=0){

# 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 one of the quantitative variables transformed following Reist's transformation,  the regressor being previously chosen by the user

Reitra.va<-function(dat,clm,re){
dat=dat[is.finite(dat[,re]),];
log.dat=dat;
mea=mean(dat[is.finite(dat[,clm]),re]);
log.dat[,clm]=log(dat[,clm],base=10);
log.dat[,re]=log(dat[,re],base=10);
mea.clm=mean(log.dat[is.finite(log.dat[,clm]),clm],na.rm=TRUE);
mea.reg=mean(log.dat[is.finite(log.dat[,clm]),re],na.rm=TRUE);
a=sum((log.dat[is.finite(log.dat[,clm]),re]-mea.reg)*log.dat[is.finite(log.dat[,clm]),clm])/sum((log.dat[is.finite(log.dat[,clm]),re]-mea.reg)*(log.dat[is.finite(log.dat[,clm]),re]-mea.reg));
dat[,clm]=log.dat[,clm]-a*(log.dat[,re]-log(mea,base=10));
return(dat);}

# to convert reg into a numerical value

nb.var=dim(data)[2]-1; 
for (i in 1:nb.var) {if (names(data)[i+1]==reg) reg=i};
if (is.numeric(reg)==FALSE) return("reg value does not exist!");

# to display the output

data=dat.rem.ind.pop(data,ind=Ri,pop=Rp);
if (reg==1) for (i in 2:nb.var) data=Reitra.va(data,clm=i+1,re=2)
else {for (i in 2:reg) data=Reitra.va(data,clm=i,re=reg+1); 
if (reg<nb.var) for (j in (reg+1):nb.var) data=Reitra.va(data,clm=j+1,re=reg+1);};
return(data[-(reg+1)]);}