R/site.pattern.R

In lliu1871/phybase: Basic functions for phylogenetic analysis

'site.pattern' <-
function(seq)
{
	numsite<-dim(seq)[2]
	numtaxa<-dim(seq)[1]
	
	result<-matrix(0,nrow=numtaxa,ncol=numsite)

	for(i in 2:numtaxa){
  		b<-rep(TRUE,numsite)
  		for(j in 1:(i-1)){
			b[seq[i,]==seq[j,]]<-FALSE			
			result[i,b]<-result[j,b]+1
   		}
	}

	result <- .sortmat(t(result),1:numtaxa)
	index<-1
    	number<-1
	numpattern<-rep(-1,numsite)
	pattern<-matrix(-1,nrow=numsite,ncol=numtaxa)

	for(i in 2:numsite){
		if(sum(abs(result[i,]-result[i-1,])) == 0){
			number<-number + 1
		}else{
			numpattern[index]<-number
			pattern[index,]<-result[i-1,]
			index<-index+1
			number<-1
		}
	}
	numpattern[index]<-number
	pattern[index,]<-result[numsite,]
	
    return(cbind(pattern[1:index,],numpattern[1:index]))
}

.sortmat <- function(mat, columns)
{
    m <- do.call("order", as.data.frame(mat[, columns]))
    mat[m, ]
}