R/is.rootedtree.R

In lliu1871/phybase: Basic functions for phylogenetic analysis

'is.rootedtree' <-
function(tree)
{
	if(is.character(tree)){
		string <- unlist(strsplit(tree, NULL))
        leftpar<-which(string=="(")
        rightpar<-which(string==")")
        
		comma<-which(string==",") 
        if(length(leftpar) != length(leftpar))
     			stop("The number of left parenthesis is NOT equal to the number of right parenthesis")
        if(length(leftpar) == length(comma))
			rooted<-TRUE
        else if(length(leftpar) == (length(comma)-1))
			rooted<-FALSE
        else
			stop("The number of comma in the tree string is wrong!")
    }else{
		rooted<-TRUE
		if(tree[.rootoftree(tree),1] == -8)
			rooted<-FALSE
    }
    return(rooted)
}

.rootoftree <- function (nodematrix)
{
    if(sum(nodematrix[,1]<0)>1)
    stop("more than two roots!")
    nodes<-sum((nodematrix[,1]<0)*(1:length(nodematrix[,1])))
    return(nodes)
}