R/sptree.maxtree.R

In lliu1871/phybase: Basic functions for phylogenetic analysis

`sptree.maxtree` <-
function(genetreevector,spname,taxaname,species.structure)
{
	ntree<-length(genetreevector)
    nodes1<-read.tree.nodes(genetreevector[1],taxaname)$nodes
    nspecies<-length(spname)
	ntaxa<-length(taxaname)

	#calculate pairwise distance
    dist<-dist.taxa(nodes1,ntaxa)
    for(i in 2:ntree){
		nodes1<-read.tree.nodes(genetreevector[i],taxaname)$nodes
		dist1<-dist.taxa(nodes1,ntaxa)
		dist<-pmin(dist,dist1)
    }
	
	spdist1<-matrix(0,nrow=nspecies,ncol=ntaxa)
	for(i in 1:nspecies){
			taxa<-species.structure[i,]*(1:ntaxa)
			taxa<-taxa[taxa>0]
			if(length(taxa)>1)  spdist1[i,]<-apply(dist[taxa,],2,min)
			else spdist1[i,]<-dist[taxa,]
    }

	spdist<-matrix(0,nrow=nspecies,ncol=nspecies)
	for(i in 1:nspecies){
			taxa<-species.structure[i,]*(1:ntaxa)
			taxa<-taxa[taxa>0]
			if(length(taxa)>1)  spdist[,i]<-apply(spdist1[,taxa],1,min)
			else spdist[,i]<-spdist1[,taxa]
    }
	dist<-spdist/2
	treestr<-tree.upgma(dist,spname,method="min")$treestr

	return(treestr)
}