#function to claculate PD using a phylogeny file (phy) and a 
#community file in the phylocom format (columns: community name, 
#spp abundance, spp name). Make sure names in community file and #phylogeny match using 'match' function.

#Marc Cadotte
#Oct 2008


PDcalc<- function (phy,com) {
	
	Community<-unique(com[,1])#generate list of community IDs
	N.coms<-length(Community)
	species<-phy$tip.label

	#for output
	PD<-numeric(N.coms)
	sp.rich<-numeric(N.coms)

	for (i in 1:N.coms) {
		
		ID<-Community[i]#select community.ID
		myclade<-com[com[,1]==ID,3]		
		if (length(myclade)==1) {
			print(paste("Community",ID,"has a single species!"))
			}
		
		sub.tree<-subTree(phy,myclade)
		
		PD[i]<-sum(sub.tree$edge.length)
		sp.rich[i]<-length(sub.tree$tip.label)


		}#end iter loop

results <- data.frame(Community,PD,sp.rich)
return(results)
	}