library(ape)

trees<-read.tree("...") # read tree file containing multiple (2) trees - read.tree uses Newick, use the read.nexus command for nexus

sp.list<-read.table("...",header=F)#read in table of species names and community ID (from 1 to number of communities) - no header

attach(sp.list)

cladeID<-unique(sp.list[,2])#generate list of community IDs
communities<-length(cladeID)

PD<-numeric(communities)
sp.rich<-numeric(communities)

iter<-length(trees)# number of trees in file

output<- data.frame()

for (j in 1:iter){
solo.tree<-trees[[j]]#select one tree at a time from file

tree.iter<-j

species<-as.list(solo.tree$tip.label)#list of species in tree


	for (iter in 1:communities) {#run for all species lists

	ID<-cladeID[iter]#select community.ID
	myclade<-sp.list[sp.list[,2]==ID,]#get list of species in that 	community
	dropme<-species[!species %in% myclade[,1]]#species in tree but 	not in community
	sub.tree<-drop.tip(solo.tree,dropme)
	PD[iter]<-sum(sub.tree$edge.length)
	sp.rich[iter]<-length(sub.tree$tip.label)



}#end iter loop
results <- data.frame(tree.iter,cladeID,PD,sp.rich)
output<-rbind(output,results)

}#loop to next tree



#OUTPUT RESULTS
output

write.table(output, file="...", col.names=T, row.names=F, quote=F, sep="\t")