###simpson's index with and without phylogenetic distances using commmunity matrix 'x', species names as colnames and community names as rownames. phy=FALSE returns traditional simpson's index

simp.phy<-function(x,tr,phy=TRUE){
	
	x<-as.matrix(x)
	x<-x[,order(colnames(x))]
	total <- apply(x, 1, sum)
	x <- sweep(x, 1, total, "/")
	
	if (phy==TRUE){
		phy.mat<-cophenetic(tr)
		phy.mat<-phy.mat[order(rownames(phy.mat)),order(colnames(phy.mat))]
		
		out<-apply(x,1,function(x) sum((x %o% x)*phy.mat))
		}
	
	if (phy==FALSE) {
		bin.mat<-matrix(1,dim(x)[2],dim(x)[2])
		diag(bin.mat)<-0
		
		out<-apply(x,1,function(x) sum((x %o% x)*bin.mat))
		}	
		
	return(out)	
	}