###Lande's (1996) scheme for additive partitioning of diversity for a site by species matrix with zeros requires vegan. Sites are columns, with the first column being species names, here is a working example.

#dat<-matrix(sample(0:10,100,replace=TRUE),ncol=10)
#coms<-c("A1","A2","A3","A4","A5","A6","A7","A8","A9","A10")
#spp<-c("SP1","SP2","SP3","SP4","SP5","SP6","SP7","SP8","SP9","SP10")
#dat<-data.frame(spp,dat)
#names(dat)[2:11]<-coms

#addPart(dat,index="richness")

#by Marc Cadotte
#Oct 2008

addPart<-function (data,index="simpson") {
	
	INDICES <- c("shannon", "simpson", "richness")
    index <- match.arg(index, INDICES)

	no.spp<-apply(data[,2:ncol(data)],MARGIN=2,sum)
		
	q<-no.spp/sum(no.spp)
	
	p.bar<-apply(data[,2:ncol(data)],
		MARGIN=1,sum)/sum(
		apply(data[,2:ncol(data)],
		MARGIN=1,sum))
			
	
	if (index == "simpson") {
		
		alph<-diversity(data[,2:ncol(data)],
			index="simpson",MARGIN=2)
		
		lmbd<-1-alph
		
		d.sqr<-sum(q*lmbd)-sum(p.bar^2)

		D.bar<-sum(alph*q)

		Dt<-d.sqr+D.bar
		
		return(rbind(D.bar,d.sqr,Dt))
		}
	
	if (index == "shannon") {
		
		alph<-diversity(data[,2:ncol(data)],
			index="shannon",MARGIN=2)
			
		H.bar<-sum(alph*q)
		
		H.among<--sum(p.bar*log(p.bar))-sum(q*alph)
		
		Ht<-H.bar+H.among
		
		return(rbind(H.bar,H.among,Ht))
		}
		
	if (index == "richness") {
		
		for (i in 2:ncol(data)) {
			for (j in 1:nrow(data)) {
				if (data[j,i] > 1) data[j,i]=1
				}
			}
		
		alph<-apply(data[,2:ncol(data)],
		MARGIN=2,sum)
		
		S.bar<-sum(alph*q)
		
		St<-nrow(data)
		
		S.among<-St-S.bar
		
		return(rbind(S.bar,S.among,St))
		}	
		
		
	}