R/mos.f.R

In simba: A Collection of functions for similarity analysis of vegetation data

## Function for calculating focal to surrounding plot singularity
"mos.f" <-
function(x, foc=NULL, d.inc=FALSE, preso=FALSE, pc=NULL){
	if(is.null(foc)){
		stop("A focal plot has to be specified!")
	}
	x <- data.frame(x)
	if(!d.inc){
		## both checks have meaning because zeros count!
		## check and elimation of non-occurring species, without warning
		x <- x[,colSums(x)!=0]
		## check for and eliminate empty plots, without warning
		x <- x[rowSums(x)!=0,]
	}
	## create selector (the species composition of the focal plot
	## determines the next steps)
	sel <- x[foc,]
	## and delete selector site from the dataset
	x <- x[-foc,]
	## calculate the sum of occurrence for all species that
	## occur on the focal plot
	occ <- colSums(x>0)[sel>0]
	## take care for zero occurring species (when the focal plot is empty)
	#if(length(occ)==0) occ <- 0
	## calculate the sum of non-occurrence for all species that
	## do not occur on the focal plot
	nocc <- colSums(x==0)[sel==0]
	## take care for zero non-occurring species
	#if(length(nocc)==0) nocc <- 0
	## sum all sums of occurrences and non-occurrences and
	## divide by the number of species and by the number of plots
	res <- sum(c(occ, nocc))/ncol(x)/nrow(x)
	fac <- 1
	if(!is.null(pc)){
		if(pc==1){
			fac <- sum(sel - c(occ > 0, nocc == ncol(x)) == 0) / length(sel)
			}
		else{
			fac <- as.numeric(1-vegdist(rbind(rep(nrow(x), length(sel)), c(occ, nocc))))
			}
		}
	
	if(preso) {
		res <- sum(occ)/length(occ)/nrow(x)
	}
	res <- res*fac
	names(res) <- "mos.f"
	return(res)
}