R/entropy.plot.R

In MDM: Multinomial Diversity Model

entropy.plot <-
function(lst, y, x, ord=TRUE, type=c("species","sites")[1], labs,
	segs = TRUE, wid.seg=0.25, pchs = c(15,19,0,2,6,2,15,17,21,17), ...) {

	plnp <- function(x) {
		x <- -x*log(x)
		x[is.na(x)] <- 0
		x
	}

	if (class(lst)!="list") stop("'lst' must be a list of fitted values from mdms !!")
	n <- length(lst)
	if (n<2) stop("needs at least two matrices")
	types <- sapply(lst,function(x) class(x)[1])
	for (i in 1:length(types)) {
		if (types[i]=="mdm") lst[[i]] <- lst[[i]]$fitted.values
	}
	rc <- (type=="species")+1
	nplt <- dim(lst[[1]])[rc]
	if (missing(labs)) labs <- dimnames(lst[[1]])[[rc]]

	for (i in 1:n) lst[[i]] <- plnp(lst[[i]])

	if(ord) {
		ords <- order(apply(lst[[1]],rc,mean))
		labs <- labs[ords]
	}
	else ords <- 1:nplt

	for (i in 1:n) lst[[i]] <- apply(lst[[i]],rc,mean)[ords]
	if (missing(y)) y <- 1:length(lst[[1]])
	if (missing(x)) xlim <- range(unlist(lst))
	plot(lst[[1]],y,type="n",xlab="Entropy",ylab="",axes=FALSE, xlim=xlim, ...)
	axis(2,at=y,labels=labs, ...)
	axis(1)
	box()
	# could use arrows below but I want to line thickness of bars #
	if (segs) {
		segments(lst[[1]],y+wid.seg,lst[[1]],y-wid.seg,lty=1,lwd=1)
		segments(lst[[2]],y+wid.seg,lst[[2]],y-wid.seg,lty=1,lwd=1)
		segments(lst[[1]],y,lst[[2]],y,lty=1)
		if (n>2) for (i in 3:n) points(lst[[i]],y,pch=pchs[i-2],...)
	}
	else {
		segments(lst[[1]],y,lst[[2]],y,lty=1, col="grey75")
		for (i in 1:n) points(lst[[i]],y,pch=pchs[i],...)
	}
	invisible(lst)
}