R/bioclim.plot.R

In dismo: Species Distribution Modeling

# Author: Robert J. Hijmans
# contact: r.hijmans@gmail.com
# Date : December 2009
# Version 0.1
# Licence GPL v3

setMethod("plot", signature(x='Bioclim', y='missing'), 
	function(x, a=1, b=2, p=0.9, ...) {
		
		d <- x@presence
	
		myquantile <- function(x, p) {
			p <- min(1, max(0, p))
			x <- sort(as.vector(stats::na.omit(x)))
			if (p == 0) return(x[1])
			if (p == 1) return(x[length(x)])
			i = (length(x)-1) * p + 1
			ti <- trunc(i)
			below = x[ti]
			above = x[ti+1]
			below + (above-below)*(i-ti)  
		}
	
		p <- min(1,  max(0, p))
		if (p > 0.5) p <- 1 - p
		p <- p / 2
		prd <- predict(x, d)
		i <- prd > p & prd < (1-p)
		plot(d[,a], d[,b], xlab=colnames(d)[a], ylab=colnames(d)[b], cex=0)
		type=6
		x1 <- quantile(d[,a], probs=p, type=type)	
		x2 <- quantile(d[,a], probs=1-p, type=type)	
		y1 <- quantile(d[,b], probs=p, type=type)	
		y2 <- quantile(d[,b], probs=1-p, type=type)	
#		x1 <- myquantile(x[,a], p)	
#		x2 <- myquantile(x[,a], 1-p)	
#		y1 <- myquantile(x[,b], p)	
#		y2 <- myquantile(x[,b], 1-p)	
		polygon(rbind(c(x1,y1), c(x1,y2), c(x2,y2), c(x2,y1), c(x1,y1)), border='blue', lwd=2)
		points(d[i,a], d[i,b], xlab=colnames(x)[a], ylab=colnames(x)[b], col='green' )
		points(d[!i,a], d[!i,b], col='red', pch=3)
	}
)