R/robustness.r

In bipartite: Visualising Bipartite Networks and Calculating Some (Ecological) Indices

robustness<- function (object)
{
    # a function to calculate robustness to extinction in the other trophic level
    # based on output by "second.extinct" (see there)
    # by Mariano Devoto, April 2009
    
    if (!is(object, "bipartite"))
        stop("This function cannot be meaningfully applied to objects of this class.")
    N <- colSums(object)
	# select the correct column, based on which level was subject to primary extinction:
    if (attr(object, "exterminated") == "lower"){
    	y <- -object[, 3]
    } else {
    	y <- -object[, 2]
    }
	# modified by CFD, 18 May 2012, on bug detection by Silvia Santamaria
    
    y <- (sum(y) - cumsum(y))/sum(y) #calculates the proportional cumulative sum of secondary extinctions
    x <- (object[, "no"]/max(object[, "no"])) #calculates the proportional primary extinctions
    ext.curve <- splinefun(x,y) #interpolates a function for the secondary extinctions
    ext.area <- integrate(ext.curve, min(x), max(x), subdivisions=max(100L, length(x))) # calculates the area below the curve
    return(as.numeric(ext.area[[1]]))
}