extCDF {popbio} | R Documentation |
Returns the extinction time cumulative distribution function using parameters derived from population counts.
extCDF(mu, sig2, Nc, Ne, tmax = 50)
mu |
estimated value of mean mu |
sig2 |
estimated value of sample variance |
Nc |
current population size |
Ne |
quasi-extinction threshold |
tmax |
latest time to calculate extinction probability, default 50 |
A vector with the cumulative probabilities of quasi-extinction from t=0 to t=tmax.
Chris Stubben
converted Matlab code from Box 3.3 and equation 3.5 in Morris and Doak (2002)
Morris, W. F., and D. F. Doak. 2002. Quantitative conservation biology: Theory and practice of population viability analysis. Sinauer, Sunderland, Massachusetts, USA.
countCDFxt
for bootstrap confidence intervals
data(grizzly) logN<-log(grizzly$N[-1]/grizzly$N[-39]) mu<-mean(logN) sig2<-var(logN) ## grizzly cdf (log scale) ex<-extCDF(mu, sig2, Nc=99, Ne=20) plot(ex, log='y', type='l', pch=16, col="blue", yaxt='n', xlab="Years", ylab="Quasi-extinction probability", main="Yellowstone Grizzly bears") pwrs<-seq(-15,-5,5) axis(2, at = 10^pwrs, labels=parse(text=paste("10^", pwrs, sep = "")), las=1) ##plot like fig 3.10 (p 90) n<-seq(20, 100, 2) exts<-numeric(length(n)) for (i in 1:length(n) ) { ex<-extCDF(mu, sig2, Nc=n[i], Ne=20) exts[i]<-ex[50] } plot(n, exts, type='l', las=1, xlab="Current population size", ylab="Probability of quasi-extinction by year 50")