extCDF: Count-based extinction time cumulative distribution function

Description Usage Arguments Value Author(s) Source References See Also Examples

View source: R/extCDF.R

Description

Returns the extinction time cumulative distribution function using parameters derived from population counts.

Usage

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extCDF(mu, sig2, Nc, Ne, tmax = 50)

Arguments

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

Value

A vector with the cumulative probabilities of quasi-extinction from t=0 to t=tmax.

Author(s)

Chris Stubben

Source

converted Matlab code from Box 3.3 and equation 3.5 in Morris and Doak (2002)

References

Morris, W. F., and D. F. Doak. 2002. Quantitative conservation biology: Theory and practice of population viability analysis. Sinauer, Sunderland, Massachusetts, USA.

See Also

countCDFxt for bootstrap confidence intervals

Examples

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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")

Example output

Warning message:
In xy.coords(x, y, xlabel, ylabel, log) :
  2 y values <= 0 omitted from logarithmic plot

popbio documentation built on May 4, 2018, 1:04 a.m.