countCDFxt {popbio} | R Documentation |
This function takes parameters derived from population counts and calculates the probability of extinction with bootstrap confidence intervals for a density-independent model, using a diffusion approximation.
countCDFxt(mu, sig2, nt, Nc, Ne, tq=nt, tmax=50, Nboot=500, plot=TRUE)
mu |
estimated value of mean mu |
sig2 |
estimated value of sample variance |
nt |
number of transitions in the data set |
Nc |
current population size |
Ne |
quasi-extinction threshold |
tq |
length of the census (in years), default is number of transitions |
tmax |
latest time to calculate extinction probability, default 50 |
Nboot |
number of bootstrap samples for calculating confidence intervals for extinction probabilities, default 500) |
plot |
draw extinction time CDF plot with log-scale on y-axis |
The function plots the cumulative probabilities of quasi-extinction through time with 95% confidence intervals. It also returns a data frame with the extinction time CDF for the best parameter estimates (Gbest), and the lower and upper bootstrap confidence limits for extinction probabilites (Glo, Gup).
Adapted to R by Patrick Nantel, 4 May 2005, from program 'extprob' of Morris & Doak (2002: 79-86)
converted Matlab code from Box 3.4 in Morris and Doak (2002)
Dennis et al. 1991, Ecological Monographs 61: 115-143.
Morris, W. F., and D. F. Doak. 2002. Quantitative conservation biology: Theory and practice of population viability analysis. Sinauer, Sunderland, Massachusetts, USA.
## plot like Figure 3.8 in Morris and Doak (2002). data(grizzly) logN<-log(grizzly$N[-1]/grizzly$N[-39]) countCDFxt(mu=mean(logN), sig2=var(logN), nt=38, tq=38, Nc=99, Ne=20)