countCDFxt {popbio} | R Documentation |
This function takes parameters derived from abundance time-series and calculates the probability of extinction with bootstrap confidence intervals for a density-independent model, using a diffusion approximation.
countCDFxt(mu, sig2, nt, tq, Nc, Ne, tmax=50, Nboot=500)
mu |
estimated value of mean mu |
sig2 |
estimated value of sample variance |
nt |
number of transitions in the data set |
tq |
length of the census (in years) |
Nc |
current population size |
Ne |
quasi-extinction threshold |
tmax |
latest time to calculate extinction probability, default 50 |
Nboot |
number of bootstrap samples for calculating confidence intervals for extinction probabilities, default 500) |
The function plots the cumulative probabilities of quasi-extinction through time, with 95% confidence interval. It also creates 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.
## Return a graph like Figure 3.8 in Morris and Doak (2002: 84). ## based on census counts of adult female grizzly bears, 1958-1998 countCDFxt(mu=0.02134, sig2=0.01305, nt=38, tq=38, Nc=99, Ne=20)