countCDFxt {popbio}R Documentation

Calculate count-based extinction probabilities and bootstrap confidence intervals

Description

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.

Usage

countCDFxt(mu, sig2, nt, tq, Nc, Ne, tmax=50, Nboot=500)

Arguments

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)

Value

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).

Author(s)

Adapted to R by Patrick Nantel, 4 May 2005, from program 'extprob' of Morris & Doak (2002: 79-86)

Source

converted Matlab code from Box 3.4 in Morris and Doak (2002)

References

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.

Examples

## 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)


[Package popbio version 1.1.2 Index]