Elizabeth E. Holmes. 2004. Beyond theory to application and evaluation: diffusion approximations for population viability analysis. Ecological Applications 14:1272–1292.
S-plus code to estimate diffusion approximation parameters and their posterior probability distributions for DA risk metrics.
Ecological Archives A014-023-S1.
Elizabeth E. Holmes
National Marine Fisheries Service
Northwest Fisheries Science Center
2725 Montlake Blvd. East
Seattle, WA 98112-2097
USA
Email: eli.holmes@noaa.gov
S-Plus code:
ParameterEst.ssc
kalman_ests.m
PostPDFPlots.ssc
All files are in ASCII text.
The file ParameterEst.ssc contains Splus code to estimate m and s2 using ML, running sums, and slope methods. The ML method allows missing data; the running sum and slope methods do not. For these methods, missing data points should be replaced with interpolated values. I use simple linear interpolation. Basic diagnostics are done also: normality, trend and autocorrelation tests. Outliers are tested for and removed using DFFITS criteria.
The file kalman_ests.m contains matlab code to estimate m and s2 using the Kalman filter algorithm.
The file PostPDFPlots.ssc calculates posterior probability distributions for the parameters, m, s2, and s2np, and the risk metrics, l, probability of eventual 90% decline, and expected total probability of 90% decline within given time frames. This code implements the algorithm given in the section Posterior probability distributions in the text and produces Figs. 8 and 9.