This program (VBA implemented in Excel) animates the path of a tagged animal in a VR2 hydrohpone network.
by eric.ward, last updated 1/8/08, sharing set to publicThese routines allow you to take a matrix of MCMC samples and calculate the Bayes factor based on the harmonic mean algorithm proposed by Gelfand and Dey (1994). Caution: Bayes factors tend to be numerically unstable!
by brice.semmens, last updated 7/8/08, sharing set to public
This set of Matlab scripts conducts a first order MAR(1) model to estimate interactive effects, and covariate effects, on a time series of data from a community.
It uses a Gibbs sampler to estimate parameters, and currently is set up with diffuse priors on all parameters for the model. It is pretty basic at this point, but it works.
Note on the Gamma distribution:
Going back and forth between Matlab/R/WinBUGS can be confusing, because of the different parameterizations of the gamma pdf. Here's the Matlab/BUGS forms and the R equivalents:
Matlab: X ~ g(a,b) E[X] = ab
R equivalent: X ~ g(shape=a,scale=b)
BUGS: X ~ g(a,b) E[X] = a/b
R equivalent: X ~ g(shape=a,rate=b) OR
X ~ g(shape=a,scale=1/b)
This is project involves estimating catastrophes in the presence of observation and process error. It was later expanded into a paper on fur seals (Ward et al. 2007, CJFAS). The model may be run in WinBugs / OpenBugs, or through R. The example has been made to be generic and includes some dummy data. The priors included have been simplified for demonstration purposes.
by brice.semmens, last updated 8/23/07, sharing set to public
This program allows one to walk through the steps required to conduct a population viability analysis, or PVA, using a population time time series. The model outputs probabilities of extinction as a function of time steps into the future, and importantly, gives confidence intervals for these probabilities.
This tool has two major advantages over traditional PVA techniques:
1) It uses a state-space Kalman filter that allows for both process and non-process error.
So what's the big deal? --Functionally it filters the data, and allows a more accurate fit for population parameters of interest.2) It uses a Bayesian sampling-importance-resampling algorithm to fully address uncertainty in the parameter estimates given the data.Rather than developing a single function that describes the probability of population extinction through time, we can use the uncertainty in parameter estimates to develop 'probabilities of probabilities', or, the uncertainty surrounding the probability of extinction through time.