Spatial Explicit Island Community Occupancy Modeling using Markov Random Field Model with Imperfect Observation, Study of Carnivore Community in Apostle Island National Lakeshore

The working repository for Yunyi's MS thesis in Wildlife Ecology.

We used a bilayer Ising Model to model occupancy of two pairs of species on APIS' lattice system, which can be extened to multiple species. We account for imperfect detection by using repeat observation and model the observation process as another smaller Ising model condition on the latent occupancy status, and reconstruct the true occupancy and the interaction/spatial auto correlation with a Gibbs-MH algorithm.

For a clean R package version of computational part of the project, see here