SPOMSIM: software for stochastic patch occupancy models of metapopulation dynamics

Classical metapopulations are groups of local populations living in networks of spatially distinct habitat patches in a balance between local extinctions and recolonizations of empty habitat. Models are needed for understanding and predicting metapopulation dynamics in changing landscapes. One particularly important question is what is the effect of habitat loss to the persistence of a metapopulation. A class of metapopulation models that have been successfully used in practical applications are called stochastic patch occupancy models (SPOMs), which model the presence/absence of the species on habitat patches as a Markov chain. The presence–absence assumption makes the model relatively parameter sparse, facilitates empirical data collection, and enables rigorous parameter estimation. This study reviews theory of SPOMs and describes a computational tool, called SPOMSIM, which allows one to simulate SPOMs and estimate parameters for them. SPOMSIM offers a range of choices for submodels; alternatives are provided for the functional forms of local extinction, the dispersal kernel, computation of connectivity, the colonization function, the implementation of the rescue effect and the implementation of regional stochasticity. SPOMSIM includes also, among other things, a utility based on hierarchical clustering for the analysis of the structure of a patch network, a reserve network optimization algorithm, and a patch system editor which makes it possible to investigate the consequences of changes in landscape structure. Potential uses for SPOMSIM include scientific metapopulation studies, teaching and conservation management.