Model code to build and run an integrated population model for the endangered Cape Sable Seaside Sparrow

The Cape Sable Seaside Sparrow (CSSS; Ammospiza maritima mirabilis) is an endangered species that has experienced population declines of more than 60% since the 1990s. The CSSS is restricted in geographic extent to a relatively small area of remaining marl prairie in the southern Florida Everglades and remains in six subpopulation areas (named A-F). There has been over two decades of field research conducted on the CSSS across its six subpopulations, but a statistically robust analysis of the bird’s demographic parameters utilizing all data has yet to be completed. To address this gap, we conducted demographic analysis of the CSSS population using an integrated population model (IPM). The IPM provides a flexible framework to incorporate three separate CSSS data types (range-wide counts, mark-recapture, productivity) into a single model to estimate demographic processes and population trajectories. We calculated: (1) annual estimates of annual population size, survival, and productivity; (2) coefficient estimates of hydrologic and environmental variables on survival and productivity; (3) estimates of annual population growth and its correlation with demographic rates; and (4) a population viability analysis (PVA) that includes predicted population size and demographic rates 10 years into the future, and probabilities of extinction and quasi-extinction. This data release contains the code to run the IPM and PVA in addition to providing the parameter estimates from the model.