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Abstract
Explaining patterns of species presence (occupancy) and if that species is present, the proportion of time it spends in an area (use), is typically the first step in understanding how species interact with their environments. I provide the first method (multi-scale occupancy modeling) to simultaneously estimate occupancy and use from detection-nondetection data while accounting for imperfect detection. Simulations with 5 repeated samples at each scale demonstrated that estimates and credible interval coverage are relatively unbiased when the probability of detecting a species at a site given the site is occupied is >/=0.3. Bias could be reduced by increasing the number of repeated samples. Then we apply the newly-developed multi-scale occupancy models to analyze the relationship between snag density, big tree density (>60.96 cm dbh), and acoustic evidence of Ivory-billed Woodpeckers in Arkansas while accounting for the proportion of area surveyed. Density of big trees (AIC weight=0.54) best predicted patch occupancy, percent area surveyed (AIC weight =0.61) best predicted the probability that evidence of Ivory-billed Woodpeckers was available within the patch (use), and density of big trees (AIC weight =0.61) best predicted the probability that evidence was detected given that it was available. The percent patch surveyed likely represented the level of nonrandom sampling within the patch and multi-level occupancy models helped control for that bias. Finally, we analyze the effect of disturbance on occupancy and use by 18 forest birds in northwest Ecuador. Both occupancy and use showed strong threshold responses at 21-40% upper canopy cover with the probability of occupancy increasing from about 0 to 1 and emigration (the probability that a species would stop using the site during the study period) decreasing from about 1 to 0. Patterns of use and occupancy suggest that disturbed habitat in the region (which is primarily abandoned pasture) may only be valuable to forest birds after a specific level of regeneration and during certain times of the season. The novel insights provided throughout this dissertation highlight the value of analyzing both occupancy and use in a variety of ecological contexts.