Dynamic occupancy models in unmarked

Dynamic occupancy models (MacKenzie et al. 2003) allow inference about the occurrence of “things” at collections of “sites” and about how changes in occurrence are driven by colonization and local extinction. These models also account for imperfect detection probability. Depending on how “thing” and “site” are defined, occupancy may have vastly different biological meanings, including the presence of a disease in an individual (disease incidence) of a species at a site (occurrence, distribution), or of an individual in a territory. Dynamic occupancy models in unmarked are fit using the function colext. All parameters can be modeled as functions of covariates, i.e., first-year occupancy with covariates varying by site (site-covariates), colonization and survival with siteand yearly-site-covariates and detection with site-, yearly-siteand sample-occasion-covariates. We give two commented example analyses: one for a simulated data set and another for a real data set on crossbills in the Swiss breeding bird survey MHB. We also give examples to show how predictions, along with standard errors and confidence intervals, can be obtained.