Introducing flocker: an R package for flexible occupancy modeling via brms and Stan

Occupancy models are a widespread tool for analyzing biological survey data, but packages for fitting these models offer a limited variety of effects structures. We developed Rpackage flocker to connect occupancy models (single- and multi- species; single- and multi-season) to the uniquely powerful formula syntax of Rpackage brms. Using familiar formula-based syntax, flocker models can readily incorporate a wide array of effects structures, including phylogenetic random effects, splines, Gaussian processes, autoregressive structures, monotonic effects, and nonlinear predictors. These are available for use in formulas for occupancy, detection, colonization, extinction, and autologistic terms (as applicable to the model type). flocker additionally provides functionality for data simulation, posterior prediction, and model comparison, following well-documented statistical decisions that we put forward as best practices. We anticipate that flocker will facilitate the work of practitioners who seek added realism in occupancy models. We further hope that flocker’s synthesis of these models will help inform best practices around occupancy modeling.