Modeling false positive detections in species occurrence data under different study designs

Abstract/Summary

The occurrence of false positive detections in presence-absence data, even when they occur infrequently, can lead to severe bias when estimating species occupancy patterns. Building upon previous efforts to account for this source of observational error (Royle & Link 2006; Miller et al. 2011, 2013), we establish a general framework to model false positives in occupancy studies and extend existing modeling approaches to encompass a broader range of sampling designs. Specifically, we identified three common sampling designs that are likely to cover most scenarios encountered by researchers. The different designs all include ambiguous detections, as well as some known-truth data, but their modeling differs in the level of the model hierarchy at which the known-truth information is incorporated (site-level or observation-level). For each model, we provide the likelihood, as well as R and BUGS code needed for implementation. We also establish a clear terminology and provide guidance to help choosing the most appropriate design and modeling approach.