How do ecologists estimate occupancy in practice?

Abstract

Over 20 years ago, ecologists were introduced to the site occupancy model (SOM) for estimating occupancy rates from detection-nondetection data. In the ensuing decades, the SOM and its hierarchical modeling extensions have become mainstays of quantitative ecology, and estimating occupancy rates has become one of the most common applications of ecological field data. Here, we review 364 peer-reviewed articles published between 2019–2021 that estimated occupancy. We first document broad patterns in study design and statistical methods to provide educators, developers of methodology and software, and ecologists with a clear picture of the landscape of methodologies used to estimate animal occupancy. Second, we conduct a focused review of a subset of 98 papers that applied the hierarchical SOM, drawing from methodological literature to identify discrepancies between SOM applications and methodological best practices. We discuss limits to statistical power, issues with model checking and model selection procedures, potential problems arising from unmodeled non-independence, and reproducibility. We highlight areas of rapid advancement in interpreting animal occupancy related to animal movement, imperfect detection, and the occupancy–density relationship. We aim to help readers understand the landscape of methods available, motivate shifts toward robust and reproducible science, and inspire new software and methodological research.