DOI: 10.5061/dryad.ttdz08m2n
title: Data from: Integrating multiple sign types to improve occupancy estimation for inconspicuous species

description: Standard occupancy models enable unbiased estimation of occupancy
 by accounting for observation errors such as missed detections (false
 negatives) and, less commonly, incorrect detections (false positives).
 Occupancy models are fitted to data from repeated site visits in which
 surveyors record evidence of species presence. Use of indirect sign (e.g.,
 scat, tracks) as evidence of presence can vastly improve survey efficiency
 for inconspicuous species but can also introduce additional sources of
 error. We developed a “multi‐sign” occupancy approach to model the
 detection process separately for unique sign types and used this method to
 improve estimates of occupancy dynamics for an inconspicuous species, the
 American pika (Ochotona princeps). We investigated how estimates of pika
 occupancy and environmental drivers differed under four increasingly
 realistic representations of the observation process: (1) perfect
 detection (commonly assumed for modeling pika occupancy), (2) standard
 occupancy model (single observation process without possibility of false
 detection), (3) multi‐sign with no false detections (non‐false positive
 model), and (4) multi‐sign with false detections (full model). For the
 multi‐sign occupancy models, we modeled the detection of each sign type
 (fresh scat, fresh haypiles, pika calls, and pika sightings) separately as
 a function of climatic and environmental covariates. Estimates of
 occupancy processes and inferences about environmental drivers were
 sensitive to different detection models. Simplified representations of the
 detection processes generally resulted in higher occupancy estimates and
 higher turnover rates than the full multi‐sign model. Environmental
 drivers also varied in their influence on occupancy models, where (e.g.)
 forb cover was estimated to more strongly influence occupancy in the full
 multi‐sign model than the simpler models. As has been reported previously
 in other contexts, unmodeled heterogeneity in the observation process can
 lead to biases in occupancy processes and uncertainty in the relationships
 between occupancy and environmental covariates. Overall, our multi‐sign
 approach to dynamic occupancy modeling, which accounts for spatiotemporal
 variation in reliability among sign types, has strong potential to
 generate more realistic estimates of occupancy dynamics for inconspicuous
 species.
description: Pika surveys were carried out between 2010 and 2021 across five
 park units within the states of Oregon, Idaho, and California in the
 Pacific Northwest, including: Crater Lake National Park (CRLA), Craters of
 the Moon National Monument and Preserve (CRMO), Lassen Volcanic National
 Park (LAVO), Lava Beds National Monument (LABE), and Newberry National
 Monument (NEWB). Newberry National Monument surveys were added starting in
 2017. Survey plots comprised a 12‐m radius circular surveyed area. An
 average of 100 plots per park were surveyed each year. Resurveys were
 conducted for 30% of the sites within 1 month of original surveys each
 year. Surveyors spent up to 30 min searching a site and recorded up to 10
 sign observations per survey. Observations comprised fresh or old scat
 (FS/OS), fresh or old haypiles (FH/OH), pika calls (PC), and pika
 sightings (PS).