Spatial capture–recapture with random thinning for unidentified encounters

• Published in: Ecology and Evolution
• Main Authors: Jiménez, José, C. Augustine, Ben, Linden, Daniel W., B. Chandler, Richard, Royle, J. Andrew
• Format: Article in Journal/Newspaper
• Language: English
• Published: Wiley 2020
• Subjects: Ursus arctos
• Online Access: http://dx.doi.org/10.1002/ece3.7091; https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.7091; https://onlinelibrary.wiley.com/doi/full-xml/10.1002/ece3.7091

Abstract Spatial capture–recapture (SCR) models have increasingly been used as a basis for combining capture–recapture data types with variable levels of individual identity information to estimate population density and other demographic parameters. Recent examples are the unmarked SCR (or spatial count model), where no individual identities are available and spatial mark–resight (SMR) where individual identities are available for only a marked subset of the population. Currently lacking, though, is a model that allows unidentified samples to be combined with identified samples when there are no separate classes of “marked” and “unmarked” individuals and when the two sample types cannot be considered as arising from two independent observation models. This is a common scenario when using noninvasive sampling methods, for example, when analyzing data on identified and unidentified photographs or scats from the same sites. Here we describe a “random thinning” SCR model that utilizes encounters of both known and unknown identity samples using a natural mechanistic dependence between samples arising from a single observation model. Our model was fitted in a Bayesian framework using NIMBLE. We investigate the improvement in parameter estimates by including the unknown identity samples, which was notable (up to 79% more precise) in low‐density populations with a low rate of identified encounters. We then applied the random thinning SCR model to a noninvasive genetic sampling study of brown bear ( Ursus arctos ) density in Oriental Cantabrian Mountains (North Spain). Our model can improve density estimation for noninvasive sampling studies for low‐density populations with low rates of individual identification, by making use of available data that might otherwise be discarded.