A Hierarchical Approach to Joint Estimation of Juvenile Salmonid Abundance and Detection Efficiency
Snorkel surveys are a widely used method of assessing salmonid abundance in small streams throughout the Pacific Northwest, however, they are imperfect in the sense that observers rarely count all fish present at a site. These counts are generally calibrated to an independent measure of fish abundance (e.g., mark-recapture) to correct for this imperfect detection, but it is often ignored that this independent measure may also be an imprecise or inaccurate estimate of the true abundance. Our objective was to develop and apply an analytical approach that accommodates uncertainty in both sources of information when estimating the detection efficiency of snorkel surveys. The model assumed that snorkel counts have binomial sampling variability in which the true abundance (a latent, free parameter) was treated as the binomial sample size and the success parameter was a logit-linear function of local covariates. Simultaneously, latent abundance was informed by an additional observation model explaining variability in paired mark-recapture data. We used Bayesian methods to fit the model to a data set in which 105 paired snorkel and mark-recapture surveys were conducted in the Grande Ronde Basin in northeastern Oregon. The selected covariates that best explained variability in snorkel detection efficiency included species, large wood density, channel unit type, depth, and visibility, though a non-negligible amount of variability was attributed to a site-level random effect. This model represents an improvement over previous snorkel calibration methods by applying a more rigorous statistical treatment of the sources of variability in the data while explicitly describing the mechanistic link between local stream conditions and efficiency of snorkel surveys.
Staton, B., C. Justice, S. White, T. Sedell, L. Burns, and M. Kaylor. 2020. A hierarchical approach to joint estimation of juvenile salmonid abundance and detection efficiency. Oregon Chapter of the American Fishery Society Annual Meeting, Bend, OR, March 3-6, 2020.