Hierarchical Bayesian estimation of unobserved salmon passage through weirs

Abstract

We developed a hierarchical Bayesian model (HBM) to estimate missing counts of Chinook salmon (Oncorhynchus tshawytscha (Walbaum in Artedi, 1792)) at a weir on the Kogrukluk River, Alaska, between 1976 and 2015. The model assumed that fish passage during a breach of the weir was typical of passage during normal operations. Counts of fish passing the weir were missing for some days during the runs, or only partial counts for a given 24-hour period were available. The HBM approach provided more defensible estimates of missing data and total escapement than ad hoc or year-by-year model estimates, because estimates of passage for a given year were informed not only by counts for the current year, but also by counts for all previous years. The results of the HBM yielded less variable estimates of escapement than did ad hoc or year-by-year model estimates. The HBM represents a standardized approach to estimate missing counts and total escapement and eliminates the need for ad hoc estimates of missing counts. The model also provides managers with a measure of uncertainty around estimates of escapement and around estimates of hyper-parameters to define run curves in subsequent years with incomplete fish counts.

Estimates of Fall-run Chinook Salmon Escapement in Two San Joaquin River Tributaries from Device-based and Survey-based Methods

“…Due to the number of consecutive missing days in 2011, it was not appropriate to use the GAM approach to estimate counts during that time. A promising alternative to acquire more complete estimates in partial operation years would be to use a hierarchical Bayesian model (Jasper et al 2018). Such models are capable of sharing information about run-timing and counts using hyperparameters to estimate run curves in years with incomplete monitoring.…”

“…In contrast, counting fish as they pass through a reference point, weir, or ladder, is potentially the most accurate and precise method for estimating absolute escapement, although certain circumstances must be met (Parsons and Skalski 2010). Infrastructure or expensive equipment is required to conduct passage counts, and river discharge and debris loads must remain low for weirs to remain operational during a migration season (Jasper et al 2018). In addition, estimation accuracy decreases when fish passages per hour are exceedingly high (>1,500 fish per hour; Shardlow and Hyatt 2004), or if morphologically similar species are present and are mistaken for target species (Bergman et al 2012).…”

“…Infrastructure or expensive equipment is required to conduct passage counts, and river discharge and debris loads must remain low for weirs to remain operational during a migration season (Jasper et al 2018). In addition, estimation accuracy decreases when fish passages per hour are exceedingly high (>1,500 fish per hour; Shardlow and Hyatt 2004), or if morphologically similar species are present and are mistaken for target species (Bergman et al 2012).…”

State‐Space Model to Estimate Salmon Escapement Using Multiple Data Sources

“…For anadromous fishes, escapement is often estimated at a fixed location in a river system prior to fish reaching their natal habitat to spawn (e.g., Woody 2004; Jasper et␣al. 2018). Escapement estimates facilitate effective fisheries management, particularly estimates of escapement for component groups (e.g., by stock, population, age, and origin [wild or hatchery]; Hess et␣al.…”