A State-Space Approach to Incorporating Environmental Effects in Stock Assessment and Biological Reference Points

There are many studies of environmental effects on fish stocks, some of which incorporate these effects mechanistically in stock assessment models. Most of these models do not account for error in environmental observations and use ad-hoc approaches to deal with missing observations. We present a state-space age-structured assessment model that treats environmental and traditional data components consistently. This approach offers a statistically appropriate method for dealing with both error in and missingness of observations as well as the stochastic nature of the environmental and population processes. State-space models also allow information-theoretic approaches to model selection and potentially multi-model inference. We demonstrate the approach with an application to Southern New England yellowtail flounder to evaluate effects of the Mid-Atlantic shelf cold pool on recruitment and further demonstrate how uncertainty in the effects can be propagated in biological reference points and population projections important for management.