Code from: Enhancing data-limited assessments with random effects: A case study on Korea chub mackerel (Scomber japonicus)

In a state-space framework, temporal variations in fishery-dependent processes can be modeled as random effects. This modeling flexibility makes state-space models (SSMs) powerful tools for data-limited assessments. Though SSMs enable the model-based inference of the unobserved processes, their flexibility can lead to overfitting and non-identifiability issues. To address these challenges, we developed a suite of state-space length-based age-structured models and applied them to the Korean chub mackerel (Scomber japonicus) stock. Our research demonstrated that incorporating temporal variations in fishery-dependent processes can rectify model mis-specification but may compromise robustness, which can be diagnosed through a series of model checking processes. To tackle non-identifiability, we used a non- degenerate estimator, implementing a gamma distribution as a penalty for the standard deviation parameters of observation errors. This penalty function enabled the simultaneous estimation of both process and observation error variances with minimal bias, a notably challenging task in SSMs. These results highlight the importance of model checking and the effectiveness of the penalized approach in estimating SSMs. Additionally, we discussed novel assessment outcomes for the mackerel stock.