Gmacs: A Generalized Size-Based Stock Assessment Modeling Framework
Gmacs has initially been designed for application to red king crab stocks of Alaska. The population sub-model is typical of those represented in most statistical size-structured models. However, the observation sub-model is designed to utilise the wide variety of data types typical of Alaskan crab stocks. Observation data types can include fishery or survey indices of abundance or effort; fishery discard data; size-composition and weight-at-size data; and tag-recapture data. The current framework allows for time-varying selectivity, time-varying natural mortality and growth, and time-varying molting probabilities, with more to come.
Gmacs is coded using Auto-Differentiation Model Builder (ADMB), so inherits its capability to efficiently estimate hundreds of parameters using maximum likelihood. The source code is heavily commented and formally structured, allowing for easy expansion. Gmacs output processing is handled by a purpose-built R package. The Gmacs model code, example model files, and associated R code is publicly available at https://github.com/awhitten/