JABBA: Just Another Bayesian Biomass Assessment

Abstract

This study presents a new, open-source modelling software entitled ‘Just Another Bayesian Biomass Assessment’ (JABBA). JABBA can be used for biomass dynamic stock assessment applications, and has emerged from the development of a Bayesian State-Space Surplus Production Model framework, already applied in stock assessments of sharks, tuna, and billfishes around the world. JABBA presents a unifying, flexible framework for biomass dynamic modelling, runs quickly, and generates reproducible stock status estimates and diagnostic tools. Specific emphasis has been placed on flexibility for specifying alternative scenarios, achieving high stability and improved convergence rates. Default JABBA features include: 1) an integrated state-space tool for averaging and automatically fitting multiple catch per unit effort (CPUE) time series; 2) data-weighting through estimation of additional observation variance for individual or grouped CPUE; 3) selection of Fox, Schaefer, or Pella-Tomlinson production functions; 4) options to fix or estimate process and observation variance components; 5) model diagnostic tools; 6) future projections for alternative catch regimes; and 7) a suite of inbuilt graphics illustrating model fit diagnostics and stock status results. As a case study, JABBA is applied to the 2017 assessment input data for South Atlantic swordfish (Xiphias gladius). We envision that JABBA will become a widely used, open-source stock assessment tool, readily improved and modified by the global scientific community.