The materials in this repository present the stock assessment tool ‘Just Another Bayesian Biomass Assessment’ JABBA. The motivation for developing JABBA was to provide a user-friendly R to JAGS (Plummer) interface for fitting generalized Bayesian State-Space SPMs with the aim to generate reproducible stock status estimates and diagnostics. Building on recent advances in optimizing the fitting procedures through the development of Bayesian state-space modelling approaches, JABBA originates from a continuous development process of a Bayesian State-Space SPM tool that has been applied and tested in many assessments across oceans. JABBA was conceived in the Hawaiian Summer of 2015 as a collaboration between young researchers from South Africa and the Pacific Islands Fisheries Science Center (NOAA) in Honolulu, HI USA. The goal was to provide a bridge between age-structured and biomass dynamic models, which are still widely used. JABBA runs quickly and by default generates many useful plots and diagnosic tools for stock assessments.
Inbuilt JABBA features include:
- Integrated state-space tool for averaging multiple CPUE series (+SE) for optional use in assessments
- Automatic fitting of multiple CPUE time series and associated standard errors
- Fox, Schaefer or Pella Tomlinson production function (optional as input Bmsy/K)
- Kobe-type biplot plotting functions
- Forecasting for alternative TACs
- Residual and MCMC diagnostics
- Estimating or fixing the process variance
- Optional estimation additional observation variance for individual or grouped CPUE time series
- Easy implementation of time-block changes in selectivity
A self-contained R package of JABBA is forthcoming.
JABBAbeta GitHub repository
JABBA development version for testing new JABBA features and stock assessment examples