#XSSA ##State-space Stock Assessment with "off-line coupling"
Development of state-space stock assessment models for application to open systems where the stock under analysis is connected to a wider population. The preliminary applications is the yellowfin tuna population which supports fisheries in the Main Hawaiian Islands. The MHI population is connected to a larger tuna population for which stock assessments are available. The estimated population size in areas surrounding the MHI used to "force" the population dynamics.
###Models
- issams6 - single population 6 parameter model with index of abundance; MSY, Fmsy parameterization
- xssams - two population model with explicit exchange; deprecated
###Directories
- ADMB - source (.tpl files) for ADMB implementation including several deprecated versions
- TMB - source (.R, .cpp and .dat files) for TMB port of ADMB implmentation
- scripts - R and bash scripts for plotting and data manipulation
- Reports - LaTeX and pdf documentaiton of models and results
- dat - data file to run isams6
- YPR - yield per recruit analysis of Main Hawaiian Islands yellowfing tuna fishery
- Modify estimation of Q to allow estimate to exceed 1.0 for augmented catch models
- Rationalize TMB code with issam6.tpl
- Compute Widely Applicable Information Criterion (WAIC)
- Update analysis in the event that WCPFC uptades regional yellowfin assessment