Man pages for zanbi/jabbamodel-JABBA
Just Another Bayesian Biomass Assessment
| build_jabba | Creates a data list used as input to JAGS |
| fit_jabba | Fit JABBA model |
| get_beta | gets beta prior paramenters |
| get_gamma | gets gamma prior paramenters |
| jabba2jags | Function to write JABBA model in JAGS |
| jabba_hindcast | jabba hindcasting function |
| jabba_plots | wrapper jbplot function |
| jbpar | jbpar() |
| jbplot_biplot | Stock Status Biplot |
| jbplot_bprior | Plot of biomass depletion prior vs posterios |
| jbplot_catch | Plots Total Catch |
| jbplot_catcherror | Plots estimated catch + CIs |
| jbplot_cpuefits | Plot of fitted CPUE indices |
| jbplot_hcxval | jbplot_hcxval |
| jbplot_kobe | KOBE phase plot |
| jbplot_logfits | log(CPUE) fits |
| jbplot_mcmc | Plot mcmc chains |
| jbplot_ppdist | Plot of prior and posterior distributions |
| jbplot_prj | Projection plot |
| jbplot_procdev | Plot of process error deviation on log(biomass) |
| jbplot_residuals | JABBA residual plot |
| jbplot_retro | jbplot_retro() to plot retrospective pattern |
| jbplot_runstest | JABBA runs test plots |
| jbplot_spphase | JABBA SP-Phase Plot |
| jbplot_stdresiduals | JABBA standardized residual plot |
| jbplot_summary | jbplot_summary() |
| jbplot_trj | Plot of estimated trajectories |
| kobeJabba | Function kobeJabba for FLR |
| kobeJabbaProj | Function to convert JABBA projections into FLR object |
| plot_lnorm | gets lognormal prior paramenters |
| runs_sig3 | Function to do runs.test and 3 x sigma limits |
