Man pages for jabbamodel/JABBA
Just Another Bayesian Biomass Assessment
| addBfrac | addBfrac() |
| build_jabba | Creates a data list used as input to JAGS |
| cmsy.bkprior | cmsy.bkprior() |
| cmsy.rprior | cmsy.prior() |
| fit_jabba | Fit JABBA model |
| fw_jabba | fw_jabba() External forward projections in JABBA |
| get_beta | gets beta prior paramenters |
| get_gamma | gets gamma prior paramenters |
| hindcast_jabba | hindcast_jabba() |
| jabba2jags | Function to write JABBA model in JAGS |
| jabba_hindcast | DEPRECIATED |
| jabba_plots | wrapper jbplot function |
| jbhcxval | jbhcxval() additional hindcast options with external foreward... |
| jbio | jbio() |
| jbleslie | jbleslie |
| jbmase | jbmase() |
| 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_Crisk | jbplot_Crisk() |
| jbplot_ensemble | jbplot_ensemble() |
| jbplot_hcxval | jbplot_hcxval |
| jbplot_indices | jbplot_indices |
| jbplot_kobe | KOBE phase plot |
| jbplot_logfits | log(CPUE) fits |
| jbplot_mcmc | Plot mcmc chains |
| jbplot_PPC | jrplot_PPC |
| 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_spdyn | JABBA SPdyn Plot |
| jbplot_spphase | JABBA SPphase Plot |
| jbplot_stdresiduals | JABBA standardized residual plot |
| jbplot_summary | jbplot_summary() |
| jbplot_trj | Plot of estimated trajectories |
| jbretro | jbretro() computes Mohn's rho and forecast rho |
| jbruns_sig3 | Function to do runs.test and 3 x sigma limits |
| jbrunstest | JABBA runs test |
| jbspr0 | spr0() |
| kobeJabba | Function kobeJabba for FLR |
| kobeJabbaProj | Function to convert JABBA projections into FLR object |
| mp_jabba | Fit JABBA model |
| normIndex | normIndex() |
| plot_lnorm | gets lognormal prior paramenters |
| range2prior | range2prior() |
| rc4 | rc4 r4ss color palette |
| ss3col | ss3col r4ss color generator |
| zage | zage() |
