| Create a jjm.config object | .getJjmConfig |
| Annex diagnostic plotting helpers | annex_diagnostics annotate_cohorts calc_mohn_rho comp_fig_height extr_agefits_fsh extr_agefits_srv extr_catch extr_catch_cv extr_cv extr_effn extr_fished_unfished extr_francis extr_indices extr_kobe extr_lenfits_fsh extr_meanage_fsh extr_meanage_srv extr_meanlen_fsh extr_q_breaks extr_q_trajectory extr_retro extr_sel_breaks extr_sel_fsh extr_sel_srv extr_sr extr_survey_skill extr_wtat_fsh extr_wtat_srv facet_fig_height has_comp jjm_label jjm_pfa_palette plot_catch_fleet plot_comp_fits plot_comp_ridge plot_effn plot_fished_unfished plot_fit_diagnostics plot_francis plot_historic_retro plot_indices_v2 plot_kobe plot_meanstat plot_metadata_overview plot_q_trajectory plot_retro plot_sel_ridge plot_sr plot_summary_sheet plot_survey_skill plot_wtat plot_wtat_cohort read_historic_retro strong_cohorts |
| Annotate strong cohort years on a ggplot | annotate_cohorts |
| Calculate Mohn's rho | calc_mohn_rho |
| Change the internal name of a model | changeNameModel |
| Coerce a vector to character or numeric | coerce |
| Combine outputs | combineModels |
| Calculate figure height for composition fits | comp_fig_height |
| Compare combined JJM outputs | compareModels |
| Generate Assessment plots from single model | diagnostics |
| Extract fishery age-composition fits | extr_agefits_fsh |
| Extract survey age-composition fits | extr_agefits_srv |
| Extract observed catch by fleet | extr_catch |
| Extract catch observation CVs | extr_catch_cv |
| Extract index CVs | extr_cv |
| Extract input composition sample sizes | extr_effn |
| Extract fished and unfished total biomass | extr_fished_unfished |
| Calculate Francis T1.8 effective sample sizes | extr_francis |
| Extract standardised survey index fits | extr_indices |
| Extract Kobe phase-plot data | extr_kobe |
| Extract fishery length-composition fits | extr_lenfits_fsh |
| Extract fishery mean age fits | extr_meanage_fsh |
| Extract survey mean age fits | extr_meanage_srv |
| Extract fishery mean length fits | extr_meanlen_fsh |
| Extract q break years | extr_q_breaks |
| Extract q trajectories | extr_q_trajectory |
| Extract retrospective data | extr_retro |
| Extract selectivity block break years | extr_sel_breaks |
| Extract fishery selectivity-at-age | extr_sel_fsh |
| Extract survey selectivity-at-age | extr_sel_srv |
| Extract stock-recruitment pairs and curve | extr_sr |
| Extract survey skill data | extr_survey_skill |
| Extract fishery weight-at-age data | extr_wtat_fsh |
| Extract survey weight-at-age data | extr_wtat_srv |
| Calculate figure height for faceted plots | facet_fig_height |
| Calculate or input a fixed Bmsy value for the jjm model Updates the msy_mt table in the jjm output with new B/Bmsy ratios. | fixed_bmsy |
| Get fits to indices | get_age_fits |
| Get estimated catchability coefficients | get_catchabilities |
| Get fishing mortality at age | get_fishing_mortality |
| Get fits to indices | get_index_fits |
| Get fits to length compositions | get_len_fits |
| Get and tidy msy_my table | get_msy_mt |
| Get estimated recruits | get_recruits |
| Get and tidy selectivity-at-age ogives over time by model and fleet | get_selectivities |
| Get total metrics (biomass, spawning biomass, and recruitment) | get_totals |
| Add hypothesis number to a model name | geth |
| Get elements of a list by string matching on name | getter |
| Compute a gray color ramp | gray_ramp |
| Check whether composition data are available | has_comp |
| Build a publication label from a JJM model name | jjm_label |
| JJM annex diagnostic palettes | jjm_pfa_palette |
| Kobe plot | kobe |
| Melt an age-or-length matrix into a long tibble | melt_matrix |
| Bar+line plot of observed vs predicted catch-at-age | plot_catch_age_fits |
| Bubble plot of catch-at-age residuals | plot_catch_age_residuals |
| Plot catch by fleet | plot_catch_fleet |
| Plot composition fits and residuals | plot_comp_fits |
| Plot observed composition ridges | plot_comp_ridge |
| Plot input composition sample sizes | plot_effn |
| Plot fished and unfished biomass | plot_fished_unfished |
| Plot weight at age in the fishery | plot_fishery_weight |
| Plot standard index fit diagnostics | plot_fit_diagnostics |
| Plot Francis T1.8 reweighting diagnostics | plot_francis |
| Plot historical retrospective diagnostics | plot_historic_retro |
| Plot index fits with input CVs | plot_indices_v2 |
| Plot Kobe phase plot | plot_kobe |
| Plot mean age or mean length fits | plot_meanstat |
| Plot metadata overview | plot_metadata_overview |
| Plot q trajectories | plot_q_trajectory |
| Plot retrospective peels | plot_retro |
| Plot selectivity ridges | plot_sel_ridge |
| Plot selectivities by age, year, fleet, and model | plot_selectivities |
| Plot stock-recruitment relationship | plot_sr |
| Plot a summary diagnostics sheet | plot_summary_sheet |
| Plot survey skill ROC curves | plot_survey_skill |
| Plot weight-at-age over time | plot_wtat |
| Plot weight-at-age by cohort | plot_wtat_cohort |
| Plot method for jjm.diag objects | plot.jjm.diag |
| Plot diagnostics | plot.jjm.diagnostics |
| Plot method for jjm.output objects | plot.jjm.output |
| Print a jjm.config object | print.jjm.config |
| Print method for jjm.diag objects | print.jjm.diag |
| Print method for jjm.output objects | print.jjm.output |
| Print a summary of jjm.config | print.summary.jjm.config |
| Print method for summary.jjm.diag objects | print.summary.jjm.diag |
| Print method for summary.jjm.output objects | print.summary.jjm.output |
| Read historical retrospective CSV data | read_historic_retro |
| Read external files | readExFiles |
| Read a model or list of models | readJJM |
| Read dat and ctl files from disk to create a jjm.config object. | readJJMConfig |
| Create a report from JJM outputs | report |
| Run a retrospective analysis diagnostic for a JJM model | retro |
| Fit, run, read and plot a JJM model | runit |
| Run a JJM model | runJJM |
| Run JJM models (default method) | runJJM.default |
| Run JJM models for jjm.config | runJJM.jjm.config |
| Run JJM models for jjm.output | runJJM.jjm.output |
| Identify strong cohorts | strong_cohorts |
| Summarize a jjm.config object | summary.jjm.config |
| Summary method for jjm.diag objects | summary.jjm.diag |
| Summarize all diagnostics from a jjm run | summary.jjm.diagnostics |
| Summary method for jjm.output objects | summary.jjm.output |
| ggplot2 theme for jjmR | theme_jjm |
| Tidy results of JJM model | tidy_JJM |
| Write dat and ctl files from a JJM model stored in R | writeJJM |
