| append_objs_to_list | Append objects to list |
| apply_hcr_om | Calculate the catch value to apply to the current year in the... |
| calc_catch_seas_country | Calculate the catch proportions by country, year, and season |
| calc_mean_age | Calculate mean age in the population |
| calc_mean_waa | Calculate the mean weights-at-age for all rows in a data... |
| calc_quantiles | Calculate quantiles across groups for a given column |
| calc_standard_error_ssb | Calculate the standard error on SSB between the Operating... |
| calc_tac_est_vs_real | Calculated the estimated TAC vs the Realized TAC (from data) |
| col2hex | Convert color name to hex string. Code borrowed from... |
| color_facet_backgrounds | Color the backgrounds of the facet labels in a ggplot object |
| compare_age_comps | Plot a comparison between age in catch for the OM and the old... |
| compare_age_in_catch | Plot the average age in catch for the OM |
| compare_biomass | Plot a comparison biomass (SSB) from the OM and the old OM,... |
| compare_move | Plot movement into each country by season. To use: p <-... |
| compare_tmb_data | Compare two data object inputs for input into... |
| conv_vec_to_mse_df | Convert a vector of aggregated values into a data.frame... |
| create_plot_objects | Create and/or load RDS file contents from multiple MSE runs |
| create_tmb_data | Create the data for 'TMB::MakeADFun()' |
| df_identical | Are matrices identical |
| extract_catch_country | Extract the catch by country using the assessment landings... |
| extract_initial_values | TMB helper function. Extract parameter from 'obj' to use as... |
| extract_params_tmb | Extract parameter estimates from the linear par vector... |
| extract_rep_table | Extract the vectors from a list into a 'tibble::tibble()'.... |
| fetch_extra_mcmc | Create and return a list of stats to attach to the main model... |
| files_exist | Test whether or not files exist. They can be URLs or regular... |
| fill_waa_years | Fill in missing year rows in a weight-at-age data frame with... |
| get_age_dat | Extract row(s) of age data from a data.frame |
| get_args | Get the arguments of the calling function |
| get_em_outputs | Get outputs from the Estimation models |
| get_f | Calculate the fishing mortality based on catch. See Methot &... |
| get_likelihoods | Get likelihood values for a model object the begin with 'ans' |
| get_ref_point | Calculate the catch and F40 value to apply to the next year... |
| get_select | Get a vector of selectivities of the same length as the... |
| get_wa_dfs | Get the weight-at-age data for a particular year |
| get_yrs_mse_list | Get a vector of the years from a list of MSEs |
| hake_theme | ggplot2 theme for hake |
| hake_violin | Violin plot of the MSE results |
| init_agebased_model | Initialize values used in the age based model |
| init_movement_mat | Initialize the movement model matrix. An alternative function... |
| load_data_om | Prepare the data for the operating model |
| load_data_table_from_web | Read in a data table from a CSV data file at a URL on the web |
| load_mse_plot_data | Load an mse plot object RDS file which holds the output of... |
| load_ss_extract_age_comps | Extract the age comp estimates from the SS assessment model... |
| load_ss_model_data | Load the SS model input and output data needed by this... |
| load_ss_parameters | Load a list of parameter estimates from the SS model output |
| load_ss_sel_parameters | Load a selectivity parameter estimates from the SS model... |
| merge_run_data | Merge the run data into individual data frames for easy... |
| modify_wage_df | Modify the 'yr' row in the 'wage' data.frame, copying data... |
| pacifichakemse | Pacific Hake MSE package |
| plot_bars_country | Plot season indicators barplots by country and scenario |
| plot_bars_country_season | Plot faceted barplots by country, season, and scenarios |
| plot_catch_quota | Plot Catch/Quota by scenario |
| plot_catch_quota_1panel | Plot Catch/Quota by scenario all in one panel |
| plot_em_timeseries | Plot the mean of the year medians SSB for all Estimation... |
| plot_exploitation_rate | Plot the exploitation rate (F0) by country and scenario |
| plotSelectivity | Plot selectivity for years |
| plot_selectivity_scenarios | Plot a 3-pane selectivity plot by country for three... |
| plot_standard_error | Plot Standard Error of the Spawning Stock Biomass between the... |
| plot_tac_est_vs_real | Plot TAC vs SSB as a simple line |
| plot_tac_vs_hcr | Plot estimated vs realized TAC (called Catch in plot) by... |
| plot_timeseries | Plot time series data from an MSE or OM simulation run |
| plot_timeseries_runs | Plot individual run output against each other as a time... |
| plotUncertainty | Plot uncertainty for a given parameter |
| plotValues | Plot the estimated or derived value from a 'TMB::MakeADFun()'... |
| plot_violins | Plot faceted violin plots for scenarios, showing performance... |
| plot_violins_country | Plot faceted violin plots by Country for scenarios |
| pr | Wrapper for the 'print()' function |
| run_mses | Run the MSE for a number of runs for any scenarios |
| run_mse_scenario | Run a single MSE scenario |
| run_om | Run the Operating Model, which is an age based model... |
| run_oms | Run OMs for a number of runs |
| run_season_loop_om | Run the Operating model for all seasons and spaces in one... |
| run_year_loop_om | Run the Operating model for all years |
| setup_blank_om_objects | Construct blank objects for Operating model outputs |
| setup_mse_plot_objects | Setup MSE plot data frames, colors, and plot names |
| table_perf_metrics | Create a 'knitr::kable()' table object |
| table_timeseries | Create a 'knitr::kable()' table object |
| update_om_data | Update the OM data for a new year |
