Files in pacific-hake/pacifichakemse

Management Strategy Evaluation of Pacific Hake

R/create-plot-objects.R R/create-tmb-data.R R/extract_catch_country.R R/fetch-extra-mcmc.R R/get_em_outputs.R R/get_f.R R/get_ref_point.R R/get_select.R R/get_wage_dataframes.R R/hake_violin.R R/init-movement-mat.R R/init_agebased_model.R R/load-ss-extract-age-comps.R R/load-ss-model-data.R R/load-ss-parameters.R R/load-ss-sel-parameters.R R/load_dat_om.R R/load_mse_plot_data.R R/merge_run_data.R R/pacifichakemse.R R/plotSelectivity.R R/plotUncertainty.R R/plotValues.R R/plot_bars_country.R R/plot_bars_country_season.R R/plot_catch_quota.R R/plot_em_timeseries.R R/plot_exploitation_rate.R R/plot_om.R R/plot_standard_error.R R/plot_tac_estimated_vs_realized.R R/plot_timeseries.R R/plot_timeseries_runs.R R/plot_violins.R R/plot_violins_country.R R/run_mse_scenario.R R/run_mses.R R/run_om.R R/run_oms.R R/run_season_loop_om.R R/run_year_loop_om.R R/setup_mse_plot_objects.R R/table_perf_metrics.R R/table_timeseries.R R/theme.R R/update_om_data.R R/utils-append-objs-to-list.R R/utils-apply-hcr-om.R R/utils-calc-catch-seas-country.R R/utils-calc-mean-age.R R/utils-calc-mean-waa.R R/utils-calc-quantiles-by-group.R R/utils-calc-quantiles.R R/utils-calc-standard-error-ssb.R R/utils-calc-tac-est-vs-real.R R/utils-calc-term-quantiles.R R/utils-col2hex.R R/utils-color-facet-backgrounds.R R/utils-compare-tmb-data.R R/utils-conv-vec-to-mse-df.R R/utils-df-identical.R R/utils-extract-initial-values.R R/utils-extract-params-tab.R R/utils-extract-rep-table.R R/utils-files-exist.R R/utils-fill-waa-years.R R/utils-get-age-dat.R R/utils-get-args.R R/utils-get-likelihoods.R R/utils-get-yrs-mse-list.R R/utils-load-data-table-from-web.R R/utils-modify-wage-df.R R/utils-pr.R R/utils-setup-blank-om-objects.R R/zzz.R README.md man/append_objs_to_list.Rd man/apply_hcr_om.Rd man/calc_catch_seas_country.Rd man/calc_mean_age.Rd man/calc_mean_waa.Rd man/calc_quantiles.Rd man/calc_standard_error_ssb.Rd man/calc_tac_est_vs_real.Rd man/col2hex.Rd man/color_facet_backgrounds.Rd man/compare_age_comps.Rd man/compare_age_in_catch.Rd man/compare_biomass.Rd man/compare_move.Rd man/compare_tmb_data.Rd man/conv_vec_to_mse_df.Rd man/create_plot_objects.Rd man/create_tmb_data.Rd man/df_identical.Rd man/extract_catch_country.Rd man/extract_initial_values.Rd man/extract_params_tmb.Rd man/extract_rep_table.Rd man/fetch_extra_mcmc.Rd man/files_exist.Rd man/fill_waa_years.Rd man/get_age_dat.Rd man/get_args.Rd man/get_em_outputs.Rd man/get_f.Rd man/get_likelihoods.Rd man/get_ref_point.Rd man/get_select.Rd man/get_wa_dfs.Rd man/get_yrs_mse_list.Rd man/hake_theme.Rd man/hake_violin.Rd man/init_agebased_model.Rd man/init_movement_mat.Rd man/load_data_om.Rd man/load_data_table_from_web.Rd man/load_mse_plot_data.Rd man/load_ss_extract_age_comps.Rd man/load_ss_model_data.Rd man/load_ss_parameters.Rd man/load_ss_sel_parameters.Rd man/merge_run_data.Rd man/modify_wage_df.Rd man/pacifichakemse.Rd man/plotSelectivity.Rd man/plotUncertainty.Rd man/plotValues.Rd man/plot_bars_country.Rd man/plot_bars_country_season.Rd man/plot_catch_quota.Rd man/plot_catch_quota_1panel.Rd man/plot_em_timeseries.Rd man/plot_exploitation_rate.Rd man/plot_selectivity_scenarios.Rd man/plot_standard_error.Rd man/plot_tac_est_vs_real.Rd man/plot_tac_vs_hcr.Rd man/plot_timeseries.Rd man/plot_timeseries_runs.Rd man/plot_violins.Rd man/plot_violins_country.Rd man/pr.Rd man/run_mse_scenario.Rd man/run_mses.Rd man/run_om.Rd man/run_oms.Rd man/run_season_loop_om.Rd man/run_year_loop_om.Rd man/setup_blank_om_objects.Rd man/setup_mse_plot_objects.Rd man/table_perf_metrics.Rd man/table_timeseries.Rd man/update_om_data.Rd tests/testthat.R tests/testthat/test-append-objs-to-list.R tests/testthat/test-calc-quantiles.R tests/testthat/test-calc-term-quantiles.R tests/testthat/test-conv-vec-to-mse-df.R tests/testthat/test-extract-age-comps.R tests/testthat/test-func-name.R tests/testthat/test-get-age-dat.R tests/testthat/test-get-select.R tests/testthat/test-get-yrs-mse-list.R tests/testthat/test-init-movement-mat.R tests/testthat/test-modify-wage-df.R tests/testthat/test-plot-bars-country-season.R tests/testthat/test-plot-bars-country.R tests/testthat/test-plot-exploitation-rate.R tests/testthat/test-plot-standard-error.R tests/testthat/test-plot-tac-estimated-vs-realized.R tests/testthat/test-plot-timeseries.R tests/testthat/test-run-om.R