| %>% |
Man page
|
| .onLoad |
Source code
|
| .onUnload |
Source code
|
| SetUpHakeBDS.fn |
Source code
|
| add_extra_ribbon_data |
Man page
Source code
|
| add_major_ticks |
Man page
Source code
|
| add_newlines |
Man page
Source code
|
| add_utm_columns |
Man page
Source code
|
| age_bubble_cohorts |
Man page
|
| age_diag_linecolor |
Man page
|
| age_diag_linetype |
Man page
|
| age_diag_linewidth |
Man page
|
| age_fillcolor |
Man page
|
| alt_text_inject_tags |
Man page
Source code
|
| as_ts_mcmc |
Man page
Source code
|
| assess_changes_df |
Man page
|
| assess_history_df |
Man page
|
| assess_history_probs_df |
Man page
|
| axis_label_color |
Man page
|
| axis_tick_font_size |
Man page
|
| axis_title_font_size |
Man page
|
| beta_get_shape_params |
Man page
Source code
|
| bind_cols_quiet |
Man page
Source code
|
| calc_ageerror |
Man page
Source code
Source code
|
| calc_fishery_ages |
Man page
Source code
|
| calc_historical_probs |
Man page
Source code
|
| calc_lw_params |
Man page
Source code
|
| calc_mcmc |
Man page
Source code
|
| calc_mcmc_param_stats |
Man page
Source code
|
| calc_proportions |
Source code
|
| calc_quantiles |
Man page
Source code
|
| calc_quantiles_by_group |
Man page
Source code
|
| calc_refpt_quants |
Man page
Source code
|
| calc_retro_stats |
Man page
Source code
|
| calc_risk |
Man page
Source code
|
| calc_sum_rec_devs |
Man page
Source code
|
| calc_yoob |
Man page
Source code
|
| calculate_is_confidential |
Source code
|
| can_catch_by_year_fn |
Man page
|
| can_ft_age_df |
Man page
|
| can_ft_age_props_fn |
Man page
|
| can_ft_bottom_depth_df |
Man page
|
| can_ft_catch_by_month_df |
Man page
|
| can_ft_catch_by_month_fn |
Man page
|
| can_ft_gear_depth_df |
Man page
|
| can_ft_num_fish |
Man page
|
| can_jv_age_props_fn |
Man page
|
| can_jv_catch_by_month_df |
Man page
|
| can_jv_catch_by_month_fn |
Man page
|
| can_jv_num_fish |
Man page
|
| can_raw_ft_age_counts_fn |
Man page
|
| can_raw_jv_age_counts_fn |
Man page
|
| can_raw_ss_age_counts_fn |
Man page
|
| can_sample_data_rds_fn |
Man page
|
| can_ss_age_df |
Man page
|
| can_ss_age_props_fn |
Man page
|
| can_ss_bottom_depth_df |
Man page
|
| can_ss_catch_by_month_df |
Man page
|
| can_ss_catch_by_month_fn |
Man page
|
| can_ss_gear_depth_df |
Man page
|
| can_ss_num_fish |
Man page
|
| can_waa_fn |
Man page
|
| canada_create_age_proportions_csv |
Man page
Source code
|
| canada_create_commercial_waa |
Man page
Source code
|
| canada_create_fleet_month_catch_csv_files |
Man page
Source code
|
| canada_create_fleet_year_catch_csv_files |
Man page
Source code
|
| canada_depth_sql_fn |
Man page
|
| canada_extract_depth_data_from_db |
Man page
Source code
|
| canada_extract_fleet_catch |
Man page
Source code
|
| canada_extract_samples_from_db |
Man page
Source code
|
| canada_extract_sampling_by_month |
Man page
Source code
|
| canada_get_fleet_samples |
Man page
Source code
|
| canada_load_catch_data |
Man page
Source code
|
| canada_load_sample_data |
Man page
Source code
|
| canada_sql_inject_fishery_filters |
Man page
Source code
|
| caption_adjustments_fn |
Man page
|
| catch_targets_biomass_fn |
Man page
|
| catch_targets_df |
Man page
|
| check_catch_levels |
Man page
Source code
|
| check_forecasts |
Man page
Source code
|
| clean |
Man page
Source code
|
| clean_all |
Man page
Source code
|
| cohort_catch |
Man page
Source code
|
| combine_historical_probs |
Man page
Source code
|
| commLFs.fn |
Source code
|
| comp_report_fn |
Man page
|
| compute_hexagon_xy |
Man page
Source code
|
| control_fn |
Man page
|
| convert_ctl_file_param_dfs |
Man page
Source code
|
| covar_fn |
Man page
|
| create_data_hake |
Man page
Source code
|
| create_depth_by_year_csv_files |
Man page
Source code
|
| create_fontsize_str |
Man page
Source code
|
| create_group_df_biomass |
Man page
Source code
|
| create_group_df_index |
Man page
Source code
|
| create_group_df_recr |
Man page
Source code
|
| create_rds_attach_forecasts |
Man page
Source code
|
| create_rds_attach_retrospectives |
Man page
Source code
|
| create_rds_file |
Man page
Source code
|
| create_rds_files_retro |
Man page
Source code
|
| create_rds_natage |
Man page
Source code
|
| create_sens_dirs |
Man page
Source code
|
| create_version_dirs |
Man page
Source code
|
| ct |
Man page
|
| ct_levels_catch_tol |
Man page
|
| ct_levels_max_iter |
Man page
|
| ct_levels_path |
Man page
|
| ct_levels_spr_tol |
Man page
|
| curr_time_date |
Man page
Source code
|
| data_fn |
Man page
|
| data_new_ssnew_fn |
Man page
|
| data_ssnew_fn |
Man page
|
| data_tables_path |
Man page
|
| dbeta_ab |
Man page
Source code
|
| default_hr_path |
Man page
|
| delete_dirs |
Man page
Source code
|
| delete_rds_files |
Man page
Source code
|
| derposts_fn |
Man page
|
| dirclip |
Man page
Source code
|
| doc_path |
Man page
|
| dointerpSimple |
Source code
|
| draw_arrows_yoob |
Man page
Source code
|
| enact_privacy_rule |
Man page
Source code
|
| estimate_tv_weight_at_age |
Man page
Source code
|
| extract_alt_text |
Man page
Source code
|
| extract_inline_rcode |
Man page
Source code
|
| extract_inside_catch |
Man page
Source code
|
| extract_label_from_figure_filename |
Man page
Source code
|
| extract_mcmc_quant |
Man page
Source code
|
| extract_rep_table |
Man page
Source code
|
| extract_sigma_r |
Man page
Source code
|
| extract_survey_index_fits |
Man page
Source code
|
| f |
Man page
Source code
|
| f_date |
Man page
Source code
|
| f_vessel_type |
Man page
Source code
|
| fill_wtage_matrix |
Source code
|
| firstup |
Man page
Source code
|
| fit_lw |
Man page
Source code
|
| fix_posteriors |
Man page
Source code
|
| fix_title_case_for_csl |
Man page
Source code
|
| forecast_descriptions_fn |
Man page
|
| forecast_fn |
Man page
|
| forecasts_path |
Man page
|
| forecasts_prepend |
Man page
|
| further_tac_details_fn |
Man page
|
| further_tac_df |
Man page
|
| get_age_comp_limits |
Man page
Source code
|
| get_age_prop |
Man page
Source code
|
| get_age_proportions_by_fleet |
Man page
Source code
|
| get_assess_yr |
Man page
Source code
|
| get_col_name_from_key_title |
Man page
Source code
|
| get_crs |
Man page
Source code
|
| get_data_yr |
Man page
Source code
|
| get_depth_by_year |
Man page
Source code
|
| get_doc_type |
Man page
Source code
|
| get_key_nuisance_posts |
Man page
Source code
|
| get_local |
Man page
Source code
|
| get_obj_sizes |
Man page
Source code
|
| get_os |
Man page
Source code
|
| get_param_est_comparison_df |
Man page
Source code
|
| get_post_cols |
Man page
Source code
|
| get_posterior_data |
Man page
Source code
|
| get_prior_data |
Man page
Source code
|
| get_prior_string |
Man page
Source code
|
| get_rate_by_month |
Source code
|
| get_rec_ci |
Man page
Source code
|
| get_ss3_exe_name |
Man page
Source code
|
| get_year_range |
Man page
|
| goback |
Man page
Source code
|
| gotest |
Man page
Source code
|
| gotest_beamer_get_src_dest_filenames |
Man page
Source code
|
| gotest_doc_get_src_dest_filenames |
Man page
Source code
|
| group_test_models |
Man page
|
| hake |
Man page
|
| hake_beamer |
Man page
Source code
|
| hake_pdf |
Man page
Source code
|
| hake_theme |
Man page
Source code
|
| hakedata_wd |
Man page
Source code
|
| heatmap_add_extrap_yrs_wa |
Man page
Source code
|
| heatmap_calc_function |
Man page
Source code
|
| heatmap_extract_sample_size |
Man page
Source code
|
| heatmap_get_wa_ggplot_vals |
Man page
Source code
|
| heatmap_set_colors |
Man page
Source code
|
| hex_coords |
Man page
|
| insert_row |
Man page
Source code
|
| key_posteriors |
Man page
|
| key_posteriors_fn |
Man page
|
| key_posteriors_titles |
Man page
|
| kriging_pars_df |
Man page
|
| landings_tac_fn |
Man page
|
| large_cohorts |
Man page
|
| latex_amp |
Man page
Source code
|
| latex_bold |
Man page
Source code
|
| latex_cline |
Man page
Source code
|
| latex_italics |
Man page
Source code
|
| latex_mcol |
Man page
Source code
|
| latex_size_str |
Man page
Source code
|
| latex_subscr |
Man page
Source code
|
| latex_under |
Man page
Source code
|
| linebreaker |
Man page
Source code
|
| load_age |
Source code
|
| load_age_fishery |
Man page
|
| load_all_models_in_subdir |
Man page
|
| load_can_age_data |
Man page
Source code
|
| load_ct_levels |
Man page
Source code
|
| load_extra_mcmc |
Man page
Source code
|
| load_extra_mcmc_age_comps |
Man page
Source code
|
| load_extra_mcmc_atage |
Man page
Source code
|
| load_extra_mcmc_biomass |
Man page
Source code
|
| load_extra_mcmc_catage_biomass |
Man page
Source code
|
| load_extra_mcmc_get_chunk |
Man page
Source code
|
| load_extra_mcmc_get_parameter_chunk |
Man page
Source code
|
| load_extra_mcmc_init_nage |
Man page
Source code
|
| load_extra_mcmc_m |
Man page
Source code
|
| load_extra_mcmc_naa |
Source code
|
| load_extra_mcmc_recr_cohorts |
Man page
Source code
|
| load_extra_mcmc_recr_devs |
Man page
Source code
|
| load_extra_mcmc_repfiles |
Man page
Source code
|
| load_extra_mcmc_sel |
Man page
Source code
|
| load_extra_mcmc_selwt |
Man page
Source code
|
| load_forecasts |
Man page
Source code
|
| load_mcmc_vals |
Man page
Source code
|
| load_parameter_priors |
Man page
Source code
|
| load_ss_files |
Man page
Source code
|
| main_alpha |
Man page
|
| main_fill |
Man page
|
| make_major_tick_labels |
Man page
Source code
|
| make_wtatage_plots |
Man page
Source code
|
| makeimage |
Source code
|
| maturity_at_age |
Man page
|
| maturity_estimates_df |
Man page
|
| maturity_samples_df |
Man page
|
| mcmc_path |
Man page
|
| minor_tick_length |
Man page
|
| model_output_log_fn |
Man page
|
| model_setup |
Man page
Source code
|
| modify_starter_mcmc_type |
Man page
Source code
|
| mutsel |
Man page
|
| nuisance_posteriors_fn |
Man page
|
| number_to_word |
Man page
Source code
|
| obj_sizes |
Man page
Source code
|
| object_placement_fn |
Man page
|
| ordered_decision_table_paths |
Man page
|
| out_csv_path |
Man page
|
| output_permissions |
Man page
|
| ovary_samples_df |
Man page
|
| pacea_save |
Man page
Source code
|
| pad_num |
Man page
Source code
|
| pad_weight_at_age |
Man page
Source code
|
| par_fn |
Man page
|
| plot_age_comp_bubbles |
Man page
Source code
|
| plot_age_comp_bubbles_data |
Man page
Source code
|
| plot_age_comp_comparison_bubbles |
Man page
Source code
|
| plot_age_comp_fit |
Man page
Source code
|
| plot_assessment_history_biomass |
Man page
Source code
|
| plot_assessment_history_disp |
Man page
Source code
|
| plot_assessment_timeline |
Man page
Source code
|
| plot_autocor |
Man page
Source code
|
| plot_biomass |
Man page
Source code
|
| plot_biomass_fished_unfished |
Man page
|
| plot_bubbles |
Man page
Source code
|
| plot_catch_by_month |
Man page
Source code
|
| plot_catchability_density |
Man page
Source code
|
| plot_catches |
Man page
Source code
|
| plot_cohort_catch |
Man page
Source code
|
| plot_color |
Man page
Source code
|
| plot_colour |
Man page
Source code
|
| plot_comparison |
Man page
|
| plot_cumulative_catch_cohorts |
Man page
Source code
|
| plot_data_summary |
Man page
Source code
|
| plot_density |
Man page
Source code
|
| plot_depl_fore_comparison |
Man page
Source code
|
| plot_depth |
Man page
Source code
|
| plot_depth_2_panel |
Man page
Source code
|
| plot_depth_4_panel |
Man page
Source code
|
| plot_during_loading |
Man page
Source code
|
| plot_exploitation_fraction |
Man page
Source code
|
| plot_fecundity |
Man page
Source code
|
| plot_fishing_intensity |
Man page
Source code
|
| plot_fore_age_comps |
Man page
Source code
|
| plot_fore_compare |
Man page
Source code
|
| plot_heatmap_sample_size_weight_at_age |
Man page
Source code
|
| plot_heatmap_weight_at_age |
Man page
Source code
|
| plot_historical_probs |
Man page
Source code
|
| plot_historical_probs_retro |
Man page
Source code
|
| plot_intensity_illustration |
Man page
Source code
|
| plot_management_catch_vs_tac |
Man page
Source code
|
| plot_management_catch_vs_tac_1_to_1 |
Man page
Source code
|
| plot_map |
Man page
Source code
|
| plot_maturity_ogives |
Man page
Source code
|
| plot_mcmc_diagnostics |
Man page
Source code
|
| plot_mcmc_diagnostics_all_params |
Man page
Source code
|
| plot_mcmc_histogram |
Man page
Source code
|
| plot_overview_map |
Man page
Source code
|
| plot_pairs |
Man page
Source code
|
| plot_param_density |
Man page
Source code
|
| plot_pearson_bubbles |
Man page
Source code
|
| plot_phase |
Man page
Source code
|
| plot_priors_vs_posts |
Man page
Source code
|
| plot_raw_age |
Man page
Source code
|
| plot_recdevs |
Man page
Source code
|
| plot_recruitment |
Man page
Source code
|
| plot_rel_biomass |
Man page
Source code
|
| plot_rel_recruitment |
Man page
Source code
|
| plot_retro_recruits |
Man page
Source code
|
| plot_retro_yrs |
Man page
|
| plot_running_quants |
Man page
Source code
|
| plot_selex_mountains |
Man page
Source code
|
| plot_selex_posteriors |
Man page
Source code
|
| plot_selex_uncertainty |
Man page
Source code
|
| plot_spatial_cpue |
Man page
Source code
|
| plot_spr_illustration |
Man page
Source code
|
| plot_squid |
Man page
Source code
|
| plot_stock_recruitment |
Man page
|
| plot_survey_biomass |
Man page
Source code
|
| plot_survey_fit_mcmc |
Man page
Source code
|
| plot_survey_index_fits |
Man page
Source code
|
| plot_theme |
Man page
Source code
|
| plot_trace |
Man page
Source code
|
| plot_weight_at_age |
Man page
Source code
Source code
|
| plot_weight_at_age_outlier |
Man page
Source code
|
| plot_weights_lengths |
Man page
Source code
|
| ports_df |
Man page
|
| post_process |
Man page
Source code
|
| post_process_add_alt_text |
Man page
Source code
|
| post_process_add_appendix_counter_resets |
Man page
Source code
|
| post_process_add_counters |
Man page
Source code
|
| post_process_add_headers_footers |
Man page
Source code
|
| post_process_add_horiz_lines_decision_table |
Man page
Source code
|
| post_process_add_picture_to_title_page |
Man page
Source code
|
| post_process_add_start_appendices_code |
Man page
Source code
|
| post_process_add_vert_space_after_header |
Man page
Source code
|
| post_process_add_xcolor_package |
Source code
|
| post_process_beamer |
Man page
Source code
|
| post_process_beamer_add_extra_headers_etc |
Man page
Source code
|
| post_process_beamer_insert_disclaimer |
Man page
Source code
|
| post_process_beamer_insert_title_page_logos |
Man page
Source code
|
| post_process_beamer_make_title_page_plain |
Man page
Source code
|
| post_process_convert_section_headers |
Man page
Source code
|
| post_process_error_check |
Man page
Source code
|
| post_process_extract_chunks |
Man page
Source code
|
| post_process_fix_landscape_issues |
Man page
Source code
|
| post_process_fix_tildes |
Man page
Source code
|
| post_process_interlace_chunks |
Man page
Source code
|
| post_process_landscape_figures |
Man page
Source code
|
| post_process_landscape_tables |
Man page
Source code
|
| post_process_longtables |
Man page
Source code
|
| post_process_modify_font_info |
Man page
Source code
|
| post_process_modify_link_colors |
Man page
Source code
|
| post_process_move_table_captions |
Man page
Source code
|
| post_process_object_placement |
Man page
Source code
|
| post_process_remove_title_page_number |
Man page
Source code
|
| post_process_repair_unnumbered_section_links |
Man page
Source code
|
| post_process_set_latex_placement_options |
Man page
Source code
|
| post_process_table_of_contents |
Man page
Source code
|
| posts_fn |
Man page
|
| probs |
Man page
|
| probs_forecast |
Man page
|
| process_age_sea |
Man page
Source code
|
| process_age_shore |
Man page
Source code
|
| process_atsea_year |
Source code
|
| process_catch_norpac |
Man page
Source code
|
| process_catch_pacfin |
Man page
Source code
|
| process_database |
Man page
Source code
|
| process_weight_at_age_survey |
Man page
Source code
|
| process_weight_at_age_us |
Man page
Source code
|
| psv_fn |
Man page
|
| pull_research_survey_file_names |
Source code
|
| pull_survey_age_proportions |
Man page
Source code
|
| pull_survey_weight_at_age |
Man page
Source code
|
| quotas |
Man page
|
| rbeta_ab |
Man page
Source code
|
| read_bookdown_file |
Man page
Source code
|
| read_research_year_bio_file |
Source code
|
| recruit_dev_start_yr |
Man page
|
| refpt_bo_linecolor |
Man page
|
| refpt_bo_linetype |
Man page
|
| refpt_bo_linewidth |
Man page
|
| refpt_lrp_linecolor |
Man page
|
| refpt_lrp_linetype |
Man page
|
| refpt_lrp_linewidth |
Man page
|
| refpt_usr_linecolor |
Man page
|
| refpt_usr_linetype |
Man page
|
| refpt_usr_linewidth |
Man page
|
| regex_eml_recdevs |
Man page
|
| regex_extra_mcmc_compreport |
Man page
|
| regex_extra_mcmc_report |
Man page
|
| regex_main_recdevs |
Man page
|
| regex_recdev_all |
Man page
|
| regex_recdev_early |
Man page
|
| remove_forecast_outputs |
Man page
Source code
|
| render |
Man page
Source code
|
| replace_dotted_paths |
Man page
Source code
|
| report_fn |
Man page
|
| retropectives_path |
Man page
|
| retrospective_yrs |
Man page
|
| retrospectives_prepend |
Man page
|
| rich.colors.short |
Source code
|
| rich_colors_short |
Man page
Source code
|
| run_adnuts |
Man page
Source code
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| run_adnuts_timed |
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| run_catch_levels_copy_input_files |
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| run_ct_levels |
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| run_ct_levels_default_hr |
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| run_ct_levels_spr_100 |
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| run_ct_levels_stable_catch |
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| run_extra_forecasts |
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| run_forecasts |
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| run_retrospectives |
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| sampling_history_df |
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| sanitize.text.function |
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| save_nuts_fits |
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| set_ct_levels |
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| set_dirs |
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| ship_to_source |
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| show_ss_output |
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| split_prior_info |
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| spr_100_path |
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| sql_path |
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| ss_executable |
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| ss_input_files |
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| sso_path |
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| stable_catch_path |
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| start_yr |
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| start_yr_age_comps |
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| starter_fn |
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| states_df |
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| stop_quietly |
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| surv_yrs |
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| survey_end_yr |
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| survey_history_df |
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| survey_start_yr |
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| system_ |
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| table_above_avg_cohorts_yrs |
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| table_age_data |
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| table_assessment_changes |
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| table_at_age |
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| table_biomass |
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| table_catch |
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| table_catch_by_fleet |
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| table_catch_tac_summary |
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| table_ci_posteriors |
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| table_cohort |
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| table_decision |
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| table_decision_original |
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| table_fishing_intensity |
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| table_fore_age_props |
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| table_input_age_data |
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| table_landings_tac |
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| table_maturity_ogive |
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| table_median_posteriors |
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| table_ovary_samples |
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| table_param_est |
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| table_param_est_bounds |
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| table_param_est_last_year_hardcoded |
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| table_parameters_long_summary |
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| table_recruitment |
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| table_reference_points |
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| table_risk |
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| table_sampling_by_month |
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| table_sampling_history |
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| table_survey_by_country |
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| table_survey_history |
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| table_yearly_model_compare |
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| test_extract_inline_rcode |
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| top_coh |
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| ts_linegap |
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| ts_linewidth |
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| ts_pointshape |
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| ts_pointsize |
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| ts_pointstroke |
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| ts_ribbon_alpha |
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| ts_ribbon_linetype |
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| ts_single_model_linecolor |
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| ts_single_model_linetype |
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| ts_single_model_linewidth |
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| ts_single_model_pointcolor |
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| ts_single_model_pointshape |
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| ts_single_model_pointsize |
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| ts_single_model_pointstroke |
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| ts_single_model_ribbon_fill |
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| ts_single_model_ribbon_linetype |
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| unfished_eq_yr |
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| update_ss3_ageing_error |
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| update_ss3_catch |
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| update_ss3_maturity |
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| update_ss3_recruitment_year |
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| update_ss3_selectivity |
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| update_ss3_weight_at_age |
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| us_atsea_bottom_depth_df |
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| us_atsea_fishing_depth_df |
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| us_cp_age_df |
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| us_cp_age_props_fn |
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| us_cp_catch_by_month_df |
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| us_cp_prop_tac |
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| us_extract_sampling_by_month |
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| us_ms_age_df |
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| us_ms_age_props_fn |
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| us_ms_catch_by_month_df |
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| us_ms_prop_tac |
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| us_research_catch_by_month_df |
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| us_sb_age_props_fn |
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| us_ss_age_df |
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| us_ss_catch_by_month_df |
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| us_ss_prop_tac |
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| us_ti_ct_by_month_df |
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| usa_get_passwords |
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| usa_pull_data |
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| usa_query_database |
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| utils_update_catch_sums |
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| vec2df |
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| weight_age_sample_sizes_df |
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| weight_at_age_estimates_df |
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| weight_at_age_fn |
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| weight_at_age_outlier |
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| weight_at_age_read |
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| weight_at_age_wide |
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| wrap_by |
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| write_wtatage_file |
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| yaml_check_margin_format |
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