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"calc_fram_scaling", "title": "*[Experimental]* Calculate match/replace df based on scaling", "topics": [ "calc_fram_scaling" ] }, { "page": "calculate_stock_comp", "title": "Plot stock composition", "topics": [ "calculate_stock_comp" ] }, { "page": "change_run_id", "title": "Changes a run's ID number in a FRAM database", "topics": [ "change_run_id" ] }, { "page": "check_bp_coverage", "title": "Check the FisheryScalers and NonRetention have valid values", "topics": [ "check_bp_coverage" ] }, { "page": "coho_mark_rates", "title": "*[Experimental]* Predict Fram encounter markrates by fisheries", "topics": [ "coho_mark_rates" ] }, { "page": "cohort_abundance", "title": "*[Experimental]* Calculate starting cohort abundance", "topics": [ "cohort_abundance" ] }, { "page": "compare_databases", "title": "*[Experimental]* Compare tables in two equivalent FRAM databases", "topics": [ "compare_databases" ] }, { "page": "compare_fishery_input_flags", "title": "Compares the fishery flags of two runs", "concept": [ "comparisons" ], "topics": [ "compare_fishery_input_flags" ] }, { "page": "compare_fishery_inputs", "title": "Compares the fishery inputs of two runs", "concept": [ "comparisons" ], "topics": [ "compare_fishery_inputs" ] }, { "page": "compare_inputs", "title": "Compare FisheryScalers tables between two runs.", "concept": [ "comparisons" ], "topics": [ "compare_inputs" ] }, { "page": "compare_inputs_chart", "title": "Generate heat map of changed values between two run inputs.", "concept": [ "comparisons" ], "topics": [ "compare_inputs_chart" ] }, { "page": "compare_non_retention_input_flags", "title": "Compares the non retention flags of two runs", "topics": [ "compare_non_retention_input_flags" ] }, { "page": "compare_non_retention_inputs", "title": "Compares the non retention inputs of two runs", "concept": [ "comparisons" ], "topics": [ "compare_non_retention_inputs" ] }, { "page": "compare_recruits", "title": "Compares the recruit scalers of two runs", "concept": [ "comparisons" ], "topics": [ "compare_recruits" ] }, { "page": "compare_runs", "title": "Compare key aspects of two FRAM runs", "concept": [ "comparisons" ], "topics": [ "compare_runs" ] }, { "page": "compare_sl_ratio", "title": "Compare Sublegal Ratio tables between two runs.", "concept": [ "comparisons" ], "topics": [ "compare_sl_ratio" ] }, { "page": "compare_stock_fishery_rate_scalers", "title": "Compares the stock fishery rate scalers of two runs", "concept": [ "comparisons" ], "topics": [ "compare_stock_fishery_rate_scalers" ] }, { "page": "connect_fram_db", "title": "Connect to FRAM database", "concept": [ "connections" ], "topics": [ "connect_fram_db" ] }, { "page": "copy_fishery_scalers", "title": "Copying scaler inputs from one run to another", "topics": [ "copy_fishery_scalers" ] }, { "page": "copy_run", "title": "*[Experimental]* Copies a run any number of times", "topics": [ "copy_run" ] }, { "page": "copy_tamm", "title": "*[Experimental]* Copy TAMM for FRAM batch runs", "topics": [ "copy_tamm" ] }, { "page": "create_soncc_pasteable", "title": "Calculate SONCC ER breakdown for STT", "concept": [ "soncc" ], "topics": [ "create_soncc_pasteable" ] }, { "page": "disconnect_all_fram_connections", "title": "Clear all connections", "concept": [ "connections" ], "topics": [ "disconnect_all_fram_connections" ] }, { "page": "disconnect_fram_db", "title": "Safely disconnect from FRAM database", "concept": [ "connections" ], "topics": [ "disconnect_fram_db" ] }, { "page": "fetch_quarto_templates", "title": "Creates quarto template files", "topics": [ "fetch_quarto_templates" ] }, { "page": "fetch_table", "title": "Fetch a complete table from a FRAM database.", "topics": [ "fetch_table", "fetch_table_" ] }, { "page": "fetch_table_bkchin", "title": "Safely fetch Chinook BackwardsFRAM table", "topics": [ "fetch_table_bkchin" ] }, { "page": "filter_ak", "title": "Filters a dataframe to Alaska (AK) fisheries.", "concept": [ "fishery_filters" ], "topics": [ "filter_ak" ] }, { "page": "filter_bc", "title": "Filters a dataframe to Canadian (BC) fisheries.", "concept": [ "fishery_filters" ], "topics": [ "filter_bc" ] }, { "page": "filter_ca", "title": "Filters a dataframe to California (CA) fisheries.", "concept": [ "fishery_filters" ], "topics": [ "filter_ca" ] }, { "page": "filter_coast", "title": "Filters a dataframe to Coastal fisheries.", "concept": [ "fishery_filters" ], "topics": [ "filter_coast" ] }, { "page": "filter_commercial_wa_nt", "title": "Filters a dataframe to WA non-treaty commercial fisheries.", "concept": [ "fishery_filters" ], "topics": [ "filter_commercial_wa_nt" ] }, { "page": "filter_hatchery", "title": "Filters a Coho stock dataframe to hatchery stocks", "concept": [ "stock_filters" ], "topics": [ "filter_hatchery" ] }, { "page": "filter_marine", "title": "Filters a dataframe to marine fisheries.", "concept": [ "fishery_filters" ], "topics": [ "filter_marine" ] }, { "page": "filter_mixed", "title": "Filters a Coho stock dataframe to mixed stocks", "concept": [ "stock_filters" ], "topics": [ "filter_mixed" ] }, { "page": "filter_net", "title": "Filters a dataframe to net fisheries.", "concept": [ "fishery_filters" ], "topics": [ "filter_net" ] }, { "page": "filter_or", "title": "Filters a dataframe to Oregon (OR) fisheries.", "concept": [ "fishery_filters" ], "topics": [ "filter_or" ] }, { "page": "filter_puget_sound", "title": "Filters a dataframe to Puget Sound fisheries.", "concept": [ "fishery_filters" ], "topics": [ "filter_puget_sound" ] }, { "page": "filter_sport", "title": "Filters a dataframe to sport fisheries.", "concept": [ "fishery_filters" ], "topics": [ "filter_sport" ] }, { "page": "filter_stt", "title": "Filters a Coho dataframe to STT fisheries", "concept": [ "fishery_filters" ], "topics": [ "filter_stt" ] }, { "page": "filter_stt_nt", "title": "Filters a Coho dataframe to non-treaty STT fisheries", "concept": [ "fishery_filters" ], "topics": [ "filter_stt_nt" ] }, { "page": "filter_wa", "title": "Filters a dataframe to fisheries in Washington state.", "concept": [ "fishery_filters" ], "topics": [ "filter_wa" ] }, { "page": "filter_wild", "title": "Filters a Coho stock dataframe to wild stocks", "concept": [ "stock_filters" ], "topics": [ "filter_wild" ] }, { "page": "fishery_mortality", "title": "Returns a tibble matching the Fishery Mortality screen.", "topics": [ "fishery_mortality" ] }, { "page": "initialize_project", "title": "*[Experimental]* Initializes a FRAM project", "topics": [ "initialize_project" ] }, { "page": "label_fisheries_db", "title": "Label fisheries based on FRAM database", "concept": [ "labelers" ], "topics": [ "label_fisheries_db" ] }, { "page": "label_flags", "title": "Provide flag translations to dataframe", "concept": [ "labelers" ], "topics": [ "label_flags" ] }, { "page": "label_stocks_db", "title": "Label stocks based on FRAM database", "concept": [ "labelers" ], "topics": [ "label_stocks_db" ] }, { "page": "label_timesteps_db", "title": "Label timesteps based on FRAM database", "concept": [ "labelers" ], "topics": [ "label_timesteps_db" ] }, { "page": "list_extant_fram_connections", "title": "Describe existing fram connections (including orphans)", "concept": [ "connections" ], "topics": [ "list_extant_fram_connections" ] }, { "page": "make_batch_runs", "title": "Make batch runs", "topics": [ "make_batch_runs" ] }, { "page": "management_week", "title": "Vectorized approach to calculating the management week", "topics": [ "management_week" ] }, { "page": "modify_table", "title": "*[Experimental]* Modify FRAM database based on match/replace dataframe", "topics": [ "modify_table" ] }, { "page": "mortality_scalers", "title": "Quantify the proportion of fishery mortalities associated with stock(s) of interest", "topics": [ "mortality_scalers" ] }, { "page": "msf_encounters", "title": "Reproduce MSF encounters screen", "topics": [ "msf_encounters" ] }, { "page": "msf_landed_catch", "title": "Reproduce MSF landed catch screen", "topics": [ "msf_landed_catch" ] }, { "page": "msf_mortalities", "title": "Reproduce MSF mortalities screen", "topics": [ "msf_mortalities" ] }, { "page": "msp_mortality", "title": "Expand Chinook mortality table using Model-Stock Proportion", "topics": [ "msp_mortality" ] }, { "page": "na_non_retention_from_flag", "title": "NA's unused CNR input columns.", "topics": [ "na_non_retention_from_flag" ] }, { "page": "na_scalers_from_flag", "title": "NA's unused scalers", "topics": [ "na_scalers_from_flag" ] }, { "page": "plot_impacts_per_catch_heatmap", "title": "Make plots to show the amount of landed catch_per_impact", "topics": [ "plot_impacts_per_catch_heatmap" ] }, { "page": "plot_stock_comp", "title": "Plot stock composition", "topics": [ "plot_stock_comp" ] }, { "page": "plot_stock_mortality", "title": "Plot total mortalities by fishery", "topics": [ "plot_stock_mortality" ] }, { "page": "plot_stock_mortality_time_step", "title": "Plot total mortalities by fishery and timestep", "topics": [ "plot_stock_mortality_time_step" ] }, { "page": "population_statistics", "title": "Replicate Population Statistics screen", "topics": [ "population_statistics" ] }, { "page": "post_season_abundance", "title": "Generates post-season January age 3 abundances by stock from post-season databases.", "topics": [ "post_season_abundance" ] }, { "page": "remove_run", "title": "Removes a run in a FRAM database", "topics": [ "remove_run" ] }, { "page": "run_info", "title": "Provides a print out of Run ID information", "topics": [ "run_info" ] }, { "page": "sensitivity_custom", "title": "*[Experimental]* Generate sensitivity analyses runs based on a list of match/replace dataframes", "concept": [ "sensitivity" ], "topics": [ "sensitivity_custom" ] }, { "page": "sensitivity_exact", "title": "*[Experimental]* Generate sensitivity analyses runs based on exact values", "concept": [ "Sensitivity" ], "topics": [ "sensitivity_exact" ] }, { "page": "sensitivity_scaled", "title": "*[Experimental]* Generate sensitivity analyses runs scaled by template values", "concept": [ "Sensitivity" ], "topics": [ "sensitivity_scaled" ] }, { "page": "statistical_week", "title": "Vectorized approach to calculating the statistical week, returns an integer", "topics": [ "statistical_week" ] }, { "page": "stock_fate", "title": "*[Experimental]*", "topics": [ "stock_fate" ] }, { "page": "stock_mortality", "title": "Replicate Stock Mortality screen", "topics": [ "stock_mortality" ] }, { "page": "terminal_fisheries", "title": "*[Experimental]* List terminal stock information", "topics": [ "terminal_fisheries" ] }, { "page": "terminal_info", "title": "*[Experimental]* Parse TAAETRS table", "topics": [ "terminal_info" ] }, { "page": "terminal_stocks", "title": "*[Experimental]* List terminal stock information", "topics": [ "terminal_stocks" ] }, { "page": "translate_nr_flag", "title": "Provides English translation of numeric non-retention flags", 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