| %||% |
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| Bioenergetic |
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| EQUATION_REQUIREMENTS |
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| FB4-TMB-Shared |
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| FB4Strategy |
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| `%||%` |
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| accumulate_validations |
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| add_confidence_bands |
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| add_plot_annotations |
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| add_strategy_metadata |
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| analysis-core |
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| analysis-extraction |
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| analysis-nutritional |
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| analysis-sensitivity |
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| analyze_composition_by_size |
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| analyze_composition_changes |
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| analyze_energy_budget |
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| analyze_feeding_performance |
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| analyze_growth_patterns |
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| analyze_growth_temperature_sensitivity |
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| analyze_population_variation |
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| assess_diet_quality |
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| assign_energy_components |
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| basic-validators |
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| binary_search_p_value |
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| bioenergetic-classes |
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| bioenergetic-methods |
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| body-composition |
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| bootstrap_p_values |
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| bootstrap_single_iteration |
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| build_composition_df |
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| build_fb4_result_unified |
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| build_individual_uncertainty |
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| build_population_uncertainty |
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| build_tmb_uncertainty |
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| calculate_activity_factor_respiration |
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| calculate_body_composition |
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| calculate_combined_survival |
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| calculate_component_from_water |
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| calculate_confidence_intervals |
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| calculate_consumption |
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| calculate_consumption_params_eq2 |
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| calculate_consumption_params_eq3 |
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| calculate_contaminant_accumulation |
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| calculate_daily_consumption |
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| calculate_daily_metabolism |
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| calculate_daily_spawn_energy |
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| calculate_daily_weight_change |
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| calculate_dissolved_fraction |
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| calculate_egestion |
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| calculate_energy_density |
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| calculate_excretion |
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| calculate_fat_by_subtraction |
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| calculate_final_weight_fb4 |
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| calculate_fish_water_partition |
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| calculate_gill_efficiency |
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| calculate_growth_metrics |
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| calculate_mortality_reproduction |
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| calculate_np_ratios |
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| calculate_nutrient_allocation |
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| calculate_nutrient_balance |
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| calculate_nutrient_efficiencies |
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| calculate_predator_energy_density |
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| calculate_progress_interval |
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| calculate_reproductive_loss |
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| calculate_respiration |
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| calculate_respiration_params_eq2 |
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| calculate_sda |
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| calculate_spawn_energy |
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| calculate_stoichiometric_balance |
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| calculate_temperature_dependent_mortality |
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| calculate_temperature_factor_consumption |
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| calculate_temperature_factor_respiration |
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| calculate_weight_dependent_mortality |
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| check_bioenergetic_readiness |
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| check_numeric_value |
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| check_target_achievement |
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| check_tmb_compilation |
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| check_weight_outliers |
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| clamp |
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| close_save_device |
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| compare_individuals |
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| compare_scenarios |
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| compare_with_redfield |
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| comprehensive_nutritional_analysis |
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| compute_likelihood_profile |
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| consumption-functions |
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| consumption_temp_eq1 |
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| consumption_temp_eq2 |
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| consumption_temp_eq3 |
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| consumption_temp_eq4 |
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| contaminant-accumulation |
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| contaminant_model_1 |
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| contaminant_model_2 |
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| contaminant_model_3 |
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| convert_daily_results_to_dataframe |
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| convert_respiration_to_energy |
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| convert_to_individual_data |
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| core-validators |
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| create_binary_search_strategy |
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| create_bootstrap_strategy |
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| create_direct_strategy |
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| create_empty_composition |
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| create_error_result |
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| create_execution_plan |
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| create_execution_summary |
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| create_fb4_strategy |
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| create_hierarchical_strategy |
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| create_individual_rankings |
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| create_individual_summary |
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| create_method_specific_data |
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| create_mle_strategy |
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| create_optim_strategy |
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| create_result_summary |
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| create_unified_fit_info |
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| create_unified_summary |
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| data-processing |
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| data-validators |
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| detect_method |
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| detect_result_type |
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| egestion-excretion |
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| egestion_model_1 |
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| egestion_model_2 |
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| egestion_model_3 |
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| egestion_model_4 |
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| excretion_model_1 |
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| excretion_model_2 |
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| excretion_model_3 |
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| excretion_model_4 |
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| execute_daily_simulation |
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| execute_hierarchical_tmb |
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| execute_mle_tmb |
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| execute_simulation_with_method |
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| extract_adreport_values |
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| extract_basic_parameters |
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| extract_data_sources |
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| extract_hierarchical_parameters |
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| extract_species_name |
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| extract_strategy_parameters |
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| extract_tmb_results |
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| fb4-analysis-plots |
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| fb4-bioenergetic-plots |
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| fb4-daily-plots |
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| fb4-plot-core |
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|
| fb4-plots |
Man page
|
| fb4package |
Man page
|
| fb4package-package |
Man page
|
| fish4_parameters |
Man page
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| fish4_parameters_metadata |
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|
| fit_fb4_binary_search |
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|
| fit_fb4_bootstrap |
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| fit_fb4_mle |
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| fit_fb4_optim |
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| format_statistics_text |
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| generate_reproduction_pattern |
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|
| get_available_plot_types |
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| get_color_scheme |
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|
| get_consumption_uncertainty |
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|
| get_efficiency_uncertainty |
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| get_energy_budget_uncertainty |
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| get_individual_results |
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|
| get_parameter_value |
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|
| get_population_results |
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|
| has_uncertainty |
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Source code
|
| identify_best_scenarios |
Man page
Source code
|
| interpolate_time_series |
Man page
Source code
|
| is.Bioenergetic |
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Source code
|
| is.fb4_result |
Man page
Source code
|
| log_execution_plan |
Man page
Source code
|
| main-validators |
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|
| mle_estimate_p_value_lognormal |
Man page
Source code
|
| mortality-reproduction |
Man page
|
| neg_log_likelihood_lognormal |
Man page
Source code
|
| normalize_diet_proportions |
Man page
Source code
|
| nutrient-regeneration |
Man page
|
| nutrient_efficiency_block |
Man page
Source code
|
| op-null-default |
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| optim_search_p_value |
Man page
Source code
|
| parameter-processing |
Man page
|
| parameter-validators |
Man page
|
| perform_scenario_tests |
Man page
Source code
|
| plot.Bioenergetic |
Man page
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|
| plot.fb4_result |
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Source code
|
| plot_bio_dashboard |
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Source code
|
| plot_bio_diet |
Man page
Source code
|
| plot_bio_energy |
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Source code
|
| plot_bio_temperature |
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Source code
|
| plot_bootstrap_distributions |
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|
| plot_bootstrap_uncertainty |
Man page
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|
| plot_consumption |
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Source code
|
| plot_dashboard |
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|
| plot_distributions.fb4_result |
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|
| plot_energy |
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|
| plot_estimate_panel |
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|
| plot_growth |
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|
| plot_growth_temperature_sensitivity |
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|
| plot_growth_vs_temperature |
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|
| plot_hierarchical_distributions |
Man page
Source code
|
| plot_hierarchical_uncertainty |
Man page
Source code
|
| plot_mle_uncertainty |
Man page
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|
| plot_sensitivity.fb4_result |
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|
| plot_temperature |
Man page
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|
| plot_uncertainty.fb4_result |
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Source code
|
| predator-energy-density |
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|
| predator_energy_eq1 |
Man page
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|
| predator_energy_eq2 |
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|
| predator_energy_eq3 |
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|
| predict_consumption_bootstrap |
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|
| predict_consumption_delta |
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Source code
|
| prepare_simulation_data |
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Source code
|
| print.Bioenergetic |
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Source code
|
| print.fb4_result |
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Source code
|
| process_bioenergetic_data |
Man page
Source code
|
| process_composition_params |
Man page
Source code
|
| process_consumption_params |
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Source code
|
| process_contaminant_params |
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Source code
|
| process_egestion_params |
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Source code
|
| process_excretion_params |
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Source code
|
| process_mortality_params |
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Source code
|
| process_nutrient_params |
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Source code
|
| process_predator_energy_data |
Man page
Source code
|
| process_predator_params |
Man page
Source code
|
| process_reproduction_data |
Man page
Source code
|
| process_reproduction_pattern |
Man page
Source code
|
| process_respiration_params |
Man page
Source code
|
| process_simulation_settings |
Man page
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|
| process_species_parameters |
Man page
Source code
|
| process_temperature |
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Source code
|
| report_simulation_progress |
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|
| report_simulation_summary |
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Source code
|
| respiration-functions |
Man page
|
| respiration_temp_eq1 |
Man page
Source code
|
| respiration_temp_eq2 |
Man page
Source code
|
| result-builders-unified |
Man page
|
| run-fb4-orchestrator |
Man page
|
| run_fb4 |
Man page
Source code
|
| run_fb4.Bioenergetic |
Man page
Source code
|
| run_fb4.default |
Man page
Source code
|
| run_fb4_direct_method |
Man page
Source code
|
| run_fb4_simulation |
Man page
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|
| run_final_simulation |
Man page
Source code
|
| run_robust_optimization |
Man page
Source code
|
| run_single_optimization |
Man page
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|
| safe_exp |
Man page
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|
| safe_extract_param |
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|
| safe_sqrt |
Man page
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|
| sdr_assign_scalars |
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|
| sdr_pull_est |
Man page
Source code
|
| sdr_pull_se |
Man page
Source code
|
| sdr_pull_vec |
Man page
Source code
|
| set_diet |
Man page
Source code
|
| set_diet.Bioenergetic |
Source code
|
| set_environment |
Man page
Source code
|
| set_environment.Bioenergetic |
Source code
|
| set_parameter_value |
Man page
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|
| set_simulation_settings |
Man page
Source code
|
| set_simulation_settings.Bioenergetic |
Source code
|
| setup_plot_layout |
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|
| setup_save_device |
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|
| should_mark_as_fitted |
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|
| simulation-engine |
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| solve_weight_iterative |
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Source code
|
| solve_weight_linear_segments |
Man page
Source code
|
| solve_weight_power_function |
Man page
Source code
|
| strategy-binary-search |
Man page
|
| strategy-bootstrap |
Man page
|
| strategy-commons |
Man page
|
| strategy-direct |
Man page
|
| strategy-hierarchical |
Man page
|
| strategy-interface |
Man page
|
| strategy-mle |
Man page
|
| strategy-optim |
Man page
|
| summary.Bioenergetic |
Man page
Source code
|
| summary.fb4_result |
Man page
Source code
|
| test_metric_differences |
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|
| transform_to_tmb_basic |
Man page
Source code
|
| transform_to_tmb_hierarchical |
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Source code
|
| uncertainty-prediction |
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|
| update_body_composition |
Man page
Source code
|
| utils |
Man page
|
| validate_backend_compatibility |
Man page
Source code
|
| validate_basic_params |
Man page
Source code
|
| validate_bioenergetic_for_simulation |
Man page
Source code
|
| validate_body_composition |
Man page
Source code
|
| validate_category_equation |
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Source code
|
| validate_common_strategy_inputs |
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|
| validate_complete_simulation_data |
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Source code
|
| validate_contaminant_params |
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Source code
|
| validate_data_consistency |
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Source code
|
| validate_diet_consistency |
Man page
Source code
|
| validate_equation_params |
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|
| validate_fb4_inputs |
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Source code
|
| validate_fb4_result |
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|
| validate_fb4_system |
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Source code
|
| validate_fit_to_strategy_concordance |
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| validate_fitting_settings |
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| validate_fraction |
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Source code
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| validate_individual_data |
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| validate_numeric_core |
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| validate_nutrient_concentrations |
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|
| validate_parameter_ranges |
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| validate_plot_data |
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| validate_positive |
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| validate_predator_energy_params |
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Source code
|
| validate_predator_requirements |
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|
| validate_range_core |
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|
| validate_respiration_requirements |
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Source code
|
| validate_species_equations |
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|
| validate_standard_requirements |
Source code
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| validate_statistical_method_inputs |
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| validate_structure_core |
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| validate_temperature |
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| validate_temporal_data |
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| validate_time_series_data |
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| validate_tmb_objective |
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| validation_result |
Man page
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| z_score |
Source code
|
