Man pages for fb4package
'Fish Bioenergetics 4.0' Model Implementation with High-Performance 'TMB' Backend
| accumulate_validations | Accumulate multiple validation results |
| add_confidence_bands | Add Confidence Bands to Plot |
| add_plot_annotations | Add Standard Plot Annotations |
| add_strategy_metadata | Add standard strategy metadata to results |
| analysis-core | Core Analysis Functions for FB4 Results |
| analysis-extraction | Basic Analysis and Extraction Functions for FB4 Results |
| analysis-nutritional | Nutritional Analysis Functions for FB4 Results |
| analysis-sensitivity | Sensitivity and Comparative Analysis Functions for FB4... |
| analyze_composition_by_size | Analyze body composition by size range |
| analyze_composition_changes | Analyze composition changes with growth |
| analyze_energy_budget | Analyze energy budget from FB4 results |
| analyze_feeding_performance | Analyze feeding performance from FB4 results |
| analyze_growth_patterns | Analyze growth patterns from FB4 results |
| analyze_growth_temperature_sensitivity | Analyze growth rate sensitivity to temperature and feeding... |
| analyze_population_variation | Analyze population variation in hierarchical models |
| assess_diet_quality | Assess nutritional quality of diet |
| assign_energy_components | Fill energy budget components from a named source list |
| basic-validators | Basic Validation Functions for FB4 |
| binary_search_p_value | Binary search for optimal p_value |
| Bioenergetic | Constructor for Bioenergetic Objects |
| bioenergetic-classes | S3 Classes for FB4 Bioenergetic Model |
| bioenergetic-methods | Methods for FB4 Bioenergetic Model |
| body-composition | Body Composition Functions for FB4 Model |
| bootstrap_p_values | Bootstrap estimation of p_values with optional parallel... |
| bootstrap_single_iteration | Execute a single bootstrap iteration |
| build_composition_df | Build a body-composition data frame from a list of... |
| build_fb4_result_unified | Build FB4 result object |
| build_individual_uncertainty | Build individual-level uncertainty list for hierarchical... |
| build_population_uncertainty | Build population-level uncertainty list for hierarchical... |
| build_tmb_uncertainty | Build TMB uncertainty list for MLE results |
| calculate_activity_factor_respiration | Calculate activity factor for respiration (Mid-level) |
| calculate_body_composition | Calculate complete body composition (Mid-level - Main... |
| calculate_combined_survival | Calculate combined daily survival (Low-level) |
| calculate_component_from_water | Estimate composition from water using Breck (2014) regression... |
| calculate_confidence_intervals | Confidence interval from estimate and standard error |
| calculate_consumption | Calculate daily consumption (Mid-level - Main function) |
| calculate_consumption_params_eq2 | Calculate additional parameters for consumption equation 2... |
| calculate_consumption_params_eq3 | Calculate additional parameters for consumption equation 3... |
| calculate_contaminant_accumulation | Calculate contaminant accumulation (Mid-level - Main... |
| calculate_daily_consumption | Calculate daily consumption with multiple methods (Low-level) |
| calculate_daily_metabolism | Calculate daily metabolic processes (Low-level) |
| calculate_daily_spawn_energy | Calculate reproductive energy loss for the day (Low-level) |
| calculate_daily_weight_change | Calculate daily weight change (Low-level) |
| calculate_dissolved_fraction | Calculate dissolved fraction of contaminant (Low-level) |
| calculate_egestion | Calculate daily egestion (Mid-level - Main function) |
| calculate_energy_density | Calculate energy density from fat and protein (Low-level) |
| calculate_excretion | Calculate daily excretion (Mid-level - Main function) |
| calculate_fat_by_subtraction | Calculate fat content by subtraction (Low-level) |
| calculate_final_weight_fb4 | Calculate final weight using FB4 equations (Mid-level) |
| calculate_fish_water_partition | Calculate fish:water partition coefficient (Low-level) |
| calculate_gill_efficiency | Calculate gill uptake efficiency (Low-level) |
| calculate_growth_metrics | Calculate Basic Growth Metrics |
| calculate_mortality_reproduction | Calculate daily mortality and reproduction (Mid-level - Main... |
| calculate_np_ratios | Calculate N:P ratios for all processes |
| calculate_nutrient_allocation | Generic nutrient allocation in bioenergetic model (Low-level) |
| calculate_nutrient_balance | Calculate nutrient balance (Mid-level - Main function) |
| calculate_nutrient_efficiencies | Calculate nutrient retention efficiencies |
| calculate_predator_energy_density | Calculate predator energy density (Mid-level - Main function) |
| calculate_progress_interval | Calculate appropriate progress reporting interval |
| calculate_reproductive_loss | Calculate reproductive weight loss (Low-level) |
| calculate_respiration | Calculate daily respiration (Mid-level - Main function) |
| calculate_respiration_params_eq2 | Calculate additional parameters for respiration equation 2... |
| calculate_sda | Calculate Specific Dynamic Action (SDA) (Low-level) |
| calculate_spawn_energy | Calculate spawning energy loss (Low-level) |
| calculate_stoichiometric_balance | Calculate stoichiometric balance |
| calculate_temperature_dependent_mortality | Calculate temperature-dependent mortality (Low-level) |
| calculate_temperature_factor_consumption | Calculate temperature factor for consumption (Mid-level) |
| calculate_temperature_factor_respiration | Calculate temperature factor for respiration (Mid-level) |
| calculate_weight_dependent_mortality | Calculate weight-dependent mortality (Low-level) |
| check_bioenergetic_readiness | Check Bioenergetic Object Readiness |
| check_numeric_value | Check Numeric Value |
| check_target_achievement | Check if target was achieved for traditional methods |
| check_tmb_compilation | Check TMB model availability (simplified for installed... |
| check_weight_outliers | Check for outliers in weight data |
| clamp | Clamp values to a range |
| close_save_device | Close graphics device after saving |
| compare_individuals | Compare individuals from hierarchical models |
| compare_scenarios | Compare multiple FB4 results |
| compare_with_redfield | Compare N:P ratios with Redfield ratios |
| comprehensive_nutritional_analysis | Comprehensive nutritional analysis |
| compute_likelihood_profile | Compute likelihood profile for p_value |
| consumption-functions | Consumption Functions for FB4 Model |
| consumption_temp_eq1 | Temperature function for consumption - Equation 1 (Low-level) |
| consumption_temp_eq2 | Temperature function for consumption - Equation 2 (Low-level) |
| consumption_temp_eq3 | Temperature function for consumption - Equation 3 (Low-level) |
| consumption_temp_eq4 | Temperature function for consumption - Equation 4 (Low-level) |
| contaminant-accumulation | Contaminant Accumulation Functions for FB4 Model |
| contaminant_model_1 | Contaminant model 1 - Food uptake only (Low-level) |
| contaminant_model_2 | Contaminant model 2 - With temperature and weight dependent... |
| contaminant_model_3 | Contaminant model 3 - Arnot & Gobas (2004) (Low-level) |
| convert_daily_results_to_dataframe | Convert list of daily results to data frame |
| convert_respiration_to_energy | Convert respiration from O2 to energy units (Utility) |
| convert_to_individual_data | Convert hierarchical observed_weights to individual_data... |
| core-validators | Core Validation Functions for FB4 |
| create_binary_search_strategy | Create Binary Search Strategy |
| create_bootstrap_strategy | Create Bootstrap Strategy |
| create_direct_strategy | Create Direct Strategy |
| create_empty_composition | Create empty composition for invalid inputs (Utility) |
| create_error_result | Create standardized error result |
| create_execution_plan | Create execution plan for FB4 strategies |
| create_execution_summary | Create execution summary for verbose output |
| create_fb4_strategy | Create FB4 strategy based on method |
| create_hierarchical_strategy | Create Hierarchical Strategy |
| create_individual_rankings | Create individual rankings across metrics |
| create_individual_summary | Create summary statistics for individual metric |
| create_method_specific_data | Create method-specific data section |
| create_mle_strategy | Create MLE Strategy |
| create_optim_strategy | Create Optim Strategy |
| create_result_summary | Comprehensive post-simulation analysis summary |
| create_unified_fit_info | Create unified fit info section |
| create_unified_summary | Build the '$summary' slot of an fb4_result object |
| data-processing | Data Processing Functions for FB4 |
| data-validators | Data Validation Functions for FB4 |
| detect_method | Detect method from raw results or execution plan |
| detect_result_type | Detect method and backend from fb4_result |
| egestion-excretion | Egestion and Excretion Functions for FB4 Model |
| egestion_model_1 | Egestion model 1 - Basic (Low-level) |
| egestion_model_2 | Egestion model 2 - Elliott (1976) (Low-level) |
| egestion_model_3 | Egestion model 3 - Stewart et al. (1983) (Low-level) |
| egestion_model_4 | Egestion model 4 - Elliott (1976) without p_value (Low-level) |
| EQUATION_REQUIREMENTS | Equation requirements for all FB4 components |
| excretion_model_1 | Excretion model 1 - Basic (Low-level) |
| excretion_model_2 | Excretion model 2 - With temperature and feeding dependence... |
| excretion_model_3 | Excretion model 3 - Variant of model 2 (Low-level) |
| excretion_model_4 | Excretion model 4 - Without feeding dependence (Low-level) |
| execute_daily_simulation | Execute single day simulation (Mid-level) |
| execute_hierarchical_tmb | Execute hierarchical TMB using unified architecture and... |
| execute_mle_tmb | Execute MLE TMB using unified architecture |
| execute_simulation_with_method | Execute simulation with any method |
| extract_adreport_values | Extract ADREPORT values from TMB report |
| extract_basic_parameters | Extract parameters for basic model |
| extract_data_sources | Extract data sources from bioenergetic object |
| extract_hierarchical_parameters | Extract parameters for hierarchical model |
| extract_species_name | Extract Species Information for Titles |
| extract_strategy_parameters | Extract common strategy parameters from execution plan |
| extract_tmb_results | Extract comprehensive results from TMB optimization |
| fb4-analysis-plots | Analysis Plots for FB4 Results (Uncertainty and Sensitivity) |
| fb4-bioenergetic-plots | Bioenergetic Object Plots for Setup Validation |
| fb4-daily-plots | Daily Simulation Plots for FB4 Results |
| fb4package-package | Fish Bioenergetics 4.0 Package |
| fb4-plot-core | Core Plotting Functions for FB4 Results |
| fb4-plots | FB4 Plotting Functions |
| FB4Strategy | FB4 Strategy Interface |
| FB4-TMB-Shared | FB4 TMB Shared Functions |
| fish4_parameters | Fish Bioenergetics 4.0 Official Parameters Database |
| fish4_parameters_metadata | Fish Bioenergetics 4.0 Parameters Database Metadata |
| fit_fb4_binary_search | Fit FB4 model using binary search |
| fit_fb4_bootstrap | Fit FB4 model using bootstrap estimation with parallel option |
| fit_fb4_mle | Fit FB4 model using Maximum Likelihood Estimation |
| fit_fb4_optim | Fit FB4 model using optim() |
| format_statistics_text | Format Statistics Text for Plots |
| generate_reproduction_pattern | Generate seasonal reproduction pattern (Low-level) |
| get_available_plot_types | Get Available Plot Types |
| get_color_scheme | Get Color Scheme for Plots |
| get_consumption_uncertainty | Get consumption results with uncertainty |
| get_efficiency_uncertainty | Get efficiency results with uncertainty |
| get_energy_budget_uncertainty | Get energy budget components with uncertainty |
| get_individual_results | Get individual results from hierarchical models |
| get_parameter_value | Get Parameter Value from Species Parameters |
| get_population_results | Get population results from hierarchical models |
| has_uncertainty | Check if result has uncertainty information |
| identify_best_scenarios | Identify best performing scenarios |
| interpolate_time_series | Interpolate time series with error handling |
| is.Bioenergetic | Test if Object is Bioenergetic |
| is.fb4_result | Test if Object is fb4_result |
| log_execution_plan | Log execution plan details |
| main-validators | Main Validation Functions for FB4 |
| mle_estimate_p_value_lognormal | Maximum Likelihood Estimation for p_value using log-normal... |
| mortality-reproduction | Mortality and Reproduction Functions for FB4 Model |
| neg_log_likelihood_lognormal | Calculate negative log-likelihood for log-normal weight... |
| normalize_diet_proportions | Normalize diet proportions to sum to 1 |
| nutrient_efficiency_block | Compute efficiency metrics for a single nutrient |
| nutrient-regeneration | Nutrient Regeneration Functions for FB4 Model |
| op-null-default | Null-coalescing operator |
| optim_search_p_value | Optimization using optim() for optimal p_value |
| parameter-processing | Parameter Processing Functions for FB4 |
| parameter-validators | Parameter Validation Functions for FB4 |
| perform_scenario_tests | Perform statistical tests between scenarios |
| plot_bio_dashboard | Plot Bioenergetic dashboard |
| plot_bio_diet | Plot Bioenergetic diet |
| plot.Bioenergetic | Plot Bioenergetic object setup |
| plot_bio_energy | Plot Bioenergetic energy |
| plot_bio_temperature | Plot Bioenergetic temperature |
| plot_bootstrap_distributions | Plot bootstrap distributions |
| plot_bootstrap_uncertainty | Plot bootstrap uncertainty |
| plot_consumption | Plot consumption patterns |
| plot_dashboard | Create dashboard overview |
| plot_distributions.fb4_result | Plot parameter distributions for bootstrap and hierarchical... |
| plot_energy | Plot energy budget components |
| plot_estimate_panel | Draw a single parameter estimate panel with confidence... |
| plot.fb4_result | Plot FB4 simulation results |
| plot_growth | Plot growth trajectory |
| plot_growth_temperature_sensitivity | Plot sensitivity analysis |
| plot_growth_vs_temperature | Plot growth rate vs temperature |
| plot_hierarchical_distributions | Plot hierarchical distributions |
| plot_hierarchical_uncertainty | Plot hierarchical uncertainty |
| plot_mle_uncertainty | Plot MLE uncertainty |
| plot_sensitivity.fb4_result | Plot temperature sensitivity analysis for a Bioenergetic... |
| plot_temperature | Plot temperature profile |
| plot_uncertainty.fb4_result | Plot parameter uncertainty for probabilistic methods |
| predator-energy-density | Predator Energy Density Functions for FB4 Model |
| predator_energy_eq1 | Energy density from interpolated data - Equation 1... |
| predator_energy_eq2 | Linear piecewise energy density - Equation 2 (Low-level) |
| predator_energy_eq3 | Power function energy density - Equation 3 (Low-level) |
| predict_consumption_bootstrap | Bootstrap method for consumption uncertainty propagation |
| predict_consumption_delta | Delta method for consumption uncertainty propagation |
| prepare_simulation_data | Prepare all simulation data |
| print.Bioenergetic | Print Method for Bioenergetic Objects |
| print.fb4_result | Print Method for fb4_result Objects |
| process_bioenergetic_data | Process Bioenergetic object temporal data for simulation |
| process_composition_params | Process body composition parameters |
| process_consumption_params | Process consumption parameters |
| process_contaminant_params | Process contaminant parameters |
| process_egestion_params | Process egestion parameters |
| process_excretion_params | Process excretion parameters |
| process_mortality_params | Process mortality parameters |
| process_nutrient_params | Process nutrient parameters |
| process_predator_energy_data | Process predator energy data for equation 1 (PREDEDEQ = 1) |
| process_predator_params | Process predator energy density parameters |
| process_reproduction_data | Process reproduction data |
| process_reproduction_pattern | Process reproduction pattern |
| process_respiration_params | Process respiration parameters |
| process_simulation_settings | Process simulation settings |
| process_species_parameters | Process all species parameters for simulation |
| process_temperature | Process single temperature with all p-values |
| report_simulation_progress | Report simulation progress |
| report_simulation_summary | Report final simulation summary |
| respiration-functions | Respiration Functions for FB4 Model |
| respiration_temp_eq1 | Temperature function for respiration - Equation 1 (Low-level) |
| respiration_temp_eq2 | Temperature function for respiration - Equation 2 (Low-level) |
| result-builders-unified | Result Builders for FB4 Model |
| run_fb4 | Run FB4 Simulation |
| run_fb4.Bioenergetic | Run FB4 simulation on Bioenergetic object |
| run_fb4_direct_method | Run FB4 with direct method |
| run-fb4-orchestrator | FB4 Main Orchestrator |
| run_fb4_simulation | Run complete FB4 simulation (Mid-level - Main function) |
| run_final_simulation | Run final simulation with optimal parameter |
| run_robust_optimization | Run robust optimization with multiple fallback strategies |
| run_single_optimization | Run single optimization attempt |
| safe_exp | Safe exponential |
| safe_extract_param | Safe parameter extraction with defaults |
| safe_sqrt | Safe square root |
| sdr_assign_scalars | Batch-assign scalar estimate/SE pairs to a results list |
| sdr_pull_est | Pull a scalar estimate from an sdreport summary |
| sdr_pull_se | Pull a scalar standard error from an sdreport summary |
| sdr_pull_vec | Pull a vector of estimates and SEs from an sdreport summary |
| set_diet | Set Diet Data for Bioenergetic Objects |
| set_environment | Set Environmental Data for Bioenergetic Objects |
| set_parameter_value | Set Parameter Value in Species Parameters |
| set_simulation_settings | Set Simulation Settings for Bioenergetic Objects |
| setup_plot_layout | Setup Plot Layout |
| setup_save_device | Setup graphics device for saving |
| should_mark_as_fitted | Determine if bio_obj should be marked as fitted |
| simulation-engine | Simulation Engine for FB4 Model |
| solve_weight_iterative | Solve weight using iterative method (Mid-level) |
| solve_weight_linear_segments | Solve weight for linear segments (Low-level) |
| solve_weight_power_function | Solve weight for power function (Low-level) |
| strategy-binary-search | Binary Search Strategy for FB4 Model |
| strategy-bootstrap | Bootstrap Estimation Strategy for FB4 Model |
| strategy-commons | Strategy Commons for FB4 Model |
| strategy-direct | Direct Strategies for FB4 Model |
| strategy-hierarchical | Hierarchical Estimation Strategy for FB4 Model |
| strategy-interface | Strategy Interface and Factory for FB4 Model |
| strategy-mle | Maximum Likelihood Estimation Strategy for FB4 Model |
| strategy-optim | Optimisation Strategy for FB4 Model |
| summary.Bioenergetic | Summary Method for Bioenergetic Objects |
| summary.fb4_result | Summary Method for fb4_result Objects |
| test_metric_differences | Test differences between metric estimates |
| transform_to_tmb_basic | Transform simulation data to TMB basic format |
| transform_to_tmb_hierarchical | Transform simulation data to TMB hierarchical format |
| uncertainty-prediction | FB4 Uncertainty Propagation Functions |
| update_body_composition | Update body composition during simulation (Mid-level) |
| utils | Utility Functions for fb4package |
| validate_backend_compatibility | Validate backend compatibility |
| validate_basic_params | Validate Basic Model Parameters |
| validate_bioenergetic_for_simulation | Comprehensive validation for Bioenergetic objects |
| validate_body_composition | Validate body composition |
| validate_category_equation | Validate equation parameters for a specific category |
| validate_common_strategy_inputs | Validate common strategy inputs |
| validate_complete_simulation_data | Validate complete simulation data |
| validate_contaminant_params | Validate contaminant parameters |
| validate_data_consistency | Validate data consistency between components |
| validate_diet_consistency | Validate Consistency Between Diet and Energy Data |
| validate_equation_params | Validate equation parameters against requirements |
| validate_fb4_inputs | Validate inputs for FB4 simulation |
| validate_fb4_result | Validate unified result object structure |
| validate_fb4_system | Validate complete FB4 system ready for simulation |
| validate_fitting_settings | Validate fitting settings |
| validate_fit_to_strategy_concordance | Validate concordance between fit_to and strategy parameters |
| validate_fraction | Validate fraction values (0-1 range) |
| validate_individual_data | Validate individual data for hierarchical models |
| validate_numeric_core | Core numeric validation with flexible handling strategies |
| validate_nutrient_concentrations | Validate nutrient concentrations |
| validate_parameter_ranges | Validate parameter ranges |
| validate_plot_data | Validate Plot Data Availability |
| validate_positive | Validate positive values |
| validate_predator_energy_params | Validate predator energy density parameters |
| validate_predator_requirements | Validate predator requirements (special data handling) |
| validate_range_core | Core range validation with multiple strategies |
| validate_respiration_requirements | Validate respiration requirements (multiple categories) |
| validate_species_equations | Main function to validate all species equations |
| validate_statistical_method_inputs | Validate statistical strategy inputs |
| validate_structure_core | Core data structure validation |
| validate_temperature | Validate temperature values |
| validate_temporal_data | Validate temporal data |
| validate_time_series_data | Validate Time Series Data Structure (Basic Level) |
| validate_tmb_objective | Validate TMB objective function |
| validation_result | Create standardized validation result |
