Bioenergetic            Constructor for Bioenergetic Objects
FB4-TMB-Shared          FB4 TMB Shared Functions
accumulate_validations
                        Accumulate multiple validation 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 Results
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 levels
analyze_population_variation
                        Analyze population variation in hierarchical
                        models
assess_diet_quality     Assess nutritional quality of diet
basic-validators        Basic Validation Functions for FB4
bioenergetic-classes    S3 Classes for FB4 Bioenergetic Model
bioenergetic-methods    Methods for FB4 Bioenergetic Model
body-composition        Body Composition Functions for FB4 Model
calculate_body_composition
                        Calculate complete body composition (Mid-level
                        - Main function)
calculate_consumption   Calculate daily consumption (Mid-level - Main
                        function)
calculate_contaminant_accumulation
                        Calculate contaminant accumulation (Mid-level -
                        Main function)
calculate_egestion      Calculate daily egestion (Mid-level - Main
                        function)
calculate_excretion     Calculate daily excretion (Mid-level - Main
                        function)
calculate_final_weight_fb4
                        Calculate final weight using FB4 equations
                        (Mid-level)
calculate_mortality_reproduction
                        Calculate daily mortality and reproduction
                        (Mid-level - Main function)
calculate_np_ratios     Calculate N:P ratios for all processes
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_respiration   Calculate daily respiration (Mid-level - Main
                        function)
calculate_stoichiometric_balance
                        Calculate stoichiometric balance
check_numeric_value     Check Numeric Value
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
consumption-functions   Consumption Functions for FB4 Model
contaminant-accumulation
                        Contaminant Accumulation Functions for FB4
                        Model
core-validators         Core Validation Functions for FB4
create_empty_composition
                        Create empty composition for invalid inputs
                        (Utility)
create_result_summary   Comprehensive post-simulation analysis summary
data-processing         Data Processing Functions for FB4
data-validators         Data Validation Functions for FB4
egestion-excretion      Egestion and Excretion Functions for FB4 Model
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
fb4-plot-core           Core Plotting Functions for FB4 Results
fb4-plots               FB4 Plotting Functions
fish4_parameters        Fish Bioenergetics 4.0 Official Parameters
                        Database
fish4_parameters_metadata
                        Fish Bioenergetics 4.0 Parameters Database
                        Metadata
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
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
main-validators         Main Validation Functions for FB4
mortality-reproduction
                        Mortality and Reproduction Functions for FB4
                        Model
nutrient-regeneration   Nutrient Regeneration Functions for FB4 Model
parameter-processing    Parameter Processing Functions for FB4
parameter-validators    Parameter Validation Functions for FB4
plot.Bioenergetic       Plot Bioenergetic object setup
plot.fb4_result         Plot FB4 simulation results
plot_distributions.fb4_result
                        Plot parameter distributions for bootstrap and
                        hierarchical methods
plot_growth_temperature_sensitivity
                        Plot sensitivity analysis
plot_sensitivity.fb4_result
                        Plot temperature sensitivity analysis for a
                        Bioenergetic object
plot_uncertainty.fb4_result
                        Plot parameter uncertainty for probabilistic
                        methods
predator-energy-density
                        Predator Energy Density Functions for FB4 Model
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_params
                        Process predator energy density parameters
process_respiration_params
                        Process respiration parameters
process_simulation_settings
                        Process simulation settings
process_species_parameters
                        Process all species parameters for simulation
respiration-functions   Respiration Functions for FB4 Model
result-builders-unified
                        Result Builders for FB4 Model
run-fb4-orchestrator    FB4 Main Orchestrator
run_fb4                 Run FB4 Simulation
run_fb4.Bioenergetic    Run FB4 simulation on Bioenergetic object
run_fb4_simulation      Run complete FB4 simulation (Mid-level - Main
                        function)
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
simulation-engine       Simulation Engine for FB4 Model
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
uncertainty-prediction
                        FB4 Uncertainty Propagation Functions
update_body_composition
                        Update body composition during simulation
                        (Mid-level)
utils                   Utility Functions for fb4package
validate_basic_params   Validate Basic Model Parameters
validate_bioenergetic_for_simulation
                        Comprehensive validation for Bioenergetic
                        objects
validate_body_composition
                        Validate body composition
validate_contaminant_params
                        Validate contaminant parameters
validate_fb4_inputs     Validate inputs for FB4 simulation
validate_fb4_system     Validate complete FB4 system ready for
                        simulation
validate_fraction       Validate fraction values (0-1 range)
validate_individual_data
                        Validate individual data for hierarchical
                        models
validate_nutrient_concentrations
                        Validate nutrient concentrations
validate_positive       Validate positive values
validate_predator_energy_params
                        Validate predator energy density parameters
validate_species_equations
                        Main function to validate all species equations
validate_temperature    Validate temperature values
validate_time_series_data
                        Validate Time Series Data Structure (Basic
                        Level)
validation_result       Create standardized validation result
