# 'Fish Bioenergetics 4.0' Model Implementation with High-Performance 'TMB' Backend

## Documentation for package ‘fb4package’ version 2.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G I M N P R S U V

## -- A --

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

## -- B --

basic-validators | Basic Validation Functions for FB4
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

## -- C --

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

## -- D --

data-processing | Data Processing Functions for FB4
data-validators | Data Validation Functions for FB4

## -- E --

egestion-excretion | Egestion and Excretion Functions for FB4 Model

## -- F --

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
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

## -- G --

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

## -- I --

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

## -- M --

main-validators | Main Validation Functions for FB4
mortality-reproduction | Mortality and Reproduction Functions for FB4 Model

## -- N --

nutrient-regeneration | Nutrient Regeneration Functions for FB4 Model

## -- P --

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

## -- R --

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.default | Run FB4 Simulation
run_fb4_simulation | Run complete FB4 simulation (Mid-level - Main function)

## -- S --

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

## -- U --

uncertainty-prediction | FB4 Uncertainty Propagation Functions
update_body_composition | Update body composition during simulation (Mid-level)
utils | Utility Functions for fb4package

## -- V --

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