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

Documentation for package ‘fb4package’ version 2.0.0

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-- 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