Package index • fb4package

Core object

Create and inspect Bioenergetic objects — the central data structure that holds all model inputs.

Bioenergetic(): Constructor for Bioenergetic Objects

is.Bioenergetic(): Test if Object is Bioenergetic

print(<Bioenergetic>): Print Method for Bioenergetic Objects

summary(<Bioenergetic>): Summary Method for Bioenergetic Objects

plot(<Bioenergetic>): Plot Bioenergetic object setup

Object configuration

Convenience functions for updating individual components of a Bioenergetic object after creation.

set_environment(): Set Environmental Data for Bioenergetic Objects

set_diet(): Set Diet Data for Bioenergetic Objects

set_simulation_settings(): Set Simulation Settings for Bioenergetic Objects

get_parameter_value(): Get Parameter Value from Species Parameters

set_parameter_value(): Set Parameter Value in Species Parameters

Run simulations

Main entry point for all FB4 simulations and parameter estimation strategies.

run_fb4(): Default run_fb4 method

run_fb4(<Bioenergetic>): Run FB4 simulation on Bioenergetic object (REFACTORED)

run_fb4(<default>): Default method for run_fb4 (error)

Simulation results

Methods for printing, summarising, and plotting fb4_result objects returned by run_fb4().

print(<fb4_result>): Print Method for fb4_result Objects

summary(<fb4_result>): Summary Method for fb4_result Objects

plot(<fb4_result>): Plot FB4 simulation results

is.fb4_result(): Test if Object is fb4_result

Result analysis

Functions that extract ecologically meaningful metrics from a finished simulation.

analyze_growth_patterns(): Analyze growth patterns from FB4 results

analyze_feeding_performance(): Analyze feeding performance from FB4 results

analyze_energy_budget(): Analyze energy budget 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

analyze_composition_by_size(): Analyze body composition by size range

analyze_composition_changes(): Analyze composition changes with growth

compare_scenarios(): Compare multiple FB4 results

comprehensive_nutritional_analysis(): Comprehensive nutritional analysis

Species database

Built-in parameter database and metadata.

fish4_parameters: Fish Bioenergetics 4.0 Official Parameters Database

Data preparation

Functions for processing and validating input data before simulation.

prepare_simulation_data(): Prepare all simulation data

process_bioenergetic_data(): Process Bioenergetic object temporal data for simulation

process_species_parameters(): Process all species parameters for simulation

interpolate_time_series(): Interpolate time series with error handling

Bioenergetics equations

Low-level equation functions for consumption, respiration, egestion, excretion, and predator energy density.

calculate_consumption(): Calculate daily consumption (Mid-level - Main function)

calculate_daily_consumption(): Calculate daily consumption with multiple methods (Low-level)

calculate_temperature_factor_consumption(): Calculate temperature factor for consumption (Mid-level)

calculate_respiration(): Calculate daily respiration (Mid-level - Main function)

calculate_sda(): Calculate Specific Dynamic Action (SDA) (Low-level)

calculate_egestion(): Calculate daily egestion (Mid-level - Main function)

calculate_excretion(): Calculate daily excretion (Mid-level - Main function)

calculate_predator_energy_density(): Calculate predator energy density (Mid-level - Main function)

calculate_final_weight_fb4(): Calculate final weight using FB4 equations (Mid-level)

Validation

Functions for validating model inputs, parameters, and results.

validate_bioenergetic_for_simulation(): Comprehensive validation for Bioenergetic objects

validate_fb4_inputs(): Validate inputs for FB4 simulation

validate_fb4_system(): Validate complete FB4 system ready for simulation

validate_species_equations(): Main function to validate all species equations

validate_diet_consistency(): Validate Consistency Between Diet and Energy Data

validate_temporal_data(): Validate temporal data

validate_complete_simulation_data(): Validate complete simulation data

Utilities

Helper functions used internally and available for advanced users.

get_color_scheme(): Get Color Scheme for Plots

check_bioenergetic_readiness(): Check Bioenergetic Object Readiness

z_score(): Z-score for a given confidence level

clamp(): Clamp values to a range

safe_sqrt(): Safe square root

safe_exp(): Safe exponential

Other functions

Additional exported functions and low-level helpers.

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

Bioenergetic(): Constructor for Bioenergetic Objects

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_respiration_params_eq2(): Calculate additional parameters for respiration equation 2 (Mid-level)

calculate_stoichiometric_balance(): Calculate stoichiometric balance

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_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

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

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 (UNIFIED)

run-fb4-orchestrator: FB4 Main Orchestrator

run_fb4(<Bioenergetic>): Run FB4 simulation on Bioenergetic object (REFACTORED)

run_fb4(<default>): Default method for run_fb4 (error)

run_fb4(): Default run_fb4 method

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: Strategy-Binary-search for FB4 Model

strategy-commons: Strategy Commons for FB4 Model

strategy-direct: Direct Strategies for FB4 Model

strategy-hierarchical: Strategy-Hierarchical for FB4 Model

strategy-interface: Strategy Interface and Factory for FB4 Model

strategy-mle: Strategy-MLE for FB4 Model

strategy-optim: Strategy-Optim 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_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

validation_result(): Create standardized validation result