Comprehensive nutritional analysis — comprehensive_nutritional

Performs a comprehensive nutritional analysis combining all nutritional metrics including N:P ratios, nutrient efficiencies, body composition, and diet quality assessment.

Usage

comprehensive_nutritional_analysis(
  result,
  nutrient_balance = NULL,
  composition_params = NULL,
  diet_quality_data = NULL
)

Arguments

result: FB4 result object
nutrient_balance: Nutrient balance results (if available)
composition_params: Body composition parameters (if available)
diet_quality_data: Diet quality data (if available)

Value

A named list with at minimum two elements: model_info (list with method and has_daily_output) and energy_budget (from analyze_energy_budget). When optional inputs are provided, the following elements are appended:

np_ratios, redfield_comparison, nutrient_efficiencies, stoichiometric_balance: Added when nutrient_balance is supplied.
initial_composition, final_composition, composition_changes: Added when composition_params is supplied and both initial and final weights are available in result.
diet_quality: Added when diet_quality_data is supplied.

Examples

# \donttest{
data(fish4_parameters)
sp   <- fish4_parameters[["Oncorhynchus tshawytscha"]]$life_stages$adult
info <- fish4_parameters[["Oncorhynchus tshawytscha"]]$species_info
bio  <- Bioenergetic(
  species_params     = sp,
  species_info       = info,
  environmental_data = list(
    temperature = data.frame(Day = 1:30, Temperature = rep(12, 30))
  ),
  diet_data = list(
    proportions = data.frame(Day = 1:30, Prey1 = 1.0),
    energies    = data.frame(Day = 1:30, Prey1 = 5000),
    prey_names  = "Prey1"
  ),
  simulation_settings = list(initial_weight = 100, duration = 30)
)
#> Bioenergetic object created for: Oncorhynchus tshawytscha
bio$species_params$predator$ED_ini <- 5000
bio$species_params$predator$ED_end <- 5500
result <- run_fb4(bio, strategy = "direct", p_value = 0.5, verbose = FALSE)
#> Validation warnings:
#> Missing optional parameters (will be calculated): CG1, CG2
#> Object is ready for simulation
#> Validation warnings:
#> Missing optional parameters (will be calculated): CG1, CG2
#> Object is ready for simulation
#> Processing species parameters...
#> Processing temporal data...
#> No indigestible fraction data provided, using default 0% for all prey (FB4 default)
#> Processing simulation settings...
#> Simulation data preparation complete. Ready for simulation.
analysis <- comprehensive_nutritional_analysis(result)
# }