compare_individuals: Compare individuals from hierarchical models

In fb4package: 'Fish Bioenergetics 4.0' Model Implementation with High-Performance 'TMB' Backend

Compare individuals from hierarchical models

Description

Compares performance metrics between individuals in hierarchical models. Provides statistical summaries and identifies outliers.

Usage

compare_individuals(result, metrics = "all", confidence_level = 0.95)

Arguments

result	FB4 result object from hierarchical method
metrics	Vector of metrics to compare ("consumption", "growth", "efficiency", "all")
confidence_level	Confidence level for comparisons (default 0.95)

Value

A named list with at minimum three context elements: n_individuals (integer), metrics_compared (character vector), and confidence_level (numeric). Depending on metrics, the following sub-lists are appended; each is produced by an internal summary helper and contains metric_name, n_valid, mean, sd, min, max, median, cv, range, outliers, and performance: consumption, efficiency, and p_value. The growth element (when requested) is itself a list with two such summaries (total_growth and relative_growth). A rankings data.frame (one row per individual; columns for per-metric ranks, composite_rank, and overall_rank) is always appended. Stops with an error if result was not produced by the hierarchical method.

Examples

data(fish4_parameters)
sp   <- fish4_parameters[["Oncorhynchus tshawytscha"]]$life_stages$adult
info <- fish4_parameters[["Oncorhynchus tshawytscha"]]$species_info
bio  <- Bioenergetic(
  species_params     = sp,
  species_info       = info,
  environmental_data = list(
    temperature = data.frame(Day = 1:30, Temperature = rep(12, 30))
  ),
  diet_data = list(
    proportions = data.frame(Day = 1:30, Prey1 = 1.0),
    energies    = data.frame(Day = 1:30, Prey1 = 5000),
    prey_names  = "Prey1"
  ),
  simulation_settings = list(initial_weight = 100, duration = 30)
)
bio$species_params$predator$ED_ini <- 5000
bio$species_params$predator$ED_end <- 5500
mr_data <- data.frame(
  individual_id  = paste0("fish_", 1:5),
  initial_weight = c(10, 12, 11, 13, 9),
  final_weight   = c(80, 95, 85, 100, 70)
)
result_hier <- run_fb4(bio, strategy = "hierarchical", backend = "tmb",
                       fit_to = "Weight", observed_weights = mr_data,
                       verbose = FALSE)
comparison <- compare_individuals(result_hier)

fb4package documentation built on May 8, 2026, 1:07 a.m.