prepare_simulation_data: Prepare all simulation data

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

Prepare all simulation data

Description

Master function that processes and validates ALL data required for FB4 simulation. Combines species parameter processing with temporal data processing.

Usage

prepare_simulation_data(
  bio_obj,
  strategy,
  fit_to = NULL,
  fit_value = NULL,
  first_day = 1,
  last_day = NULL,
  validate_inputs = TRUE,
  oxycal = 13560,
  output_format = "simulation",
  observed_weights = NULL,
  covariates = NULL
)

Arguments

bio_obj	Bioenergetic object (must be pre-validated)
strategy	Strategy to use: "binary_search", "optim", "bootstrap", "mle", "hierarchical"
fit_to	Target type for fitting (e.g., "Weight"); optional for direct strategy
fit_value	Target value to fit to; optional for direct strategy
first_day	First simulation day
last_day	Last simulation day
validate_inputs	Whether to perform comprehensive validation, default TRUE
oxycal	Oxycalorific coefficient (J/g O2), default 13560
output_format	Output format: "simulation", "tmb_basic", "tmb_hierarchical"
observed_weights	Data frame with columns: individual_id, initial_weight and observed_weight
covariates	Optional covariate matrix or data frame or choose a column of individual_data

Value

For output_format = "simulation" (default), a named list with seven elements: species_params (processed species parameter sub-lists), temporal_data (processed temporal arrays), simulation_settings (processed settings), metadata (processing timestamp, duration, prey species, data sources), n_days (integer), temperatures (numeric vector), and initial_weight (numeric scalar). For output_format = "tmb_basic" or "tmb_hierarchical", returns a list formatted for TMB model fitting (structure differs).

Examples

# Requires a fully-configured Bioenergetic object; see ?Bioenergetic
# bio <- Bioenergetic(...)
# sim_data <- prepare_simulation_data(bio, strategy = "direct")

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