fb4package (version 2.0.0)

prepare_simulation_data: 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
)

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).

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

Examples

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