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