Generate simulated data from TMB models in SAMtool

A convenient wrapper function (simulate) to simulate data (and process error) from the likelihood function.

simulate(object, ...)

# S4 method for Assessment
simulate(
  object,
  nsim = 1,
  seed = NULL,
  process_error = FALSE,
  refit = FALSE,
  cores = 1,
  ...
)

# S4 method for RCModel
simulate(
  object,
  nsim = 1,
  seed = NULL,
  process_error = FALSE,
  refit = FALSE,
  cores = 1,
  ...
)

Arguments

object: An object of class Assessment or RCModel containing the fitted model.
...: Additional arguments
nsim: Number of simulations
seed: Used for the random number generator
process_error: Logical, indicates if process error is re-sampled in the simulation.
refit: Logical, whether to re-fit the model for each simulated dataset.
cores: The number of CPUs for parallel processing for model re-fitting if refit = TRUE.

Value

A sim-class object returning the original data, simulated data, original parameters, parameters estimated from simulated data, and process error used to simulate data. then a nested list of model output (`opt`, `SD`, and `report`).

Details

Process error, e.g., recruitment deviations, will be re-sampled in the simulation.

Author

Q. Huynh