Growth deviations in the operating model

Stores what each replicate needs to rebuild growth from its own deviations: the fit's time variation codes, the semi-parametric form and its ages, the deviation maps, the process error parameters, the Get_Growth arguments and, under selectivity at length, the report's selectivity at length the rebuilt keys are read through. With the fit's own penalty on the deviations, draw_sim_growth_devs keeps the fit's values over the simulation list's n_cond_yrs and draws the years after them in Setup_sim_env. With a dsem holding or linking any growth deviation, Setup_Sim_DSEM builds both arrays itself and nothing is stored here, so the deviations of a parameter outside the arrows keep the fit's values. Nothing is stored either when growth is data or has no deviations.

Usage

Setup_Sim_Growth_RE(
  sim_list,
  data,
  pars,
  rep = NULL,
  pars_by_sim = NULL,
  rep_by_sim = NULL
)

Arguments

sim_list

Simulation list with n_yrs and n_sims.

data

Data list of the fit.

pars

Parameter list at the fitted values.

rep

Report of the fit, needed under selectivity at length.

pars_by_sim, rep_by_sim

Optional lists of one parameter list and one report per replicate, for replicates that each run on their own parameter draw (sim_type = "joint" in simulation_self_test). Each replicate's growth is then rebuilt from its own parameters and deviations. NULL (default) gives every replicate pars and rep.

Value

sim_list with growth_args and the fields above added.