Set up mapping for growth

Builds the estimation maps for the growth parameters, for the deviations of any parameter that varies over time, and for the semi-parametric surface on mean length at age. Called by Setup_Mod_Biologicals once the parameter list is populated, since every map is dimensioned off its parameter.

Usage

do_growth_mapping(
  input_list,
  growth_spec,
  growth_fix,
  tv_vals,
  tv_active,
  growth_tv_spec,
  growth_tv_sigma_spec,
  semipar_val,
  growth_semipar_spec,
  semipar_age_idx,
  semipar_yr_idx
)

Arguments

input_list

List containing data, parameter, and map lists, with the growth parameters already populated.

growth_spec

Character. How the growth parameters are estimated, one of "est_all", "est_shared_r", "est_shared_s", "est_shared_r_s" or "fix".

growth_fix

Logical vector, one entry per growth parameter, naming any kept at its starting value while the others are estimated.

tv_vals

Integer vector, one entry per growth parameter, of the time variation each has (0 none, 1 iid, 2 random walk).

tv_active

Matrix [n_years x n_gpars] of ones in the years each parameter's deviations are estimated in.

growth_tv_spec

Character. How the deviation series are shared across regions and sexes.

growth_tv_sigma_spec

Character. "fix" holds the process error standard deviations, "est" estimates them.

semipar_val

Integer code of the semi-parametric form (0 none, 1 iid, 2 random walk, 3 3dmarg, 4 3dcond, 5 2dar1).

growth_semipar_spec

Character. Whether the surface's process error parameters are estimated.

semipar_age_idx, semipar_yr_idx

Integer vectors of the age and year indices the surface is estimated over.

Value

The input input_list with $map$ln_growth_pars, $map$ln_growth_devs, $map$growth_pe_pars and $map$ln_growth_semipar_devs set, along with the $data$map_ln_growth_devs and $data$map_ln_growth_semipar_devs mirrors the deviation penalties read.