Map retained fishery selectivity process error hyperparameters

Constructs the factor map for retsel_pe_pars, which contains the variance and correlation hyperparameters governing continuous time-varying selectivity. The set of active parameters depends on the time-variation type (cont_tv_ret_sel): iid/random-walk forms use up to 2 parameters (log-sigma); 3D GMRF forms use up to 4 (partial correlations for age, year, cohort dimensions plus log-sigma); the 2D AR1 form uses 3 (bin AR1, year AR1, log-sigma). Correlation components can be selectively suppressed via ret_sel_corr_opt_semipar.

Usage

do_retsel_pe_pars_mapping(
  input_list,
  retsel_pe_pars_spec,
  ret_sel_corr_opt_semipar,
  bins
)

Arguments

input_list

Named list with $data, $par, and $map sublists.

retsel_pe_pars_spec

Character vector of length n_fish_fleets. Options:

"est_all": Separate hyperparameters per region × sex.
"est_shared_r": Shared across regions; unique per sex.
"est_shared_s": Shared across sexes; unique per region.
"est_shared_r_s": Shared across regions and sexes.
"est_shared_f_x": Copy hyperparameters from fleet x.
"fix" or "none": All parameters fixed (mapped to NA).

ret_sel_corr_opt_semipar

Character vector of length n_fish_fleets specifying which correlation components to suppress for semi-parametric models. Valid values per fleet: NA (no suppression), "corr_zero_y", "corr_zero_b", "corr_zero_y_b", "corr_zero_c", "corr_zero_y_c", "corr_zero_b_c", "corr_zero_y_b_c". Cohort options ("corr_zero_c", etc.) are only valid for 3D GMRF forms and will error if applied to the 2D AR1 (cont_tv_ret_sel == 5).

Value

The input input_list with $map$retsel_pe_pars set to a factor vector. Index numbering is reset after any correlation suppression to maintain contiguous integer indices.

Details

Fleet sharing ("est_shared_f_x") is handled in a second pass.