Map retained fishery selectivity fixed-effect parameters

Constructs the factor map for ret_fixed_sel_pars (e.g., \(a_{50}\), \(k\), \(a_{max}\)), controlling whether selectivity shape parameters are estimated independently or shared across regions, sexes, or fleets. Cells with no catch data (UseCatch == 0 and UseCatch_pop == 0) are automatically mapped to NA.

Usage

do_ret_fixed_sel_pars_mapping(
  input_list,
  ret_fixed_sel_pars_spec,
  bins,
  ret_sel_nonpar_est_bins
)

Arguments

input_list

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

ret_fixed_sel_pars_spec

Character vector of length n_fish_fleets. Each element specifies the estimation structure for one fleet. Options:

"est_all"

Separate parameters per region × sex × block × bin.

"est_shared_r"

Shared across regions; unique per sex × block × bin.

"est_shared_s"

Shared across sexes; unique per region × block × bin.

"est_shared_r_s"

Shared across regions and sexes; unique per block × bin.

"est_shared_f_x"

Copy parameter mapping from fleet x. Fleet x must not itself use "est_shared_f_y".

"fix" / "fixed_ret_sel_input"

All parameters fixed (mapped to NA).

bins

Number of selectivity bins.

ret_sel_nonpar_est_bins

Optional list specifying bin groupings for non-parametric selectivity. Structure is [[fleet]][[block]], where each element is a list of bin index vectors defining grouped parameters.

Value

Updated input_list with $map$ret_fixed_sel_pars as a factor array.

Details

Non-parametric selectivity (model sel_model == 5) is supported via ret_sel_nonpar_est_bins, which defines bin groupings that are treated as individual estimated parameters.

Fleet sharing ("est_shared_f_x") is applied in a second pass after all base mappings are constructed, copying the full parameter index structure from the reference fleet.