Map fishery selectivity fixed-effect parameters — do_fish_fixed_sel_pars

Constructs the factor map for fish_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) are automatically mapped to NA.

Usage

do_fish_fixed_sel_pars_mapping(
  input_list,
  fish_fixed_sel_pars_spec,
  bins,
  fish_sel_nonpar_est_bins
)

Arguments

input_list

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

fish_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": Parameters shared across regions; unique per sex × block × bin.
"est_shared_s": Parameters shared across sexes; unique per region × block × bin.
"est_shared_r_s": Parameters 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": All parameters fixed at starting values (mapped to NA).

bins

Number of selectivity bins.

fish_sel_nonpar_est_bins

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

Value

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

Details

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

Fleet sharing ("est_shared_f_x") is handled in a second pass after all base fleet mappings are established, copying the reference fleet's index assignments into the sharing fleet.