Map fixed selectivity parameters (fishery, retention, or survey)

Constructs the factor map for fixed-effects selectivity parameters (fish_fixed_sel_pars, ret_fixed_sel_pars, or srv_fixed_sel_pars) across region, bin, block, sex, and fleet, handling every parametric selectivity form (logistic, gamma, exponential, double normal, asymptotic logistic, bicubic spline) as well as non-parametric selectivity with user-defined bin groupings. Fleet sharing ("est_shared_f_x") is handled in a second pass, copying the full mapping from a reference fleet.

Usage

do_fixed_sel_pars_mapping(
  input_list,
  sel_pars_spec,
  bins,
  sel_nonpar_est_bins,
  prefix,
  fleet_field,
  use_field,
  fleet_label
)

Arguments

input_list: Named list with $data, $par, and $map sublists.
sel_pars_spec: Character vector of length n_<fleet_field>. Options: "est_all", "est_shared_r", "est_shared_s", "est_shared_r_s", "fix", "fix_<prefix>_sel_input", or "est_shared_f_x" (copy from fleet x).
bins: Number of selectivity bins.
sel_nonpar_est_bins: Optional list [[fleet]][[block]] of bin index groupings for non-parametric selectivity (model 5).
prefix: Character, one of "fish", "ret", or "srv". Drives the domain-specific field names: use_fixed_<prefix>_sel, <prefix>_sel_blocks, <prefix>_sel_model, <prefix>_sel_bicubic_binnodes/_yrnodes, <prefix>_fixed_sel_pars (par/map name).
fleet_field: Character. Name of the $data field giving the number of fleets to loop over ("n_fish_fleets" for both "fish" and "ret", since retention shares fishery fleets; "n_srv_fleets" for "srv").
use_field: Character. Stub for the usage-indicator fields read by sel_has_data: Use<use_field> and its at-age counterpart Use<use_field>AA, each with a _pop variant. "Catch" for "fish"/"ret"; "SrvIdx" for "srv".
fleet_label: Character. Used only in the collected setup message, e.g. "fishery fleet" or "survey fleet".

Value

The input input_list with $map$<prefix>_fixed_sel_pars set to a factor vector.

Details

Serves fishery, retention, and survey selectivity. prefix is "fish", "ret", or "srv"; retention takes its own use_field because it is switched on by the fishery side rather than by a retention specific flag.