Map survey selectivity deviation parameters

Internal helper called by Setup_Mod_Srvsel_and_Q to construct the TMB/RTMB factor map for ln_srvsel_devs [n_regions × (n_years + n_proj_yrs_devs) × n_bins × n_sexes × n_srv_fleets], where n_bins is n_ages for age-based selectivity or n_lens for length-based selectivity. For iid and random walk forms, the bin dimension indexes selectivity parameters (1, 2, or 6 depending on functional form); for semi-parametric forms (3D GMRF, 2D AR1), it indexes age or length bins directly.

Usage

do_srvsel_devs_mapping(
  input_list,
  srv_sel_devs_spec,
  srvsel_devs_shared_bins,
  bins
)

Arguments

input_list

Named list with $data, $par, and $map sublists. Requires $data$n_srv_fleets, $data$n_regions, $data$n_sexes, $data$cont_tv_srv_sel, $data$srv_sel_model, $data$UseSrvIdx, $data$UseSrvIdx_pop, $data$n_proj_yrs_devs, and $data$srv_selex_type.

srv_sel_devs_spec

Character vector [n_srv_fleets] specifying the sharing structure for selectivity deviations. One of:

"est_all"

Separate deviation time series per region, sex, bin, and fleet.

"est_shared_r"

Shared across regions; separate by sex and bin.

"est_shared_s"

Shared across sexes; separate by region and bin.

"est_shared_r_s"

Shared across regions and sexes.

"est_shared_b"

Shared across bin groups defined by srvsel_devs_shared_bins. Semi-parametric forms only.

"est_shared_r_b"

Shared across regions and bin groups. Semi-parametric forms only.

"est_shared_b_s"

Shared across bin groups and sexes. Semi-parametric forms only.

"est_shared_r_b_s"

Shared across regions, bin groups, and sexes. Semi-parametric forms only.

"est_shared_f_x"

Copy the map from fleet x. Fleet x must not itself use "est_shared_f_x".

"fix"/"none"

All deviations fixed at zero (mapped to NA).

srvsel_devs_shared_bins

List of integer vectors defining bin groups for age/length sharing. Each element specifies the bin indices within one group (e.g., list(1:5, 6:10, 11:30)). Required when srv_sel_devs_spec includes "est_shared_b" or its variants; ignored otherwise.

bins

Number of seletivity bins

Value

The input input_list with $map$ln_srvsel_devs set to a factor vector and $data$map_ln_srvsel_devs set to the equivalent integer array [n_regions × (n_years + n_proj_yrs_devs) × n_bins × n_sexes × n_srv_fleets]. Active parameters receive sequential integer indices; inactive parameters are NA.

Details

Bin-sharing options ("est_shared_b" and variants) are only valid for semi-parametric forms and require srvsel_devs_shared_bins to define which bin groups share a common deviation. Fleet-sharing ("est_shared_f_x") is handled in a second pass. Parameters are automatically fixed for fleets with no continuous time-variation or no active survey index data. The integer-valued map is also stored in $data$map_ln_srvsel_devs for use within the TMB objective function.