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Map retained fishery selectivity deviation parameters

do_retsel_devs_mapping.Rd

Constructs the factor map for ln_retsel_devs, the annual deviations in continuous time-varying retained fishery selectivity. For iid and random-walk forms, the deviation dimension corresponds to selectivity parameters (up to 6 for double-normal); for semi-parametric forms (3D GMRF, 2D AR1), it corresponds to age or length bins. Cells with no time-variation (cont_tv_ret_sel == 0) or no catch data are mapped to NA.

Usage

do_retsel_devs_mapping(
  input_list,
  ret_sel_devs_spec,
  retsel_devs_shared_bins,
  bins
)

Arguments

input_list

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

ret_sel_devs_spec

Character vector of length n_fish_fleets. Options:

"est_all"

Separate deviation series per region × sex × bin.

"est_shared_r"

Shared across regions.

"est_shared_s"

Shared across sexes.

"est_shared_r_s"

Shared across regions and sexes.

"est_shared_b"

Shared across bin groups defined by retsel_devs_shared_bins.

"est_shared_r_b"

Shared across regions and bin groups.

"est_shared_b_s"

Shared across bin groups and sexes.

"est_shared_r_b_s"

Shared across regions, bin groups, and sexes.

"est_shared_f_x"

Copy deviation map from fleet x.

"fix" or "none"

All deviations fixed at zero (mapped to NA).

Bin-sharing options ("est_shared_b", etc.) are only valid with semi-parametric time-varying forms (cont_tv_ret_sel is in c(3,4,5)).

retsel_devs_shared_bins

List of integer vectors defining bin groupings for bin-sharing options. Each element groups bins that share a single deviation series, e.g., list(1:5, 6:10, 11:30). Only used when ret_sel_devs_spec includes "est_shared_b".

bins

Number of selectivity bins

Value

The input input_list with $map$ln_retsel_devs set to a factor vector and $data$map_ln_retsel_devs set to the corresponding integer array (for use in the RTMB template).

Details

Bin-sharing ("est_shared_b" and related options) groups bins into blocks defined by retsel_devs_shared_bins, reducing the number of estimated deviation series. Fleet sharing ("est_shared_f_x") is handled in a second pass. The resulting integer map is also stored as $data$map_ln_retsel_devs for use in the RTMB objective function.