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

do_sel_devs_mapping.Rd

Constructs the factor map for continuous time-varying selectivity deviations (ln_fishsel_devs, ln_retsel_devs, or ln_srvsel_devs) across region, year, bin, sex, and fleet. For iid/random-walk forms, active bins are governed by the fitted selectivity model's parameter count; for 3D GMRF/2D AR1 forms, every age bin is active. Bin groupings (sel_devs_shared_bins, used by "est_shared_b" and its combinations) apply wherever the deviations are indexed by bin: the GMRF and AR1 forms, and the non-parametric selectivity forms under iid or a random walk. Fleet sharing ("est_shared_f_x") is handled in a second pass.

Usage

do_sel_devs_mapping(
  input_list,
  sel_devs_spec,
  sel_devs_shared_bins,
  bins,
  dont_est_dev_first = NULL,
  prefix,
  fleet_field,
  use_field,
  fleet_label
)

Arguments

input_list

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

sel_devs_spec

Character vector of length n_<fleet_field>. Options: "est_all", "est_shared_r", "est_shared_s", "est_shared_r_s", "est_shared_b", "est_shared_r_b", "est_shared_b_s", "est_shared_r_b_s", "fix"/"none", or "est_shared_f_x".

sel_devs_shared_bins

List of integer vectors, each defining a group of bins that share a single estimated deviation. Required when sel_devs_spec includes "est_shared_b" or its variants.

bins

Number of selectivity bins.

dont_est_dev_first

Integer vector [n_<fleet_field>] of 0/1, or NULL. Where 1, the deviations of year one are dropped from the map so the walk starts in year two and the fixed selectivity parameters hold year one. Refused for the GMRF and 2D AR1 forms, whose deviations are a field rather than a walk anchored at year one.

prefix

Character, one of "fish", "ret", or "srv". Drives the domain-specific field names: cont_tv_<prefix>_sel, <prefix>_sel_model, ln_<prefix>sel_devs (par/map name, no underscore before "sel").

fleet_field

Character. Name of the $data field giving the number of fleets ("n_fish_fleets" for "fish"/"ret"; "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.

Value

The input input_list with $map$ln_<prefix>sel_devs set to a factor vector, and $data$map_ln_<prefix>sel_devs set to the equivalent integer array.

Details

Serves fishery, retention, and survey selectivity, selected by prefix exactly as in do_fixed_sel_pars_mapping.