Map selectivity process error hyperparameters (fishery, retention, or survey)

Constructs the factor map for the variance/correlation hyperparameters governing continuous time-varying selectivity (fishsel_pe_pars, retsel_pe_pars, or srvsel_pe_pars). The set of active parameters depends on the time-variation type: iid/random-walk forms use up to 2 parameters (log-sigma); 3D GMRF forms use up to 4 (partial correlations for age, year, cohort dimensions plus log-sigma); the 2D AR1 form uses 3 (bin AR1, year AR1, log-sigma). Correlation components can be selectively suppressed via corr_opt_semipar. Fleet sharing ("est_shared_f_x") is handled in a second pass.

Usage

do_sel_pe_pars_mapping(
  input_list,
  pe_pars_spec,
  corr_opt_semipar,
  bins,
  sel_devs_spec,
  sel_devs_shared_bins,
  prefix,
  fleet_field,
  use_field,
  fleet_label
)

Arguments

input_list

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

pe_pars_spec

Character vector of length n_<fleet_field>. Options: "est_all", "est_shared_r", "est_shared_s", "est_shared_r_s", the same four with _b added ("est_shared_b", "est_shared_r_b", "est_shared_b_s", "est_shared_r_b_s"), which put one standard deviation across every bin the fleet reads, "fix"/"none", or "est_shared_f_x".

corr_opt_semipar

Character vector of length n_<fleet_field> specifying which correlation components to suppress for semi-parametric models (NA, "corr_zero_y", "corr_zero_b", "corr_zero_y_b", "corr_zero_c", "corr_zero_y_c", "corr_zero_b_c", "corr_zero_y_b_c"). Cohort options are only valid for 3D GMRF forms.

bins

Number of selectivity bins.

sel_devs_spec

Character vector of length n_<fleet_field>, the deviation specification passed to do_sel_devs_mapping. Read only to recognize which dimensions the deviations are shared over. "est_shared_f_x" resolves to the referenced fleet's specification.

sel_devs_shared_bins

List of integer vectors grouping bins that share a single estimated deviation, as passed to do_sel_devs_mapping.

prefix

Character, one of "fish", "ret", or "srv". Drives the domain-specific field names: cont_tv_<prefix>_sel, <prefix>_sel_model, <prefix>_selex_type, <prefix>sel_pe_pars (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 $map$<prefix>sel_pe_pars set to a factor vector.

Details

The hyperparameters have to match the deviation series the likelihood actually evaluates, which is one per shared group, read at the group's lowest bin and first sex. Under iid or a random walk on a non-parametric fleet the log-sigmas are indexed by bin, so "est_shared_b" leaves one log-sigma per bin group. Sharing deviations across sexes ("est_shared_s" and its combinations) leaves one set for the first sex, under every time-variation form. The rest are fixed.

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