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Map survey selectivity process error (variance/correlation) parameters

do_srvsel_pe_pars_mapping.Rd

Internal helper called by Setup_Mod_Srvsel_and_Q to construct the TMB/RTMB factor map for srvsel_pe_pars [n_regions × max(max_sel_pars, 4) × n_sexes × n_srv_fleets], the hyperparameters governing the variance and correlation structure of continuous time-varying survey selectivity. The second dimension is padded to at least 4 to accommodate the maximum number of process error parameters across all semi-parametric forms:

iid or random walk (cont_tv_srv_sel 1–2)

Up to max_sel_pars variance parameters (1, 2, or 6 depending on selectivity model).

3D GMRF (cont_tv_srv_sel 3–4)

4 parameters: age partial correlation (index 1), year partial correlation (index 2), cohort partial correlation (index 3), log-sigma (index 4).

2D AR1 (cont_tv_srv_sel 5)

3 parameters at indices 1, 2, and 4 (bin, year, log-sigma); index 3 is always NA.

Usage

do_srvsel_pe_pars_mapping(
  input_list,
  srvsel_pe_pars_spec,
  corr_opt_semipar,
  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, and $data$srv_selex_type.

srvsel_pe_pars_spec

Character vector [n_srv_fleets] specifying the sharing structure. Same options as do_srvsel_devs_mapping: "est_all", "est_shared_r", "est_shared_s", "est_shared_r_s", "est_shared_f_x", "fix", "none".

corr_opt_semipar

Character vector [n_srv_fleets] or NULL. Specifies which correlation components to suppress for 3D GMRF or 2D AR1 likelihoods by setting the corresponding parameter indices to NA. Valid values: NA, "corr_zero_y", "corr_zero_b", "corr_zero_y_b", "corr_zero_c" (3D GMRF only), "corr_zero_y_c" (3D GMRF only), "corr_zero_b_c" (3D GMRF only), "corr_zero_y_b_c" (3D GMRF only). After suppression, remaining non-NA parameters are re-indexed sequentially.

bins

Number of selectivity bins

Value

The input input_list with $map$srvsel_pe_pars set to a factor vector. Active parameters receive sequential integer indices; fixed, inactive, and correlation-suppressed parameters are NA.

Details

When corr_opt_semipar is non-NULL, specified correlation indices are set to NA and the remaining active parameters are re-indexed sequentially. Fleet-sharing ("est_shared_f_x") is handled in a second pass. Parameters are automatically fixed for fleets with no continuous time-variation (cont_tv_srv_sel = 0) or no active survey index data.