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

Builds the factor map for the variance and correlation hyperparameters of continuous time-varying selectivity (fishsel_pe_pars, retsel_pe_pars or srvsel_pe_pars), selected by prefix exactly as in do_fixed_sel_pars_mapping. Which parameters are active follows the time-variation form: the iid and random walk forms use up to two log sigmas, the 3D GMRF forms up to four (the partial correlations over age, year and cohort plus a log sigma), and the 2D AR1 form three (the bin and year correlations plus a log sigma). Fleet sharing 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.

pe_pars_spec

Character vector, one entry per fleet: "est_all", "est_shared_r", "est_shared_s", "est_shared_r_s", those four with _b added, which put one standard deviation across every bin the fleet reads, "fix" or "none", or "est_shared_f_x".

corr_opt_semipar

Character vector, one entry per fleet, of which correlation components to suppress under the semi-parametric forms: NA, "corr_zero_y", "corr_zero_b", "corr_zero_y_b", "corr_zero_c", "corr_zero_y_c", "corr_zero_b_c" or "corr_zero_y_b_c". The cohort options are valid for the 3D GMRF forms only.

bins

Number of selectivity bins.

sel_devs_spec

Character vector, one entry per fleet, the deviation specification passed to do_sel_devs_mapping. Read only to recognize which dims the deviations are shared over, and "est_shared_f_x" resolves to the referenced fleet's.

sel_devs_shared_bins

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

prefix

"fish", "ret" or "srv", which drives the field names cont_tv_<prefix>_sel, <prefix>_sel_model, <prefix>_selex_type and <prefix>sel_pe_pars.

fleet_field

Name of the $data field giving the number of fleets: "n_fish_fleets" for "fish" and "ret", "n_srv_fleets" for "srv".

use_field

Stub for the use indicator fields sel_has_data reads, Use<use_field> and Use<use_field>AA with their _pop variants: "Catch" for "fish" and "ret", "SrvIdx" for "srv".

fleet_label

Used only in the collected setup message.

Value

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 per bin group, and sharing deviations across sexes leaves one set for the first sex under every form. The rest are fixed. Deviations shared across regions share their sigmas across regions, read at the fleet's first region with data, and a fleet using another fleet's deviations ("est_shared_f_x") uses that fleet's sigmas, whatever pe_pars_spec says, since one series has one variance.