Map AR1 correlation parameter for recruitment deviations

Constructs the RecDevs_rho factor map. RecDevs_rho is only read when RecDevs_model = "ar1" (see Setup_Mod_Rec); under any other RecDevs_model every RecDevs_rho parameter is mapped to NA regardless of RecDevs_rho_spec, since the recruitment penalty never reads it.

Usage

do_RecDevs_rho_mapping(input_list, RecDevs_rho_spec)

Arguments

input_list

Named list with $data, $par, and $map sublists, as constructed by upstream setup functions.

RecDevs_rho_spec

Character string controlling the sharing and estimation structure for RecDevs_rho: one of "est_all", "est_shared_pop", "est_shared_r", "est_shared_pop_r", or "fix".

Value

The input input_list with $map$RecDevs_rho set to a factor vector of length prod(dim(par$RecDevs_rho)).