Map initial age-structure deviation parameters — do_InitDevs

Builds the factor map for ln_InitDevs [n_pop x n_regions x (n_ages - 1) x n_sexes], the log-scale deviations from the equilibrium initial age structure. Population, region and age are resolved on a single-sex slice and then expanded across sexes by InitDevs_sex_spec. Called by Setup_Mod_Rec.

Usage

do_InitDevs_mapping(
  input_list,
  InitDevs_spec,
  rec_dd,
  init_age_devs_shared,
  InitDevs_sex_spec = "est_shared_s"
)

Arguments

input_list: Named list with $data, $par and $map. Requires $data$equil_init_age_strc, $data$rec_region_prop_spec, $data$natal_region and $data$rec_dd.
InitDevs_spec: Sharing structure for ln_InitDevs. "est_shared_pop_r" gives one set of age deviations across every population and region, required when rec_dd = "global" and n_regions > 1. "est_shared_r" gives one set per population, shared across its regions. "fix" holds every deviation at zero. NULL (default) estimates all independently, which is not permitted when rec_region_prop_spec = 1 and n_pop > 1.
rec_dd: Density dependence inherited from Setup_Mod_Rec. "global" restricts InitDevs_spec to "est_shared_r" or "est_shared_pop_r" when n_regions > 1.
init_age_devs_shared: Integer vector of length n_ages - 1 giving the factor level of each age position; positions sharing a value share one parameter. Read under equil_init_age_strc = 3, and respected by InitDevs_spec = "est_shared_r" (per population, with a population offset) and "est_shared_pop_r" (globally, no offset). c(1:42, rep(42, 9)) gives 42 free parameters for a 52-age model with 43 data ages. Default NULL.
InitDevs_sex_spec: "est_shared_s" (default) maps every sex onto one age curve penalized once; "est_all" offsets the factor levels per sex so each has its own, each penalized. Also builds data$init_devs_pen_use, which flags one penalized copy of every estimated parameter.

Value

input_list with $map$ln_InitDevs set to a factor vector of length prod(dim(par$ln_InitDevs)). Active parameters take sequential integers; plus-group slots under equil_init_age_strc = 1 and non-natal region slots under rec_region_prop_spec = 1 are NA, and their starting values are reset to 0.