Map recruitment variability (sigma_R) parameters

Internal helper called by Setup_Mod_Rec to construct the TMB/RTMB factor map for ln_sigmaR, the log-scale standard deviation of recruitment deviations. The ln_sigmaR array has dimensions [2 x n_pop x n_regions], where the first index distinguishes initial age-structure deviations (i = 1) from annual recruitment deviations (i = 2).

Usage

do_sigmaR_mapping(input_list, sigmaR_spec)

Arguments

input_list

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

sigmaR_spec

Character string specifying the estimation structure for ln_sigmaR. One of:

"est_all"

Estimate ln_sigmaR separately for both the initial deviation period (i = 1) and the annual deviation period (i = 2), and for every population and region.

"est_shared_r"

Separate per deviation period and population, shared across regions within each.

"est_shared_all"

Single ln_sigmaR shared across both deviation periods, all populations, and all regions.

"fix_early_est_late"

Fix ln_sigmaR for the initial deviation period (i = 1) at its starting value; estimate ln_sigmaR for the annual deviation period (i = 2), per population and region. Useful when initial age-structure uncertainty is assumed known.

"fix"

Fix all ln_sigmaR parameters at their starting values (all mapped to NA).

Value

The input input_list with $map$ln_sigmaR set to a factor vector of length prod(dim(par$ln_sigmaR)). Active parameters receive sequential integer indices; fixed parameters are NA.

Details

The map decides what is shared, and the recruitment penalty reads each region's own slot. Under rec_region_prop_spec = 1 with multiple populations, a population's non-natal region slots have no deviations and are mapped off automatically.