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), respecting the density-dependence sharing rules described above.

"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). 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

Sharing behaviour adapts to the density-dependence structure: under local density dependence (rec_dd = 0) with a single population, each region receives its own ln_sigmaR estimate; under global density dependence or with multiple populations, a single ln_sigmaR is shared across regions within each population.