Map recruitment regional apportionment parameters

Internal helper called by Setup_Mod_Rec to construct the TMB/RTMB factor map for rec_region_prop_pars, the logit-scale parameters controlling the proportion of recruits assigned to each region. The array has dimensions [n_pop x (n_regions - 1)], using a sum-to-one soft-max parameterisation with one reference region omitted.

Usage

do_rec_region_prop_mapping(input_list, rec_region_prop_spec)

Arguments

input_list

Named list with $data, $par, and $map sublists. Requires $data$n_pop, $data$n_regions, and $data$natal_region to be set by upstream setup functions.

rec_region_prop_spec

Character string specifying the dispersal structure, or NULL to estimate all regional proportions freely. Options when non-NULL:

"no_dispersal"

Recruits are assigned entirely to their natal region. Starting values for rec_region_prop_pars are overwritten with large-magnitude values (-20 for non-natal regions, +20 for the natal region when natal_region > 1), and all elements are mapped to NA so the parameters are not estimated. Requires n_pop > 1 and n_regions > 1.

NULL

All rec_region_prop_pars are estimated independently. Only available when n_regions > 1.

Value

The input input_list with $map$rec_region_prop_pars set to a factor vector of length n_pop * (n_regions - 1), or NULL when n_regions = 1. Under "no_dispersal", $par$rec_region_prop_pars starting values are also overwritten.

Details

When n_regions = 1, the parameter is structurally irrelevant and both $par$rec_region_prop_pars and $map$rec_region_prop_pars are set to NULL.