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Map annual recruitment deviation parameters

Source: R/setup_recruitment.R
do_RecDevs_mapping.Rd

Builds the factor map for ln_RecDevs [n_pop x n_regions x n_years], the log-scale annual recruitment deviations. When rec_region_prop_spec = 1 and n_pop > 1, non-natal regions get no recruitment, so their deviations are fixed to NA whatever RecDevs_spec asks for and the rest are re-numbered. Called by Setup_Mod_Rec.

Usage

do_RecDevs_mapping(input_list, RecDevs_spec, rec_dd, dont_pen_recdev_first = 0)

Arguments

input_list

Named list with $data, $par and $map. Requires $data$rec_region_prop_spec, $data$natal_region, $data$rec_dd and $data$n_pop.

RecDevs_spec

Sharing structure for ln_RecDevs. "est_shared_r" gives one deviation series per population, shared across its regions. "est_shared_pop_r" gives one series across every population and region, required when rec_dd = "global" and n_regions > 1. "fix" holds every deviation at zero. NULL 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 RecDevs_spec to "est_shared_r" or "est_shared_pop_r" when n_regions > 1.

Value

input_list with $map$ln_RecDevs set to a factor vector of length prod(dim(par$ln_RecDevs)). Active parameters take sequential integers; non-natal region slots and fixed deviations are NA, and their starting values are reset to 0.

See also

do_InitDevs_mapping, which shares the same options.