Map recruitment seasonal apportionment parameters

Builds the factor map for rec_seas_prop_pars [n_pop x (n_seas - 1)], the logit-scale share of annual recruitment per season, under a softmax with one reference season omitted. Called by Setup_Mod_Rec. When rec_lag = 0 and spawn_seas > 1 the seasons before spawn_seas are fixed at zero by a restricted softmax in the model, so the trailing unused columns are forced to NA whatever rec_seas_prop_spec asks for.

Usage

do_rec_seas_prop_mapping(input_list, rec_seas_prop_spec)

Arguments

input_list

Named list with $data, $par and $map. Requires $data$n_pop, $data$n_seas and $data$use_fixed_rec_seas_prop.

rec_seas_prop_spec

Seasonal apportionment structure. "est_shared_pop" estimates one set of n_seas - 1 parameters for every population and is only valid when n_seas > 1. "fix" holds every parameter at its starting value. NULL estimates all n_pop x (n_seas - 1) independently. The first and last reset use_fixed_rec_seas_prop to 0 with a warning if it was 1.

Value

input_list with $map$rec_seas_prop_pars set to a factor vector of length n_pop * (n_seas - 1), or NULL when n_seas = 1. Both $par$rec_seas_prop_pars and its map are NULL in that case. $data$use_fixed_rec_seas_prop may change as a side effect.