Map discard mortality deviation parameters

Constructs the logit_dmr_devs factor map, assigning unique estimation indices to region-year-season-fleet cells that are fished and mapping true closures to NA. A cell is fished when aggregated or any population-specific catch is used, or when the aggregate catch observation is missing (NA) rather than a recorded zero, which is the same condition under which the objective computes a non-zero dmr.

Usage

do_dmr_dev_mapping(input_list, dmr_dev_spec)

Arguments

input_list

Named list with $data, $par, and $map sublists. Requires $data$UseCatch, $data$UseCatch_pop, and $data$ObsCatch to be populated by Setup_Mod_Catch_and_F.

dmr_dev_spec

Character string specifying whether to estimate or fix deviations. Currently supports "est_all" and "fix".

Value

The input input_list with $map$logit_dmr_devs set to a factor vector. Fished cells are assigned unique integer indices; true closures are NA.

Details

Discard observations are not required for a deviation to be estimable. dmr enters the likelihood through total mortality (ZAA), so it is informed by retained catch, indices, and compositions in any fished cell where retention is less than one. get_dmr_penalty keys on the same condition, so the estimated and penalized sets coincide.