Discard mortality rate deviation penalty

IID penalty on every estimated discard mortality rate deviation, called once from the "Discard Mortality Rate (Penalty)" section of SPoRC_rtmb.R.

Usage

get_dmr_penalty(
  logit_dmr_devs,
  ln_sigma_dmr,
  map_logit_dmr_devs,
  n_fish_fleets,
  n_yrs,
  n_regions,
  n_seas
)

Arguments

logit_dmr_devs

Array [region, year, season, fish_fleet] of discard mortality rate deviations on the logit scale.

ln_sigma_dmr

Array [region, season, fish_fleet] of log-sigma for the deviation penalty.

map_logit_dmr_devs

Array [region, year, season, fish_fleet] mirroring $map$logit_dmr_devs: an estimation index where a deviation is estimated, NA where it is fixed.

n_fish_fleets, n_yrs, n_regions, n_seas

Dimension sizes.

Value

Array [region, year, season, fish_fleet] of negative log-likelihood penalties (0 where the deviation is not estimated).

Details

The penalized set is read off map_logit_dmr_devs rather than recomputed, so it always matches what is estimated, including deviations mapped off by hand after setup. By default do_dmr_dev_mapping estimates a deviation in every cell the objective does not treat as a true closure. Discard observations are not the boundary: dmr is identified through total mortality (ZAA) wherever a cell is fished and retention is less than one, and it cancels out of PredDiscard itself.