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Set likelihood and penalty weights for the estimation model

Setup_Mod_Weighting.Rd

Assigns lambda (\(\lambda\)) multipliers to each likelihood component and penalty term in the TMB/RTMB objective function. Weights scale the relative contribution of each data source during estimation and can be used to down-weight noisy data, implement iterative reweighting schemes (e.g., Francis), or disable a component entirely by setting its weight to 1. Must be called after all data setup functions.

Usage

Setup_Mod_Weighting(
  input_list,
  Wt_Catch = 1,
  Wt_FishIdx = 1,
  Wt_SrvIdx = 1,
  Wt_Catch_pop = 1,
  Wt_FishIdx_pop = 1,
  Wt_SrvIdx_pop = 1,
  Wt_Rec = 1,
  Wt_F = 1,
  Wt_Tagging = 1,
  Wt_FishAgeComps = array(1, dim = c(input_list$data$n_regions,
    length(input_list$data$years), input_list$data$n_seas, input_list$data$n_sexes,
    input_list$data$n_fish_fleets)),
  Wt_SrvAgeComps = array(1, dim = c(input_list$data$n_regions,
    length(input_list$data$years), input_list$data$n_seas, input_list$data$n_sexes,
    input_list$data$n_srv_fleets)),
  Wt_FishLenComps = array(1, dim = c(input_list$data$n_regions,
    length(input_list$data$years), input_list$data$n_seas, input_list$data$n_sexes,
    input_list$data$n_fish_fleets)),
  Wt_SrvLenComps = array(1, dim = c(input_list$data$n_regions,
    length(input_list$data$years), input_list$data$n_seas, input_list$data$n_sexes,
    input_list$data$n_srv_fleets)),
  Wt_FishAgeComps_pop = array(1, dim = c(input_list$data$n_pop,
    input_list$data$n_regions, length(input_list$data$years), input_list$data$n_seas,
    input_list$data$n_sexes, input_list$data$n_fish_fleets)),
  Wt_SrvAgeComps_pop = array(1, dim = c(input_list$data$n_pop, input_list$data$n_regions,
    length(input_list$data$years), input_list$data$n_seas, input_list$data$n_sexes,
    input_list$data$n_srv_fleets)),
  Wt_FishLenComps_pop = array(1, dim = c(input_list$data$n_pop,
    input_list$data$n_regions, length(input_list$data$years), input_list$data$n_seas,
    input_list$data$n_sexes, input_list$data$n_fish_fleets)),
  Wt_SrvLenComps_pop = array(1, dim = c(input_list$data$n_pop, input_list$data$n_regions,
    length(input_list$data$years), input_list$data$n_seas, input_list$data$n_sexes,
    input_list$data$n_srv_fleets)),
  Wt_Discard = 1,
  Wt_Discard_pop = 1,
  Wt_D = 1,
  Wt_FishAgeComps_discard = array(1, dim = c(input_list$data$n_regions,
    length(input_list$data$years), input_list$data$n_seas, input_list$data$n_sexes,
    input_list$data$n_fish_fleets)),
  Wt_FishLenComps_discard = array(1, dim = c(input_list$data$n_regions,
    length(input_list$data$years), input_list$data$n_seas, input_list$data$n_sexes,
    input_list$data$n_fish_fleets)),
  Wt_FishAgeComps_discard_pop = array(1, dim = c(input_list$data$n_pop,
    input_list$data$n_regions, length(input_list$data$years), input_list$data$n_seas,
    input_list$data$n_sexes, input_list$data$n_fish_fleets)),
  Wt_FishLenComps_discard_pop = array(1, dim = c(input_list$data$n_pop,
    input_list$data$n_regions, length(input_list$data$years), input_list$data$n_seas,
    input_list$data$n_sexes, input_list$data$n_fish_fleets)),
  fish_sel_pen_wts = NULL,
  ret_sel_pen_wts = NULL,
  srv_sel_pen_wts = NULL
)

Arguments

input_list

Named list with $data, $par, $map, and $verbose sublists, as returned by upstream setup functions.

Wt_Catch

Weight applied to the catch likelihood. Either a scalar applied uniformly across all fleets, regions, years, and seasons, or a numeric array [n_regions × n_years × n_seas × n_fish_fleets] for fleet- or time-specific weighting. Default 1.

Wt_FishIdx

Weight applied to the fishery index likelihood. Accepts the same scalar or array format as Wt_Catch, dimensioned [n_regions × n_years × n_seas × n_fish_fleets]. Default 1.

Wt_SrvIdx

Weight applied to the survey index likelihood. Accepts the same scalar or array format, dimensioned [n_regions × n_years × n_seas × n_srv_fleets]. Default 1.

Wt_Catch_pop

Weight applied to the population-specific catch likelihood. Either a scalar applied uniformly or a numeric array [n_pop × n_regions × n_years × n_seas × n_fish_fleets]. Default 1.

Wt_FishIdx_pop

Weight applied to the population-specific fishery index likelihood. Same scalar or array format as Wt_Catch_pop, dimensioned [n_pop × n_regions × n_years × n_seas × n_fish_fleets]. Default 1.

Wt_SrvIdx_pop

Weight applied to the population-specific survey index likelihood. Same scalar or array format as Wt_Catch_pop, dimensioned [n_pop × n_regions × n_years × n_seas × n_srv_fleets]. Default 1.

Wt_Rec

Scalar weight applied to the recruitment deviation penalty (ln_RecDevs). Default 1.

Wt_F

Scalar weight applied to the fishing mortality deviation penalty (ln_F_devs). Default 1.

Wt_Tagging

Scalar weight applied to the tag-recovery likelihood. Default 1.

Wt_FishAgeComps

Weight applied to the fishery age composition likelihood. Either a scalar or a numeric array [n_regions × n_years × n_seas × n_sexes × n_fish_fleets]. Default: array of 1s.

Wt_SrvAgeComps

Weight applied to the survey age composition likelihood. Either a scalar or a numeric array [n_regions × n_years × n_seas × n_sexes × n_srv_fleets]. Default: array of 1s.

Wt_FishLenComps

Weight applied to the fishery length composition likelihood. Same format as Wt_FishAgeComps, [n_regions × n_years × n_seas × n_sexes × n_fish_fleets]. Default: array of 1s.

Wt_SrvLenComps

Weight applied to the survey length composition likelihood. Same format as Wt_SrvAgeComps, [n_regions × n_years × n_seas × n_sexes × n_srv_fleets]. Default: array of 1s.

Wt_FishAgeComps_pop

Weight applied to the population-specific fishery age composition likelihood. Either a scalar or a numeric array [n_pop × n_regions × n_years × n_seas × n_sexes × n_fish_fleets]. Default: array of 1s.

Wt_SrvAgeComps_pop

Weight applied to the population-specific survey age composition likelihood. Either a scalar or a numeric array [n_pop × n_regions × n_years × n_seas × n_sexes × n_srv_fleets]. Default: array of 1s.

Wt_FishLenComps_pop

Weight applied to the population-specific fishery length composition likelihood. Same format as Wt_FishAgeComps_pop, [n_pop × n_regions × n_years × n_seas × n_sexes × n_fish_fleets]. Default: array of 1s.

Wt_SrvLenComps_pop

Weight applied to the population-specific survey length composition likelihood. Same format as Wt_SrvAgeComps_pop, [n_pop × n_regions × n_years × n_seas × n_sexes × n_srv_fleets]. Default: array of 1s.

Wt_Discard

Weight applied to the aggregated discard amount or fraction likelihood. Either a scalar applied uniformly or a numeric array [n_regions × n_years × n_seas × n_fish_fleets]. Default 1.

Wt_Discard_pop

Weight applied to the population-specific discard likelihood. Either a scalar or a numeric array [n_pop × n_regions × n_years × n_seas × n_fish_fleets]. Default 1.

Wt_D

Scalar weight applied to the discard mortality rate deviation penalty (logit_dmr_devs). Default 1.

Wt_FishAgeComps_discard

Weight applied to the discard fishery age composition likelihood. Either a scalar or a numeric array [n_regions × n_years × n_seas × n_sexes × n_fish_fleets]. Default: array of 1s.

Wt_FishLenComps_discard

Weight applied to the discard fishery length composition likelihood. Same format as Wt_FishAgeComps_discard, [n_regions × n_years × n_seas × n_sexes × n_fish_fleets]. Default: array of 1s.

Wt_FishAgeComps_discard_pop

Weight applied to the population-specific discard fishery age composition likelihood. Either a scalar or a numeric array [n_pop × n_regions × n_years × n_seas × n_sexes × n_fish_fleets]. Default: array of 1s.

Wt_FishLenComps_discard_pop

Weight applied to the population-specific discard fishery length composition likelihood. Same format as Wt_FishAgeComps_discard_pop, [n_pop × n_regions × n_years × n_seas × n_sexes × n_fish_fleets]. Default: array of 1s.

fish_sel_pen_wts

NULL (default), or a named numeric vector/list with independent weights for any subset of nine selectivity penalty terms (see resolve_sel_pen_wts), replacing single implicit-weight-1 on/off flags with independently settable weights for the total fishery selectivity penalty:

"yr_devs"

First-difference-across-years penalty on the continuous time-varying deviations (TimeVary_Model 1-2 only).

"bin_curve", "yr_curve"

Second-difference (curvature) penalties on the realized log-selectivity surface across bins and across years, respectively (TimeVary_Model 3-5 only).

"smooth_bin_curve", "smooth_bin_diff", "smooth_yr_diff", "smooth_yr_curve", "smooth_dome", "smooth_mean_center"

see Get_Selex_Smoothness_Penalty: bin curvature, unconditional bin first difference, inter-annual first difference, inter-annual second difference, dome-shape, and a per-year mean-centering regularization. These six terms operate directly on the fleet's realized selectivity surface (not on any particular parameterization's deviations), so they apply to any selectivity functional form – e.g. a nonparametric (Selex_Model == 5) fleet with discrete time blocks can use them to regularize curvature/stability across those blocks, bridging an ADMB assessment's coefficient selectivity held constant between "selectivity change years" (see the model equations vignette for a worked example).

When NULL, the first three terms fall back to weight 1 and the six "smooth_*" terms are always 0. Must be called after Setup_Mod_Fishsel_and_Q.

ret_sel_pen_wts

Same format as fish_sel_pen_wts, for the retained fishery selectivity penalty. Falls back to the legacy cont_tv_ret_sel_penalty flag (set via Setup_Mod_Fishsel_and_Q) when NULL.

srv_sel_pen_wts

Same format as fish_sel_pen_wts, for the survey selectivity penalty. Falls back to the legacy cont_tv_srv_sel_penalty flag (set via Setup_Mod_Srvsel_and_Q) when NULL. Must be called after Setup_Mod_Srvsel_and_Q.

Value

The input input_list with all weight values stored in $data under their respective names (Wt_Catch, Wt_FishIdx, Wt_SrvIdx, Wt_Catch_pop, Wt_FishIdx_pop, Wt_SrvIdx_pop, Wt_FishAgeComps, Wt_SrvAgeComps, Wt_FishLenComps, Wt_SrvLenComps, Wt_FishAgeComps_pop, Wt_SrvAgeComps_pop, Wt_FishLenComps_pop, Wt_SrvLenComps_pop, Wt_Rec, Wt_F, Wt_Tagging, Wt_Discard, Wt_Discard_pop, Wt_D, Wt_FishAgeComps_discard, Wt_FishLenComps_discard, Wt_FishAgeComps_discard_pop, Wt_FishLenComps_discard_pop).

See also

Other Model Setup: Setup_Mod_Biologicals(), Setup_Mod_Catch_and_F(), Setup_Mod_Dim(), Setup_Mod_Discard_Comps(), Setup_Mod_FishIdx_and_Comps(), Setup_Mod_Fishsel_and_Q(), Setup_Mod_Movement(), Setup_Mod_Rec(), Setup_Mod_Retsel(), Setup_Mod_SrvIdx_and_Comps(), Setup_Mod_Srvsel_and_Q(), Setup_Mod_Tagging()