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Get Composition Proportions from RTMB Output

get_comp_prop.Rd

Extracts and standardizes age and length composition data for fishery and survey fleets from RTMB model output. The function processes both observed and expected compositions for pooled (all populations combined) and population-specific data streams, returning results in both long-format data frames and array formats suitable for diagnostics and likelihood evaluation.

Usage

get_comp_prop(data, rep, age_labels, len_labels, year_labels)

Arguments

data

List. RTMB input data containing observed compositions, usage flags, composition types, ageing error matrices, and fleet/region/season/ population dimensions.

rep

List. RTMB model output containing predicted compositions (CAA, CAL, DAA, DAL, SrvIAA, SrvIAL) with a leading population dimension that is summed to produce pooled outputs.

age_labels

Vector. Age bin labels used in composition data.

len_labels

Vector. Length bin labels used in composition data.

year_labels

Vector. Labels for model years corresponding to projection or estimation periods.

Value

A named list containing:

Fishery_Ages, Fishery_Lens

Long-format data frames of observed and predicted pooled fishery age and length compositions, including metadata (Region, Year, Season, Age/Len, Sex, Fleet, Type).

Fishery_Discard_Ages, Fishery_Discard_Lens

Long-format data frames for discard compositions.

Survey_Ages, Survey_Lens

Long-format data frames for survey-based compositions.

Pop_Fishery_Ages, Pop_Fishery_Lens, Pop_Survey_Ages, Pop_Survey_Lens

Population-specific long-format composition outputs with an additional Pop column.

Obs_*_mat

Arrays of observed compositions indexed by Region × Year × Season × Bin × Sex × Fleet (and Pop where applicable).

Pred_*_mat

Arrays of model-predicted compositions with matching dimensions to observed arrays.

Details

Compositions include retained catch, discard catch, and survey observations, and are aligned across regions, years, seasons, fleets, sexes, and age/length bins. Observed compositions are optionally filtered by usage flags defined in the input data object.

See also

Other Model Diagnostics: do_jitter(), do_likelihood_profile(), do_retrospective(), do_runs_test(), get_catch_fits_plot(), get_idx_fits(), get_idx_fits_plot(), get_model_rep_from_mcmc(), get_nLL_plot(), get_osa(), get_retrospective_plot(), get_retrospective_relative_difference(), plot_resids()

Examples

if (FALSE) { # \dontrun{
comp_props <- get_comp_prop(
  data = data,
  rep = rep,
  age_labels = 2:31,
  len_labels = seq(41, 99, 2),
  year_labels = 1960:2024
)
} # }