Extract Index Fit Results

Generates a tidy dataframe of observed and predicted survey and fishery indices from a fitted RTMB model, including standard errors, confidence intervals, residuals, and catchability blocks. Both pooled and population-specific indices are returned when the corresponding Use*_pop flags contain any ones.

Usage

get_idx_fits(data, rep, year_labs)

Arguments

data

List. Input data used in the RTMB model. Must contain ObsSrvIdx, ObsSrvIdx_SE, ObsFishIdx, ObsFishIdx_SE, Wt_SrvIdx, Wt_FishIdx, srv_q_blocks, fish_q_blocks, UseFishIdx, and UseSrvIdx. For population-specific indices, also requires ObsSrvIdx_pop, ObsSrvIdx_pop_SE, ObsFishIdx_pop, ObsFishIdx_pop_SE, Wt_SrvIdx_pop, Wt_FishIdx_pop, UseSrvIdx_pop, and UseFishIdx_pop.

rep

List. RTMB report output containing PredSrvIdx and PredFishIdx, both dimensioned [n_pop × n_regions × n_years × n_seas × n_fleets]. Pooled indices are obtained by summing across the population dimension; population-specific indices use each population slice directly.

year_labs

Vector. Year labels assigned to the year dimension of predicted and observed index arrays.

Value

A dataframe containing pooled and, when active, population-specific survey and fishery indices with the following columns:

Region

Region label (prefixed with "Region").

Year

Year.

Seas

Season.

Fleet

Fleet identifier.

Type

One of "Survey", "Fishery", "Pop Survey", or "Pop Fishery".

obs

Observed index value.

value

Predicted index value.

se

Standard error of the observed index (weight-adjusted).

lci, uci

95% log-normal confidence interval for the observed index.

q_block

Catchability block identifier.

resid

Log-scale residual (\(\log(\text{obs}) - \log(\text{predicted})\)).

Category

Combined label of Type, population (for pop rows), Fleet, Season, and Q-block.

See also

Other Model Diagnostics: do_jitter(), do_likelihood_profile(), do_retrospective(), do_runs_test(), get_catch_fits_plot(), get_comp_prop(), 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{
idx_fits <- get_idx_fits(
  data = data,
  rep = rep,
  year_labs = seq(1960, 2024, 1)
)
} # }