Plot gene-tagging (GT) matches

Plot observed and predicted gene-tagging matches by release year.

Usage

plot_gt(
  fit = NULL,
  object = NULL,
  level = 0.95,
  observed_color = "#D55E00",
  predicted_color = "#0072B2",
  data = NULL
)

Arguments

fit

An sbt_fit object. This diagnostic uses its fitted point estimate; posterior intervals are not materialized.

object

Legacy RTMB objective used only with a legacy data-list input.

level

Numeric confidence level for the binomial prediction interval. The default is 0.95.

observed_color

Color used for observed gene-tagging matches.

predicted_color

Color used for predicted gene-tagging matches and intervals.

data

Legacy named alias for a model data list; supply object as well.

Value

A ggplot2 object displaying observed and predicted gene-tagging matches.

Details

Prediction intervals are plug-in binomial intervals conditional on the fitted probability. They do not include parameter uncertainty or the optional beta-binomial observation model.

See also

Other diagnostic plots: plot_af(), plot_biomass_spawning(), plot_cpue(), plot_hsps(), plot_lf(), plot_pops(), plot_recruitment(), plot_selectivity(), plot_tags(), plot_tags_residuals()

Examples

fit <- sbt_example_fit()
#> Warning: Dependency versions differ: RTMBdist, TMB
#> Warning: Dependency versions differ: RTMBdist, TMB
plot_gt(fit)