Plot age frequency

Plot fit to age frequency (AF) observations.

Usage

plot_af(
  fit = NULL,
  object = NULL,
  posterior = NULL,
  probs = c(0.025, 0.975),
  years = NULL,
  fishery = "Indonesian",
  iters = NULL,
  observed_color = "#D55E00",
  predicted_color = "#0072B2",
  data = NULL,
  ...
)

Arguments

fit

An sbt_fit object. Stored MCMC is used by default when the plot supports posterior output.

object

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

posterior

Use NULL to plot the fit's required embedded composition posterior summary, or FALSE for point estimates only. External posterior objects are not accepted.

probs

A numeric vector of length 2 with probabilities in [0,1] for plotting quantiles of the posterior distribution. Default is c(0.025, 0.975).

years

A numeric vector of years to plot. If NULL (default), all years are plotted.

fishery

A character string specifying the fishery to plot. Options are "Indonesian" or "Australian". Default is "Indonesian".

iters

Retained for compatibility. It must be NULL when plotting an embedded posterior summary, which always covers every retained draw.

observed_color

Color used for observed proportions.

predicted_color

Color used for predicted proportions and intervals.

data

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

...

Retained for backward compatibility and currently ignored.

Value

A ggplot2 object displaying observed and predicted age frequencies by year.

See also

Other diagnostic plots: plot_biomass_spawning(), plot_cpue(), plot_gt(), 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_af(fit, posterior = FALSE, years = 2020:2022)