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Plot one-step-ahead (OSA) residual diagnostics

Source: R/7-plot_osa.R
plot.rceattle_osa.Rd

Diagnostic plots for an rceattle_osa object (from osa_residuals()), following the recommendations of Stewart and Monnahan (2025) and the styling of the NOAA-AFSC afscOSA package. Under a correctly specified model OSA residuals are iid standard normal, so the headline diagnostic is statistical (the Q-Q plot with its annotated SDNR / tail statistics).

Up to two separate figures are drawn, depending on which data are present:

  1. Aggregate (index / catch): a Q-Q panel faceted by data source. These series have no age/length bin, so no bubble plots are drawn.

  2. Composition (comp / caal): a Q-Q panel, a signed OSA-residual bubble panel, and a signed Pearson-residual bubble panel (the Pearson residuals carried on the rceattle_osa object). By default age-based bins (age composition and conditional age-at-length) are shown in the left column and length-based bins in the right column, each with its own bin axis; set combine = FALSE to draw the age and length composition as two separate figures instead (useful when a model has many fleets/species).

Panel headers use the fleet name from fleet_control. Process residuals (from process_residuals()) are drawn as a Q-Q panel plus a residual-by-year panel.

Usage

# S3 method for class 'rceattle_osa'
plot(x, source = "all", species = NULL, combine = TRUE, ...)

Arguments

x

An rceattle_osa object from osa_residuals() or process_residuals().

source

Data source(s) to plot: any of "index", "catch", "comp", "caal", "diet", or "all" (default). Mirrors the source argument of residuals.Rceattle(); filters which figures are produced.

species

Optional species code(s) to include (matched against the species column). Default NULL keeps all species.

combine

Logical. When TRUE (default), age and length composition share one figure (age in the left column, length in the right). When FALSE, they are drawn as separate composition_age / composition_length figures.

...

Unused.

Value

Invisibly, a named list of the assembled ggplot / cowplot objects (some of aggregate, composition / composition_age / composition_length, and process). Called for its side effect of drawing the plot(s).

References

Stewart, I.J., and Monnahan, C.C. 2025. Can. J. Fish. Aquat. Sci. 82:1-13.

See also

osa_residuals(), osa_diagnostics()