R: Plot diagnostics for an 'asreml' object

plot.asreml {asreml}

R Documentation

Plot diagnostics for an `asreml` object

Description

Four plots are generated: a histogram of the residuals, a Normal Q-Q plot, a plot of residuals against fitted values and a plot of residuals against unit number.

Usage

## S3 method for class 'asreml'
plot(
  x,
  res = "default",
  spatial = "trend",
  facet = TRUE,
  distribution = "norm",
  conf = 0.95,
  labels = FALSE,
  no_semi_transparency = FALSE,
  ...
)

Arguments

x

An asreml object.

res

The type of residuals to be plotted; see residuals.asreml (default = default).

spatial

If "plot" and an independent error has been fitted with units in the random formula, these are added to the residuals, otherwise if "trend" then units are not added even if present in the model (default = "trend").

If TRUE, multi-panel conditioning plots are produced for models with multi-section residual structures (default = TRUE).

distribution

A character string specifying the distribution for Q-Q plots. Density and quantile functions for many standard probability distributions are available in the "stats" package. The distribution name is automatically prefixed with "d" and "q" (default = "norm").

conf

Value specifying confidence level (0 to 1) to be used to present confidence intervals (default = 0.95).

labels

If TRUE, points are labelled by unit number (default = FALSE).

no_semi_transparency

This should be set to TRUE if the device being used does not support semi-transparency (default = FALSE).

...

Additional arguments.

Details

If the residual structure of the model contains multiple sections, the default plots are conditioned on the factor whose levels define the sections; Normal Q-Q plots are only produced if facet = TRUE. For multivariate analyses, the plots are conditioned on trait.

Value

An invisible list of ggplot2 objects.