Skip to contents

Plot Residual Diagnostics

Source: R/plot.R
plot.resid.Rd

Residual-based diagnostic plots for cumulative link and general regression models using tinyplot::tinyplot() graphics.

Usage

# S3 method for class 'resid'
plot(
  x,
  y = NULL,
  what = c("qq", "fitted", "covariate"),
  covariate = NULL,
  fit = NULL,
  distribution = qnorm,
  ncol = NULL,
  alpha = 1,
  xlab = NULL,
  ylab = NULL,
  main = NULL,
  smooth = TRUE,
  ...
)

# S3 method for class 'clm'
plot(
  x,
  y = NULL,
  what = c("qq", "fitted", "covariate"),
  covariate = NULL,
  fit = NULL,
  distribution = qnorm,
  ncol = NULL,
  alpha = 1,
  xlab = NULL,
  ylab = NULL,
  main = NULL,
  smooth = TRUE,
  ...
)

# S3 method for class 'glm'
plot(
  x,
  y = NULL,
  what = c("qq", "fitted", "covariate"),
  covariate = NULL,
  fit = NULL,
  distribution = qnorm,
  ncol = NULL,
  alpha = 1,
  xlab = NULL,
  ylab = NULL,
  main = NULL,
  smooth = TRUE,
  ...
)

# S3 method for class 'lrm'
plot(
  x,
  y = NULL,
  what = c("qq", "fitted", "covariate"),
  covariate = NULL,
  fit = NULL,
  distribution = qnorm,
  ncol = NULL,
  alpha = 1,
  xlab = NULL,
  ylab = NULL,
  main = NULL,
  smooth = TRUE,
  ...
)

# S3 method for class 'orm'
plot(
  x,
  y = NULL,
  what = c("qq", "fitted", "covariate"),
  covariate = NULL,
  fit = NULL,
  distribution = qnorm,
  ncol = NULL,
  alpha = 1,
  xlab = NULL,
  ylab = NULL,
  main = NULL,
  smooth = TRUE,
  ...
)

# S3 method for class 'polr'
plot(
  x,
  y = NULL,
  what = c("qq", "fitted", "covariate"),
  covariate = NULL,
  fit = NULL,
  distribution = qnorm,
  ncol = NULL,
  alpha = 1,
  xlab = NULL,
  ylab = NULL,
  main = NULL,
  smooth = TRUE,
  ...
)

# S3 method for class 'vglm'
plot(
  x,
  y = NULL,
  what = c("qq", "fitted", "covariate"),
  covariate = NULL,
  fit = NULL,
  distribution = qnorm,
  ncol = NULL,
  alpha = 1,
  xlab = NULL,
  ylab = NULL,
  main = NULL,
  smooth = TRUE,
  ...
)

Arguments

x

An object of class "resid" (returned by resids()), or a fitted model object of class ordinal::clm(), stats::glm(), rms::lrm(), rms::orm(), MASS::polr(), or VGAM::vglm().

y

Ignored.

what

Character string specifying what to plot. Default is "qq" which produces a quantile-quantile plot of the residuals.

covariate

A vector giving the covariate values to use for residual-by- covariate plots (i.e., when what = "covariate").

fit

The fitted model from which the residuals were extracted. (Only required if what = "fitted" and x inherits from class "resid".)

distribution

Function that computes the quantiles for the reference distribution to use in the quantile-quantile plot. Default is qnorm which is only appropriate for models using a probit link function. When jitter_scale = "probability", the reference distribution is always U(-0.5, 0.5).

ncol

Integer specifying the number of columns to use for the plot layout (if requesting multiple plots). Default is NULL.

alpha

A single value in the interval [0, 1] controlling the opacity alpha of the plotted points. Only used when nsim > 1.

xlab

Character string giving the text to use for the x-axis label. Default is NULL.

ylab

Character string giving the text to use for the y-axis label. Default is NULL.

main

Character string giving the plot title. Default is NULL.

smooth

Logical indicating whether or not to add a nonparametric smooth to certain plots. Default is TRUE.

...

Additional optional arguments to be passed onto tinyplot::tinyplot() (e.g., col, pch, cex, etc.) or resids() (if calling the plot method directly on a fitted model object).

Value

No return value, called for plotting.

Note

For vglm (and vgam) objects, the VGAM package defines its own S4 plot method which will override this S3 method if VGAM is loaded. In such cases, we recommend extracting the residuals first using resids() and then plotting the resulting resid object (e.g. plot(resids(fit))), which will correctly dispatch to plot.resid().