Extended Plot Diagnostics for (g)lm Models

Source: R/plotlm6.R

These plots are an extension of the original plots provided by plot.lm.

Six plots are currently available: residuals versus fitted, Scale-Location of \(\sqrt{| residuals|}\) against fitted values, residuals against leverages, Cook's distance, Normal Q-Q plot and histogram of residuals.

Also provided is the summary plot which shows all diagnostic plots arranged in a 2 by 3 grid. By default, this is shown first, then each of the individual plots in turn.

plotlm6(
  x,
  which = 1:6,
  panel = if (add.smooth) panel.smooth else points,
  sub.caption = NULL,
  main = "",
  ask = prod(par("mfcol")) < length(which) && dev.interactive(),
  id.n = 3,
  labels.id = names(residuals(x)),
  cex.id = 0.75,
  qqline = TRUE,
  cook.levels = c(0.5, 1),
  add.smooth = getOption("add.smooth", TRUE),
  label.pos = c(4, 2),
  cex.caption = 1,
  showBootstraps = nrow(x$model) >= 30 && nrow(x$model) < 4000,
  use.inzightplots = FALSE,
  env = parent.frame(),
  ...
)

Arguments

x

an lm object, typically the result of lm or glm. Can also take svyglm objects.

which

numeric, if a subset of the plots is required, specify a subset of the numbers 1:6. 7 will produce a summary plot showing all of the plots arranged in a a grid. 1:6 will show the summary plot followed by each of the single plots one by one (default).

panel

panel function. the useful alternative to points, panel.smooth can be chosen by add.smooth = TRUE.

sub.caption

common title. Above the figures if there are more than one; used as sub (s.title) otherwise. If NULL, as by default, a possible abbreviated version of deparse(x$call) is used.

main

title to each plot, in addition to caption.

ask

logical, if TRUE, the user is asked before each plot, see par(ask=.). Ignored when only one plot is being shown.

id.n

number of points to be labelled in each plot, starting with the most extreme.

labels.id

vector of labels, from which the labels for extreme plots will be chosen. NULL uses observation numbers.

cex.id

magnification of point labels.

qqline

logical, if TRUE, a qqline() is added to the normal QQ plot.

cook.levels

levels of the Cook's distance at which to draw contours.

add.smooth

logical, if TRUE, a smoother is drawn to the appropriate plots; see also panel above.

label.pos

positioning of labels, for the left half and right half of the graph respectively, for plots 1--3.

cex.caption

controls the size of caption.

showBootstraps

logical, if TRUE, bootstrap loess smoothers are drawn in the first 4 plots. By default, only drawn for sample sizes of at least 30.

use.inzightplots

logical, if set to TRUE, the iNZightPlots package will be used for plotting, rather than base R graphics.

env

environment for performing bootstrap simulations (i.e., to find the dataset!)

...

other arguments to be passed to through to plotting functions.

Value

No return value; called for the side-effect of producing a plot.

Details

For the residuals versus fitted values plot, we add bootstrapped smoothers to illustrate variance. The smoother is also added to the Scale-Location plot.

The Normal Q-Q and histogram plots are taken from the normcheck function in the s20x package.

Author

Simon Potter, David Banks, Tom Elliott.

Examples


m <- lm(Sepal.Length ~ Sepal.Width + Petal.Width, data = iris)
plotlm6(m, which = 1)


# the summary grid:
plotlm6(m, which = 7)


# the default cycles through all 6 plots
plotlm6(m)