Normal Plot of Residuals or Random Effects from an lme Object
DESCRIPTION:
Diagnostic plots for assessing the normality of residuals and random
effects in the linear mixed-effects fit are obtained. The
form
argument gives considerable flexibility in the type of
plot specification. A conditioning expression (on the right side of a
`|' operator) always implies that different panels are used for
each level of the conditioning factor, according to a Trellis
display.
an object inheriting from class
lme, representing
a fitted linear mixed-effects model.
OPTIONAL ARGUMENTS:
form
an optional one-sided formula specifying the desired type of
plot. Any variable present in the original data frame used to obtain
object can be referenced. In addition,
object itself
can be referenced in the formula using the symbol
".". Conditional expressions on the right of a |
operator can be used to define separate panels in a Trellis
display. The expression on the right hand side of
form and to
the left of a `|' operator must evaluate to a residuals vector,
or a random effects matrix. Default is `~ resid(., type = "p")',
corresponding to a normal plot of the standardized residuals
evaluated at the innermost level of nesting.
abline
an optional numeric value, or numeric vector of length
two. If given as a single value, a horizontal line will be added to the
plot at that coordinate; else, if given as a vector, its values are
used as the intercept and slope for a line added to the plot. If
missing, no lines are added to the plot.
id
an optional numeric value, or one-sided formula. If given as
a value, it is used as a significance level for a two-sided outlier
test for the standardized residuals (random effects). Observations with
absolute standardized residuals (random effects) greater than the
1 - value/2 quantile of the standard normal distribution are
identified in the plot using
idLabels. If given as a one-sided
formula, its right hand side must evaluate to a logical, integer, or
character vector which is used to identify observations in the
plot. If missing, no observations are identified.
idLabels
an optional vector, or one-sided formula. If given as a
vector, it is converted to character and used to label the
observations identified according to
id. If given as a
one-sided formula, its right hand side must evaluate to a vector
which is converted to character and used to label the identified
observations. Default is the innermost grouping factor.
grid
an optional logical value indicating whether a grid should
be added to plot. Defaults to
FALSE.
...
optional arguments passed to the Trellis plot function.
VALUE:
a diagnostic Trellis plot for assessing normality of residuals or
random effects.
SEE ALSO:
,
EXAMPLES:
fm1 <- lme(distance ~ age, Orthodont, random = ~ age | Subject)
# normal plot of standardized residuals by gender
qqnorm(fm1, ~ resid(., type = "p") | Sex, abline = c(0, 1))
# normal plots of random effects
qqnorm(fm1, ~ranef(.))