\HeaderA{qqnorm.lme}{Normal Plot of Residuals or Random Effects from an lme Object}{qqnorm.lme}
\aliasA{qqnorm.lm}{qqnorm.lme}{qqnorm.lm}
\aliasA{qqnorm.lmList}{qqnorm.lme}{qqnorm.lmList}
\aliasA{qqnorm.nls}{qqnorm.lme}{qqnorm.nls}
\keyword{models}{qqnorm.lme}
\begin{Description}\relax
Diagnostic plots for assessing the normality of residuals and random
effects in the linear mixed-effects fit are obtained. The
\code{form} argument gives considerable flexibility in the type of
plot specification. A conditioning expression (on the right side of a
\code{|} operator) always implies that different panels are used for
each level of the conditioning factor, according to a Trellis
display.
\end{Description}
\begin{Usage}
\begin{verbatim}
## S3 method for class 'lme':
qqnorm(y, form, abline, id, idLabels, grid, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{y}] an object inheriting from class \code{lme}, representing
a fitted linear mixed-effects model or from class \code{lmList},
representing a list of \code{lm} objects, or from class \code{lm},
representing a fitted linear model, or from class \code{nls},
representing a nonlinear least squares fitted model.
\item[\code{form}] an optional one-sided formula specifying the desired type of
plot. Any variable present in the original data frame used to obtain
\code{y} can be referenced. In addition, \code{y} itself
can be referenced in the formula using the symbol
\code{"."}. Conditional expressions on the right of a \code{|}
operator can be used to define separate panels in a Trellis
display. The expression on the right hand side of \code{form} and to
the left of a \code{|} operator must evaluate to a residuals vector,
or a random effects matrix. Default is \code{\textasciitilde{} resid(., type = "p")},
corresponding to a normal plot of the standardized residuals
evaluated at the innermost level of nesting.
\item[\code{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.
\item[\code{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
\eqn{1 - value/2}{} quantile of the standard normal distribution are
identified in the plot using \code{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.
\item[\code{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 \code{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.
\item[\code{grid}] an optional logical value indicating whether a grid should
be added to plot. Default is \code{FALSE}.
\item[\code{...}] optional arguments passed to the Trellis plot function.
\end{ldescription}
\end{Arguments}
\begin{Value}
a diagnostic Trellis plot for assessing normality of residuals or
random effects.
\end{Value}
\begin{Author}\relax
Jose Pinheiro \email{Jose.Pinheiro@pharma.novartis.com} and Douglas Bates \email{bates@stat.wisc.edu}
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{lme}{lme}}, \code{\LinkA{plot.lme}{plot.lme}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## Not run: 
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(.))
## End(Not run)
\end{ExampleCode}
\end{Examples}

