\HeaderA{qqnorm.gls}{Normal Plot of Residuals from a gls Object}{qqnorm.gls}
\keyword{models}{qqnorm.gls}
\begin{Description}\relax
Diagnostic plots for assessing the normality of residuals the
generalized least squares 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 'gls':
qqnorm(y, form, abline, id, idLabels, grid, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{y}] an object inheriting from class \code{gls}, representing
a generalized 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. Default is \code{\textasciitilde{} resid(., type = "p")}, 
corresponding to a normal plot of the standardized residuals.
\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 depends on the type of Trellis plot used:
if \code{xyplot} defaults to \code{TRUE}, else defaults to
\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.
\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{gls}{gls}}, \code{\LinkA{plot.gls}{plot.gls}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
fm1 <- gls(follicles ~ sin(2*pi*Time) + cos(2*pi*Time), Ovary,
           correlation = corAR1(form = ~ 1 | Mare))
qqnorm(fm1, abline = c(0,1))
\end{ExampleCode}
\end{Examples}

