\Header{pairs.lme}{Pairs Plot of an lme Object}
\keyword{models}{pairs.lme}
\begin{Description}\relax
Diagnostic plots for 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. The expression on the right hand side of the formula, before
a \code{|} operator, must evaluate to a data frame with at least two
columns. If the data frame has two columns, a scatter plot of the two
variables is displayed (the Trellis function \code{xyplot} is
used). Otherwise, if more than two columns are present, a scatter plot
matrix with pairwise scatter plots of the columns in the data frame is
displayed (the Trellis function \code{splom} is used).
\end{Description}
\begin{Usage}
\begin{verbatim}
## S3 method for class 'lme':
pairs(x, form, label, id, idLabels, grid, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] an object inheriting from class \code{lme}, representing
a fitted linear mixed-effects 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{x} can be referenced. In addition, \code{x} 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 the \code{|} operator, must evaluate to a data frame with
at least two columns. Default is \code{\textasciitilde{} coef(.) }, corresponding to
a pairs plot of the coefficients evaluated at the innermost level of
nesting.
\item[\code{label}] an optional character vector of labels for the variables
in the pairs 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 an outlier
test based on the Mahalanobis distances of the estimated random
effects. Groups with random effects distances greater than the
\eqn{1-value}{} percentile of the appropriate chi-square 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 points in the
plot. If missing, no points 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
points 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
points. 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.
\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{\Link{lme}}, \code{\Link{xyplot}},
\code{\Link{splom}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
data(Orthodont)
fm1 <- lme(distance ~ age, Orthodont, random = ~ age | Subject)
# scatter plot of coefficients by gender, identifying unusual subjects
pairs(fm1, ~coef(., augFrame = TRUE) | Sex, id = 0.1, adj = -0.5)    
# scatter plot of estimated random effects
## Not run: 
pairs(fm1, ~ranef(.))
## End(Not run)
\end{ExampleCode}
\end{Examples}

