\Header{plot.nffGroupedData}{Plot an nffGroupedData Object}
\keyword{models}{plot.nffGroupedData}
\begin{Description}\relax
A Trellis dot-plot of the response by group is generated. If outer
variables are specified, the combination of their levels are used to
determine the panels of the Trellis display. The Trellis function
\code{dotplot} is used.
\end{Description}
\begin{Usage}
\begin{verbatim}
## S3 method for class 'nffGroupedData':
plot(x, outer, inner, innerGroups, xlab, ylab, strip, panel, key,
     grid, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] an object inheriting from class \code{nffGroupedData},
representing a \code{groupedData} object with a factor primary
covariate and a single grouping level.

\item[\code{outer}] an optional logical value or one-sided formula,
indicating covariates that are outer to the grouping factor, which
are used to determine the panels of the Trellis plot. If
equal to \code{TRUE}, \code{attr(object, "outer")} is used to indicate the
outer covariates. An outer covariate is invariant within the sets
of rows defined by the grouping factor.  Ordering of the groups is
done in such a way as to preserve adjacency of groups with the same
value of the outer variables. Defaults to \code{NULL}, meaning that
no outer covariates are to be used.

\item[\code{inner}] an optional logical value or one-sided formula, indicating
a covariate that is inner to the grouping factor, which is used to
associate points within each panel of the Trellis plot. If
equal to \code{TRUE}, \code{attr(object, "inner")} is used to indicate the
inner covariate. An inner covariate can change within the sets of
rows defined by the grouping  factor. Defaults to \code{NULL},
meaning that no inner covariate  is present. 

\item[\code{innerGroups}] an optional one-sided formula specifying a factor
to be used for grouping the levels of the \code{inner}
covariate. Different colors, or symbols, are used for each level
of the \code{innerGroups} factor. Default is \code{NULL}, meaning
that no \code{innerGroups} covariate is present.

\item[\code{xlab}] an optional character string with the label for the
horizontal axis. Default is the \code{y} elements of \code{attr(object,
     "labels")} and \code{attr(object, "units")} pasted together.

\item[\code{ylab}] an optional character string with the label for the
vertical axis. Default is the grouping factor name.

\item[\code{strip}] an optional function passed as the \code{strip} argument to
the \code{dotplot} function. Default is \code{strip.default(..., style
     = 1)} (see \code{trellis.args}).

\item[\code{panel}] an optional function used to generate the individual
panels in the Trellis display, passed as the \code{panel} argument
to the \code{dotplot} function.

\item[\code{key}] an optional logical function or function. If \code{TRUE}
and either \code{inner} or \code{innerGroups} are non-\code{NULL}, a
legend for the different \code{inner} (\code{innerGroups}) levels is 
included at the top of the plot. If given as a function, it is passed
as the \code{key} argument to the \code{dotplot} function. Default is
\code{TRUE} is either \code{inner} or \code{innerGroups} are
non-\code{NULL} and \code{FALSE} otherwise.

\item[\code{grid}] this argument is included for consistency with the
\code{plot.nfnGroupedData} method calling sequence. It is
ignored in this method function.
\item[\code{...}] optional arguments passed to the \code{dotplot} function.
\end{ldescription}
\end{Arguments}
\begin{Value}
a Trellis dot-plot of the response by group.
\end{Value}
\begin{Author}\relax
Jose Pinheiro \email{Jose.Pinheiro@pharma.novartis.com} and Douglas Bates \email{bates@stat.wisc.edu}
\end{Author}
\begin{References}\relax
Bates, D.M. and Pinheiro, J.C. (1997), "Software Design for Longitudinal
Data", in "Modelling Longitudinal and Spatially Correlated Data:
Methods, Applications and Future Directions", T.G. Gregoire (ed.),
Springer-Verlag, New York.

Pinheiro, J.C. and Bates, D.M. (1997) "Future Directions in
Mixed-Effects Software: Design of NLME 3.0" available at
http://franz.stat.wisc.edu/pub/NLME.
\end{References}
\begin{SeeAlso}\relax
\code{\Link{groupedData}}, \code{\Link{dotplot}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
data(Machines)
plot(Machines)
plot(Machines, inner = TRUE)
\end{ExampleCode}
\end{Examples}

