\HeaderA{collapse.groupedData}{Collapse a groupedData Object}{collapse.groupedData}
\keyword{models}{collapse.groupedData}
\begin{Description}\relax
If \code{object} has a single grouping factor, it is returned
unchanged. Else, it is summarized by the values of the
\code{displayLevel} grouping factor (or the combination of its values
and the values of the covariate indicated in \code{preserve}, if any is
present). The collapsed data is used to produce a new
\code{groupedData} object, with grouping factor given by the
\code{displayLevel} factor.
\end{Description}
\begin{Usage}
\begin{verbatim}
## S3 method for class 'groupedData':
collapse(object, collapseLevel, displayLevel,
       outer, inner, preserve, FUN, subset, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] an object inheriting from class \code{groupedData},
generally with multiple grouping factors.

\item[\code{collapseLevel}] an optional positive integer or character string
indicating the grouping level to use when collapsing the data. Level
values increase from outermost to innermost grouping. Default is the
highest or innermost level of grouping.

\item[\code{displayLevel}] an optional positive integer or character string
indicating the grouping level to use as the grouping factor for the
collapsed data. Default is \code{collapseLevel}.

\item[\code{outer}] an optional logical value or one-sided formula,
indicating covariates that are outer to the \code{displayLevel}
grouping factor. If equal to \code{TRUE}, the \code{displayLevel}
element \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 \code{displayLevel} grouping
factor. If equal to \code{TRUE}, \code{attr(object, "outer")} 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{preserve}] an optional one-sided formula indicating a covariate
whose levels should be preserved when collapsing the data according
to the \code{collapseLevel} grouping factor. The collapsing factor is
obtained by pasting together the levels of the \code{collapseLevel}
grouping factor and the values of the covariate to be
preserved. Default is \code{NULL}, meaning that no covariates need to
be preserved.

\item[\code{FUN}] an optional summary function or a list of summary functions
to be used for collapsing the data.  The function or functions are
applied only to variables in \code{object} that vary within the
groups defined by \code{collapseLevel}.  Invariant variables are 
always summarized by group using the unique value that they assume
within that group.  If \code{FUN} is a single
function it will be applied to each non-invariant variable by group
to produce the summary for that variable.  If \code{FUN} is a list of
functions, the names in the list should designate classes of
variables in the data such as \code{ordered}, \code{factor}, or
\code{numeric}.  The indicated function will be applied to any
non-invariant variables of that class.  The default functions to be
used are \code{mean} for numeric factors, and \code{Mode} for both
\code{factor} and \code{ordered}.  The \code{Mode} function, defined
internally in \code{gsummary}, returns the modal or most popular
value of the variable.  It is different from the \code{mode} function
that returns the S-language mode of the variable.
\item[\code{subset}] an optional named list. Names can be either positive
integers representing grouping levels, or names of grouping
factors. Each element in the list is a vector indicating the levels
of the corresponding grouping factor to be preserved in the collapsed
data. Default is \code{NULL}, meaning that all levels are
used.

\item[\code{...}] some methods for this generic require additional
arguments.  None are used in this method.
\end{ldescription}
\end{Arguments}
\begin{Value}
a \code{groupedData} object with a single grouping factor given by the
\code{displayLevel} grouping factor, resulting from collapsing
\code{object} over the levels of the \code{collapseLevel} grouping
factor.
\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
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{\LinkA{groupedData}{groupedData}}, \code{\LinkA{plot.nmGroupedData}{plot.nmGroupedData}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
# collapsing by Dog
collapse(Pixel, collapse = 1)  # same as collapse(Pixel, collapse = "Dog")
\end{ExampleCode}
\end{Examples}

