\Header{coef.lme}{Extract lme Coefficients}
\keyword{models}{coef.lme}
\begin{Description}\relax
The estimated coefficients at level \eqn{i}{} are obtained by adding
together the fixed effects estimates and the corresponding random
effects estimates at grouping levels less or equal to \eqn{i}{}. The
resulting estimates are returned as a data frame, with rows
corresponding to groups and columns to coefficients. Optionally, the
returned data frame may be augmented with covariates summarized over
groups.
\end{Description}
\begin{Usage}
\begin{verbatim}
## S3 method for class 'lme':
coef(object, augFrame, level, data, which, FUN, 
       omitGroupingFactor, subset, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] an object inheriting from class \code{lme}, representing
a fitted linear mixed-effects model.
\item[\code{augFrame}] an optional logical value. If \code{TRUE}, the returned
data frame is augmented with variables defined in \code{data}; else,
if \code{FALSE}, only the coefficients are returned. Defaults to
\code{FALSE}.
\item[\code{level}] an optional positive integer giving the level of grouping
to be used in extracting the coefficients from an object with
multiple nested grouping levels. Defaults to the highest or innermost
level of grouping.
\item[\code{data}] an optional data frame with the variables to be used for
augmenting the returned data frame when \code{augFrame =
     TRUE}. Defaults to the data frame used to fit \code{object}.
\item[\code{which}] an optional positive integer or character vector
specifying which columns of \code{data} should be used in the
augmentation of the returned data frame. Defaults to all columns in
\code{data}.
\item[\code{FUN}] an optional summary function or a list of summary functions
to be applied to group-varying variables, when collapsing \code{data}
by groups.  Group-invariant variables are always summarized by 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 frame such as \code{ordered}, \code{factor}, or
\code{numeric}.  The indicated function will be applied to any
group-varying 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{omitGroupingFactor}] an optional logical value.  When \code{TRUE}
the grouping factor itself will be omitted from the group-wise
summary of \code{data} but the levels of the grouping factor will
continue to be used as the row names for the returned data frame.
Defaults to \code{FALSE}.
\item[\code{subset}] an optional expression specifying a subset
\item[\code{...}] some methods for this generic require additional
arguments.  None are used in this method.
\end{ldescription}
\end{Arguments}
\begin{Value}
a data frame inheriting from class \code{coef.lme} with the estimated
coefficients at level \code{level} and, optionally, other covariates
summarized over groups. The returned object also inherits from classes
\code{ranef.lme} and \code{data.frame}.
\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{ranef.lme}},
\code{\Link{plot.ranef.lme}}, \code{\Link{gsummary}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
data(Orthodont)
fm1 <- lme(distance ~ age, Orthodont, random = ~ age | Subject)
coef(fm1)
coef(fm1, augFrame = TRUE)
\end{ExampleCode}
\end{Examples}

