\HeaderA{lmeObject}{Fitted lme Object}{lmeObject}
\keyword{models}{lmeObject}
\begin{Description}\relax
An object returned by the \code{lme} function, inheriting from class
\code{lme} and representing a fitted linear mixed-effects
model. Objects of this class have methods for the generic functions 
\code{anova}, \code{coef}, \code{fitted}, \code{fixed.effects},
\code{formula}, \code{getGroups}, \code{getResponse},
\code{intervals}, \code{logLik}, \code{pairs}, \code{plot},
\code{predict}, \code{print}, \code{random.effects}, \code{residuals},
\code{summary}, and \code{update}.
\end{Description}
\begin{Value}
The following components must be included in a legitimate \code{lme}
object. 
\begin{ldescription}
\item[\code{apVar}] an approximate covariance matrix for the
variance-covariance coefficients. If \code{apVar = FALSE} in the list
of control values used in the call to \code{lme}, this
component is equal to \code{NULL}.
\item[\code{call}] a list containing an image of the \code{lme} call that
produced the object.
\item[\code{coefficients}] a list with two components, \code{fixed} and
\code{random}, where the first is a vector containing the estimated
fixed effects and the second is a list of matrices with the estimated
random effects for each level of grouping. For each matrix in the
\code{random} list, the columns refer to the random effects and the
rows to the groups.
\item[\code{contrasts}] a list with the contrasts used to represent factors
in the fixed effects formula  and/or random effects formula. This
information is important for making predictions from a new data
frame in which not all levels of the original factors are
observed. If no factors are used in the lme model, this component
will be an empty list.
\item[\code{dims}] a list with basic dimensions used in the lme fit,
including the components \code{N} - the number of observations in
the data, \code{Q} - the number of grouping levels, \code{qvec} -
the number of random effects at each level from innermost to
outermost (last two values are equal to zero and correspond to the
fixed effects and the response), \code{ngrps} - the number of groups
at each level from innermost to outermost (last two values are one
and correspond to the fixed effects and the response), and
\code{ncol} - the number of columns in the model matrix for each
level of grouping from innermost to outermost (last two values are
equal to the number of fixed effects and one).
\item[\code{fitted}] a data frame with the fitted values as columns. The
leftmost column corresponds to the population fixed effects
(corresponding to the fixed effects only) and successive columns
from left to right correspond to increasing levels of grouping.
\item[\code{fixDF}] a list with components \code{X} and \code{terms}
specifying the denominator degrees of freedom for, respectively,
t-tests for the individual fixed effects and F-tests for the
fixed-effects terms in the models.
\item[\code{groups}] a data frame with the grouping factors as
columns. The grouping level increases from left to right.
\item[\code{logLik}] the (restricted) log-likelihood at convergence.
\item[\code{method}] the estimation method: either \code{"ML"} for maximum
likelihood, or \code{"REML"} for restricted maximum likelihood.
\item[\code{modelStruct}] an object inheriting from class \code{lmeStruct},
representing a list of mixed-effects model components, such
as \code{reStruct}, \code{corStruct}, and \code{varFunc} objects.
\item[\code{numIter}] the number of iterations used in the iterative
algorithm.
\item[\code{residuals}] a data frame with the residuals as columns. The
leftmost column corresponds to the population residuals
and successive columns from left to right correspond to increasing
levels of grouping.
\item[\code{sigma}] the estimated within-group error standard deviation.
\item[\code{varFix}] an approximate covariance matrix of the
fixed effects estimates.
\end{ldescription}
\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{lme}{lme}}, \code{lmeStruct}
\end{SeeAlso}

