

   FFiitttteedd llmmee OObbjjeecctt

   DDeessccrriippttiioonn::

        An object returned by the `lme' function, inheriting
        from class `lme' and representing a fitted linear
        mixed-effects model. Objects of this class have methods
        for the generic functions `anova', `coef', `fitted',
        `fixed.effects', `formula', `getGroups', `getResponse',
        `intervals', `logLik', `pairs', `plot', `predict',
        `print', `random.effects', `residuals', `summary', and
        `update'.

   VVaalluuee::

        The following components must be included in a legiti-
        mate `lme' object.

      apVar: an approximate covariance matrix for the variance-
             covariance coefficients. If `apVar = FALSE' in the
             list of control values used in the call to `lme',
             this component is equal to `NULL'.

       call: a list containing an image of the `lme' call that
             produced the object.

   coefficients: a list with two components, `fixed' and `ran-
             dom', 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
             `random' list, the columns refer to the random
             effects and the rows to the groups.

   contrasts: a list with the contrasts used to represent fac-
             tors 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.

       dims: a list with basic dimensions used in the lme fit,
             including the components `N' - the number of
             observations in the data, `Q' - the number of
             grouping levels, `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), `ngrps' -
             the number of groups at each level from innermost
             to outermost (last two values are one and corre-
             spond to the fixed effects and the response), and
             `ncol' - the number of columns in the model matrix
             for each level of grouping from innermost to out-
             ermost (last two values are equal to the number of
             fixed effects and one).

   estMethod: the estimation method: either `"ML"' for maximum
             likelihood, or `"REML"' for restricted maximum
             likelihood.

     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.

     groups: a data frame with the grouping factors as columns.
             The grouping level increases from left to right.

   lmeStruct: an object inheriting from class `lmeStruct', rep-
             resenting a list of linear mixed-effects model
             components, such as `reStruct', `corStruct', and
             `varFunc' objects.

     logLik: the (restricted) log-likelihood at convergence.

    numIter: the number of iterations used in the iterative
             algorithm.

   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.

      sigma: the estimated within-group error standard devia-
             tion.

   varFixed: an approximate covariance matrix of the fixed
             effects estimates.

   AAuutthhoorr((ss))::

        Jose Pinheiro and Douglas Bates

   SSeeee AAllssoo::

        `lme', `lmeStruct'

