predict.lme               package:nlme               R Documentation

Predictions from an lme Object

Description:

     The predictions at level i are obtained by adding together the
     population predictions (based only on the fixed effects estimates)
     and the estimated contributions of the random effects to the
     predictions at grouping levels less or equal to i. The resulting
     values estimate the best linear unbiased predictions (BLUPs) at
     level i. If group values not included in the original grouping
     factors are present in 'newdata', the corresponding predictions
     will be set to 'NA' for levels greater or equal to the level at
     which the unknown groups occur.

Usage:

     ## S3 method for class 'lme':
     predict(object, newdata, level, asList, na.action, ...)

Arguments:

  object: an object inheriting from class 'lme', representing a fitted
          linear mixed-effects model.

 newdata: an optional data frame to be used for obtaining the
          predictions. All variables used in the fixed and random
          effects models, as well as the grouping factors, must be
          present in the data frame. If missing, the fitted values are
          returned.

   level: an optional integer vector giving the level(s) of grouping to
          be used in obtaining the predictions. Level values increase
          from outermost to innermost grouping, with level zero
          corresponding to the population predictions. Defaults to the
          highest or innermost level of grouping.

  asList: an optional logical value. If 'TRUE' and a single value is
          given in 'level', the returned object is a list with the
          predictions split by groups; else the returned value is
          either a vector or a data frame, according to the length of
          'level'. 

na.action: a function that indicates what should happen when 'newdata'
          contains 'NA's.  The default action ('na.fail') causes the
          function to print an error message and terminate if there are
          any incomplete observations.

     ...: some methods for this generic require additional arguments. 
          None are used in this method.

Value:

     if a single level of grouping is specified in 'level', the
     returned value is either a list with the predictions split by
     groups ('asList = TRUE') or a vector with the predictions ('asList
     = FALSE'); else, when multiple grouping levels are specified in
     'level', the returned object is a data frame with columns given by
     the predictions at different levels and the grouping factors.

Author(s):

     Jose Pinheiro Jose.Pinheiro@pharma.novartis.com and Douglas Bates
     bates@stat.wisc.edu

See Also:

     'lme', 'fitted.lme'

Examples:

     fm1 <- lme(distance ~ age, Orthodont, random = ~ age | Subject)
     newOrth <- data.frame(Sex = c("Male","Male","Female","Female","Male","Male"),
                           age = c(15, 20, 10, 12, 2, 4),
                           Subject = c("M01","M01","F30","F30","M04","M04"))
     predict(fm1, newOrth, level = 0:1)

