augPred {nlme}

Augmented Predictions

Description

Predicted values are obtained at the specified values of primary. If object has a grouping structure (i.e. getGroups(object) is not NULL), predicted values are obtained for each group. If level has more than one element, predictions are obtained for each level of the max(level) grouping factor. If other covariates besides primary are used in the prediction model, their average (numeric covariates) or most frequent value (categorical covariates) are used to obtain the predicted values. The original observations are also included in the returned object.

Usage

augPred(object, primary, minimum, maximum, length.out, ...)
## S3 method for class 'lme'
augPred(object, primary = NULL,
        minimum = min(primary), maximum = max(primary),
        length.out = 51, level = Q, ...)

Arguments

object

a fitted model object from which predictions can be extracted, using a predict method.

primary

an optional one-sided formula specifying the primary covariate to be used to generate the augmented predictions. By default, if a covariate can be extracted from the data used to generate object (using getCovariate), it will be used as primary.

minimum

an optional lower limit for the primary covariate. Defaults to min(primary).

maximum

an optional upper limit for the primary covariate. Defaults to max(primary).

length.out

an optional integer with the number of primary covariate values at which to evaluate the predictions. Defaults to 51.

level

an optional integer vector specifying the desired prediction levels. Levels increase from outermost to innermost grouping, with level 0 representing the population (fixed effects) predictions. Defaults to the innermost level.

...

some methods for the generic may require additional arguments.

Value

a data frame with four columns representing, respectively, the values of the primary covariate, the groups (if object does not have a grouping structure, all elements will be 1), the predicted or observed values, and the type of value in the third column: original for the observed values and predicted (single or no grouping factor) or predict.groupVar (multiple levels of grouping), with groupVar replaced by the actual grouping variable name (fixed is used for population predictions). The returned object inherits from class "augPred".

Note

This function is generic; method functions can be written to handle specific classes of objects. Classes which already have methods for this function include: gls, lme, and lmList.

Author(s)

José Pinheiro and Douglas Bates [e-mail]

References

Pinheiro, J. C. and Bates, D. M. (2000), Mixed-Effects Models in S and S-PLUS, Springer, New York.

See Also

plot.augPred, getGroups, predict

Examples

fm1 <- lme(Orthodont, random = ~1)
augPred(fm1, length.out = 2, level = c(0,1))