coef.lme {nlme}

Extract lme Coefficients

Description

The estimated coefficients at level i are obtained by adding together the fixed effects estimates and the corresponding random effects estimates at grouping levels less or equal to 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.

Usage

## S3 method for class 'lme'
coef(object, augFrame, level, data, which, FUN, 
       omitGroupingFactor, subset, ...)

Arguments

object

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

augFrame

an optional logical value. If TRUE, the returned data frame is augmented with variables defined in data; else, if FALSE, only the coefficients are returned. Defaults to FALSE.

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.

data

an optional data frame with the variables to be used for augmenting the returned data frame when augFrame = TRUE. Defaults to the data frame used to fit object.

which

an optional positive integer or character vector specifying which columns of data should be used in the augmentation of the returned data frame. Defaults to all columns in data.

FUN

an optional summary function or a list of summary functions to be applied to group-varying variables, when collapsing data by groups. Group-invariant variables are always summarized by the unique value that they assume within that group. If FUN is a single function it will be applied to each non-invariant variable by group to produce the summary for that variable. If FUN is a list of functions, the names in the list should designate classes of variables in the frame such as ordered, factor, or numeric. The indicated function will be applied to any group-varying variables of that class. The default functions to be used are mean for numeric factors, and Mode for both factor and ordered. The Mode function, defined internally in gsummary, returns the modal or most popular value of the variable. It is different from the mode function that returns the S-language mode of the variable.

omitGroupingFactor

an optional logical value. When TRUE the grouping factor itself will be omitted from the group-wise summary of data but the levels of the grouping factor will continue to be used as the row names for the returned data frame. Defaults to FALSE.

subset

an optional expression specifying a subset

...

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

Value

a data frame inheriting from class "coef.lme" with the estimated coefficients at level level and, optionally, other covariates summarized over groups. The returned object also inherits from classes "ranef.lme" and "data.frame".

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, esp. pp. 455-457.

See Also

lme, ranef.lme, plot.ranef.lme, gsummary

Examples

fm1 <- lme(distance ~ age, Orthodont, random = ~ age | Subject)
coef(fm1)
coef(fm1, augFrame = TRUE)