A question on lme in R

Zonghui Hu <zhu at stat.tamu.edu> writes:

I have a question on using lme on a mixed effects model with nested
error structure. After applying lme to the data, and put the outcome
in, say TR.lme. I can extract the fixed effects by
TR.lme$coef$fixed. However, when I use TR.lme$coef$random.effects, it
does not give the variance components that I need, but a vector of
values at each nested level. What I want are the estimated variance
components that show up with summary(TR.lme), but I can not extract
them from TR.lme.

It is better to use the extractor functions fixef (or fixed.effects)
and ranef (of random.effects) to extract the estimated coefficients.
You should not depend on a particular internal representation of the
object returned from a model-fitting function.  For example, objects
returned by the version of lme in the lme4 package uses a different
internal representation.

As indicated in the output from
 help(package = "nlme")
the function VarCorr returns the variance and correlation components.

Douglas Bates                            bates at stat.wisc.edu
Statistics Department                    608/262-2598
University of Wisconsin - Madison        http://www.stat.wisc.edu/~bates/