Hi, everyone, 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. Could you please give any suggestion? I have tried ranef( ), but it seems not to be the right function. Thank you very much! Zonghui
A question on lme in R
2 messages · Zonghui Hu, Douglas Bates
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/