Re: [R] bVar slot of lmer objects and standard errors

From: Ulrich Keller <>
Date: Tue 21 Feb 2006 - 11:04:02 EST


I'm sorry to resurrect this thread that I started almost two months ago. I've been pretty busy since I posted my question and the issue is not that high on my priority list. Thanks to all those who replied, and I hope I can tickle your interest again.

As a reminder, my question was how one can extract the conditional posterior variance of a random effect from the bVar slot of an lmer model. Thanks to your answers, I now understand that I have to use the diagonal elements of the conditional matrices. However, I am not quite sure what this means:

Douglas Bates wrote:
> I'd have to go back and check but I think that these are the upper
> triangles of the symmetric matrix (as Spencer suggested) that are the
> conditional variance-covariance matrices of the two-dimensional
> random effects for each school up to a scale factor. That is, I think
> each face needs to be multiplied by s^2 to get the actual
> variance-covariance matrix.

What is s^2? Where can I find it in the lmer object? I tried reading the source, but gave up fairly quickly. Thanks in advance for your replies, and this time I promise I'll be more responsive.


My original post:
> Hello,
> I am looking for a way to obtain standard errors for emprirical Bayes estimates of a model fitted with lmer (like the ones plotted on page 14 of the document available at Harold Doran mentioned ( that the posterior modes' variances can be found in the bVar slot of lmer objects. However, when I fit e.g. this model:
> lmertest1<-lmer(mathtot~1+(m_escs_c|schoolid),hlmframe)
> then lmertest1@bVar$schoolid is a three-dimensional array with dimensions (2,2,28). The factor schoolid has 28 levels, and there are random effects for the intercept and m_escs_c, but what does the third dimension correspond to? In other words, what are the contents of bVar, and how can I use them to get standard errors?
> Thanks in advance for your answers and Merry Christmas,
> Uli Keller mailing list PLEASE do read the posting guide! Received on Tue Feb 21 11:09:10 2006

This archive was generated by hypermail 2.1.8 : Fri 03 Mar 2006 - 03:42:38 EST