[R] Using lme (nlme) to find the conditional variance of therandom effects

[Douglas Bates]

On Nov 13, 2007 1:02 AM, Rick Bilonick <bilonickra at upmc.edu> wrote:
> On Tue, 2007-11-13 at 01:03 -0500, Rick Bilonick wrote:
>
> >
> > Is there some way to get ranef with postVar=TRUE to show what the
> > variances are, or what the lower and upper bounds are? qqmath makes nice
> > plots but I need to obtain the numerical values.
> >
> > Rick B.
> >
> I found a way:
>
> attr(ranef(lmer.13,postVar=TRUE)[[2]],"postVar")
>
> But I still don't understand why it's not OK to access the bVar slot
> directly.

Because the class definitions can (and do, in the case of lme4)
change.  If you were to install the development version of the lme4
package

install.packages("lme4", repos = "http://R-forge.R-project.org")

you would find that the bVar slot doesn't exist any more.  However,
the ranef extractor with postVar = TRUE still does return the
conditional variances of the random effects.

> Also, the code I originally showed and the results from ranef are very
> similar with a correlation of 0.9983 (it varies very slightly from
> subject to subject):
>
> >
> round(data.frame(a=as.numeric(lmer.13 at bVar[[2]]*(attr(VarCorr(lmer.13),"sc")^2)[1]),
>   b=as.numeric(attr(ranef(lmer.13,postVar=TRUE)[[2]],"postVar"))),10)
>           a        b
> 1  5.41e-08 5.44e-08
> 2  4.77e-08 4.83e-08
> 3  6.24e-08 6.25e-08
> 4  4.44e-08 4.52e-08
> 5  6.50e-08 6.50e-08
> 6  2.67e-08 2.92e-08
> 7  5.07e-08 5.12e-08
> 8  6.43e-08 6.43e-08
> 9  3.64e-08 3.79e-08
> 10 4.86e-08 4.92e-08
> 11 6.33e-08 6.33e-08
> 12 3.44e-08 3.60e-08
> 13 4.16e-08 4.26e-08
> 14 3.69e-08 3.83e-08
> 15 5.96e-08 5.97e-08
> 16 6.46e-08 6.46e-08
> 17 3.28e-08 3.46e-08
> 18 4.71e-08 4.77e-08
> 19 5.18e-08 5.22e-08
> 20 2.81e-08 3.04e-08
> 21 3.97e-08 4.09e-08
> 22 5.70e-08 5.72e-08
> 23 6.06e-08 6.07e-08
> 24 3.23e-08 3.42e-08
> 25 4.94e-08 4.99e-08
> 26 5.35e-08 5.38e-08
> 27 3.86e-08 3.98e-08
> 28 6.73e-08 6.73e-08
> 29 4.68e-08 4.74e-08
> 30 6.15e-08 6.16e-08
> 31 4.67e-08 4.74e-08
> 32 2.04e-08 2.37e-08
> 33 3.45e-08 3.61e-08
> 34 6.28e-08 6.29e-08
> 35 5.53e-08 5.55e-08
>
> Not sure why they are not exactly the same.
>
>
> Rick B.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>