[R-sig-ME] crossed random effects example

Jeroen Ooms j.c.l.ooms at uu.nl
Sun Mar 1 17:12:33 CET 2009

Hello Gabor,

I don't understand what you mean. lmer reports a variance of treatment
that is practically 0:

Random effects:
Groups    Name        Variance   Std.Dev.
airport   (Intercept) 1.0369e-01 3.2202e-01
treatment (Intercept) 1.0140e-23 3.1844e-12
Residual              4.6991e-02 2.1677e-01

It seems as if lmer shows there is no variance at all for the
treatment effect. I think this is quite different than the 0.04
reported in the slide. Are you sure I did not did use the correct

On Sun, Mar 1, 2009 at 4:27 PM, Gabor Grothendieck
<ggrothendieck at gmail.com> wrote:
> I suspect that the slide you are referencing mislabeled the
> standard deviations as variances since there is reasonable
> correspondence between your output and the slides if that
> were the case.
> Also check out:
> http://www.stat.columbia.edu/~gelman/arm/examples/pilots/
> On Sat, Feb 28, 2009 at 6:00 PM, Jeroen Ooms <j.c.l.ooms at uu.nl> wrote:
>> I am trying to learn about crossed random effects modeling in lme4. I
>> found this presentation that provides a small crossed dataset.
>> http://www.biostat.jhsph.edu/~fdominic/teaching/bio656/lectures/5addsin.crosslevels.ppt
>> I would like to reproduce the variance components as reported on slide
>> 9 of the powerpoint. Here is my code:
>> y <- c(0.38,0,0.38,0,.33,1,.12,1,.25,0,.5,.12,.5,1,.12,.86,.5,.67,.33,0,.14,1,0,1,.14,0,.71,0,.29,1,.14,1,.43,0,.29,.86,.86,.86,.14,.75)
>> x2 <- rep(paste("airport",1:8,sep=""),5)
>> x1 <- rep(paste("treatment",1:5,sep=""),rep(8,5))
>> mydata <- data.frame(y=y,airport=x2,treatment=x1)
>> lmer(y~1+(1|airport)+(1|treatment),data=mydata)
>> However, the variance components as reported by lmer are different
>> from the ones in the slides. What formula should I use? thank you!
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