[R-sig-ME] Comparison of crossed ranom effects: lmer vs. MCMCglmm

[Jarrod Hadfield]

Hi Linus,

The point estimates are almost identical if the posterior mode is used:

hist(mcmc$VCV[,"plate"], breaks=30)

abline(v=VarCorr(ml)[["plate"]][1], col="red")

The posterior mean (which is reported in the summary) is often not a  
good measure of central tendency for variance components because of  
the skew. Posterior modes have high Monte Carlo error though.

Cheers,

Jarrod




Quoting Linus Holtermann <holtermann at hwwi.org> on Mon, 19 Jan 2015  
18:39:52 +0100:

> Hello,
>
> I read that lmer can handle independent (often labelled as crossed)  
> random effets in mixed models. It seems to be possible with MCMCglmm  
> as long as groups for the random effects are uniquely labelled. I  
> use the "Penicllin" data in the lme4-package to compare both  
> approaches:
>
> library(lme4)
> library(MCMCglmm)
>
> str(Penicillin)
> attach(Penicillin)
>
> ml <- lmer(diameter~ 1 + (1|plate)+ (1|sample))
> summary(ml)
>
> mcmc <- MCMCglmm(diameter~ 1, random=~ plate + sample,verbose=F,  
> nitt=110000,burn=10000,thin=10,data=Penicillin)
> summary(mcmc)
>
> Why are the result for the plate-variance differ by a large amount?  
> Is it because MCMCglmm applies Gibbs sampling? Or is MCMCglmm doing  
> something else here, instead of fitting independent random effects?
>
>
> Best regards,
>
>
> Linus Holtermann
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