[R-sig-ME] Another case of -1.0 correlation of random effects

[Jarrod Hadfield]

Hi,

As a solution to suggestion 2: an inverse-Wishart prior with null  
scale matrix and degree of belief parameter equal to 3 (for a 2X2  
case) is non-informative for the correlation.  As a quick stab you  
could try:

prior<-list(R=list(V=1, nu=0), G=list(G1=list(V=diag(2)*1e-6, nu=3)))

m1<-MCMCglmm(iAUC~Dose, random=~us(Dose):Subject, prior=prior,  
data=gluc)

plot(posterior.cor(m1$VCV[,1:4]))


NOTE: I do not advocate this prior as it does not imply non- 
informativeness for the (co)variances (amongst other things). It is  
just useful to know the uncertainty regarding the correlation.

Jarrod




On 9 Apr 2010, at 14:03, Ben Bolker wrote:

> Ken Knoblauch wrote:
>> Kevin E. Thorpe <kevin.thorpe at ...> writes:
>>
>>> My data come from a crossover trial and are balanced.
>>>
>>>> str(gluc)
>>> 'data.frame':	96 obs. of  4 variables:
>>>  $ Subject  : int  1 2 3 5 6 7 10 11 12 13 ...
>>>  $ Treatment: Factor w/ 2 levels "Barley","Oat": 1 1 1 1 1 1 1 1 1  
>>> 1 ...
>>>  $ Dose     : int  8 8 8 8 8 8 8 8 8 8 ...
>>>  $ iAUC     : num  110 256 129 207 244 ...
>>>
>>
>>> clip>
>>
>> Shouldn't you make Subject into a factor?
>>
>> Ken
>>
>
>  It would make the plot a little bit prettier but I don't think it
> matters in this case because variable that appears as a grouping
> variable (i.e. on the right of the | ) is automatically treated as a
> factor?  I think?
>
>  Since it is really a crossover trial, it would seem reasonable in
> principle to have the (Treatment|Subject) random effect in there as
> well. I'm not sure what to do about the -1 correlation: it seems the
> choices (not necessarily in order) are (1) throw up your hands and say
> there's not enough data to estimate independently; (2) try WinBUGS,
> possibly with slightly informative priors; (3) try using lme4a to  
> create
> profiles of the parameters and see if you can figure out what's  
> happening.
>
>
>
> -- 
> Ben Bolker
> Associate professor, Biology Dep't, Univ. of Florida
> bolker at ufl.edu / people.biology.ufl.edu/bolker
> GPG key: people.biology.ufl.edu/bolker/benbolker-publickey.asc
>
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