[R-sig-ME] MCMCglmm troubles

Jarrod Hadfield j.hadfield at ed.ac.uk
Thu Jun 24 10:46:59 CEST 2010

Hi Mike,

Sorry for the delay on this.  I'm not sure you want "multinomial3" as  
your family given that the three response variables are normally  
distributed. Specifying family=rep("gaussian", 3) would be more  
appropriate.  You will still get an error message because the default   
residual term is ~units which specifies a residual for each row of the  
response. For univariate models this is equivalent to IID residuals.  
For multi-response models it is more usual to allow different residual  
variances for each response, and often residual covariances between  
responses. rcov=~idh(trait):units fits different variances across  
responses (trait)  but sets the covariances to zero. rcov=  
~us(trait):units  estimates the covariances too. There are other less  
general possibilities too (see CourseNotes) which may be usefull. For  
example  rcov=~trait:units fits a common variance across responses and  
fixes the covariances to zero.

Having random=~sid also assumes that each sid effect is identical  
across responses so you may want to relax this assumption as above.



On 17 Jun 2010, at 13:43, Mike Lawrence wrote:

> Hi folks,
> I'm trying to do a mixed multinomial model with 3 response variables,
> but I'm getting the error "please use idh() or us() error structure".
> I believe that idh() and us() are used to specify the nature of the
> interaction between multiple random variables, but I don't have
> multiple random variables, so I'm not sure why I'm getting that error.
> Some example data are below, but note that in my real data, the dv's
> are indeed non-independent (they are in fact the number of trials
> classified into each of three categories).
> a = expand.grid(
> 	sid = 1:20
> 	, condition = factor(1:2)
> )
> a$group = factor(a$sid%%2)
> a$sid = factor(a$sid)
> a$dv1 = rnorm(nrow(a))
> a$dv2 = rnorm(nrow(a))
> a$dv3 = rnorm(nrow(a))
> MCMCglmm(
> 	cbind(dv1,dv2,dv3)~condition*group
> 	, random = ~ sid
> 	, family = 'multinomial3'
> 	, data = a
> )
> -- 
> Mike Lawrence
> Graduate Student
> Department of Psychology
> Dalhousie University
> Looking to arrange a meeting? Check my public calendar:
> http://tr.im/mikes_public_calendar
> ~ Certainty is folly... I think. ~
> _______________________________________________
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