# [R-sig-ME] MCMCglmm troubles

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.

Cheers,

Jarrod

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
> 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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>

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```