[R] MCMCglmm multinomial model results

[Michelle Kline]

Hi David,

Thanks for your comment. I haven't posted the data because they are
unpublished and include human subjects so there are issues with sharing on
a list serv, but I thought perhaps someone had encountered a similar
problem and would already know the answer.

I will reconsider whether my University's ethics approval would allow me to
post the data and update the question if I think it is allowable.

Michelle

On Fri, Mar 23, 2018, 10:13 AM David Winsemius <dwinsemius at comcast.net>
wrote:

>
> > On Mar 22, 2018, at 1:31 PM, Michelle Kline <
> michelle.ann.kline at gmail.com> wrote:
> >
> > Hi,
> >
> > Thanks in advance for any help on this question. I'm running multinomial
> > models using the MCMCglmm package. The models have 5 outcome variables
> > (each with count data), and an additional two random effects built into
> the
> > models. The issue is that when I use the following code, the summary only
> > gives me results for four of the outcome variables.
> >
> > Here is the code for my model:
> >
> > m3.random <- MCMCglmm(cbind(Opp_teacher , Dir_teacher, Enh_teacher,
> > SocTol_teacher, Eval_teacher) ~ trait -1,
> >               random = ~ us(trait):other + us(trait):focal,
> >               rcov = ~ us(trait):units,
> >               prior = list(
> >                 R = list(fix=1, V=0.5 * (I + J), n = 4),
> >                 G = list(
> >                   G1 = list(V = diag(4), n = 4),
> >                   G2 = list(V = diag(4), n = 4))),
> >               burnin = burn,
> >               nitt = iter,
> >               family = "multinomial5",
> >               data = data,
>
> We have no way to debug this without the data. Perhaps you should contact
> the maintainer and in your message attach the data?
>
>  maintainer('MCMCglmm')
> [1] "Jarrod Hadfield <j.hadfield at ed.ac.uk>"
>
>
> An equally effective approach would be to post (again with data that
> reproduces the error)  on the R-SIG-mixed-models mailing list since
> Hadfield is a regular contributor on that list. (To me it suggests not an
> error since you got output but rather a warning. Generally warnings and
> errors are properly labeled so you may not have included the full output.)
>
> --
> David.
> >               pr=TRUE,
> >               pl=TRUE,
> >               DIC = TRUE,
> >               verbose = FALSE)
> >
> > And the summary of the main effects:
> >
> > post.mean  l-95% CI  u-95% CI eff.samp        pMCMC
> > traitOpp_teacher    -3.828752 -4.616731 -3.067424 184.4305 5.263158e-05
> > traitDir_teacher    -3.400481 -4.041069 -2.813063 259.1084 5.263158e-05
> > traitEnh_teacher    -1.779129 -2.197415 -1.366496 624.9759 5.263158e-05
> > traitSocTol_teacher -2.852684 -3.429799 -2.332909 468.7098 5.263158e-05
> >
> >
> > It is not an issue of the suppressing the intercept, since I'm already
> > doing that (see the -1 term. When I remove that term, the model solutions
> > includes an intercept and only 3 additional main effects).
> >
> > The model does throw the following error, but after searching previous
> > messages on this list, I've concluded that this error message doesn't
> have
> > to do with  my current problem. Just in case: " observations with zero
> > weight not used for calculating dispersion"
> >
> > I have also posted a similar question on stackoverflow about a week ago,
> > but with no response, so I thought I would try here. Link in case people
> > want to gain reputation points for a
> > response:
> https://stackoverflow.com/questions/49309027/missing-term-in-mcmcglmm-multinomial-model-results-not-in-intercept-issue
> > <
> https://stackoverflow.com/questions/49309027/missing-term-in-mcmcglmm-multinomial-model-results-not-in-intercept-issue
> >
> >
> > And of course I've checked various other sources including the course
> > notes, but can't make sense of why the 5th term is dropped from the
> model.
> > Any help is much appreciated.
> >
> > Best,
> >
> > Michelle
> >
> > --
> > Michelle A. Kline, PhD
> >
> > Assistant Professor
> > Department of Psychology
> > Simon Fraser University
> >
> >       [[alternative HTML version deleted]]
> >
> > ______________________________________________
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> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
> David Winsemius
> Alameda, CA, USA
>
> 'Any technology distinguishable from magic is insufficiently advanced.'
>  -Gehm's Corollary to Clarke's Third Law
>
>
>
>
>
>

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