[R] MCMCglmm multinomial model results

Michelle Kline michelle.ann.kline at gmail.com
Thu Mar 22 21:31:27 CET 2018


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,
               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

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.



Michelle A. Kline, PhD

Assistant Professor
Department of Psychology
Simon Fraser University

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