[R-sig-ME] post hoc tests for glmmTMB

Guillaume Adeux guill@ume@imon@@2 @ending from gm@il@com
Fri Nov 9 15:42:54 CET 2018


Hi Aoibheann,

I think that anova on glmmTMB objects only produce Wald tests, which don't
seem to be very reliable.
You might want to look at the monet package (or its little brother afex)
that can produce LRT tests or parametric bootstrap.

Moreover, emmeans should work fine with glmmTMB but I remember having a
similar problem.

Maybe this thread and the following discussion can help you out:
https://stackoverflow.com/questions/48609432/error-message-lsmeans-for-beta-mixed-regression-model-with-glmmtmb

GA2



Le ven. 9 nov. 2018 à 15:24, Aoibheann Gaughran <gaughra using tcd.ie> a écrit :

> Update: lsmeans works if I use an older version of lsmeans (2.27-62) - can
> I rely on the results?
>
> Many thanks, Aoibheann
>
> On Fri, 9 Nov 2018 at 12:24, Aoibheann Gaughran <gaughra using tcd.ie> wrote:
>
> > Dear list,
> >
> > I am trying to perform post hoc tests on a glmmTMB model. I would
> normally
> > use car::Anova and mulgcomp::glht on my glmms (lmers). However, these
> > functions do not appear to be working for glmmTMB (when I run the model
> as
> > an lmer they work fine). I have also tried lsmeans and emmeans but they
> do
> > not appear to support glmmTMB either (although it appears they used to).
> I
> > have found various treads online suggesting that these functions should
> > work with TMB but they date back a few months.
> >
> > I am using the most up to date versions of R (3.5.1) and have updated all
> > of my packages e.g. glmmTMB 0.2.2.0, lsmeans 2.30-0
> >
> > The following are the error messages that I receive:
> >
> > > Anova(topmodTRFETE, type = 2)Error in I.p[c(subs.relatives,
> subs.term), , drop = FALSE] :
> >   subscript out of bound
> >
> > > summary(glht(topmodTRFETE, linfct = mcp(roadworks = "Tukey")), test =
> adjusted("holm"))Error in modelparm.default(model, ...) :
> >   dimensions of coefficients and covariance matrix don't match
> > >
> source(system.file("other_methods","lsmeans_methods.R",package="glmmTMB"))>
> lsmeans(topmodTRFETE, pairwise ~ roadworks, adjustSigma = TRUE, adjust =
> "holm")Error in ref_grid(object, ...) :
> >   Can't handle an object of class  “glmmTMB”
> >  Use help("models", package = "emmeans") for information on supported
> models.> rw.emm.s <- emmeans(topmodTRFETE, "roadworks")Error in
> ref_grid(object, ...) :
> >   Can't handle an object of class  “glmmTMB”
> >  Use help("models", package = "emmeans") for information on supported
> models.
> >
> >
> > Can any point me in the direction of a workaround for performing posthocs
> > on my glmmTMB model?
> >
> > Many thanks,
> >
> > --
> > Aoibheann Gaughran
> >
> > Behavioural and Evolutionary Ecology Research Group
> > Zoology Building
> > School of Natural Sciences
> > Trinity College Dublin
> > Dublin 2
> > Ireland
> > Phone: +353 (86) 3812615
> >
>
>
> --
> Aoibheann Gaughran
>
> Behavioural and Evolutionary Ecology Research Group
> Zoology Building
> School of Natural Sciences
> Trinity College Dublin
> Dublin 2
> Ireland
> Phone: +353 (86) 3812615
>
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>
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