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

[Aoibheann Gaughran]

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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