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

[Aoibheann Gaughran]

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

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