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

Fox, John jfox @ending from mcm@@ter@c@
Fri Nov 9 16:37:43 CET 2018


Dear Aoibheann,

There is no specific Anova() method for "glmmTMB" objects, so the default method is invoked. This won't work because of the structure of "glmmTMB" models. I think that ideally one would want two tables of Wald tests of fixed effects, one for the conditional nonzero part of the model and one for the zero-inflation part of the model. 

This seems to me of sufficient interest that I'll look into writing "glmmTMB" methods for Anova() and for the linearHypothesis() function in the car package, on which Anova() depends. I can't promise, however, when I'll get to this.

Best,
 John

--------------------------------------
John Fox, Professor Emeritus
McMaster University
Hamilton, Ontario, Canada
Web: socialsciences.mcmaster.ca/jfox/



> -----Original Message-----
> From: R-sig-mixed-models [mailto:r-sig-mixed-models-bounces using r-
> project.org] On Behalf Of Aoibheann Gaughran
> Sent: Friday, November 9, 2018 10:23 AM
> To: Ben Bolker <bbolker using gmail.com>
> Cc: r-sig-mixed-models using r-project.org
> Subject: Re: [R-sig-ME] post hoc tests for glmmTMB
> 
> Great, thank you - I will keep plugging on. I will reconsider my use of
> the Anova function in car as well!
> 
> On Fri, 9 Nov 2018 at 15:19, Ben Bolker <bbolker using gmail.com> wrote:
> 
> >
> >   The point about Wald tests is correct, although their reliability
> > depends very much on context (they should be pretty good for tests of
> > fixed effects when the data set is reasonably large and predicted
> > probabilities/counts are not too extreme, i.e. not too close to zero
> > (counts) or 0/1 (probabilities)).
> >
> >   There are a lot of improvements in the development version with
> > respect to post hoc tests etc. on glmmTMB fits, as documented here:
> > <
> > https://github.com/glmmTMB/glmmTMB/blob/master/glmmTMB/vignettes/model
> > _evaluation.rmd
> > >
> >
> >   If you can install the development version (see
> > https://github.com/glmmTMB/glmmTMB/blob/master/README.md), that should
> > help a lot.
> >
> >  If you can't, most of these improvements will probably get to CRAN in
> > the next week or two; we're planning a new release soon.
> >
> >   In any case, I think that running the following code should make
> > multcomp work with glmmTMB objects (not quite sure what that first
> > function is doing ... ???)
> >
> > glht_glmmTMB <- function (model, ..., component="cond") {
> >     glht(model, ...,
> >          coef. = function(x) fixef(x)[[component]],
> >          vcov. = function(x) vcov(x)[[component]],
> >          df = NULL)
> > }
> > modelparm.glmmTMB <- function (model, coef. = function(x)
> > fixef(x)[[component]],
> >                                vcov. = function(x)
> vcov(x)[[component]],
> >                                df = NULL, component="cond", ...) {
> >     multcomp:::modelparm.default(model, coef. = coef., vcov. = vcov.,
> >                         df = df, ...)
> > }
> >
> > ## example
> > g1 <- glht(cbpp_b1, linfct = mcp(period = "Tukey"))
> >
> >
> >
> > On 2018-11-09 9:42 a.m., Guillaume Adeux wrote:
> > > 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="glmmTM
> > B"))>
> > >> 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
> > >>
> > >>         [[alternative HTML version deleted]]
> > >>
> > >> _______________________________________________
> > >> R-sig-mixed-models using r-project.org mailing list
> > >> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> > >>
> > >
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> > >
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> >
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> >
> 
> 
> --
> Aoibheann Gaughran
> 
> Behavioural and Evolutionary Ecology Research Group Zoology Building
> School of Natural Sciences Trinity College Dublin Dublin 2 Ireland
> Phone: +353 (86) 3812615
> 
> 	[[alternative HTML version deleted]]
> 
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