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

[Ben Bolker]

  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="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
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> R-sig-mixed-models using r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>>
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> R-sig-mixed-models using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>