[R-sig-ME] Plotting post-fitting inference effects in a glmmTMB model

[Ben Bolker]

  Yes, quite weird as effects:::plot.eff (the relevant method) appears
to check that variables are factors every time it tries to applies
droplevels().  A reproducible example would be great (although
technically maybe not this list's problem, as it's not clear it's
directly mixed-model-related?)

On 2019-08-27 8:06 a.m., Daniel Lüdecke wrote:
> Dear Julian,
> 
> without a reproducible example, it's a bit difficult to guess how to solve
> your issue. Is one of your predictors of class "character" and should
> probably be coerced to factor before you fit your model?
> 
> Else, you could also try the "ggeffects" package
> (https://strengejacke.github.io/ggeffects/), where you have three functions:
> ggpredict(), ggeffect() and ggemmeans(), each calling the related functions
> "predict()", "effects::effect()" or "emmeans::emmeans()" internally to
> compute marginal effects. There is a plot() method as well, based on ggplot2
> (see examples here
> https://strengejacke.github.io/ggeffects/articles/introduction_plotcustomize
> .html or here
> https://strengejacke.github.io/ggeffects/articles/introduction_plotmethod.ht
> ml). 
> 
> Best
> Daniel
> 
> -----Ursprüngliche Nachricht-----
> Von: R-sig-mixed-models [mailto:r-sig-mixed-models-bounces using r-project.org] Im
> Auftrag von Julian Gaviria Lopez
> Gesendet: Dienstag, 27. August 2019 12:01
> An: r-sig-mixed-models using r-project.org
> Betreff: [R-sig-ME] Plotting post-fitting inference effects in a glmmTMB
> model
> 
> Hello,
> 
> 
> I have the next model:
> 
>> zipoisson2  <- glmmTMB(Observations ~ CAP * Condition + (1|ID), 
>> contrasts=list(CAP="contr.sum",Condition="contr.sum"), data=mDATA, 
>> ziformula=~ 1 , family=poisson)
> 
> 
> Plotting the effects ("effects" package), I obtain:
> 
> (ae <- allEffects(zipoisson2))
> 
> model: Observations ~ CAP * Condition
>  CAP*Condition effect
>         Condition
> CAP        aapaff      aff      neu     pneu
>   apreC3 3.222636 2.731724 2.777021 2.573694
>   insC5  1.406698 3.173030 2.104875 1.420336
>   preC1  2.883115 3.641252 2.541221 2.635991
>   preC5  2.184075 2.310564 3.137734 1.995430
> 
> plot(ae)
> Error in UseMethod("droplevels") :
>   no applicable method for 'droplevels' applied to an object of class
> "character"
> 
> Question 1: Has anyone encountered the same issue? Any hint to solve it?
> 
> Question 2: Maybe is there any other package works better with glmmTMB model
> 
> Thanks in advance for any hint about it.
> 
> Julian,
> 
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