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

[Daniel Lüdecke]

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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