glmmTMB objects and residual plots

[Rosie Lennon]

Hi, 

I have been trying to find a function that to create residual plots for several glmmTMB objects (approx size: 2.3Mb). I have tried:

residuals.glmmTMB() # function does not exist
simulate() # only exists in bblme and does not recognise glmmTMB object
simulateResiduals() # via DHARMa package, but glmmTMB object not recognised
plot() # glmmTMB object not recognised
qqnorm(resid(), main="normal qq-plot, residuals") # glmmTMB object not recognised
qqline(resid()) # glmmTMB object not recognised

Either the function does not exist (TMB version 1.7.13, glmmTMB version 0.2.0, bblme version 1.0.20), or the glmmTMB object is not recognised with the error message: 

 Error in is.data.frame(data) : object 'x' not found

Apologies if this is a simple issue to fix, but I have not been able to find a solution on any forum I have come across. Does anyone know of an up to date function within glmmTMB that works?

Many thanks,

Rosie 

[Koen van Benthem]

Dear Rosie,

on my machine the following code runs and seems to return the residuals:

m1 <- glmmTMB(count~ mined + (1|site), zi=~mined, family=poisson, data=Salamanders)
residuals(m1)

If you  want to explicitly force the usage of the glmmTMB function, you could try:

glmmTMB:::residuals.glmmTMB(m1)

I hope this helps.

Best,

Koen

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[Mollie Brooks]

Hi Rosie,

Newer versions of DHARMa can handle glmmTMB. There is a discussion here 

https://github.com/florianhartig/DHARMa/issues/16

You probably also need to update glmmTMB.

simulateResiduals() can be a bit slow with large data sets, but it works.

This is more of a question for the R-sig-mixed list. 

cheers,

Mollie

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