CODEWITHSUNDEEP
rsjplot
Romy Frömer
Romy Frömer

Reputation: 13

Can't get "kr" p-value computation in tab_model (sjPlot) to work

I'm trying to summarize a lmer model with sjPlot::tab_model. It works until I try to get "kr" p-values to also obtain degrees of freedom. I have pbkrtest installed, and can use it separately, but it's unsuccessfully called by tab_model. Does anyone know what I'm missing?

I ran a linear mixed effects model. I can generate a table using 

tab_model(BWRTmod1b,show.stat = TRUE)

When I change the call to get p-values based on the Kenward-Roger approximated degrees of freedom like this: 

tab_model(BWRTmod1b,p.val= "kr" ,show.stat = TRUE)

I get the following error message:

Error in round(attr(pv, "df.kr", exact = TRUE)) : non-numeric argument to mathematical function

I have googled the problem and the only thing I found was a missing pbkrtest package, but that's not the case here. I also googled the error message itself and found that this can happen when a data frame is fed into a function that wants numerical input. I have also updated R and reinstalled/updated all packages and that didn't help.

I don't know whether and how I can fix this and it's also entirely possible that I am missing something else. Any hints would be appreciated.

Link to the model output

# working
tab_model(BWRTmod1b,show.stat = TRUE)

# not working
tab_model(BWRTmod1b,p.val= "kr" ,show.stat = TRUE) 

# long term goal
tab_model(BWRTmod1b,p.val= "kr", show.df=TRUE ,show.stat = TRUE)

I expected to generate a table of my linear mixed effects model results that includes degrees of freedom. I can generate a table with a summary based on Wald approximation, but I cannot get the Kenward-Roger version with degrees of freedom.

Upvotes: 1

Views: 565

Answers (1)

Ben Bolker
Ben Bolker

Reputation: 226597

This turns out to be a bug/infelicitous interaction between the lmerTest and sjPlot packages. Reproducible example:

library(lmerTest)
fm3 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy,
            REML=TRUE)
sjPlot::tab_model(fm3,p.val="kr")
## Error in round(attr(pv, "df.kr", exact = TRUE)) : 
## non-numeric argument to mathematical function

whereas the same thing works if you start with library(lme4) instead of library(lmerTest). It should now be fixed in the development version of sjPlot

Not sure how this interacts with REML=TRUE ...

Upvotes: 0

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