When trying to graph the conditional fixed effects of a glmmTMB
model with two random intercepts in GGally
I get the error:
There was an error calling "tidy_fun()". Most likely, this is because the function supplied in "tidy_fun=" was misspelled, does not exist, is not compatible with your object, or was missing necessary arguments (eg "conf.level=" or "conf.int="). See error message below. Error: Error in "stop_vctrs()": ! Can't recycle "..1" (size 3) to match "..2" (size 2).`
I have tinkered with figuring out the issue and it seems to be related to the two random intercepts included in the model. I have also tried extracting the coefficient and standard error information separately through broom.mixed::tidy
and then feeding the data frame into GGally:ggcoef()
with no avail. Any suggestions?
# Example with built-in randu data set
data(randu)
randu$A <- factor(rep(c(1,2), 200))
randu$B <- factor(rep(c(1,2,3,4), 100))
# Model
test <- glmmTMB(y ~ x + z + (0 +x|A) + (1|B), family="gaussian", data=randu)
# A few of my attempts at graphing--works fine when only one random effects term is in model
ggcoef_model(test)
ggcoef_model(test, tidy_fun = broom.mixed::tidy)
ggcoef_model(test, tidy_fun = broom.mixed::tidy, conf.int = T, intercept=F)
ggcoef_model(test, tidy_fun = broom.mixed::tidy(test, effects="fixed", component = "cond", conf.int = TRUE))
There are some (old!) bugs that have recently been fixed ( here , here ) that would make confidence interval reporting on RE parameters break for any model with multiple random terms (I think). I believe that if you are able to install updated versions of both glmmTMB
and broom.mixed
:
remotes::install_github("glmmTMB/glmmTMB/glmmTMB@ci_tweaks")
remotes::install_github("bbolker/broom.mixed")
then ggcoef_model(test)
will work.
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