I have been attempting to run a zero-inflated poisson model with the attached data and following code:

Example.csv (21.5 KB)

example<-read.csv(“Example.csv”,header=T)

as.factor(example$ID)->example$ID

as.factor(example$Sex)->example$Sex

as.factor(example$Level)->example$Level

as.factor(example$LesionType)->example$LesionType

formula<-bf(LesionNumber ~ Level + LesionType + Level:LesionType + Sex + AgeDeath + DD + PMI + (1 | ID), zi ~ Level + LesionType + Level:LesionType + Sex + AgeDeath + DD + PMI + (1 | ID))

model<-brm(formula=formula, data=example, family=“zero_inflated_poisson”,warmup=2000,iter=4000,seed=34)

I then received errors about treedepth, Rhat, bulk ESS, and tail ESS. Therefore, I tried to adjust the code with the following:

model.updated<-brm(formula=formula, data=lesion_number_total_staged, family=“zero_inflated_poisson”,warmup=4000,iter=8000,seed=34,control=list(max_treedepth=15))

However, I then get an R Session Aborted error. I’ve never encountered this with recent models and have narrowed down that it only happens when inputting control parameters. Any insight on why this is happening? I’ve tried uninstalling brms, rstan, and rstantools and reinstalling but that didn’t seem to help.

I’m using a MacBook Pro with 16GB memory on Mojave Version 10.14.6 and RStudio version Version 1.4.1717.