I am trying to fit the following model:
The simulated data is a logDose/Response dataset with 5 doses and the responses are 0’s and 1’s, with two samples and two blocks, and 20 replicates at each dose.
I am running into convergence issues;
1: There were 43 divergent transitions after warmup. Increasing adapt_delta above 0.999 may help. See
2: Examine the pairs() plot to diagnose sampling problems
The RHat and effective sample space metrics both give results that are consistent with convergence, whereas the divergent transitions do not. I looked at the pairs plot and the divergent transitions are all “below the diagonal”.
I am happy to provide the data.
I am just not clear on how effective reparameterization happens with an rstanarm model, or if you have any other suggestions.
Thank you in advance,
- Operating System: Centos 7
- rstanarm Version: 2.17.3