Ctsem

General
1

Hi all,

I am running ctsem and I have been getting some issues. Looking for help on how to fix them.

Warning messages:
1: There were 336 divergent transitions after warmup. See
https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
to find out why this is a problem and how to eliminate them.
2: There were 4 chains where the estimated Bayesian Fraction of Missing Information was low. See
https://mc-stan.org/misc/warnings.html#bfmi-low
3: Examine the pairs() plot to diagnose sampling problems

4: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#bulk-ess
5: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
Running the chains for more iterations may help. See
https://mc-stan.org/misc/warnings.html#tail-ess

Thanks,

2

@Charles_Driver

3

Discussion section at ctsem github is usually the best way to ask ctsem questions. These are just standard stan warnings telling you the estimates are unreliable. Why that is can be many reasons, inappropriate model for the data and not enough sampling iterations are two likely causes. Try simplify the model, tighten priors, or increase iterations.

1 Like
4

Thanks!

5

Thanks @Charles_Driver

Odd that I did not get these warning messages during the first run which I have used same model, with the same data.