Our code is on GitHub here: https://github.com/ImperialCollegeLondon/covid19model/

I’m running base.r from Rscript (i.e. Rscript base.r; this runs 4 chains for 200 iterations, 100 warmup; takes < 4 minutes).

Everything runs out of the box on my Macbook Pro, with R version 3.5.1 and RStan version 2.18.2. 100 warmup iterations isn’t actually enough, so it hits maximum treedepth, but I’m pretty sure 1000 would be fine:

```
Warning messages:
1: There were 3 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
2: Examine the pairs() plot to diagnose sampling problems
```

Here’s the issue–on an Ubuntu server I’ve just spun up on the cloud, R version 3.6.3, RStan version 2.19.3, I get these mystifying messages–but when I check shinystan everything looks fine in terms of R-hat, etc:

```
Warning messages:
1: There were 1 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
2: Examine the pairs() plot to diagnose sampling problems
3: The largest R-hat is NA, indicating chains have not mixed.
Running the chains for more iterations may help. See
http://mc-stan.org/misc/warnings.html#r-hat
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
http://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
http://mc-stan.org/misc/warnings.html#tail-ess
```

As you can imagine, debugging this is a priority, so if anyone is available to help in real-time today or tomorrow, feel free to contact me off-site: s.flaxman@imperial.ac.uk

RData image from the run on the server is available here (100 MB): https://www.dropbox.com/s/zrmpltaic7kwm98/base-568665.Rdata?dl=0