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Convergence Diagnostics

Open lbybee opened this issue 10 years ago • 9 comments

Would there be interest in some code for a couple of convergence diagnostics?

lbybee avatar Jul 08 '14 04:07 lbybee

Yes, there would; which convergence diagnostics would you be interested in coding?

papamarkou avatar Jul 08 '14 08:07 papamarkou

Yes, Julia provides all the required machinery for implementing r-hat (it is not one of those mcmc diagnostics relying on AR processes), so go for it. Here is some sample R code for it:

http://www.stat.cmu.edu/~hseltman/rube/rube0.3-7/R/Rhat.R

papamarkou avatar Jul 08 '14 18:07 papamarkou

Sorry, I've caused the thread to look confusing by leaving a comment suggesting Rhat and then changed my mind and deleted it right away (since I figured you guys are all familiar with that diagnostic and I had second thoughts about butting in).

dchudz avatar Jul 08 '14 18:07 dchudz

There is nothing wrong with your suggestion, it would be very helpful if you would like to code Rhat and open a PR; we haven't implemented it (we haven't simply taken the time to do it), so it would be a nice contribution.

papamarkou avatar Jul 08 '14 18:07 papamarkou

We need to figure out what license that code was released under before we can use. I suspect it's not MIT-licensed.

johnmyleswhite avatar Jul 08 '14 18:07 johnmyleswhite

I am not familiar with licensing issues when it comes to coding as the boundaries are sometimes blur; would it make sense for example to simply reference Gelman's paper that introduces Rhat? Otherwise we could simply ask for the aurhors' permission to use their code as a reference point to reproduce the routine in Julia perhaps.

papamarkou avatar Jul 08 '14 18:07 papamarkou

I was thinking about r-hat, since there seems to be some interest I'd be happy to start on that. I'm not sure about the licencing either, though I know PyMC has a version. I can look into that.

lbybee avatar Jul 08 '14 18:07 lbybee

Ok, keep us posted here once you know more about the licensing issue and you have progressed with coding - I am sure you won't be writing to us from prison next time we hear from you.

papamarkou avatar Jul 08 '14 18:07 papamarkou

It's definitely fine if you work based on the paper or book instead of the code.

dchudz avatar Jul 08 '14 21:07 dchudz