Closed matsen closed 6 years ago
I ran the 125-pruned version of our data for 500 million iterations of BEAST. I have all the resultant files, but @dunleavy005, do I just use tracer to generate the caterpillar graphic you made a while ago? I can do that for the 500 million run. Our default setting is 10 million, so I can run tracer on all the ecgtheow runs I'm about to do with the new partis runs Duncan's done.
Yes, use tracer, it has a nice GUI so it should spit out the trace plot almost immediately.
@dunleavy005 uploaded this caterpillar trace plot for the run I did on 500 million iterations. I think we decided it was sufficiently random? @matsen
Oh, yes, it's lovely.
Can now dynamically tweak mcmc iters from #21
What sort of convergence should we be seeing in terms of ESS of various parameters in order to think that the ancestral lineage graph is stable (i.e. it won't change with longer MCMC runs)?