Speedemon coalescent rates

[Jacob Christensen]

Greetings,

I'm running speedemon on some SNP data I have and an getting generally good convergence on all parameters. However, on subsequent runs, it appears that a few of the snapperCoalescentRates are switching positions in the log file, which makes me question combining them with LogCombiner. Here you can see it in Tracer:

Does anyone have experience with this?

Best,

Jacob

[Jordan Douglas]

Hi Jacob,

It looks like you have 6 taxa, which means that the first 6 coalescent rates correspond to the leaves, which indices 7-10 are the internal nodes, and 11 is the root. The numbering behind the internal nodes is completely arbitrary between and within runs. Therefore, they are often multimodal in the trace file, which is nothing to be concerned about. The important part is that the leaf and root traces have high ESS (which they generally do). Note that this logic also applies for theta, as well as other models with branch parameters like the relaxed clock.

Jordan