Re: obtaining Markov jump statistics

[Sikandar Azam]

Hi oshin,

As far as I understand, simply selecting "State Change Count" in BEAUti may not be sufficient to log Markov jump statistics. I generally manually edit the XML file to include the appropriate Markov jump and reward blocks, as described in the BEAST documentation: https://beast.community/markov_jumps_rewards. 

In addition, I include the completeHistoryLogger to obtain the full history of state transitions, including the timing of each jump. It would be helpful if others could confirm whether this remains the recommended workflow for the current BEAST version 

Best,  

Sikandar

On Tue, Jun 16, 2026 at 5:10 AM Oshin Ley Garcia <oshi...@gmail.com> wrote:

Dear users, I hope you are doing well. I am working on a discrete phylogeographic analysis (find picture enclosed) and would like to confirm the correct workflow for obtaining Markov jump statistics in BEAST.

In BEAUti, I enabled "State Change Count" under the discrete trait settings. However, after running the analysis, the resulting .log file did not include the expected Markov jump outputs (number of jumps, 95% HPD, or jump proportions).

From what I understand, BEAUti does not automatically add the MarkovJumpsStatistic loggers to the XML file. To obtain the jump counts, it seems necessary to manually insert the MarkovJumpsStatistic entries into the <logger> section of the XML.

Could you please confirm whether this is the correct approach, or if there is an updated workflow for enabling Markov jumps in BEAST?

Thank you very much for your guidance.

Best regards, Oshin

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[Oshin Ley Garcia]

Hi Sikandar, thanks for your time.

I download the ''batRABV.jumpHistory.log''  example from tutorial and check line by line. 

I got so many errors but now is running. I will cross finger to see if that works