How to visually check chain convergence with large number of iterations?

[Ruiqi-CUB]

Hi there,

I was running ~20k iterations/chain and 3 chains for phylobayes. I would like to visualize the convergence of the 3 chains. I have done it with Tracer in the past, however, with 20k iterations, Tracer is having a hard time to open the chain files. Is there any other way to visually check chain convergence?

Thanks a lot!

[bayesiancook]

Dear Ruiqi,

are you trying to open the .trace files (the .chain files will not be readable by tracer) ?

best, bayesiancook

[Ruiqi-CUB]

Yes! I was able to visualize them with less iterations. I understand that I can use build-in program to calculate if they converge but it's still nice to visualize them. Do you have any suggestions?

On Thu, Mar 16, 2023 at 4:24 AM bayesiancook @.***> wrote:

Dear Ruiqi,

are you trying to open the .trace files (the .chain files will not be readable by tracer) ?

best, bayesiancook

— Reply to this email directly, view it on GitHub https://github.com/bayesiancook/phylobayes/issues/5#issuecomment-1471682659, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALEILISOHGO65PE3YJVO3FDW4LS5LANCNFSM6AAAAAAV4VRDKU . You are receiving this because you authored the thread.Message ID: @.***>

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[bayesiancook]

Hi,

not clear to me what the problem is here. the trace files are not that big, so tracer should be able to open them. I would need more information:

• could you send me an example of problematic trace file ?
• command used for running phylobayes (which model - the exact data are unimportant).

best,