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bayesiancook / pbmpi

phylobayes mpi
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How to determine burin in bpcomp and tracecomp #21

Closed dongzhang0725 closed 3 years ago

dongzhang0725 commented 3 years ago

Hi all,

I wanna to know what is the proper burin threshold, now I set 25% of the total generation as burin, but I am not sure it is reasonable. Could anybody help me with this question?

Thank you for your help,

Dong

bayesiancook commented 3 years ago

Dear Dong,

there is no simple rule to set up the burnin; you need to have a look at the trace plot of the summary statistics that are in the trace file (starting from column number 4, which is also the most important one, the log likelihood): the burnin should be chosen such that the traces are stationary.

I hope this helps

best,

Nicolas

dongzhang0725 commented 3 years ago

Dear Nicolas,

Thank you for your useful answer, now I know what to do with the burin strategy.

Best,

Dong