burn-in for log files

[JHallas]

Hi all,

trying to figure out to calculate the burn-in for the log files so i can see if my sampling converged.  Can anyone help me out. 


thanks,

Josh

[Natalia]

Hello Josh,

You should open your log files in Tracer and see if they have converged. Look at the traces from all runs together but colored with different colors. You can also look at the distributions and see if they are overlapping. The beginning of each trace is grayed out. This is the default burn-in. Depending if and when the runs converge, you can change the burn in from the table in tracer in the upper left. The first number on the table is the total of samples, the second number is the number of samples disregarded as burn-in. Then you can use this number to calculate the number of trees that should be disregarded as burn in for Tree annotator (the number is not the same, in Tracer the number is in generations, while in Tree annotator it is the number of samples, so it depends on how often you sample for your run).

hope this helps,

Natalia