I installed the MODEL_SELECTION package and restarted the program, but I'm still not seeing where I can apply the PS and SS methods in BEAUti for my XML. Most of the tutorials and help I've found online talks about adjusting the XML file itself, but if one must do that, the question then becomes what is the point of this package in BEAUti?
Thank you for any and all help.
Hi,
You can easily do this in BEAUti version 1.8 and higher. In the MCMC panel there is a check box "Perform marginal likelihood estimation (MLE) using path/stepping-stone sampling". Checking it will cause BEAST to output a yourfilename.mle.log.txt file which you can load in TRACER and calculate Bayes factors.
Hope this helps.
Hello,
It's different in BEAST2, you can do it with the AppStore, if you're using this version, check out this page : http://beast2.org/tag/model-selection-v-1-0-2/
It's all explained and really easy to use!
Best,
Marie
Hello,
I am facing same confusion. I've gone through BEAST2 model selection tutorial but can't find how to estimate SS score. Can anybody give a clue?
BR,
Arafat
Hello,
For BEAST 2.x, path sampling analysis could be performed by either editing the XML or using a GUI as well. Here are the tutorials.
All the best,
Fangluan
Editing the xml file for Path sampling:
http://www.beast2.org/path-sampling/
Path sampling with a GUI:
http://www.beast2.org/2014/07/14/path-sampling-with-a-gui
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