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evolvedmicrobe / beast-mcmc

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BEAST: tree prior expansion + growth not working #266

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
use BEAUTi to generate XML with tree prior expansion + growth:

8/12/2009 17:56:33 dr.evomodel.coalescent.CoalescentLikelihood
calculateLogLikelihood
SEVERE: CoalescentLikelihood is -Infinity; expansion.popSize=0.0213278684;
expansion.ancestralProportion=0.4514403426; expansion.growthRate=0.0000000001; 
8/12/2009 17:56:33 dr.evomodel.coalescent.CoalescentLikelihood
calculateLogLikelihood
SEVERE: CoalescentLikelihood is -Infinity; expansion.popSize=0.0220526214;
expansion.ancestralProportion=0.2478997426; expansion.growthRate=0.0000000003; 
8/12/2009 17:56:33 dr.evomodel.coalescent.CoalescentLikelihood
calculateLogLikelihood
SEVERE: CoalescentLikelihood is -Infinity; expansion.popSize=0.0220526214;
expansion.ancestralProportion=0.0655718444; expansion.growthRate=0.0000000008;

Original issue reported on code.google.com by dong.w.xie@gmail.com on 8 Dec 2009 at 4:57

GoogleCodeExporter commented 9 years ago 
Removed BEAUti-based workaround (i.e., disabling the option). Adjusted the 
starting values for some of the parameters and it seems to be working now. Was 
probably a numerical issue with inappropriate starting values.

Original comment by ramb...@gmail.com on 18 Aug 2010 at 11:27