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danieljue / beast-mcmc

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Speciation: Birth-death serially sampled model update #563

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
2) The "Speciation: Birth-death serially sampled model", the ideal 
parameterization would be (instead of bdss.birthRate, bdss.relativeDeathRate, 
bdss.psi):
bdss.birthRate (=lambda keep as it is),
relativeExtinctionRate (=(mu+psi)/lambda; uniform distribution on [0,1]),  
samplingProbability (=psi/(mu+psi) equivalent to the " birth-death basic 
reproductive number model", prior beta distribution)
bdss.sampleProbability as already there

We didn't add the alternative parameterization yet (and unfortunately I do not 
know how to do this...)

These changes will make the method equivalent to Denise's Beast2 implementation.

Thanks!!
Tanja

Original issue reported on code.google.com by dong.w.xie@gmail.com on 8 Dec 2011 at 10:15

GoogleCodeExporter commented 9 years ago

Original comment by dong.w.xie@gmail.com on 1 Feb 2012 at 10:26