Dear Remco,
I used the the BirthDeathSkyContemporary prior to run the analyisis in BEAST 2.1.3, but an initialise error occurred:
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Start likelihood: -Infinity after 11 initialisation attempts
P(posterior) = -Infinity (was NaN)
P(prior) = -Infinity (was NaN)
P(BirthDeathSkyContemporary.t:Clade3) = -Infinity (was NaN)
P(R0Prior.t:Clade3) = -184.20680743952371 (was NaN)
P(becomeUninfectiousRatePrior.t:Clade3) = -138.15510557964274 (was NaN)
P(ClockPrior.c:Clade3) = -13.815510557964274 (was NaN)
P(ClockPrior.c:newTrait) = -13.815510557964274 (was NaN)
P(GammaShapePrior.s:Clade3) = -13.815510557964274 (was NaN)
P(MutationRatePrior.s:Clade3) = -13.815510557964274 (was NaN)
P(origRootPrior.t:Clade3) = -18.420680743952367 (was NaN)
P(RateACPrior.s:Clade3) = -16.11809565095832 (was NaN)
P(RateAGPrior.s:Clade3) = -13.815510557964274 (was NaN)
P(RateATPrior.s:Clade3) = -13.815510557964274 (was NaN)
P(RateCGPrior.s:Clade3) = -13.815510557964274 (was NaN)
P(RateGTPrior.s:Clade3) = -13.815510557964274 (was NaN)
P(rhoPrior.t:Clade3) = 0.0 (was NaN)
P(rootPrior.newTrait) = NaN (was NaN)
P(likelihood) = NaN (was NaN)
P(treeLikelihood.Clade3) = NaN (was NaN)
P(locationtreeLikelihood.newTrait) = NaN (was NaN)
java.lang.Exception: Could not find a proper state to initialise. Perhaps try another seed.
at beast.core.MCMC.run(Unknown Source)
at beast.app.BeastMCMC.run(Unknown Source)
at beast.app.beastapp.BeastMain.<init>(Unknown Source)
at beast.app.beastapp.BeastMain.main(Unknown Source)
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Please tell me how this error occurred and give me some suggestion about how to address this problem. Thanks very much!
Cheers,
Jie