Closed GoogleCodeExporter closed 8 years ago
But it seems some BEAUti default boundaries have problem:
- <logNormalPrior mean="1.0" stdev="1.25" offset="0.0" meanInRealSpace="false">
<parameter idref="CP1+2.kappa" />
</logNormalPrior>
- <logNormalPrior mean="1.0" stdev="1.25" offset="0.0" meanInRealSpace="false">
<parameter idref="CP3.kappa" />
</logNormalPrior>
- <uniformPrior lower="0.0" upper="Infinity">
<parameter idref="CP1+2.mu" />
</uniformPrior>
- <uniformPrior lower="0.0" upper="Infinity">
<parameter idref="CP3.mu" />
</uniformPrior>
- <uniformPrior lower="0.0" upper="1.0">
<parameter idref="CP1+2.frequencies" />
</uniformPrior>
- <uniformPrior lower="0.0" upper="1.0">
<parameter idref="CP3.frequencies" />
</uniformPrior>
- <uniformPrior lower="0.0" upper="1000.0">
<parameter idref="CP1+2.alpha" />
</uniformPrior>
- <uniformPrior lower="0.0" upper="1000.0">
<parameter idref="CP3.alpha" />
</uniformPrior>
- <oneOnXPrior>
<parameter idref="exponential.popSize" />
</oneOnXPrior>
- <uniformPrior lower="-Infinity" upper="Infinity">
<parameter idref="exponential.growthRate" />
</uniformPrior>
<coalescentLikelihood idref="coalescent" />
Result:
CompoundLikelihood(compoundModel)=(
DistributionLikelihood=-1.8654,
DistributionLikelihood=-1.8654,
DistributionLikelihood=-Inf,
DistributionLikelihood=-Inf,
DistributionLikelihood=0.0,
DistributionLikelihood=0.0,
DistributionLikelihood=-6.9078,
DistributionLikelihood=-6.9078,
OneOnX(exponential.popSize)=4.0174,
DistributionLikelihood=-Inf,
CoalescentLikelihood(coalescentLikelihood)=54.4972
),
CompoundLikelihood(compoundModel)=(
TreeLikelihood(treeLikelihood)=-2061.0466,
TreeLikelihood(treeLikelihood)=-916.1405
)
Original comment by dong.w.xie@gmail.com
on 8 Oct 2010 at 2:02
Attachments:
Do not add explicit uniform prior if one or other bound is infinity. The issue
was if you (say) set a uniform prior on clock.rate of [0, 100], BEAUti
generates this by setting the upper limit on the parameter which obscures the
fact this prior is there. I think the upper and lower on the parameters should
only be used to define 'hard' bounds.
Original comment by ramb...@gmail.com
on 8 Oct 2010 at 6:44
Original comment by dong.w.xie@gmail.com
on 20 Mar 2011 at 11:00
Original issue reported on code.google.com by
ramb...@gmail.com
on 30 Sep 2010 at 9:58