BEAUti should explicitly generate uniform priors

[msuchard]

Originally reported on Google Code with ID 409

Currently, BEAUti generates uniform priors between bounds by setting upper and lower
attributes on the parameters. This should change to adding a <uniformPrior> element
to the priors block so all priors are explicitly defined in one place. As a consequence
the 'upper' and 'lower' attributes of a parameter should reflect the actual range of
values the parameter can take (i.e., in most cases these will be some combination of
-Inf, +Inf, 0 or 1).

Reported by rambaut on 2010-09-30 21:58:04

[msuchard]

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
  )

Reported by dong.w.xie on 2010-10-08 02:02:55

---

• Attachment: x2.xml

[msuchard]

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.

Reported by rambaut on 2010-10-08 06:44:14

[msuchard]

Reported by dong.w.xie on 2011-03-20 23:00:26

• Status changed: Fixed
• Labels added: Priority-High
• Labels removed: Priority-Medium