Hello,
I am trying to use BEAST1.10.4 to run a continuous phylogeography analysis assuming a directional RRW. I selected this option in Beauti, which I think produced this xml block:
<multivariateTraitLikelihood id="location.traitLikelihood" traitName="location" useTreeLength="true" scaleByTime="true" reportAsMultivariate="true" reciprocalRates="true" integrateInternalTraits="true">
<multivariateDiffusionModel idref="location.diffusionModel"/>
<treeModel idref="treeModel"/>
<traitParameter>
<parameter id="leaf.location"/>
</traitParameter>
<driftModels>
<strictClockBranchRates>
<parameter id="location.driftRate" value="0.0"/>
</strictClockBranchRates>
</driftModels>
<jitter window="1.0 1.0" duplicatesOnly="true">
<parameter idref="leaf.location"/>
</jitter>
<conjugateRootPrior>
<meanParameter>
<parameter value="0.0 0.0"/>
</meanParameter>
<priorSampleSize>
<parameter value="0.000001"/>
</priorSampleSize>
</conjugateRootPrior>
<arbitraryBranchRates idref="location.diffusion.branchRates"/>
</multivariateTraitLikelihood>
<correlation id="location.correlation" dimension1="1" dimension2="2">
<matrixParameter idref="location.precision"/>
</correlation>
<matrixInverse id="location.varCovar">
<matrixParameter idref="location.precision"/>
</matrixInverse>
<continuousDiffusionStatistic id="location.diffusionRate" greatCircleDistance="true">
<multivariateTraitLikelihood idref="location.traitLikelihood"/>
</continuousDiffusionStatistic>
BEAST is crashing because of the driftModels block:
SEVERE: Parsing error - poorly formed BEAST file, sib.complete_cds.directional.xml:
The '<strictClockBranchRates>' element, nested within an element with id, 'location.traitLikelihood', is incorrectly constructed.
The following was expected:
Exactly one ELEMENT of name rate REQUIRED containing
Exactly one ELEMENT of type Parameter REQUIRED
Am I missing something? Was this option tested in 1.10.4?
Thank you,
Ksenia