This tutorial is based on the BEAST community tutorial available here.
This tutorial will cover,
- Create XML to log Markov jump history.
- Create XML to log Markov jump history using an empirical tree distribution.
For this tutorial you can downlaod the BEAST jar files from here.
Complete history logger
<log id="completeJumpHistory" logEvery="100" fileName="batRABV.jumpHistory.log">
<completeHistoryLogger>
<markovJumpsTreeLikelihood idref="host.treeLikelihood"/>
</completeHistoryLogger>
</log>
For complete history logger you need to add useUniformization=”true” numberOfSimulants=”1” saveCompleteHistory=”true” to the markovJumpsTreeLikelihood block.
<!-- Likelihood for tree given discrete trait data -->
<markovJumpsTreeLikelihood id="state.treeLikelihood" stateTagName="state.states" useUniformization="true" numberOfSimulants="1" saveCompleteHistory="true">
<attributePatterns idref="state.pattern"/>
<treeModel idref="treeModel"/>
<siteModel idref="state.siteModel"/>
<generalSubstitutionModel idref="state.model"/>
<generalSubstitutionModel idref="state.model"/>
<strictClockBranchRates idref="state.branchRates"/>
<!-- START Ancestral state reconstruction -->
<!-- <parameter id="state.count" value=" 0.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 0.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 0.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 0.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 0.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 0.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 0.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 0.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 0.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 0.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 0.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 0.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 0.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 0.0"/> -->
<!-- END Ancestral state reconstruction -->
</markovJumpsTreeLikelihood>
Empirical tree distribution
<empiricalTreeDistributionModel id="treeModel" fileName="batRABV.trees">
<taxa idref="taxa"/>
</empiricalTreeDistributionModel>
<statistic id="treeModel.currentTree" name="Current Tree">
<empiricalTreeDistributionModel idref="treeModel"/>
</statistic>
Operator for currentTree
<empiricalTreeDistributionOperator weight="1">
<empiricalTreeDistributionModel idref="treeModel"/>
</empiricalTreeDistributionOperator>