contraband/examples/testing/BMMVNLikelihoodOneTrait_fixedtree.xml at master · fkmendes/contraband · GitHub

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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<beast namespace="beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.util:beast.base.math:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.alignment:beast.base.evolution.likelihood" required="BEAST v2.5.0" version="2.5">

  <run id="mcmc" spec="MCMC" chainLength="5000000">
    <state id="state" storeEvery="5000">
      <stateNode idref="rateValue"/>
      <stateNode idref="rootValue"/>
    </state>

    <!-- START posterior -->
    <distribution id="posterior" spec="beast.base.inference.CompoundDistribution">

      <!-- START prior -->
      <distribution id="prior" spec="beast.base.inference.CompoundDistribution">
	<distribution id="RateValuePrior" spec="beast.base.inference.distribution.Prior" x="@rateValue">
	  <distr id="Exp.rateValue" spec="beast.base.inference.distribution.Exponential" offset="0.0" mean="0.2"/>
	</distribution>

        <distribution id="RootValuePrior" spec="beast.base.inference.distribution.Prior" x="@rootValue">
	  <distr id="Normal.RootValue" spec="beast.base.inference.distribution.Normal" mean="0.0" sigma="2.0"/>
        </distribution>
      </distribution>
      <!-- END prior -->

      <!-- START likelihood -->
      <distribution id="likelihood" spec="beast.base.inference.CompoundDistribution" useThreads="false">
	<distribution id="BMMVN" spec="contraband.mvnlikelihood.BMMVNLikelihoodOneTrait">

	  <tree id="FixedTree" spec="beast.base.evolution.tree.TreeParser" IsLabelledNewick="true" adjustTipHeights="false" newick="(((sp1:1.0,sp2:1.0):1.0,sp3:2.0):1.0,sp4:3.0):0.0;" offset="0" singlechild="false">
	    <taxonset id="TaxonSet" spec="TaxonSet">
	      <taxon id="sp1" spec="Taxon"/>
	      <taxon id="sp2" spec="Taxon"/>
	      <taxon id="sp3" spec="Taxon"/>
	      <taxon id="sp4" spec="Taxon"/>
	    </taxonset>
	  </tree>

	  <!-- (DEPRECATED) Original implementation used OneValueContTraits as a data wrapper, prior to Parameter having the "keys" argument -->
	  <!-- <oneTraitData id="oneTraitData" spec="contraband.valuewrappers.OneValueContTraits" nTraits="1" spNames="sp1,sp2,sp3,sp4"> -->
	  <!--   <traitValues id="fixedTraitValues" spec="parameter.RealParameter">4.1 4.5 5.9 0.0</traitValues> -->
	  <!-- </oneTraitData> -->

	  <oneTraitData id="oneTraitData" spec="outercore.parameter.KeyRealParameter" keys="sp1 sp2 sp3 sp4" value="4.1 4.5 5.9 0.0"/>

	  <sigmaSq id="rateValue" dimension="1" spec="parameter.RealParameter">1.4822794118</sigmaSq>

	  <rootValue id="rootValue" dimension="1" spec="parameter.RealParameter">3.079142</rootValue>
	</distribution>
      </distribution> <!-- END likelihood -->
    </distribution> <!-- END posterior -->

    <operator id="RateValueSqScaler" spec="ScaleOperator" parameter="@rateValue" scaleFactor="0.75" weight="3.0"/>
    <operator id="RootValueScaler" spec="RealRandomWalkOperator" parameter="@rootValue" windowSize="10.0" weight="3.0"/>

    <logger id="tracelog" fileName="example_BMMVNLikelihoodOneTrait_fixedtree.log" logEvery="5000" model="@posterior" sanitiseHeaders="true" sort="smart">
      <log idref="posterior"/>
      <log idref="likelihood"/>
      <log idref="prior"/>
      <log idref="rateValue"/>
      <log idref="rootValue"/>
    </logger>

    <logger id="screenlog" logEvery="1">
      <log idref="posterior"/>
      <log id="ESS.0" spec="util.ESS" arg="@posterior"/>
      <log idref="likelihood"/>
      <log idref="prior"/>
    </logger>

    <logger id="treelog.t:firsthalf" fileName="example_BMMVNLikelihoodOneTrait_fixedtree.trees" logEvery="5000000" mode="tree">
      <log id="TreeWithMetaDataLogger" spec="beast.base.evolution.tree.TreeWithMetaDataLogger" tree="@FixedTree"/>
    </logger>
  </run>
</beast>