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reparameteris beauti template
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@rbouckaert
rbouckaert committed Jun 25, 2019
1 parent 847fa0e commit 38d673c
Showing 1 changed file with 14 additions and 10 deletions.
24 changes: 14 additions & 10 deletions templates/snapper.xml
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snapper.SnapperTreeLikelihood.proportions,
snapper.SnapperTreeLikelihood.threads,
snapper.SnapSubstitutionModel.mutationRateU,
snapper.SnapSubstitutionModel.mutationRateV
snapper.SnapSubstitutionModel.mutationRateV,
snapper.SnapSubstitutionModel.theta
"
buttonLabelMap="beast.app.beauti.BeautiInitDlg.>> details=Edit parameters"
>
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<rawdata idref='$(n)'/>
</data>
<parameter name="stateNode" id="snapperTheta.t:$(n)" lower="1e-10" upper="10" spec="parameter.RealParameter">0.008</parameter>
<parameter name="stateNode" id="snapperCoalescentRate.t:$(n)" lower="1e-10" upper="10" spec="parameter.RealParameter">0.008</parameter>
<parameter name="stateNode" id="snapperU.s:$(n)" value="1.0" lower="0.0" spec="parameter.RealParameter" estimate="false"/>
<parameter name="stateNode" id="snapperV.s:$(n)" value="1.0" lower="0.0" spec="parameter.RealParameter" estimate="false"/>
<distribution spec="snapper.SnapperTreeLikelihood" id="snapperTreeLikelihood.$(n)" initFromTree="false" pattern="theta" >
<distribution spec="snapper.SnapperTreeLikelihood" id="snapperTreeLikelihood.$(n)" initFromTree="false" pattern="coalescentRate" >
<data idref="snapper.$(n)"/>
<tree idref="Tree.t:$(n)"/>
<siteModel spec="sitemodel.SiteModel" id="SnapperSiteModel.s:$(n)">
<substModel spec="snapper.SnapSubstitutionModel" id="SnapperSubstModel.s:$(n)">
<mutationRateU idref="snapperU.s:$(n)"/>
<mutationRateV idref="snapperV.s:$(n)"/>
<theta idref="snapperTheta.t:$(n)"/>
<coalescentRate idref="snapperCoalescentRate.t:$(n)"/>
</substModel>
</siteModel>
<branchRateModel spec="StrictClockModel" id="StrictClock.c:$(n)">
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<prior id="ClockPrior.c:$(n)" x="@clockRate.c:$(n)"><distr spec="beast.math.distributions.Uniform" upper="Infinity"/></prior>
<prior id="SnapperMutationRateUPrior.s:$(n)" x="@snapperU.s:$(n)"><distr spec="Gamma" alpha="1000" beta="0.001"/></prior>
<prior id="SnapperMutationRateVPrior.s:$(n)" x="@snapperV.s:$(n)"><distr spec="Gamma" alpha="1000" beta="0.001"/></prior>
<prior id="SnapperThetaPrior.s:$(n)" x="@snapperTheta.t:$(n)"><distr spec="Gamma" alpha="1000" beta="0.001"/></prior>
<prior id="SnapperCoalescentRatePrior.s:$(n)" x="@snapperCoalescentRate.t:$(n)"><distr spec="Gamma" alpha="1000" beta="0.001"/></prior>
<!-- tree and its properties -->
<taxonset id="TaxonSet.$(n)" spec="beast.evolution.alignment.TaxonSet" alignment="@snapper.$(n)" />
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<plugin id="TreeHeight.t:$(n)" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:$(n)"/>
<log id='ThetaLogger' spec='snap.ThetaLogger' coalescenceRate='@snapperCoalescentRate.t:$(n)'/>
<logger id="treelog.t:$(n)" spec="beast.core.Logger" logEvery="1000" fileName="$(tree).trees" mode="tree">
<log id="TreeWithMetaDataLogger.t:$(n)" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:$(n)">
</log>
Expand All @@ -244,8 +247,8 @@
<operator id="SnapperNodeSwapper.t:$(n)" spec="snap.operators.NodeSwapper" weight="0.5" tree="@Tree.t:$(n)"/>
<operator id="SnapperNodeBudger.t:$(n)" spec="snap.operators.NodeBudger" weight="5" size="0.5" tree="@Tree.t:$(n)"/>
<operator id="SnapperGammaMover.t:$(n)" spec="snap.operators.GammaMover" scale="0.75" weight="1" coalescenceRate="@snapperTheta.t:$(n)"/>
<operator id="SnapperRateMixer.t:$(n)" spec="snap.operators.RateMixer" scaleFactors="0.25" weight="1" tree="@Tree.t:$(n)" coalescenceRate="@snapperTheta.t:$(n)"/>
<operator id="SnapperGammaMover.t:$(n)" spec="snap.operators.GammaMover" scale="0.75" weight="1" coalescenceRate="@snapperCoalescentRate.t:$(n)"/>
<operator id="SnapperRateMixer.t:$(n)" spec="snap.operators.RateMixer" scaleFactors="0.25" weight="1" tree="@Tree.t:$(n)" coalescenceRate="@snapperCoalescentRate.t:$(n)"/>
<operator id='SnapperMutationMover.s:$(n)' spec='snap.operators.MutationMover' window="0.1" weight="1" u='@snapperU.s:$(n)' v='@snapperV.s:$(n)'/>
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<connect srcID="SnapperMutationRateUPrior.s:$(n)" targetID="prior" inputName="distribution" if="inlikelihood(snapperU.s:$(n)) and snapperU.s:$(n)/estimate=true"/>
<connect srcID="SnapperMutationRateVPrior.s:$(n)" targetID="prior" inputName="distribution" if="inlikelihood(snapperV.s:$(n)) and snapperV.s:$(n)/estimate=true"/>
<connect srcID="SnapperThetaPrior.t:$(n)" targetID="prior" inputName="distribution" if="inlikelihood(snapperTheta.t:$(n)) and snapperTheta.t:$(n)/estimate=true"/>
<connect srcID="SnapperCoalescentRatePrior.t:$(n)" targetID="prior" inputName="distribution" if="inlikelihood(snapperCoalescentRate.t:$(n)) and snapperCoalescentRate.t:$(n)/estimate=true"/>

<connect srcID="Tree.t:$(n)" targetID="state" inputName="stateNode" if="inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true"/>
<connect srcID="snapperU.s:$(n)" targetID="state" inputName="stateNode" if="inlikelihood(snapperU.s:$(n)) and snapperU.s:$(n)/estimate=true"/>
<connect srcID="snapperV.s:$(n)" targetID="state" inputName="stateNode" if="inlikelihood(snapperV.s:$(n)) and snapperV.s:$(n)/estimate=true"/>
<connect srcID="snapperTheta.t:$(n)" targetID="state" inputName="stateNode" if="inlikelihood(snapperTheta.t:$(n)) and snapperTheta.t:$(n)/estimate=true"/>
<connect srcID="snapperCoalescentRate.t:$(n)" targetID="state" inputName="stateNode" if="inlikelihood(snapperCoalescentRate.t:$(n)) and snapperCoalescentRate.t:$(n)/estimate=true"/>
<connect srcID="clockRate.c:$(n)" targetID="state" inputName="stateNode" if="inlikelihood(clockRate.c:$(n)) and clockRate.c:$(n)/estimate=true"/>
<connect srcID="birthRate.t:$(n)" targetID="state" inputName="stateNode" if="inposterior(YuleModel.t:$(n)) and inposterior(Tree.t:$(n)) and birthRate.t:$(n)/estimate=true"/>

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<connect srcID="TreeHeight.t:$(n)" targetID="tracelog" inputName="log" if="inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true"/>
<connect srcID="snapperU.s:$(n)" targetID="tracelog" inputName="log" if="inposterior(snapperU.s:$(n)) and snapperU.s:$(n)/estimate=true"/>
<connect srcID="snapperV.s:$(n)" targetID="tracelog" inputName="log" if="inlikelihood(snapperV.s:$(n)) and snapperV.s:$(n)/estimate=true"/>
<connect srcID="snapperTheta.t:$(n)" targetID="tracelog" inputName="log" if="inlikelihood(snapperTheta.t:$(n)) and snapperTheta.t:$(n)/estimate=true"/>
<connect srcID="snapperCoalescentRate.t:$(n)" targetID="tracelog" inputName="log" if="inlikelihood(snapperCoalescentRate.t:$(n)) and snapperCoalescentRate.t:$(n)/estimate=true"/>
<connect srcID="clockRate.c:$(n)" targetID="tracelog" inputName="log" if="inlikelihood(clockRate.c:$(n)) and clockRate.c:$(n)/estimate=true"/>
<connect srcID="YuleModel.t:$(n)" targetID="tracelog" inputName="log" if="inposterior(YuleModel.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true"/>
<connect srcID="birthRate.t:$(n)" targetID="tracelog" inputName="log" if="inposterior(YuleModel.t:$(n)) and birthRate.t:$(n)/estimate=true"/>
<connect srcID='ThetaLogger' targetID='tracelog' inputName='log' if="inlikelihood(snapperCoalescentRate.t:$(n)) and snapperCoalescentRate.t:$(n)/estimate=true"/>

<connect srcID="YuleBirthRatePrior.t:$(n)" targetID="prior" inputName="distribution" if="inposterior(YuleModel.t:$(n)) and inposterior(Tree.t:$(n)) and birthRate.t:$(n)/estimate=true">Prior on Yule birth rate for partition s:$(n)</connect>

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