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add template for birth-death parametrization
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| <beast version='2.0' | ||
| namespace='beast.app.beauti:beast.core:beast.evolution.branchratemodel:beast.evolution.speciation:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood:beast.evolution:beast.math.distributions'> | ||
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| <!-- tree priors --> | ||
| <mergewith point='treePriorTemplates'> | ||
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| <subtemplate id='BirthDeathSkylineContemporaryBDSParam' class='beast.evolution.speciation.BirthDeathSkylineModel' mainid='BirthDeathSkyContemporaryBDSParam.t:$(n)' | ||
| suppressInputs='beast.evolution.speciation.BirthDeathSkylineModel.intervalTimes, | ||
| beast.evolution.speciation.BirthDeathSkylineModel.reproductiveNumber, | ||
| beast.evolution.speciation.BirthDeathSkylineModel.becomeUninfectiousRate, | ||
| beast.evolution.speciation.BirthDeathSkylineModel.samplingProportion, | ||
| beast.evolution.speciation.BirthDeathSkylineModel.samplingRate, | ||
| beast.evolution.speciation.BirthDeathSkylineModel.contemp, | ||
| beast.evolution.speciation.BirthDeathSkylineModel.S0, | ||
| beast.evolution.speciation.BirthDeathSkylineModel.tree, | ||
| beast.evolution.speciation.BirthDeathSkylineModel.treeIntervals, | ||
| beast.evolution.speciation.BirthDeathSkylineModel.forceRateChange, | ||
| beast.evolution.speciation.BirthDeathSkylineModel.conditionOnSurvival, | ||
| beast.evolution.speciation.BirthDeathSkylineModel.conditionOnRoot, | ||
| beast.math.distributions.MarkovChainDistribution.parameter, | ||
| beast.evolution.speciation.BirthDeathSkylineModel.birthRateTimesRelative, | ||
| beast.evolution.speciation.BirthDeathSkylineModel.deathRateTimesRelative, | ||
| beast.evolution.speciation.BirthDeathSkylineModel.samplingRateTimesRelative, | ||
| beast.evolution.speciation.BirthDeathSkylineModel.reverseTimeArrays, | ||
| beast.evolution.speciation.BirthDeathSkylineModel.originIsRootEdge, | ||
| beast.evolution.speciation.BirthDeathSkylineModel.origin, | ||
| beast.evolution.speciation.BirthDeathSkylineModel.rhoSamplingTimes, | ||
| beast.evolution.speciation.BirthDeathSkylineModel.deathRateChangeTimes, | ||
| beast.evolution.speciation.BirthDeathSkylineModel.samplingRateChangeTimes, | ||
| beast.evolution.speciation.BirthDeathSkylineModel.birthRateChangeTimes, | ||
| beast.evolution.speciation.BirthDeathSkylineModel.removalProbabilityChangeTimes, | ||
| beast.evolution.speciation.BirthDeathSkylineModel.removalProbability, | ||
| beast.evolution.speciation.BirthDeathSkylineModel.turnOver, | ||
| beast.evolution.speciation.BirthDeathSkylineModel.netDiversification, | ||
| beast.evolution.speciation.BirthDeathSkylineModel.conditionOnRhoSampling'> | ||
| <![CDATA[ | ||
| <!-- Sequential Birth Death Skyline model--> | ||
| <BirthDeathSkylineModel spec="beast.evolution.speciation.BirthDeathSkylineModel" id="BirthDeathSkyContemporaryBDSParam.t:$(n)" tree="@Tree.t:$(n)" conditionOnRoot="true"> | ||
| <parameter name="birthRate" id="birthRateBDS.t:$(n)" value="2.0" lower="0." upper="Infinity" dimension="1"/> | ||
| <parameter name="deathRate" id="deathRateBDS.t:$(n)" value="0.5" lower="0." upper="Infinity" dimension="1"/> | ||
| <parameter name="samplingRate" id="samplingRateBDS.t:$(n)" value="0."/> | ||
| <parameter name="rho" id="rhoBDS.t:$(n)" value="0.8" lower="0." upper="1."/> | ||
| </BirthDeathSkylineModel> | ||
| <distribution id="rhoPriorContemp.t:$(n)" spec="beast.math.distributions.Prior" x="@rhoBDS.t:$(n)"> | ||
| <distr spec="beast.math.distributions.Beta" offset="0."> | ||
| <parameter name="alpha" value="80" estimate="false"/> | ||
| <parameter name="beta" value="20" estimate="false"/> | ||
| </distr> | ||
| </distribution> | ||
| <distribution id="deathRatePriorContemp.t:$(n)" spec="beast.math.distributions.Prior" x="@deathRateBDS.t:$(n)"> | ||
| <distr spec='beast.math.distributions.Uniform' lower="0." upper="100"/> | ||
| </distribution> | ||
| <distribution id="birthRatePriorContemp.t:$(n)" spec="beast.math.distributions.Prior" x="@birthRateBDS.t:$(n)"> | ||
| <distr spec='beast.math.distributions.Uniform' lower="0." upper="100"/> | ||
| </distribution> | ||
| <!-- tree operators --> | ||
| <operator id='BDSKY_contemptreeScaler.t:$(n)' spec='ScaleOperator' scaleFactor="0.5" weight="3" tree="@Tree.t:$(n)"/> | ||
| <operator id='BDSKY_contemptreeRootScaler.t:$(n)' spec='ScaleOperator' scaleFactor="0.5" weight="3" tree="@Tree.t:$(n)" rootOnly='true'/> | ||
| <operator id='BDSKY_contempUniformOperator.t:$(n)' spec='Uniform' weight="30" tree="@Tree.t:$(n)"/> | ||
| <operator id='BDSKY_contempSubtreeSlide.t:$(n)' spec='SubtreeSlide' weight="15" gaussian="true" size="1.0" tree="@Tree.t:$(n)"/> | ||
| <operator id='BDSKY_contempnarrow.t:$(n)' spec='Exchange' isNarrow='true' weight="15" tree="@Tree.t:$(n)"/> | ||
| <operator id='BDSKY_contempwide.t:$(n)' spec='Exchange' isNarrow='false' weight="3" tree="@Tree.t:$(n)"/> | ||
| <operator id='BDSKY_contempWilsonBalding.t:$(n)' spec='WilsonBalding' weight="3" tree="@Tree.t:$(n)"/> | ||
| <!-- BDSKY operators --> | ||
| <operator id='deathRateScaler.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="2" parameter="@deathRateBDS.t:$(n)"/> | ||
| <operator id='rhoScaler.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="1" parameter="@rhoBDS.t:$(n)"/> | ||
| <operator id='birthRateScaler.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="10" parameter="@birthRateBDS.t:$(n)"/> | ||
| <operator id="updownBD.t:$(n)" spec="UpDownOperator" scaleFactor=".75" weight="2"> | ||
| <up idref="birthRateBDS.t:$(n)"/> | ||
| <down idref="deathRateBDS.t:$(n)"/> | ||
| </operator> | ||
| ]]> | ||
| <connect srcID='BirthDeathSkyContemporaryBDSParam.t:$(n)' targetID='prior' inputName='distribution' if='inposterior(BirthDeathSkyContemporaryBDSParam.t:$(n)) and inlikelihood(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'/> | ||
| <connect srcID='RandomTree.t:$(n)' targetID='mcmc' inputName='init' if='inposterior(Tree.t:$(n))'/> | ||
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| <connect srcID='rhoPriorContemp.t:$(n)' targetID='prior' inputName='distribution' if='inposterior(BirthDeathSkyContemporaryBDSParam.t:$(n)) and rhoBDS.t:$(n)/estimate=true'>prior on sampling proportion t:$(n)</connect> | ||
| <connect srcID='deathRatePriorContemp.t:$(n)' targetID='prior' inputName='distribution' if='inposterior(BirthDeathSkyContemporaryBDSParam.t:$(n)) and deathRateBDS.t:$(n)/estimate=true'>prior on deathRateBDS.t:$(n)</connect> | ||
| <connect srcID='birthRatePriorContemp.t:$(n)' targetID='prior' inputName='distribution' if='inposterior(BirthDeathSkyContemporaryBDSParam.t:$(n)) and birthRateBDS.t:$(n)/estimate=true'>prior on birthRateBDS.t:$(n)</connect> | ||
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| <connect srcID='BDSKY_contemptreeScaler.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporaryBDSParam.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Scales all internal nodes for tree t:$(n)</connect> | ||
| <connect srcID='BDSKY_contemptreeRootScaler.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporaryBDSParam.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Scales root node for tree t:$(n)</connect> | ||
| <connect srcID='BDSKY_contempUniformOperator.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporaryBDSParam.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Draws new internal node heights uniformally for tree t:$(n)</connect> | ||
| <connect srcID='BDSKY_contempSubtreeSlide.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporaryBDSParam.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Performs subtree slide rearrangement of tree t:$(n)</connect> | ||
| <connect srcID='BDSKY_contempnarrow.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporaryBDSParam.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Narrow exchange performs local rearrangement of tree t:$(n)</connect> | ||
| <connect srcID='BDSKY_contempwide.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporaryBDSParam.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Wide exchange performs global rearrangement of tree t:$(n)</connect> | ||
| <connect srcID='BDSKY_contempWilsonBalding.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporaryBDSParam.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Performs Wilson-Balding global rearrangement of tree t:$(n)</connect> | ||
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| <connect srcID='deathRateScaler.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporaryBDSParam.t:$(n)) and deathRateBDS.t:$(n)/estimate=true'/> | ||
| <connect srcID='rhoScaler.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporaryBDSParam.t:$(n)) and rhoBDS.t:$(n)/estimate=true'/> | ||
| <connect srcID='birthRateScaler.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporaryBDSParam.t:$(n)) and birthRateBDS.t:$(n)/estimate=true'/> | ||
| <connect srcID='updownBD.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporaryBDSParam.t:$(n)) and birthRateBDS.t:$(n)/estimate=true and deathRateBDS.t:$(n)/estimate=true'/> | ||
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| <connect srcID='BirthDeathSkyContemporaryBDSParam.t:$(n)' targetID='tracelog' inputName='log' if='inposterior(BirthDeathSkyContemporaryBDSParam.t:$(n))'/> | ||
| <plate var='p' range='birthRateBDS,deathRateBDS,rhoBDS'> | ||
| <connect srcID='$(p).t:$(n)' targetID='state' inputName='stateNode' if='inposterior(BirthDeathSkyContemporaryBDSParam.t:$(n)) and $(p).t:$(n)/estimate=true'/> | ||
| <connect srcID='$(p).t:$(n)' targetID='tracelog' inputName='log' if='inposterior(BirthDeathSkyContemporaryBDSParam.t:$(n)) and $(p).t:$(n)/estimate=true'/> | ||
| </plate> | ||
| </subtemplate> | ||
| </mergewith> | ||
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| </beast> | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,3 @@ | ||
| <addon name='BDSKY' version='1.4.1'> | ||
| <addon name='BDSKY' version='1.4.2'> | ||
| <depends on='beast2' atleast='2.5.0'/> | ||
| </addon> |