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Merge pull request #34 from jugne/master
BDSky template for morphological analyses with serial sampling
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| <beast version='2.0' | ||
| namespace='beast.app.beauti:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.branchratemodel:beast.base.evolution.speciation:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood:beast.evolution:beast.base.math.distributions'> | ||
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| <!-- tree priors --> | ||
| <mergewith point='treePriorTemplates'> | ||
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| <subtemplate id='BirthDeathSkylineSerialBDSParam' class='bdsky.evolution.speciation.BirthDeathSkylineModel' mainid='BirthDeathSkySerialBDSParam.t:$(n)' | ||
| suppressInputs='bdsky.evolution.speciation.BirthDeathSkylineModel.intervalTimes, | ||
| bdsky.evolution.speciation.BirthDeathSkylineModel.reproductiveNumber, | ||
| bdsky.evolution.speciation.BirthDeathSkylineModel.becomeUninfectiousRate, | ||
| bdsky.evolution.speciation.BirthDeathSkylineModel.samplingProportion, | ||
| bdsky.evolution.speciation.BirthDeathSkylineModel.S0, | ||
| bdsky.evolution.speciation.BirthDeathSkylineModel.tree, | ||
| bdsky.evolution.speciation.BirthDeathSkylineModel.treeIntervals, | ||
| bdsky.evolution.speciation.BirthDeathSkylineModel.forceRateChange, | ||
| bdsky.evolution.speciation.BirthDeathSkylineModel.conditionOnSurvival, | ||
| bdsky.evolution.speciation.BirthDeathSkylineModel.conditionOnRoot, | ||
| beast.base.inference.distribution.MarkovChainDistribution.parameter, | ||
| bdsky.evolution.speciation.BirthDeathSkylineModel.birthRateTimesRelative, | ||
| bdsky.evolution.speciation.BirthDeathSkylineModel.deathRateTimesRelative, | ||
| bdsky.evolution.speciation.BirthDeathSkylineModel.samplingRateTimesRelative, | ||
| bdsky.evolution.speciation.BirthDeathSkylineModel.reverseTimeArrays, | ||
| bdsky.evolution.speciation.BirthDeathSkylineModel.originIsRootEdge, | ||
| bdsky.evolution.speciation.BirthDeathSkylineModel.origin, | ||
| bdsky.evolution.speciation.BirthDeathSkylineModel.rhoSamplingTimes, | ||
| bdsky.evolution.speciation.BirthDeathSkylineModel.deathRateChangeTimes, | ||
| bdsky.evolution.speciation.BirthDeathSkylineModel.samplingRateChangeTimes, | ||
| bdsky.evolution.speciation.BirthDeathSkylineModel.birthRateChangeTimes, | ||
| bdsky.evolution.speciation.BirthDeathSkylineModel.removalProbabilityChangeTimes, | ||
| bdsky.evolution.speciation.BirthDeathSkylineModel.removalProbability, | ||
| bdsky.evolution.speciation.BirthDeathSkylineModel.turnOver, | ||
| bdsky.evolution.speciation.BirthDeathSkylineModel.netDiversification, | ||
| bdsky.evolution.speciation.BirthDeathSkylineModel.conditionOnRhoSampling'> | ||
| <![CDATA[ | ||
| <!-- Sequential Birth Death Skyline model--> | ||
| <BirthDeathSkylineModel spec="bdsky.evolution.speciation.BirthDeathSkylineModel" id="BirthDeathSkySerialBDSParam.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="0.2" lower="0." upper="Infinity" dimension="1"/> | ||
| <parameter name="rho" id="rhoBDS.t:$(n)" value="0.8" lower="0." upper="1."/> | ||
| </BirthDeathSkylineModel> | ||
| <distribution id="rhoPriorSerialBDS.t:$(n)" spec="beast.base.inference.distribution.Prior" x="@rhoBDS.t:$(n)"> | ||
| <distr spec="beast.base.inference.distribution.Beta" offset="0."> | ||
| <parameter name="alpha" value="80" estimate="false"/> | ||
| <parameter name="beta" value="20" estimate="false"/> | ||
| </distr> | ||
| </distribution> | ||
| <distribution id="deathRatePriorSerialBDS.t:$(n)" spec="beast.base.inference.distribution.Prior" x="@deathRateBDS.t:$(n)"> | ||
| <distr spec='beast.base.inference.distribution.Uniform' lower="0." upper="100"/> | ||
| </distribution> | ||
| <distribution id="birthRatePriorSerialBDS.t:$(n)" spec="beast.base.inference.distribution.Prior" x="@birthRateBDS.t:$(n)"> | ||
| <distr spec='beast.base.inference.distribution.Uniform' lower="0." upper="100"/> | ||
| </distribution> | ||
| <distribution id="samplingRatePriorSerialBDS.t:$(n)" spec="beast.base.inference.distribution.Prior" x="@samplingRateBDS.t:$(n)"> | ||
| <distr spec='beast.base.inference.distribution.Uniform' lower="0." upper="100"/> | ||
| </distribution> | ||
| <!-- tree operators --> | ||
| <operator id='BDSKY_Serial_bds_treeScaler.t:$(n)' spec='ScaleOperator' scaleFactor="0.5" weight="3" tree="@Tree.t:$(n)"/> | ||
| <operator id='BDSKY_Serial_bds_treeRootScaler.t:$(n)' spec='ScaleOperator' scaleFactor="0.5" weight="3" tree="@Tree.t:$(n)" rootOnly='true'/> | ||
| <operator id='BDSKY_Serial_bds_UniformOperator.t:$(n)' spec='Uniform' weight="30" tree="@Tree.t:$(n)"/> | ||
| <operator id='BDSKY_Serial_bds_SubtreeSlide.t:$(n)' spec='SubtreeSlide' weight="15" gaussian="true" size="1.0" tree="@Tree.t:$(n)"/> | ||
| <operator id='BDSKY_Serial_bds_narrow.t:$(n)' spec='Exchange' isNarrow='true' weight="15" tree="@Tree.t:$(n)"/> | ||
| <operator id='BDSKY_Serial_bds_wide.t:$(n)' spec='Exchange' isNarrow='false' weight="3" tree="@Tree.t:$(n)"/> | ||
| <operator id='BDSKY_Serial_bds_WilsonBalding.t:$(n)' spec='WilsonBalding' weight="3" tree="@Tree.t:$(n)"/> | ||
| <!-- BDSKY operators --> | ||
| <operator id='BDSKY_Serial_bds_deathRateScaler.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="2" parameter="@deathRateBDS.t:$(n)"/> | ||
| <operator id='BDSKY_Serial_bds_rhoScaler.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="1" parameter="@rhoBDS.t:$(n)"/> | ||
| <operator id='BDSKY_Serial_bds_birthRateScaler.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="10" parameter="@birthRateBDS.t:$(n)"/> | ||
| <operator id='BDSKY_Serial_bds_samplingRateScaler.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="10" parameter="@samplingRateBDS.t:$(n)"/> | ||
| <operator id="BDSKY_Serial_bds_updownBD.t:$(n)" spec="UpDownOperator" scaleFactor=".75" weight="2"> | ||
| <up idref="birthRateBDS.t:$(n)"/> | ||
| <down idref="deathRateBDS.t:$(n)"/> | ||
| </operator> | ||
| ]]> | ||
| <connect srcID='BirthDeathSkySerialBDSParam.t:$(n)' targetID='prior' inputName='distribution' if='inposterior(BirthDeathSkySerialBDSParam.t:$(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='rhoPriorSerialBDS.t:$(n)' targetID='prior' inputName='distribution' if='inposterior(BirthDeathSkySerialBDSParam.t:$(n)) and rhoBDS.t:$(n)/estimate=true'>prior on sampling proportion t:$(n)</connect> | ||
| <connect srcID='samplingRatePriorSerialBDS.t:$(n)' targetID='prior' inputName='distribution' if='inposterior(BirthDeathSkySerialBDSParam.t:$(n)) and samplingRateBDS.t:$(n)/estimate=true'>prior on samplingRateBDSt:$(n)</connect> | ||
| <connect srcID='deathRatePriorSerialBDS.t:$(n)' targetID='prior' inputName='distribution' if='inposterior(BirthDeathSkySerialBDSParam.t:$(n)) and deathRateBDS.t:$(n)/estimate=true'>prior on deathRateBDS.t:$(n)</connect> | ||
| <connect srcID='birthRatePriorSerialBDS.t:$(n)' targetID='prior' inputName='distribution' if='inposterior(BirthDeathSkySerialBDSParam.t:$(n)) and birthRateBDS.t:$(n)/estimate=true'>prior on birthRateBDS.t:$(n)</connect> | ||
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| <connect srcID='BDSKY_Serial_bds_treeScaler.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkySerialBDSParam.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Scales all internal nodes for tree t:$(n)</connect> | ||
| <connect srcID='BDSKY_Serial_bds_treeRootScaler.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkySerialBDSParam.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Scales root node for tree t:$(n)</connect> | ||
| <connect srcID='BDSKY_Serial_bds_UniformOperator.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkySerialBDSParam.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Draws new internal node heights uniformally for tree t:$(n)</connect> | ||
| <connect srcID='BDSKY_Serial_bds_SubtreeSlide.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkySerialBDSParam.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_Serial_bds_narrow.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkySerialBDSParam.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Narrow exchange performs local rearrangement of tree t:$(n)</connect> | ||
| <connect srcID='BDSKY_Serial_bds_wide.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkySerialBDSParam.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_Serial_bds_WilsonBalding.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkySerialBDSParam.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Performs Wilson-Balding global rearrangement of tree t:$(n)</connect> | ||
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| <connect srcID='BDSKY_Serial_bds_deathRateScaler.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkySerialBDSParam.t:$(n)) and deathRateBDS.t:$(n)/estimate=true'/> | ||
| <connect srcID='BDSKY_Serial_bds_rhoScaler.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkySerialBDSParam.t:$(n)) and rhoBDS.t:$(n)/estimate=true'/> | ||
| <connect srcID='BDSKY_Serial_bds_birthRateScaler.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkySerialBDSParam.t:$(n)) and birthRateBDS.t:$(n)/estimate=true'/> | ||
| <connect srcID='BDSKY_Serial_bds_samplingRateScaler.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkySerialBDSParam.t:$(n)) and samplingRateBDS.t:$(n)/estimate=true'/> | ||
| <connect srcID='BDSKY_Serial_bds_updownBD.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkySerialBDSParam.t:$(n)) and birthRateBDS.t:$(n)/estimate=true and deathRateBDS.t:$(n)/estimate=true'/> | ||
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| <connect srcID='BirthDeathSkySerialBDSParam.t:$(n)' targetID='tracelog' inputName='log' if='inposterior(BirthDeathSkySerialBDSParam.t:$(n))'/> | ||
| <plate var='p' range='birthRateBDS,deathRateBDS,rhoBDS,samplingRateBDS'> | ||
| <connect srcID='$(p).t:$(n)' targetID='state' inputName='stateNode' if='inposterior(BirthDeathSkySerialBDSParam.t:$(n)) and $(p).t:$(n)/estimate=true'/> | ||
| <connect srcID='$(p).t:$(n)' targetID='tracelog' inputName='log' if='inposterior(BirthDeathSkySerialBDSParam.t:$(n)) and $(p).t:$(n)/estimate=true'/> | ||
| </plate> | ||
| </subtemplate> | ||
| </mergewith> | ||
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| </beast> | ||
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