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| <beast version='2.0' | ||
| namespace='beast.app.beauti | ||
| :beast.core | ||
| :beast.core.util | ||
| :beast.evolution | ||
| :beast.evolution.nuc | ||
| :beast.evolution.operators | ||
| :beast.evolution.sitemodel | ||
| :beast.evolution.substitutionmodel | ||
| :beast.evolution.likelihood | ||
| :beast.evolution.branchratemodel | ||
| :beast.evolution.speciation | ||
| :beast.evolution.tree.coalescent | ||
| :beast.math.distributions | ||
| :bsp.distributions | ||
| :bsp.util'> | ||
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| <mergewith point='misc' fragment="@TreeOperators"/> | ||
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| <mergewith point='misc'> | ||
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| <fragment id="BESP_params" spec="beast.app.beauti.Fragment"> | ||
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| <![CDATA[ | ||
| <!-- Population size prior --> | ||
| <distribution id='$(b)MarkovChainedPopSizes.t:$(n)' spec="beast.math.distributions.MarkovChainDistribution" | ||
| jeffreys="true" | ||
| parameter="@$(b)PopSizes.t:$(n)"/> | ||
| <!-- Sampling intensity prior --> | ||
| <prior id="$(b)SamplingIntensityPrior.t:$(n)" name="distribution" x="@$(b)SamplingIntensity.t:$(n)"> | ||
| <Exponential name="distr" mean="1.0"/> | ||
| </prior> | ||
| <!-- Operators --> | ||
| <operator id='$(b)PopSizesScaler.t:$(n)' spec='ScaleOperator' scaleFactor="0.75" weight="15" parameter="@$(b)PopSizes.t:$(n)"/> | ||
| <operator id='$(b)GroupSizesDelta.t:$(n)' spec='DeltaExchangeOperator' delta="1" weight="6" integer="true" | ||
| intparameter="@$(b)GroupSizes.t:$(n)"/> | ||
| <operator id="$(b)SamplingIntensityScaler.t:$(n)" spec="ScaleOperator" parameter="@$(b)SamplingIntensity.t:$(n)" scaleFactor="0.5" weight="2.0"/> | ||
| <!-- Change-point time loggers --> | ||
| <plugin id="$(b)PopSizeChangeTimes.t:$(n)" spec="bsp.util.popSizeChangeTimeLogger" skyline="@$(b).t:$(n)"/> | ||
| <plugin id="$(b)SamplingIntensityChangeTimes.t:$(n)" spec="bsp.util.samplingIntensityChangeTimeLogger" skyline="@$(b).t:$(n)"/> | ||
| ]]> | ||
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| <!-- Connect parameters to state --> | ||
| <connect srcID='$(b)PopSizes.t:$(n)' targetID='state' inputName='stateNode' | ||
| if='inposterior($(b).t:$(n)) and $(b)PopSizes.t:$(n)/estimate=true'/> | ||
| <connect srcID='$(b)SamplingIntensity.t:$(n)' targetID='state' inputName='stateNode' | ||
| if='inposterior($(b).t:$(n)) and $(b)SamplingIntensity.t:$(n)/estimate=true'/> | ||
| <connect srcID='$(b)GroupSizes.t:$(n)' targetID='state' inputName='stateNode' | ||
| if='inposterior($(b).t:$(n)) and $(b)GroupSizes.t:$(n)/estimate=true'/> | ||
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| <!-- Connect prior distributions to prior --> | ||
| <connect srcID='$(b).t:$(n)' targetID='prior' inputName='distribution' | ||
| if='inposterior($(b).t:$(n)) and Tree.t:$(n)/estimate=true'>Coalescent with BESP tree t:$(n) | ||
| </connect> | ||
| <connect srcID='$(b)MarkovChainedPopSizes.t:$(n)' targetID='prior' inputName='distribution' | ||
| if='inposterior($(b).t:$(n)) and $(b)PopSizes.t:$(n)/estimate=true'>Markov chained prior on population sizes of BESP | ||
| </connect> | ||
| <connect srcID='$(b)SamplingIntensityPrior.t:$(n)' targetID='prior' inputName='distribution' | ||
| if='inposterior($(b).t:$(n)) and $(b)SamplingIntensity.t:$(n)/estimate=true'>Prior on sampling intensity of BESP | ||
| </connect> | ||
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| <!-- Connect operators --> | ||
| <connect srcID='$(b)PopSizesScaler.t:$(n)' targetID='mcmc' inputName='operator' | ||
| if='inposterior($(b).t:$(n)) and $(b)PopSizes.t:$(n)/estimate=true'>Scale population size of BESP prior of tree t:$(n) | ||
| </connect> | ||
| <connect srcID='$(b)SamplingIntensityScaler.t:$(n)' targetID='mcmc' inputName='operator' | ||
| if='inposterior($(b).t:$(n)) and $(b)SamplingIntensity.t:$(n)/estimate=true'>Scale sampling intensity of BESP prior of tree t:$(n) | ||
| </connect> | ||
| <connect srcID='$(b)GroupSizesDelta.t:$(n)' targetID='mcmc' inputName='operator' | ||
| if='inposterior($(b).t:$(n)) and $(b)GroupSizes.t:$(n)/estimate=true'>Exchange group sizes of BESP prior of tree t:$(n) | ||
| </connect> | ||
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| <!-- Connect parameters to tracelog --> | ||
| <connect srcID='$(b).t:$(n)' targetID='tracelog' inputName='log' | ||
| if='inposterior($(b).t:$(n))'/> | ||
| <connect srcID='$(b)PopSizes.t:$(n)' targetID='tracelog' inputName='log' | ||
| if='inposterior($(b).t:$(n)) and $(b)PopSizes.t:$(n)/estimate=true'/> | ||
| <connect srcID='$(b)SamplingIntensity.t:$(n)' targetID='tracelog' inputName='log' | ||
| if='inposterior($(b).t:$(n)) and $(b)SamplingIntensity.t:$(n)/estimate=true'/> | ||
| <connect srcID='$(b)GroupSizes.t:$(n)' targetID='tracelog' inputName='log' | ||
| if='inposterior($(b).t:$(n)) and $(b)GroupSizes.t:$(n)/estimate=true'/> | ||
| <connect srcID='$(b)PopSizeChangeTimes.t:$(n)' targetID='tracelog' inputName='log' | ||
| if='inposterior($(b).t:$(n))'/> | ||
| <connect srcID='$(b)SamplingIntensityChangeTimes.t:$(n)' targetID='tracelog' inputName='log' | ||
| if='inposterior($(b).t:$(n))'/> | ||
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| </fragment> | ||
| </mergewith> | ||
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| <!-- BESP tree prior configurations --> | ||
| <mergewith point='treePriorTemplates'> | ||
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| <!-- Coalescent BESP --> | ||
| <subtemplate id='CoalescentBESP' class='bsp.distributions.BESP' | ||
| mainid='BESP.t:$(n)' | ||
| suppressInputs='beast.math.distributions.MarkovChainDistribution.parameter, | ||
| bsp.distributions.BESP.tree, | ||
| bsp.distributions.BESP.treeIntervals, | ||
| bsp.distributions.BESP.popSizeEpochTimes, | ||
| bsp.distributions.BESP.samplingIntensityGroupSizes, | ||
| bsp.distributions.BESP.samplingEpochTimes, | ||
| bsp.distributions.BESP.numInitializationAttempts'> | ||
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| <plate var="b" range="BESP"> | ||
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| <![CDATA[ | ||
| <distribution spec="bsp.distributions.BESP" id='$(b).t:$(n)'> | ||
| <parameter name='popSizes' id='$(b)PopSizes.t:$(n)' dimension="5" value="380.0" lower="0.0" estimate='true'/> | ||
| <parameter name='samplingIntensity' id='$(b)SamplingIntensity.t:$(n)' dimension="1" value="1" lower="0.0" estimate='true'/> | ||
| <popSizeGroupSizes spec='parameter.IntegerParameter' id='$(b)GroupSizes.t:$(n)' dimension='5' value='1' estimate='true'/> | ||
| <treeIntervals spec='TreeIntervals' id='$(b)TreeIntervals.t:$(n)' tree='@Tree.t:$(n)'/> | ||
| </distribution> | ||
| ]]> | ||
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| </plate> | ||
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| <plate fragment="TreeOperators" var="m" range="BESP"/> | ||
| <plate fragment="BESP_params" var="b" range="BESP"/> | ||
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| </subtemplate> | ||
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| </mergewith> | ||
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| </beast> |
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