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Added missing operators to beauti templates. #36

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Added missing operators to beauti templates. #36

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204923a
Added missing operators to beauti templates.
tgvaughan Jun 15, 2023
6bb8405
Improved build script.
tgvaughan Jun 19, 2023
77032cc
Converted all BDMM inputs to Functions.
tgvaughan Dec 6, 2023
a326518
Version bump.
tgvaughan Dec 6, 2023
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301 changes: 187 additions & 114 deletions build.xml
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57 changes: 53 additions & 4 deletions fxtemplates/MultiTypeBirthDeath.xml
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Expand Up @@ -299,10 +299,6 @@

<!-- Parameter operators -->

<operator id='proportionInvariantScaler.s:$(n)' spec='ScaleOperator' scaleFactor="0.5" weight="0.1" parameter="@proportionInvariant.s:$(n)"/>
<operator id='mutationRateScaler.s:$(n)' spec='ScaleOperator' scaleFactor="0.5" weight="0.1" parameter="@mutationRate.s:$(n)"/>
<operator id='gammaShapeScaler.s:$(n)' spec='ScaleOperator' scaleFactor="0.5" weight="0.1" parameter="@gammaShape.s:$(n)"/>

<operator id="R0Scaler.t:$(n)" parameter="@R0.t:$(n)" scaleFactor="0.8" spec="ScaleOperator" weight="3" />
<operator id="becomeUninfectiousRateScaler.t:$(n)" parameter="@becomeUninfectiousRate.t:$(n)" scaleFactor="0.9" spec="ScaleOperator" weight="1" scaleAll="true" optimise="false"/>
<operator id="samplingScaler.t:$(n)" parameter="@samplingProportion.t:$(n)" scaleFactor="0.9" spec="ScaleOperator" weight="3.0" />
Expand All @@ -327,6 +323,59 @@

<operator id='rateMatrixScaler.t:$(n)' spec='ScaleOperator' scaleFactor="0.8" weight="1" parameter="@rateMatrix.t:$(n)"/>


<operator id="AVMNOperator.$(n)" spec="beast.base.evolution.operator.kernel.AdaptableVarianceMultivariateNormalOperator" weight="0.1"
coefficient="1.0"
scaleFactor="1"
beta="0.05"
initial="800"
burnin="400"
every="1" allowNonsense="true">
<transformations id="AVMNSumTransform.$(n)" spec="beast.base.inference.operator.kernel.Transform$LogConstrainedSumTransform" sum="1.0">
<!-- frequencies -->
</transformations>
<transformations id="AVMNLogTransform.$(n)" spec="beast.base.inference.operator.kernel.Transform$LogTransform">
<!-- site and substitution model parameters -->
</transformations>
<transformations id="AVMNNoTransform.$(n)" spec="beast.base.inference.operator.kernel.Transform$NoTransform">
<!-- tree -->
</transformations>
</operator>

<operator id="StrictClockRateScaler.c:$(n)" spec="beast.base.evolution.operator.AdaptableOperatorSampler" weight="1.5">
<parameter idref="clockRate.c:$(n)"/>
<operator idref="AVMNOperator.$(n)"/>
<operator id='StrictClockRateScalerX.c:$(n)' spec='kernel.BactrianScaleOperator' scaleFactor="0.75" weight="3" parameter='@clockRate.c:$(n)'/>
</operator>

<operator id="strictClockUpDownOperator.c:$(n)" spec="beast.base.evolution.operator.AdaptableOperatorSampler" weight="1.5">
<parameter idref="clockRate.c:$(n)"/>
<tree idref="Tree.t:$(n)"/>
<operator idref="AVMNOperator.$(n)"/>
<operator id='strictClockUpDownOperatorX.c:$(n)' spec='kernel.BactrianUpDownOperator' scaleFactor="0.75" weight="3">
<up idref="clockRate.c:$(n)"/>
<down idref="Tree.t:$(n)"/>
</operator>
</operator>

<operator id="proportionInvariantScaler.s:$(n)" spec="beast.base.evolution.operator.AdaptableOperatorSampler" weight="0.05">
<parameter idref="proportionInvariant.s:$(n)"/>
<operator idref="AVMNOperator.$(n)"/>
<operator id='proportionInvariantScalerX.s:$(n)' spec='kernel.BactrianScaleOperator' scaleFactor="0.5" weight="0.1" parameter="@proportionInvariant.s:$(n)"/>
</operator>

<operator id="mutationRateScaler.s:$(n)" spec="beast.base.evolution.operator.AdaptableOperatorSampler" weight="0.05">
<parameter idref="mutationRate.s:$(n)"/>
<operator idref="AVMNOperator.$(n)"/>
<operator id='mutationRateScalerX.s:$(n)' spec='kernel.BactrianScaleOperator' scaleFactor="0.5" weight="0.1" parameter="@mutationRate.s:$(n)"/>
</operator>

<operator id="gammaShapeScaler.s:$(n)" spec="beast.base.evolution.operator.AdaptableOperatorSampler" weight="0.05">
<parameter idref="gammaShape.s:$(n)"/>
<operator idref="AVMNOperator.$(n)"/>
<operator id='gammaShapeScalerX.s:$(n)' spec='kernel.BactrianScaleOperator' scaleFactor="0.5" weight="0.1" parameter="@gammaShape.s:$(n)"/>
</operator>

<!-- Multi-type tree operators -->

<operator spec='multitypetree.operators.TypedSubtreeExchange' id='STX.t:$(n)' weight="10" multiTypeTree="@Tree.t:$(n)" migrationModel="@migModel.t:$(n)"/>
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47 changes: 43 additions & 4 deletions fxtemplates/MultiTypeBirthDeathUncoloured.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -307,10 +307,6 @@

<!-- Parameter operators -->

<operator id='proportionInvariantScaler.s:$(n)' spec='ScaleOperator' scaleFactor="0.5" weight="0.1" parameter="@proportionInvariant.s:$(n)"/>
<operator id='mutationRateScaler.s:$(n)' spec='ScaleOperator' scaleFactor="0.5" weight="0.1" parameter="@mutationRate.s:$(n)"/>
<operator id='gammaShapeScaler.s:$(n)' spec='ScaleOperator' scaleFactor="0.5" weight="0.1" parameter="@gammaShape.s:$(n)"/>

<operator id="R0Scaler.t:$(n)" parameter="@R0.t:$(n)" scaleFactor="0.8" spec="ScaleOperator" weight="3" />
<operator id="becomeUninfectiousRateScaler.t:$(n)" parameter="@becomeUninfectiousRate.t:$(n)" scaleFactor="0.9" spec="ScaleOperator" weight="1" scaleAll="true" optimise="false"/>
<operator id="samplingScaler.t:$(n)" parameter="@samplingProportion.t:$(n)" scaleFactor="0.9" spec="ScaleOperator" weight="3.0" />
Expand All @@ -336,6 +332,49 @@

<operator id='rateMatrixScaler.t:$(n)' spec='ScaleOperator' scaleFactor="0.8" weight="1" parameter="@rateMatrix.t:$(n)"/>


<operator id="AVMNOperator.$(n)" spec="beast.base.evolution.operator.kernel.AdaptableVarianceMultivariateNormalOperator" weight="0.1"
coefficient="1.0"
scaleFactor="1"
beta="0.05"
initial="800"
burnin="400"
every="1" allowNonsense="true">
<transformations id="AVMNSumTransform.$(n)" spec="beast.base.inference.operator.kernel.Transform$LogConstrainedSumTransform" sum="1.0">
<!-- frequencies -->
</transformations>
<transformations id="AVMNLogTransform.$(n)" spec="beast.base.inference.operator.kernel.Transform$LogTransform">
<!-- site and substitution model parameters -->
</transformations>
<transformations id="AVMNNoTransform.$(n)" spec="beast.base.inference.operator.kernel.Transform$NoTransform">
<!-- tree -->
</transformations>
</operator>

<operator id="StrictClockRateScaler.c:$(n)" spec="beast.base.evolution.operator.AdaptableOperatorSampler" weight="1.5">
<parameter idref="clockRate.c:$(n)"/>
<operator idref="AVMNOperator.$(n)"/>
<operator id='StrictClockRateScalerX.c:$(n)' spec='kernel.BactrianScaleOperator' scaleFactor="0.75" weight="3" parameter='@clockRate.c:$(n)'/>
</operator>

<operator id="proportionInvariantScaler.s:$(n)" spec="beast.base.evolution.operator.AdaptableOperatorSampler" weight="0.05">
<parameter idref="proportionInvariant.s:$(n)"/>
<operator idref="AVMNOperator.$(n)"/>
<operator id='proportionInvariantScalerX.s:$(n)' spec='kernel.BactrianScaleOperator' scaleFactor="0.5" weight="0.1" parameter="@proportionInvariant.s:$(n)"/>
</operator>

<operator id="mutationRateScaler.s:$(n)" spec="beast.base.evolution.operator.AdaptableOperatorSampler" weight="0.05">
<parameter idref="mutationRate.s:$(n)"/>
<operator idref="AVMNOperator.$(n)"/>
<operator id='mutationRateScalerX.s:$(n)' spec='kernel.BactrianScaleOperator' scaleFactor="0.5" weight="0.1" parameter="@mutationRate.s:$(n)"/>
</operator>

<operator id="gammaShapeScaler.s:$(n)" spec="beast.base.evolution.operator.AdaptableOperatorSampler" weight="0.05">
<parameter idref="gammaShape.s:$(n)"/>
<operator idref="AVMNOperator.$(n)"/>
<operator id='gammaShapeScalerX.s:$(n)' spec='kernel.BactrianScaleOperator' scaleFactor="0.5" weight="0.1" parameter="@gammaShape.s:$(n)"/>
</operator>

<!-- Tree operators -->


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