bella-companion 0.0.28__py3-none-any.whl → 0.0.30__py3-none-any.whl
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- bella_companion/eucovid/beast_configs/GLM.xml +125 -405
- bella_companion/eucovid/beast_configs/MLP.xml +108 -288
- bella_companion/eucovid/run_beast.py +11 -17
- bella_companion/platyrrhine/beast_config.xml +2 -2
- bella_companion/platyrrhine/run_beast.py +4 -7
- bella_companion/simulations/beast_configs/epi-multitype/MLP.xml +1 -1
- bella_companion/simulations/beast_configs/epi-skyline/MLP.xml +1 -1
- bella_companion/simulations/beast_configs/fbd-2traits/MLP.xml +2 -2
- bella_companion/simulations/beast_configs/fbd-no-traits/MLP.xml +2 -2
- {bella_companion-0.0.28.dist-info → bella_companion-0.0.30.dist-info}/METADATA +1 -1
- {bella_companion-0.0.28.dist-info → bella_companion-0.0.30.dist-info}/RECORD +13 -13
- {bella_companion-0.0.28.dist-info → bella_companion-0.0.30.dist-info}/WHEEL +0 -0
- {bella_companion-0.0.28.dist-info → bella_companion-0.0.30.dist-info}/entry_points.txt +0 -0
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<?xml version="1.0"
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<beast
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<map name="
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<map name="
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<map name="
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<
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<
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<
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fileName = "$(aligned_fasta)"/>
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<typeSet id="typeSetBDMMPrime" spec="TypeSet">
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<typeTraitSet id="typeTraitSet" spec="TraitSetFromTaxonSet"
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traitname="type"
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delimiter="|"
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takeGroup="1">
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<taxa spec="TaxonSet" alignment="@alignment"/>
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</typeTraitSet>
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</typeSet>
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<trait id="dateTrait" spec="TraitSetFromTaxonSet"
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traitname="date"
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dateFormat="yyyy-M-dd"
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delimiter= "|"
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everythingAfterLast="true">
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<taxa spec="TaxonSet" alignment="@alignment"/>
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</trait>
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<!-- BDMMPrime Population Model -->
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<processLength id="originBDMMPrime" spec="RealParameter">10.0</processLength>
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<Re id="ReSV" spec="SkylineVectorParameter"
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timesAreAges="true" processLength="@originBDMMPrime" typeSet="@typeSetBDMMPrime">
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<skylineValues id="ReValues" spec="RealParameter">1.0 1.1 1.2 1.3 1.4 1.01 1.1 1.2 1.3 1.4</skylineValues>
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<changeTimes id="ReRateChangeTimes" spec="RealParameter">0.123</changeTimes>
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</Re>
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<samplingProportion id="samplingProportionSV" spec="SkylineVectorParameter"
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timesAreAges="true" processLength="@originBDMMPrime" typeSet="@typeSetBDMMPrime">
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<skylineValues id="samplingProportionValues" spec="RealParameter" dimension="15" lower="0.0" upper="1.0">1.11E-5 1.2E-5 1.3E-5 1.4E-5 1.5E-5 1.1E-5 1.2E-5 1.3E-5 1.4E-5 1.5E-5 0.0 0.0 0.0 0.0 0.0</skylineValues>
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<changeTimes id="samplingProportionChangeTimes" spec="RealParameter">0.123 0.205</changeTimes>
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</samplingProportion>
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<becomeUninfectiousRate id="becomeUninfectiousRateSV" spec="SkylineVectorParameter"
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typeSet="@typeSetBDMMPrime">
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<skylineValues id="becomeUninfectiousValues" spec="RealParameter">36.5</skylineValues>
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</becomeUninfectiousRate>
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<migrationRate id="migrationRateSM" spec="SkylineMatrixParameter"
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timesAreAges="true" processLength="@originBDMMPrime" typeSet="@typeSetBDMMPrime">
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<skylineValues id="migrationRateValues" spec="glmprior.util.GLMLogLinear" transform="false">
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<plate var="predictor" range="$(GLMpredictor_files)">
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<predictor spec="RealParameterFromXSV" id="$(predictor)" fileName="$(predictor)"/>
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</plate>
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<parameter id="coefficientsGLM" spec="RealParameter" name="coefficients" value="0.1"/>
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<parameter id="scaleFactorGLM" spec="RealParameter" name="scaleFactor" value="1"/>
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<parameter id="indicatorGLM" spec="BooleanParameter" name="indicators" value="1"/>
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<!-- <parameter id="errorTermGLM" spec="RealParameter" name="error" value="0.01" dimension="30"/> -->
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</skylineValues>
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<changeTimes id="migrationRateChangeTimes" spec="RealParameterFromXSV"
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fileName="$(GLMpredictor_changetimes)"/>
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</migrationRate>
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<removalProb id="removalProbSV" spec="SkylineVectorParameter" skylineValues="1.0"
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processLength="@originBDMMPrime" typeSet="@typeSetBDMMPrime"/>
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<startTypePriorProbs id="typeFrequencies" spec="RealParameter"
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estimate="false" lower="0.0" upper="1.0">1.0 0.0 0.0 0.0 0.0</startTypePriorProbs>
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<!-- Site Model -->
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<siteModel id="siteModel" spec="SiteModel" gammaCategoryCount="4">
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<parameter id="gammaShape" name="shape" value="1.0"/>
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<parameter name="mutationRate" estimate="false" value="1.0"/>
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<parameter name="proportionInvariant" estimate="false" value="0.0"/>
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<substModel spec="HKY">
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<kappa id="kappa" spec="RealParameter" value="2.0"/>
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<frequencies id="empiricalFreqs" spec="Frequencies" data="@alignment"/>
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</substModel>
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</siteModel>
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<!-- Branch rate Model -->
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<branchRateModel id="branchRateModel" spec="StrictClockModel">
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<parameter id="clockRate" name="clock.rate" estimate="false">8.0E-4</parameter>
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</branchRateModel>
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<!-- Population Model for Tree initialiser -->
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<popFunc id="popFunc" spec="ConstantPopulation">
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<popSize spec="RealParameter" value="0.1"/>
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</popFunc>
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<!-- MCMC -->
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<run id="mcmc" spec="MCMC" chainLength="10000000" numInitializationAttempts="100">
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<!-- State -->
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<?xml version="1.0"?>
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<beast
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namespace="
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:beast.base.evolution
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:beast.base.evolution.alignment
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:beast.base.evolution.branchratemodel
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:beast.base.evolution.likelihood
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:beast.base.evolution.operator
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:beast.base.evolution.operator.kernel
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:beast.base.evolution.sitemodel
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:beast.base.evolution.substitutionmodel
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:beast.base.evolution.tree
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:beast.base.evolution.tree.coalescent
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:beast.base.inference
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:beast.base.inference.parameter
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:beast.base.inference.operator.kernel
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:bdmmprime.distribution
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:bdmmprime.mapping
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:bdmmprime.trajectories
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:bdmmprime.parameterization
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:bdmmprime.util
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:bdmmprime.util.operators
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:bdmmprime.util.priors
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:feast.fileio"
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version="2.7"
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>
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<map name="Uniform">beast.base.inference.distribution.Uniform</map>
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<map name="Exponential">beast.base.inference.distribution.Exponential</map>
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<map name="LogNormal">beast.base.inference.distribution.LogNormalDistributionModel</map>
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<map name="Normal">beast.base.inference.distribution.Normal</map>
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<map name="prior">beast.base.inference.distribution.Prior</map>
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<map name="AlignmentFromFasta">feast.fileio.AlignmentFromFasta</map>
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<map name="TaxonSet">beast.base.evolution.alignment.TaxonSet</map>
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<map name="TraitSetFromTaxonSet">feast.fileio.TraitSetFromTaxonSet</map>
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<map name="TypeSet">bdmmprime.parameterization.TypeSet</map>
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<map name="TypeMappedTree">bdmmprime.mapping.TypeMappedTree</map>
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<AlignmentFromFasta id="alignment" fileName="$(msa_file)"/>
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<TaxonSet id="taxonSet" alignment="@alignment"/>
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<TraitSetFromTaxonSet id="typeTraitSet" traitname="type" delimiter="|" takeGroup="1" taxa="@taxonSet"/>
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<TypeSet id="typeSet" typeTraitSet="@typeTraitSet"/>
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<TraitSetFromTaxonSet id="dateTrait" traitname="date" dateFormat="yyyy-M-dd" delimiter="|" everythingAfterLast="true" taxa="@taxonSet"/>
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<TypeMappedTree id="typeMappedTree" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@startTypePriorProbs" mapOnInit="false" remapOnLog="true" typeLabel="type" typeTraitSet="@typeTraitSet" untypedTree="@tree"/>
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<run spec="MCMC" chainLength="10000000">
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<state id="state" spec="State">
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taxa="@alignment"
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populationModel="@popFunc"
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trait="@dateTrait">
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<stateNode id="tree" spec="RandomTree" taxa="@alignment" trait="@dateTrait">
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<populationModel spec="ConstantPopulation" popSize="0.1"/>
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<stateNode
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<stateNode idref="kappa"/>
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<stateNode idref="gammaShape"/>
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<stateNode id="Re" spec="RealParameter" value="1.0 1.1 1.2 1.3 1.4 1.01 1.1 1.2 1.3 1.4"/>
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<stateNode id="samplingProportion" spec="RealParameter" value="1.11E-5 1.2E-5 1.3E-5 1.4E-5 1.5E-5 1.1E-5 1.2E-5 1.3E-5 1.4E-5 1.5E-5 0.0 0.0 0.0 0.0 0.0"/>
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<stateNode id="migrationRateW" spec="RealParameter" value="0"/>
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<stateNode id="migrationRateScaler" spec="RealParameter" value="0.1"/>
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<stateNode id="processLength" spec="RealParameter" value="10.0"/>
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<stateNode id="gammaShape" spec="RealParameter" value="1.0"/>
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<stateNode id="kappa" spec="RealParameter" value="2.0"/>
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</state>
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<!-- Posterior Distribution -->
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<distribution id="posterior" spec="CompoundDistribution">
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<!-- Tree Likelihood -->
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<distribution id="likelihood" spec="CompoundDistribution" useThreads="true">
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<distribution id="treeLikelihood" spec="ThreadedTreeLikelihood" data="@alignment" tree="@tree">
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<siteModel spec="SiteModel" gammaCategoryCount="4" shape="@gammaShape" mutationRate="1.0">
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<substModel spec="HKY" kappa="@kappa">
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<frequencies spec="Frequencies" data="@alignment"/>
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</substModel>
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</siteModel>
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<branchRateModel spec="StrictClockModel" clock.rate="8.0E-4"/>
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</distribution>
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<distribution id="prior" spec="CompoundDistribution">
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<distribution id="BDMMPrime" spec="BirthDeathMigrationDistribution" tree="@tree" conditionOnSurvival="true" typeTraitSet="@typeTraitSet">
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<parameterization id="EpiBDMMPrimeParameterization" spec="EpiParameterization" processLength="@processLength" typeSet="@typeSet">
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<Re id="ReSP" spec="SkylineVectorParameter" skylineValues="@Re" changeTimes="0.123" timesAreAges="true" processLength="@processLength" typeSet="@typeSet"/>
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<samplingProportion id="samplingProportionSP" spec="SkylineVectorParameter" skylineValues="@samplingProportion" changeTimes="0.123 0.205" timesAreAges="true" processLength="@processLength" typeSet="@typeSet"/>
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<becomeUninfectiousRate spec="SkylineVectorParameter" skylineValues="36.5" typeSet="@typeSet"/>
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<migrationRate id="migrationRateSP" spec="SkylineMatrixParameter" timesAreAges="true" processLength="@processLength" typeSet="@typeSet">
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<skylineValues spec="glmprior.util.GLMLogLinear" coefficients="@migrationRateW" scaleFactor="@migrationRateScaler" transform="false">
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<plate var="predictorFile" range="$(predictorFiles)">
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<predictor spec="RealParameterFromXSV" fileName="$(predictorFile)"/>
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</plate>
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<indicators spec="BooleanParameter" value="1"/>
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</skylineValues>
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<changeTimes spec="RealParameterFromXSV" fileName="$(changeTimesFile)"/>
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</migrationRate>
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<removalProb spec="SkylineVectorParameter" skylineValues="1.0" typeSet="@typeSet"/>
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</parameterization>
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<startTypePriorProbs id="startTypePriorProbs" spec="RealParameter" value="1.0 0.0 0.0 0.0 0.0"/>
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</distribution>
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<distribution id="BDMMPrime" spec="BirthDeathMigrationDistribution"
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tree="@treeBDMMPrime"
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conditionOnSurvival="true"
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finalSampleOffset="0.0"
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typeTraitSet="@typeTraitSet"
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startTypePriorProbs="@typeFrequencies">
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<parameterization id="EpiBDMMPrimeParameterization" spec="EpiParameterization"
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processLength="@originBDMMPrime"
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Re="@ReSV"
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samplingProportion="@samplingProportionSV"
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becomeUninfectiousRate="@becomeUninfectiousRateSV"
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migrationRate="@migrationRateSM"
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removalProb="@removalProbSV"
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typeSet="@typeSetBDMMPrime"/>
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</distribution>
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|
|
206
|
-
<!-- Priors on parameters -->
|
|
207
|
-
<!-- BDMMPrime parameters priors -->
|
|
208
|
-
|
|
209
|
-
<prior id="originBDMMPrimePrior" name="distribution" x="@originBDMMPrime">
|
|
91
|
+
<prior name="distribution" x="@processLength">
|
|
210
92
|
<LogNormal name="distr" M="-1.0" S="0.2"/>
|
|
211
93
|
</prior>
|
|
212
|
-
|
|
213
|
-
<!-- Reproductive number Prior -->
|
|
214
|
-
<distribution id="RePrior" spec="SmartZeroExcludingPrior" x="@ReValues">
|
|
94
|
+
<distribution spec="SmartZeroExcludingPrior" x="@Re">
|
|
215
95
|
<LogNormal name="distr" M="0.8" S="0.5"/>
|
|
216
96
|
</distribution>
|
|
217
|
-
|
|
218
|
-
<!-- Prior for sampling proportion for China -->
|
|
219
|
-
<distribution id="spChinaE2Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
|
|
220
|
-
classesToExclude="1.2E-5 1.3E-5 1.4E-5 1.5E-5">
|
|
97
|
+
<distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.2E-5 1.3E-5 1.4E-5 1.5E-5">
|
|
221
98
|
<Uniform name="distr" lower="0" upper="0.15"/>
|
|
222
99
|
</distribution>
|
|
223
|
-
|
|
224
|
-
<distribution id="spFranceE1Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
|
|
225
|
-
classesToExclude="1.1E-5 1.3E-5 1.4E-5 1.5E-5">
|
|
100
|
+
<distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.3E-5 1.4E-5 1.5E-5">
|
|
226
101
|
<Uniform name="distr" lower="0" upper="0.093"/>
|
|
227
102
|
</distribution>
|
|
228
|
-
|
|
229
|
-
<distribution id="spGermanyE1Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
|
|
230
|
-
classesToExclude="1.1E-5 1.2E-5 1.4E-5 1.5E-5">
|
|
103
|
+
<distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.4E-5 1.5E-5">
|
|
231
104
|
<Uniform name="distr" lower="0" upper="0.10"/>
|
|
232
105
|
</distribution>
|
|
233
|
-
|
|
234
|
-
<distribution id="spItalyE1Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
|
|
235
|
-
classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.5E-5">
|
|
106
|
+
<distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.5E-5">
|
|
236
107
|
<Uniform name="distr" lower="0" upper="0.005"/>
|
|
237
108
|
</distribution>
|
|
238
|
-
|
|
239
|
-
<distribution id="spOEE1Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
|
|
240
|
-
classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.4E-5">
|
|
109
|
+
<distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.4E-5">
|
|
241
110
|
<Uniform name="distr" lower="0" upper="0.057"/>
|
|
242
111
|
</distribution>
|
|
243
|
-
|
|
244
|
-
|
|
245
|
-
<!-- Migration rate GLM Prior -->
|
|
246
|
-
<!-- <prior id="migRatePrior" name="distribution" x="@migrationRateValues">
|
|
247
|
-
<Uniform id="Uniform.migRate" name="distr" lower="0.0" upper="50.0"/>
|
|
248
|
-
</prior> -->
|
|
249
|
-
|
|
250
|
-
<!-- <prior id="migRatePrior" name="distribution" x="@migrationRateValues">
|
|
251
|
-
<LogNormal name="distr" M="0" S="1.5"/>
|
|
252
|
-
</prior> -->
|
|
253
|
-
|
|
254
|
-
<prior id="coefficientsPrior" name="distribution" x="@coefficientsGLM">
|
|
255
|
-
<Normal name="distr">
|
|
256
|
-
<parameter spec="RealParameter" estimate="false" name="mean">0.0</parameter>
|
|
257
|
-
<parameter spec="RealParameter" estimate="false" name="sigma">1.0</parameter>
|
|
258
|
-
</Normal>
|
|
112
|
+
<prior name="distribution" x="@migrationRateW">
|
|
113
|
+
<Normal name="distr" mean="0.0" sigma="1.0"/>
|
|
259
114
|
</prior>
|
|
260
|
-
|
|
261
|
-
|
|
262
|
-
<LogNormal name="distr">
|
|
263
|
-
<parameter spec="RealParameter" estimate="false" name="M">0.0</parameter>
|
|
264
|
-
<parameter spec="RealParameter" estimate="false" name="S">0.8</parameter>
|
|
265
|
-
</LogNormal>
|
|
115
|
+
<prior name="distribution" x="@migrationRateScaler">
|
|
116
|
+
<LogNormal name="distr" M="0.0" S="0.8"/>
|
|
266
117
|
</prior>
|
|
267
|
-
|
|
268
|
-
|
|
269
|
-
<x id="indicatorSumGLM" spec="Sum" arg="@indicatorGLM"/>
|
|
270
|
-
<Poisson name="distr" lambda='0.693'/>
|
|
271
|
-
</prior> -->
|
|
272
|
-
|
|
273
|
-
<!-- Substitution model parameter priors -->
|
|
274
|
-
<prior id="GammaShapePrior" name="distribution" x="@gammaShape">
|
|
275
|
-
<Exponential name="distr">
|
|
276
|
-
<parameter spec="RealParameter" estimate="false" name="mean">0.5</parameter>
|
|
277
|
-
</Exponential>
|
|
118
|
+
<prior name="distribution" x="@gammaShape">
|
|
119
|
+
<Exponential name="distr" mean="0.5"/>
|
|
278
120
|
</prior>
|
|
279
|
-
|
|
280
121
|
<prior id="KappaPrior" name="distribution" x="@kappa">
|
|
281
|
-
<LogNormal name="distr"
|
|
282
|
-
<parameter spec="RealParameter" estimate="false" name="M">1.0</parameter>
|
|
283
|
-
<parameter spec="RealParameter" estimate="false" name="S">1.25</parameter>
|
|
284
|
-
</LogNormal>
|
|
122
|
+
<LogNormal name="distr" M="1.0" S="1.25"/>
|
|
285
123
|
</prior>
|
|
286
|
-
|
|
287
124
|
</distribution>
|
|
288
125
|
</distribution>
|
|
289
126
|
|
|
290
|
-
|
|
291
|
-
|
|
292
|
-
|
|
293
|
-
<operator
|
|
294
|
-
|
|
295
|
-
|
|
296
|
-
<operator
|
|
297
|
-
|
|
298
|
-
|
|
299
|
-
<operator
|
|
300
|
-
|
|
301
|
-
|
|
302
|
-
<operator
|
|
303
|
-
|
|
304
|
-
|
|
305
|
-
<operator id="BDMMPrimeWide" spec="Exchange" tree="@treeBDMMPrime"
|
|
306
|
-
isNarrow="false" weight="3.0"/>
|
|
307
|
-
|
|
308
|
-
<operator id="BDMMPrimeWilsonBalding" spec="WilsonBalding" tree="@treeBDMMPrime"
|
|
309
|
-
weight="3.0"/>
|
|
310
|
-
|
|
311
|
-
<operator id="BDMMPrimeBICEPSEpochTop" spec="EpochFlexOperator" tree="@treeBDMMPrime"
|
|
312
|
-
scaleFactor="0.1" weight="2.0"/>
|
|
313
|
-
|
|
314
|
-
<operator id="BDMMPrimeBICEPSEpochAll" spec="EpochFlexOperator" tree="@treeBDMMPrime"
|
|
315
|
-
fromOldestTipOnly="false" scaleFactor="0.1" weight="2.0"/>
|
|
316
|
-
|
|
317
|
-
<operator id="BDMMPrimeBICEPSTreeFlex" spec="TreeStretchOperator" tree="@treeBDMMPrime"
|
|
318
|
-
scaleFactor="0.01" weight="2.0"/>
|
|
319
|
-
|
|
320
|
-
|
|
321
|
-
<!-- Population model operators -->
|
|
322
|
-
|
|
323
|
-
<operator id="originBDMMPrimeScaler" spec="BactrianScaleOperator" parameter="@originBDMMPrime"
|
|
324
|
-
scaleFactor="0.25" weight="3.0" />
|
|
325
|
-
|
|
326
|
-
<operator id="ReScaler" spec="SmartScaleOperator" parameter="@ReValues" scaleFactor="0.25"
|
|
327
|
-
weight="10.0" />
|
|
328
|
-
<!-- <operator id="ReScalerAll" spec="BactrianScaleOperator" parameter="@ReValues" scaleFactor="0.25"
|
|
329
|
-
weight="3.0" scaleAll="true" /> -->
|
|
330
|
-
|
|
331
|
-
<operator id="samplingProportionScaler" spec="SmartScaleOperator" parameter="@samplingProportionValues"
|
|
332
|
-
weight="3.0" />
|
|
333
|
-
|
|
334
|
-
<!-- <operator id="scaleFactorGLMScaler" spec="BactrianScaleOperator" parameter="@scaleFactorGLM" scaleFactor="0.25" weight="3.0" /> -->
|
|
335
|
-
|
|
336
|
-
<operator id="coefficientsGLMScaler" spec="BactrianRandomWalkOperator" parameter="@coefficientsGLM"
|
|
337
|
-
weight="5.0" scaleFactor="0.1"/>
|
|
338
|
-
|
|
339
|
-
<operator id="AVNMOperator" spec="beast.base.evolution.operator.kernel.AdaptableVarianceMultivariateNormalOperator" weight="5.0"
|
|
340
|
-
coefficient="1.0"
|
|
341
|
-
scaleFactor="0.5"
|
|
342
|
-
beta="0.05"
|
|
343
|
-
initial="800"
|
|
344
|
-
burnin="400"
|
|
345
|
-
every="1">
|
|
346
|
-
<transformations spec="beast.base.inference.operator.kernel.Transform$NoTransform">
|
|
347
|
-
<f idref="coefficientsGLM"/>
|
|
348
|
-
</transformations>
|
|
349
|
-
</operator>
|
|
350
|
-
|
|
351
|
-
<!-- <operator id="indicatorParamGLMFlip" spec="BitFlipOperator" parameter="@indicatorGLM"
|
|
352
|
-
weight="10.0" uniform="false" />
|
|
353
|
-
|
|
354
|
-
<operator id="indicatorSwap" spec="glmprior.operator.ExtendedSwapOperator" boolparameter="@indicatorGLM" weight="5.0" />
|
|
355
|
-
|
|
356
|
-
<operator id="indicatorParamGLMPick" spec="glmprior.operator.PickIndicatorOperator"
|
|
357
|
-
parameter="@indicatorGLM" weight="3.0" />
|
|
358
|
-
|
|
359
|
-
<operator id="BSSVSGLMoperator" spec="glmprior.operator.BitFlipBSSVSOperator" indicator="@indicatorGLM" mu="@scaleFactorGLM" weight="10"/>
|
|
360
|
-
|
|
361
|
-
<operator id="multiSwapOperator" spec="glmprior.operator.MultiSwapOperator" boolparameter="@indicatorGLM" parameter="@coefficientsGLM" weight="10.0" />
|
|
362
|
-
|
|
363
|
-
<operator id="JointSwapGLM1" spec="JointOperator" weight="3.0">
|
|
364
|
-
<operator idref="indicatorSwap"/>
|
|
365
|
-
<operator idref="AVNMOperator"/>
|
|
127
|
+
<operator spec="BactrianScaleOperator" tree="@tree" rootOnly="true" scaleFactor="0.25" weight="5.0"/>
|
|
128
|
+
<operator spec="BactrianNodeOperator" tree="@tree" weight="30.0"/>
|
|
129
|
+
<operator spec="BactrianSubtreeSlide" tree="@tree" weight="15.0"/>
|
|
130
|
+
<operator spec="Exchange" tree="@tree" weight="15.0"/>
|
|
131
|
+
<operator spec="Exchange" tree="@tree" isNarrow="false" weight="3.0"/>
|
|
132
|
+
<operator spec="WilsonBalding" tree="@tree" weight="3.0"/>
|
|
133
|
+
<operator spec="EpochFlexOperator" tree="@tree" scaleFactor="0.1" weight="2.0"/>
|
|
134
|
+
<operator spec="EpochFlexOperator" tree="@tree" fromOldestTipOnly="false" scaleFactor="0.1" weight="2.0"/>
|
|
135
|
+
<operator spec="TreeStretchOperator" tree="@tree" scaleFactor="0.01" weight="2.0"/>
|
|
136
|
+
<operator spec="BactrianScaleOperator" parameter="@processLength" scaleFactor="0.25" weight="3.0"/>
|
|
137
|
+
<operator spec="SmartScaleOperator" parameter="@Re" scaleFactor="0.25" weight="10.0"/>
|
|
138
|
+
<operator spec="SmartScaleOperator" parameter="@samplingProportion" weight="3.0"/>
|
|
139
|
+
<operator spec="BactrianRandomWalkOperator" parameter="@migrationRateW" weight="5.0" scaleFactor="0.1"/>
|
|
140
|
+
<operator spec="AdaptableVarianceMultivariateNormalOperator" weight="5.0" coefficient="1.0" scaleFactor="0.5" beta="0.05" initial="800" burnin="400" every="1">
|
|
141
|
+
<transformations spec="Transform$NoTransform" f="@migrationRateW"/>
|
|
366
142
|
</operator>
|
|
143
|
+
<operator spec="BactrianScaleOperator" parameter="@gammaShape" weight="1.0"/>
|
|
144
|
+
<operator spec="BactrianScaleOperator" parameter="@kappa" weight="1.0"/>
|
|
367
145
|
|
|
368
|
-
<
|
|
369
|
-
<operator idref="coefficientsGLMScaler"/>
|
|
370
|
-
<operator idref="scaleFactorGLMScaler"/>
|
|
371
|
-
</operator>
|
|
372
|
-
-->
|
|
373
|
-
<!-- <operator id="errorTermGLMScaler" spec="BactrianScaleOperator" parameter="@errorTermGLM"
|
|
374
|
-
weight="5.0" upper="20.0"/> -->
|
|
375
|
-
|
|
376
|
-
|
|
377
|
-
<!-- Substitution model operators -->
|
|
378
|
-
<operator id="gammaShapeScaler" spec="BactrianScaleOperator" parameter="@gammaShape"
|
|
379
|
-
weight="1.0"/>
|
|
380
|
-
|
|
381
|
-
<operator id="KappaScaler" spec="BactrianScaleOperator" parameter="@kappa"
|
|
382
|
-
weight="1.0"/>
|
|
383
|
-
|
|
384
|
-
|
|
385
|
-
<!-- Loggers -->
|
|
386
|
-
<logger id="tracelog" spec="Logger" fileName="$(filebase).log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
|
|
146
|
+
<logger spec="Logger" fileName="MCMC.log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
|
|
387
147
|
<log idref="posterior"/>
|
|
388
148
|
<log idref="likelihood"/>
|
|
389
149
|
<log idref="prior"/>
|
|
390
|
-
<log idref="treeLikelihood"/>
|
|
391
|
-
<log idref="gammaShape"/>
|
|
392
|
-
<log idref="kappa"/>
|
|
393
|
-
<log id="TreeHeight" spec="TreeStatLogger" tree="@treeBDMMPrime"/>
|
|
394
|
-
<log id="typedTreeStats" spec="TypedTreeStatsLogger" includeRootEdge="true"
|
|
395
|
-
typeLabel="type" typeSet="@typeSetBDMMPrime">
|
|
396
|
-
<typedTree id="typeMappedTree" spec="TypeMappedTree" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@typeFrequencies" mapOnInit="false" remapOnLog="true" typeLabel="type" typeTraitSet="@typeTraitSet" untypedTree="@treeBDMMPrime"/>
|
|
397
|
-
</log>
|
|
398
|
-
<log idref="originBDMMPrime"/>
|
|
399
|
-
<log idref="ReSV"/>
|
|
400
|
-
<log idref="becomeUninfectiousRateSV"/>
|
|
401
|
-
<log idref="samplingProportionSV"/>
|
|
402
|
-
<log idref="migrationRateSM"/>
|
|
403
|
-
<log idref="coefficientsGLM"/>
|
|
404
|
-
<log idref="scaleFactorGLM"/>
|
|
405
|
-
<log idref="indicatorGLM"/>
|
|
406
|
-
<log id="coefbyindGLM" spec="ExpCalculator" value="coefficientsGLM*indicatorGLM" useCaching="false">
|
|
407
|
-
<arg idref="coefficientsGLM"/>
|
|
408
|
-
<arg idref="indicatorGLM"/>
|
|
409
|
-
</log>
|
|
410
|
-
<plate var="predictor" range="$(GLMpredictor_files)">
|
|
411
|
-
<log idref="$(predictor)"/>
|
|
412
|
-
</plate>
|
|
413
|
-
<!-- <log idref="errorTermGLM"/> -->
|
|
414
|
-
<log idref="removalProbSV"/>
|
|
415
|
-
<log idref="typeFrequencies"/>
|
|
416
|
-
</logger>
|
|
417
|
-
|
|
418
|
-
<logger id="screenlog" spec="Logger" logEvery="1000">
|
|
419
|
-
<log idref="posterior"/>
|
|
420
|
-
<log arg="@posterior" id="ESS_posterior" spec="util.ESS"/>
|
|
421
|
-
<log idref="likelihood"/>
|
|
422
|
-
<log arg="@likelihood" id="ESS_likelihood" spec="util.ESS"/>
|
|
423
|
-
<log idref="prior"/>
|
|
424
|
-
<log arg="@prior" id="ESS_prior" spec="util.ESS"/>
|
|
425
150
|
<log idref="BDMMPrime"/>
|
|
426
|
-
<log
|
|
427
|
-
|
|
428
|
-
|
|
429
|
-
|
|
430
|
-
<log
|
|
151
|
+
<log idref="gammaShape"/>
|
|
152
|
+
<log idref="kappa"/>
|
|
153
|
+
<log idref="processLength"/>
|
|
154
|
+
<log idref="ReSP"/>
|
|
155
|
+
<log idref="samplingProportionSP"/>
|
|
156
|
+
<log idref="migrationRateSP"/>
|
|
157
|
+
<log idref="migrationRateW"/>
|
|
158
|
+
<log idref="migrationRateScaler"/>
|
|
431
159
|
</logger>
|
|
432
|
-
|
|
433
|
-
<logger id="typedTreeLogger" spec="OptionalLogger" enableLogger="true"
|
|
434
|
-
fileName="$(filebase).typed.trees" logEvery="10000" mode="tree">
|
|
160
|
+
<logger spec="Logger" fileName="typedTrees.trees" logEvery="10000" mode="tree">
|
|
435
161
|
<log idref="typeMappedTree"/>
|
|
436
162
|
</logger>
|
|
437
|
-
<logger
|
|
438
|
-
|
|
439
|
-
<log id="nodeTypedTree" spec="TypedNodeTreeLogger" typedTree="@typeMappedTree"/>
|
|
163
|
+
<logger spec="Logger" fileName="TypedNodeTrees.trees" logEvery="10000" mode="tree">
|
|
164
|
+
<log spec="TypedNodeTreeLogger" typedTree="@typeMappedTree"/>
|
|
440
165
|
</logger>
|
|
441
|
-
<logger
|
|
442
|
-
<log
|
|
443
|
-
startTypePriorProbs="@typeFrequencies" typeMappedTree="@typeMappedTree" useTauLeaping="true"/>
|
|
166
|
+
<logger spec="Logger" fileName="trajectories.csv" logEvery="10000">
|
|
167
|
+
<log spec="SampledTrajectory" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@startTypePriorProbs" typeMappedTree="@typeMappedTree" useTauLeaping="true"/>
|
|
444
168
|
</logger>
|
|
445
|
-
|
|
446
|
-
<operatorschedule id="OperatorSchedule" spec="OperatorSchedule"/>
|
|
447
|
-
|
|
448
169
|
</run>
|
|
449
|
-
|
|
450
170
|
</beast>
|