bella-companion 0.0.25__py3-none-any.whl → 0.0.27__py3-none-any.whl
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- bella_companion/eucovid/beast_configs/GLM.xml +377 -128
- bella_companion/eucovid/beast_configs/Nonparametric.xml +331 -146
- bella_companion/eucovid/run_beast.py +15 -13
- bella_companion/platyrrhine/run_beast.py +1 -1
- bella_companion/utils/slurm.py +7 -2
- {bella_companion-0.0.25.dist-info → bella_companion-0.0.27.dist-info}/METADATA +1 -1
- {bella_companion-0.0.25.dist-info → bella_companion-0.0.27.dist-info}/RECORD +9 -9
- {bella_companion-0.0.25.dist-info → bella_companion-0.0.27.dist-info}/WHEEL +0 -0
- {bella_companion-0.0.25.dist-info → bella_companion-0.0.27.dist-info}/entry_points.txt +0 -0
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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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<beast
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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="prior">beast.base.inference.distribution.Prior</map>
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<beast namespace="beast.base.inference
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:beast.base.inference.parameter
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:beast.base.inference.distribution
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:beast.base.evolution.branchratemodel
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:beast.base.evolution.substitutionmodel
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:beast.base.evolution.sitemodel
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:beast.base.evolution.tree.coalescent
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:beast.base.evolution.tree
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:beast.base.evolution.likelihood
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:beast.base.evolution.alignment
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:beast.base.evolution.operator.kernel
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:beast.base.inference.operator.kernel
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:beast.base.inference.operator
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:beast.base.math.distributions
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:beast.base.evolution
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:beast.base.evolution.operator
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:bdmmprime.util
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:bdmmprime.util.operators
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:bdmmprime.util.priors
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:bdmmprime.distribution
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:bdmmprime.parameterization
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:bdmmprime.mapping
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:bdmmprime.trajectories
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:feast
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:feast.parameter
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:feast.fileio
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:feast.function
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:feast.expressions
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:glmprior.util"
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required="BEAST.base v2.7.7:BDMM-Prime v2.2.2" version="2.7">
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<!-- Map elements -->
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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="prior" >beast.base.inference.distribution.Prior</map>
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<!-- Adapted from https://github.com/SarahNadeau/cov-europe-bdmm/blob/master/analyses/with_hubei_migration_decrease/with_hubei_migration_decrease_scrubbed.xml -->
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<!-- Sequence data loaded from GISAID with the gisaid EPI ISLs -->
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<!-- Alignment -->
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<alignment id="alignment" spec= "AlignmentFromFasta"
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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">1.0</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="
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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">0.12 0.205</changeTimes>
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</samplingProportion>
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<becomeUninfectiousRate id="
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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_scaled" name="skylineValues" spec="feast.expressions.ExpCalculator">
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<![CDATA[
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migrationRateValues *
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{ f,f,f,f,
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f, 1,1,1,
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f,1, 1,1,
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f,1,1, 1,
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f,1,1,1,
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1,1,1,1,
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1, 1,1,1,
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1,1, 1,1,
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1,1,1, 1,
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1,1,1,1 }
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]]>
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<arg id="migrationRateValues" spec="RealParameter" dimension="40">
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0.11 0.15 0.2 0.24
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0.0 0.12 0.16 0.25
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0.0 0.13 0.17 0.21
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0.11 0.15 0.2 0.24
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</arg>
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<arg id="f" spec="RealParameter">0.5</arg>
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</skylineValues>
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<changeTimes id="migrationRateChangeTimes" spec="RealParameter">0.123</changeTimes>
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</migrationRate>
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<removalProb id="removalProbSP" spec="SkylineVectorParameter" skylineValues="1.0" processLength="@processLength" typeSet="@typeSet"/>
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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 spec="Frequencies" data="@alignment"/>
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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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<branchRateModel id="branchRateModel" spec="StrictClockModel" clock.rate="8.0E-4"/>
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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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<state id="state" spec="State" storeEvery="5000">
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<stateNode
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<stateNode id="treeBDMMPrime" spec="RandomTree"
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taxa="@alignment"
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populationModel="@popFunc"
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trait="@dateTrait">
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</stateNode>
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<stateNode idref="originBDMMPrime"/>
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<stateNode idref="ReValues"/>
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<stateNode idref="samplingProportionValues"/>
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<stateNode idref="migrationRateValues"/>
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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"
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data="@alignment"
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tree="@treeBDMMPrime"
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siteModel="@siteModel"
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branchRateModel="@branchRateModel"/>
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</distribution>
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<!-- BDMM-Prime tree prior 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 BDMM-Prime -->
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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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<!-- Priors on parameters -->
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<!-- BDMMPrime parameters priors -->
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<prior id="originBDMMPrimePrior" name="distribution" x="@originBDMMPrime">
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<LogNormal name="distr" M="-1.0" S="0.2"/>
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</prior>
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|
-
|
|
226
|
+
|
|
227
|
+
<!-- Reproductive number Prior -->
|
|
228
|
+
<distribution id="RePrior" spec="SmartZeroExcludingPrior" x="@ReValues">
|
|
138
229
|
<LogNormal name="distr" M="0.8" S="0.5"/>
|
|
139
230
|
</distribution>
|
|
140
|
-
|
|
231
|
+
|
|
232
|
+
<!-- Prior for sampling proportion for China -->
|
|
233
|
+
<distribution id="spChinaE2Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
|
|
234
|
+
classesToExclude="1.2E-5 1.3E-5 1.4E-5 1.5E-5">
|
|
141
235
|
<Uniform name="distr" lower="0" upper="0.15"/>
|
|
142
236
|
</distribution>
|
|
143
|
-
|
|
237
|
+
<!-- Prior for sampling proportion for France -->
|
|
238
|
+
<distribution id="spFranceE1Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
|
|
239
|
+
classesToExclude="1.1E-5 1.3E-5 1.4E-5 1.5E-5">
|
|
144
240
|
<Uniform name="distr" lower="0" upper="0.093"/>
|
|
145
241
|
</distribution>
|
|
146
|
-
|
|
242
|
+
<!-- Prior for sampling proportion for Germany Epoch -->
|
|
243
|
+
<distribution id="spGermanyE1Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
|
|
244
|
+
classesToExclude="1.1E-5 1.2E-5 1.4E-5 1.5E-5">
|
|
147
245
|
<Uniform name="distr" lower="0" upper="0.10"/>
|
|
148
246
|
</distribution>
|
|
149
|
-
|
|
247
|
+
<!-- Prior for sampling proportion for Italy -->
|
|
248
|
+
<distribution id="spItalyE1Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
|
|
249
|
+
classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.5E-5">
|
|
150
250
|
<Uniform name="distr" lower="0" upper="0.005"/>
|
|
151
251
|
</distribution>
|
|
152
|
-
|
|
252
|
+
<!-- Prior for sampling proportion for OtherEuropean -->
|
|
253
|
+
<distribution id="spOEE1Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
|
|
254
|
+
classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.4E-5">
|
|
153
255
|
<Uniform name="distr" lower="0" upper="0.057"/>
|
|
154
256
|
</distribution>
|
|
155
|
-
|
|
257
|
+
|
|
258
|
+
<!-- Migration rate Prior -->
|
|
259
|
+
<distribution id="migRatePrior" name="distribution" spec="SmartZeroExcludingPrior" x="@migrationRateValues">
|
|
156
260
|
<LogNormal name="distr" M="0.0" S="1.0"/>
|
|
157
261
|
</distribution>
|
|
158
|
-
|
|
262
|
+
|
|
263
|
+
<distribution id="fPrior" name="distribution" spec="ZeroExcludingPrior" x="@f">
|
|
159
264
|
<Uniform name="distr" lower="0.0" upper="1.0"/>
|
|
160
265
|
</distribution>
|
|
161
|
-
|
|
162
|
-
|
|
266
|
+
|
|
267
|
+
<!-- Substitution model parameter priors -->
|
|
268
|
+
<prior id="GammaShapePrior" name="distribution" x="@gammaShape">
|
|
269
|
+
<Exponential name="distr">
|
|
270
|
+
<parameter spec="RealParameter" estimate="false" name="mean">0.5</parameter>
|
|
271
|
+
</Exponential>
|
|
163
272
|
</prior>
|
|
164
|
-
|
|
165
|
-
|
|
273
|
+
|
|
274
|
+
<prior id="KappaPrior" name="distribution" x="@kappa">
|
|
275
|
+
<LogNormal name="distr">
|
|
276
|
+
<parameter spec="RealParameter" estimate="false" name="M">1.0</parameter>
|
|
277
|
+
<parameter spec="RealParameter" estimate="false" name="S">1.25</parameter>
|
|
278
|
+
</LogNormal>
|
|
166
279
|
</prior>
|
|
280
|
+
|
|
167
281
|
</distribution>
|
|
168
282
|
</distribution>
|
|
169
283
|
|
|
170
|
-
|
|
171
|
-
|
|
172
|
-
|
|
173
|
-
<operator spec="
|
|
174
|
-
|
|
175
|
-
|
|
176
|
-
<operator spec="
|
|
177
|
-
|
|
178
|
-
|
|
179
|
-
<operator
|
|
180
|
-
|
|
181
|
-
|
|
182
|
-
<operator
|
|
183
|
-
|
|
184
|
-
|
|
185
|
-
<operator
|
|
186
|
-
|
|
187
|
-
|
|
284
|
+
|
|
285
|
+
<!-- Operators -->
|
|
286
|
+
<!-- Tree operators -->
|
|
287
|
+
<operator id="BDMMPrimeTreeRootScaler" spec="BactrianScaleOperator" tree="@treeBDMMPrime"
|
|
288
|
+
rootOnly="true" scaleFactor="0.25" weight="5.0"/>
|
|
289
|
+
|
|
290
|
+
<operator id="BDMMPrimeUniformOperator" spec="BactrianNodeOperator" tree="@treeBDMMPrime"
|
|
291
|
+
weight="30.0"/>
|
|
292
|
+
|
|
293
|
+
<operator id="BDMMPrimeSubtreeSlideScaler" spec="BactrianSubtreeSlide" tree="@treeBDMMPrime"
|
|
294
|
+
weight="15.0"/>
|
|
295
|
+
|
|
296
|
+
<operator id="BDMMPrimeNarrow" spec="Exchange" tree="@treeBDMMPrime"
|
|
297
|
+
weight="15.0"/>
|
|
298
|
+
|
|
299
|
+
<operator id="BDMMPrimeWide" spec="Exchange" tree="@treeBDMMPrime"
|
|
300
|
+
isNarrow="false" weight="3.0"/>
|
|
301
|
+
|
|
302
|
+
<operator id="BDMMPrimeWilsonBalding" spec="WilsonBalding" tree="@treeBDMMPrime"
|
|
303
|
+
weight="3.0"/>
|
|
304
|
+
|
|
305
|
+
<operator id="BDMMPrimeBICEPSEpochTop" spec="EpochFlexOperator" tree="@treeBDMMPrime"
|
|
306
|
+
scaleFactor="0.1" weight="2.0"/>
|
|
307
|
+
|
|
308
|
+
<operator id="BDMMPrimeBICEPSEpochAll" spec="EpochFlexOperator" tree="@treeBDMMPrime"
|
|
309
|
+
fromOldestTipOnly="false" scaleFactor="0.1" weight="2.0"/>
|
|
310
|
+
|
|
311
|
+
<operator id="BDMMPrimeBICEPSTreeFlex" spec="TreeStretchOperator" tree="@treeBDMMPrime"
|
|
312
|
+
scaleFactor="0.01" weight="2.0"/>
|
|
313
|
+
|
|
314
|
+
|
|
315
|
+
<!-- Population model operators -->
|
|
316
|
+
<operator id="originBDMMPrimeScaler" spec="BactrianScaleOperator" parameter="@originBDMMPrime"
|
|
317
|
+
scaleFactor="0.25" weight="5.0" />
|
|
318
|
+
|
|
319
|
+
<!-- <operator id="ReScaler" spec="BactrianScaleOperator" parameter="@ReValues"
|
|
320
|
+
weight="5.0" />
|
|
321
|
+
<operator id="ReScalerAll" spec="BactrianScaleOperator" parameter="@ReValues"
|
|
322
|
+
weight="5.0" scaleAll="true" /> -->
|
|
323
|
+
|
|
324
|
+
<operator id="ReScaler" spec="SmartScaleOperator" parameter="@ReValues"
|
|
325
|
+
weight="5.0" />
|
|
326
|
+
|
|
327
|
+
<operator id="samplingProportionScaler" spec="SmartScaleOperator" parameter="@samplingProportionValues"
|
|
328
|
+
weight="3.0" />
|
|
329
|
+
|
|
330
|
+
<operator id="migrationRateScaler" spec="SmartScaleOperator" parameter="@migrationRateValues"
|
|
331
|
+
weight="5.0" />
|
|
332
|
+
<operator id="fScaler" spec="BactrianScaleOperator" parameter="@f"
|
|
333
|
+
weight="5.0"/>
|
|
334
|
+
|
|
335
|
+
<!-- Substitution model operators -->
|
|
336
|
+
<operator id="gammaShapeScaler" spec="BactrianScaleOperator" parameter="@gammaShape"
|
|
337
|
+
weight="1.0"/>
|
|
338
|
+
|
|
339
|
+
<operator id="KappaScaler" spec="BactrianScaleOperator" parameter="@kappa"
|
|
340
|
+
weight="1.0"/>
|
|
341
|
+
|
|
342
|
+
|
|
343
|
+
<!-- Loggers -->
|
|
344
|
+
<logger id="tracelog" spec="Logger" fileName="$(filebase).log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
|
|
188
345
|
<log idref="posterior"/>
|
|
189
346
|
<log idref="likelihood"/>
|
|
190
347
|
<log idref="prior"/>
|
|
191
|
-
<log idref="
|
|
192
|
-
<log idref="
|
|
193
|
-
<log idref="
|
|
194
|
-
<log
|
|
195
|
-
<log spec="TypedTreeStatsLogger" includeRootEdge="true"
|
|
348
|
+
<log idref="treeLikelihood"/>
|
|
349
|
+
<log idref="gammaShape"/>
|
|
350
|
+
<log idref="kappa"/>
|
|
351
|
+
<log id="TreeHeight" spec="TreeStatLogger" tree="@treeBDMMPrime"/>
|
|
352
|
+
<log id="typedTreeStats" spec="TypedTreeStatsLogger" includeRootEdge="true"
|
|
353
|
+
typeLabel="type" typeSet="@typeSetBDMMPrime">
|
|
196
354
|
<typedTree id="typeMappedTree" spec="TypeMappedTree" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@typeFrequencies" mapOnInit="false" remapOnLog="true" typeLabel="type" typeTraitSet="@typeTraitSet" untypedTree="@treeBDMMPrime"/>
|
|
197
355
|
</log>
|
|
356
|
+
<log idref="originBDMMPrime"/>
|
|
357
|
+
<log idref="ReSV"/>
|
|
358
|
+
<log idref="becomeUninfectiousRateSV"/>
|
|
359
|
+
<log idref="samplingProportionSV"/>
|
|
360
|
+
<log idref="migrationRateSM"/>
|
|
361
|
+
<log idref="migrationRateValues"/>
|
|
362
|
+
<log idref="f"/>
|
|
363
|
+
<log idref="removalProbSV"/>
|
|
364
|
+
<log idref="typeFrequencies"/>
|
|
198
365
|
</logger>
|
|
199
366
|
|
|
200
|
-
<logger
|
|
201
|
-
<log idref="
|
|
367
|
+
<logger id="screenlog" spec="Logger" logEvery="1000">
|
|
368
|
+
<log idref="posterior"/>
|
|
369
|
+
<log arg="@posterior" id="ESS_posterior" spec="util.ESS"/>
|
|
370
|
+
<log idref="likelihood"/>
|
|
371
|
+
<log arg="@likelihood" id="ESS_likelihood" spec="util.ESS"/>
|
|
372
|
+
<log idref="prior"/>
|
|
373
|
+
<log arg="@prior" id="ESS_prior" spec="util.ESS"/>
|
|
374
|
+
<log idref="BDMMPrime"/>
|
|
375
|
+
<log arg="@BDMMPrime" id="ESS_BDMMPrime" spec="util.ESS"/>
|
|
202
376
|
</logger>
|
|
203
377
|
|
|
204
|
-
<logger
|
|
205
|
-
<log spec="
|
|
378
|
+
<logger id="treelog" spec="Logger" fileName="$(filebase).trees" logEvery="1000" mode="tree">
|
|
379
|
+
<log id="TreeWithMetaDataLogger" spec="TreeWithMetaDataLogger" tree="@treeBDMMPrime"/>
|
|
206
380
|
</logger>
|
|
207
|
-
|
|
208
|
-
<logger spec="OptionalLogger" enableLogger="true"
|
|
209
|
-
|
|
381
|
+
|
|
382
|
+
<logger id="typedTreeLogger" spec="OptionalLogger" enableLogger="true"
|
|
383
|
+
fileName="$(filebase).typed.trees" logEvery="10000" mode="tree">
|
|
384
|
+
<log idref="typeMappedTree"/>
|
|
385
|
+
</logger>
|
|
386
|
+
<logger id="nodeTypedTreeLogger.t:eubdmm_alignment" spec="OptionalLogger" enableLogger="true"
|
|
387
|
+
fileName="$(filebase).typed.node.trees" logEvery="10000" mode="tree">
|
|
388
|
+
<log id="nodeTypedTree" spec="TypedNodeTreeLogger" typedTree="@typeMappedTree"/>
|
|
210
389
|
</logger>
|
|
390
|
+
<logger id="trajLogger" spec="OptionalLogger" enableLogger="true" fileName="$(filebase).traj" logEvery="10000">
|
|
391
|
+
<log id="typedTraj" spec="SampledTrajectory" bdmmDistrib="@BDMMPrime"
|
|
392
|
+
startTypePriorProbs="@typeFrequencies" typeMappedTree="@typeMappedTree" useTauLeaping="true"/>
|
|
393
|
+
</logger>
|
|
394
|
+
|
|
395
|
+
<operatorschedule id="OperatorSchedule" spec="OperatorSchedule"/>
|
|
211
396
|
|
|
212
397
|
</run>
|
|
213
398
|
|