bella-companion 0.0.26__py3-none-any.whl → 0.0.28__py3-none-any.whl
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- bella_companion/eucovid/beast_configs/MLP.xml +241 -88
- bella_companion/eucovid/run_beast.py +5 -6
- bella_companion/utils/slurm.py +2 -2
- {bella_companion-0.0.26.dist-info → bella_companion-0.0.28.dist-info}/METADATA +1 -1
- {bella_companion-0.0.26.dist-info → bella_companion-0.0.28.dist-info}/RECORD +7 -7
- {bella_companion-0.0.26.dist-info → bella_companion-0.0.28.dist-info}/WHEEL +0 -0
- {bella_companion-0.0.26.dist-info → bella_companion-0.0.28.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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<beast
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namespace="
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beast.base.inference
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:beast.base.inference
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:beast.base.inference.parameter
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:beast.base.evolution.branchratemodel
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:beast.base.evolution.substitutionmodel
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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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:feast.expressions
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:glmprior.util"
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required="BEAST.base v2.7.7:BDMM-Prime v2.2.2"
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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="
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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="Poisson" >beast.base.inference.distribution.Poisson</map>
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<map name="prior" >beast.base.inference.distribution.Prior</map>
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<alignment id="alignment" spec= "AlignmentFromFasta" fileName = "$(aligned_fasta)"/>
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<typeSet id="typeSetBDMMPrime" spec="TypeSet">
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<typeTraitSet id="typeTraitSet" spec="TraitSetFromTaxonSet" traitname="type" delimiter="|" 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" traitname="date" dateFormat="yyyy-M-dd" delimiter= "|" everythingAfterLast="true">
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<taxa spec="TaxonSet" alignment="@alignment"/>
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</trait>
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<processLength id="originBDMMPrime" spec="RealParameter">10.0</processLength>
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<Re id="ReSV" spec="SkylineVectorParameter" 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">0.123 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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<
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<migrationRate id="migrationRateSM" spec="SkylineMatrixParameter"
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timesAreAges="true" processLength="@originBDMMPrime" typeSet="@typeSetBDMMPrime">
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<predictor spec="RealParameterFromXSV" fileName="$(predictorFile)"/>
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<skylineValues id="migrationRateValues" spec="bella.BayesMLP" nodes="$(nodes)">
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<plate var="predictor" range="$(GLMpredictor_files)">
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<predictor spec="RealParameterFromXSV" id="$(predictor)" fileName="$(predictor)"/>
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</plate>
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<plate var="n" range="$(layersRange)">
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<weights idref="migrationW$(n)"/>
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</plate>
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</skylineValues>
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<changeTimes spec="RealParameterFromXSV" fileName="$(changeTimesFile)"/>
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</migrationRate>
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<changeTimes id="migrationRateChangeTimes" spec="RealParameterFromXSV"
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fileName="$(GLMpredictor_changetimes)"/>
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</migrationRate>
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<startTypePriorProbs id="typeFrequencies" spec="RealParameter" value="1.0 0.0 0.0 0.0 0.0"/>
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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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<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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<stateNode
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<!-- State -->
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<state id="state" spec="State">
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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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<plate var="n" range="$(layersRange)">
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<stateNode spec="RealParameter" id="migrationW$(n)" value="0"/>
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</plate>
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<stateNode idref="kappa"/>
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<stateNode idref="gammaShape"/>
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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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<!-- Prior distribution -->
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<distribution id="prior" spec="CompoundDistribution">
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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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<!-- Reproductive number Prior -->
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<distribution id="RePrior" spec="SmartZeroExcludingPrior" x="@ReValues">
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<LogNormal name="distr" M="0.8" S="0.5"/>
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</distribution>
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<!-- Prior for sampling proportion for China -->
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<distribution id="spChinaE2Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
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classesToExclude="1.2E-5 1.3E-5 1.4E-5 1.5E-5">
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<Uniform name="distr" lower="0" upper="0.15"/>
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</distribution>
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<!-- Prior for sampling proportion for France -->
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<distribution id="spFranceE1Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
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classesToExclude="1.1E-5 1.3E-5 1.4E-5 1.5E-5">
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</distribution>
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<!-- Prior for sampling proportion for Germany Epoch -->
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<distribution id="spGermanyE1Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
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classesToExclude="1.1E-5 1.2E-5 1.4E-5 1.5E-5">
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</distribution>
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<!-- Prior for sampling proportion for Italy -->
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<distribution id="spItalyE1Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
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classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.5E-5">
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</distribution>
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<!-- Prior for sampling proportion for OtherEuropean -->
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<distribution id="spOEE1Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
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classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.4E-5">
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<Uniform name="distr" lower="0" upper="0.057"/>
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</distribution>
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<plate var="n" range="$(layersRange)">
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<prior name="distribution" x="@migrationW$(n)">
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<Normal name="distr" mean="0.0" sigma="1.0"/>
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</prior>
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<prior id="GammaShapePrior" name="distribution" x="@gammaShape">
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<Exponential name="distr">
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<parameter spec="RealParameter" estimate="false" name="mean">0.5</parameter>
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</Exponential>
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<prior id="KappaPrior" name="distribution" x="@kappa">
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<LogNormal name="distr">
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<parameter spec="RealParameter" estimate="false" name="M">1.0</parameter>
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<parameter spec="RealParameter" estimate="false" name="S">1.25</parameter>
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</LogNormal>
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<operator id="BDMMPrimeTreeRootScaler" spec="BactrianScaleOperator" tree="@treeBDMMPrime"
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rootOnly="true" scaleFactor="0.25" weight="5.0"/>
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<operator id="BDMMPrimeUniformOperator" spec="BactrianNodeOperator" tree="@treeBDMMPrime"
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weight="30.0"/>
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254
|
+
<operator id="BDMMPrimeSubtreeSlideScaler" spec="BactrianSubtreeSlide" tree="@treeBDMMPrime"
|
|
255
|
+
weight="15.0"/>
|
|
256
|
+
|
|
257
|
+
<operator id="BDMMPrimeNarrow" spec="Exchange" tree="@treeBDMMPrime"
|
|
258
|
+
weight="15.0"/>
|
|
259
|
+
|
|
260
|
+
<operator id="BDMMPrimeWide" spec="Exchange" tree="@treeBDMMPrime"
|
|
261
|
+
isNarrow="false" weight="3.0"/>
|
|
262
|
+
|
|
263
|
+
<operator id="BDMMPrimeWilsonBalding" spec="WilsonBalding" tree="@treeBDMMPrime"
|
|
264
|
+
weight="3.0"/>
|
|
265
|
+
|
|
266
|
+
<operator id="BDMMPrimeBICEPSEpochTop" spec="EpochFlexOperator" tree="@treeBDMMPrime"
|
|
267
|
+
scaleFactor="0.1" weight="2.0"/>
|
|
268
|
+
|
|
269
|
+
<operator id="BDMMPrimeBICEPSEpochAll" spec="EpochFlexOperator" tree="@treeBDMMPrime"
|
|
270
|
+
fromOldestTipOnly="false" scaleFactor="0.1" weight="2.0"/>
|
|
271
|
+
|
|
272
|
+
<operator id="BDMMPrimeBICEPSTreeFlex" spec="TreeStretchOperator" tree="@treeBDMMPrime"
|
|
273
|
+
scaleFactor="0.01" weight="2.0"/>
|
|
274
|
+
|
|
275
|
+
<operator id="originBDMMPrimeScaler" spec="BactrianScaleOperator" parameter="@originBDMMPrime"
|
|
276
|
+
scaleFactor="0.25" weight="3.0" />
|
|
277
|
+
|
|
278
|
+
<operator id="ReScaler" spec="SmartScaleOperator" parameter="@ReValues" scaleFactor="0.25"
|
|
279
|
+
weight="10.0" />
|
|
280
|
+
|
|
281
|
+
<operator id="samplingProportionScaler" spec="SmartScaleOperator" parameter="@samplingProportionValues"
|
|
282
|
+
weight="3.0" />
|
|
283
|
+
|
|
162
284
|
<plate var="n" range="$(layersRange)">
|
|
163
285
|
<operator spec="BactrianRandomWalkOperator" parameter="@migrationW$(n)" weight="5.0"/>
|
|
164
286
|
</plate>
|
|
165
|
-
<operator id="gammaShapeScaler" spec="BactrianScaleOperator" parameter="@gammaShape" weight="1.0"/>
|
|
166
|
-
<operator id="KappaScaler" spec="BactrianScaleOperator" parameter="@kappa" weight="1.0"/>
|
|
167
|
-
<operatorschedule spec="OperatorSchedule"/>
|
|
168
287
|
|
|
169
|
-
<
|
|
288
|
+
<operator id="gammaShapeScaler" spec="BactrianScaleOperator" parameter="@gammaShape"
|
|
289
|
+
weight="1.0"/>
|
|
290
|
+
|
|
291
|
+
<operator id="KappaScaler" spec="BactrianScaleOperator" parameter="@kappa"
|
|
292
|
+
weight="1.0"/>
|
|
293
|
+
|
|
294
|
+
|
|
295
|
+
<!-- Loggers -->
|
|
296
|
+
<logger id="tracelog" spec="Logger" fileName="$(filebase).log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
|
|
170
297
|
<log idref="posterior"/>
|
|
171
298
|
<log idref="likelihood"/>
|
|
172
299
|
<log idref="prior"/>
|
|
173
|
-
<log idref="
|
|
174
|
-
<log idref="
|
|
175
|
-
<log idref="
|
|
176
|
-
<log
|
|
177
|
-
<log
|
|
178
|
-
|
|
300
|
+
<log idref="treeLikelihood"/>
|
|
301
|
+
<log idref="gammaShape"/>
|
|
302
|
+
<log idref="kappa"/>
|
|
303
|
+
<log id="TreeHeight" spec="TreeStatLogger" tree="@treeBDMMPrime"/>
|
|
304
|
+
<log id="typedTreeStats" spec="TypedTreeStatsLogger" includeRootEdge="true"
|
|
305
|
+
typeLabel="type" typeSet="@typeSetBDMMPrime">
|
|
179
306
|
<typedTree id="typeMappedTree" spec="TypeMappedTree" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@typeFrequencies" mapOnInit="false" remapOnLog="true" typeLabel="type" typeTraitSet="@typeTraitSet" untypedTree="@treeBDMMPrime"/>
|
|
180
307
|
</log>
|
|
181
|
-
|
|
308
|
+
<log idref="originBDMMPrime"/>
|
|
309
|
+
<log idref="ReSV"/>
|
|
310
|
+
<log idref="becomeUninfectiousRateSV"/>
|
|
311
|
+
<log idref="samplingProportionSV"/>
|
|
312
|
+
<log idref="migrationRateSM"/>
|
|
182
313
|
|
|
183
|
-
|
|
184
|
-
<log idref="
|
|
314
|
+
<log idref="removalProbSV"/>
|
|
315
|
+
<log idref="typeFrequencies"/>
|
|
185
316
|
</logger>
|
|
186
317
|
|
|
187
|
-
<logger
|
|
188
|
-
<log
|
|
318
|
+
<logger id="screenlog" spec="Logger" logEvery="1000">
|
|
319
|
+
<log idref="posterior"/>
|
|
320
|
+
<log arg="@posterior" id="ESS_posterior" spec="util.ESS"/>
|
|
321
|
+
<log idref="likelihood"/>
|
|
322
|
+
<log arg="@likelihood" id="ESS_likelihood" spec="util.ESS"/>
|
|
323
|
+
<log idref="prior"/>
|
|
324
|
+
<log arg="@prior" id="ESS_prior" spec="util.ESS"/>
|
|
325
|
+
<log idref="BDMMPrime"/>
|
|
326
|
+
<log arg="@BDMMPrime" id="ESS_BDMMPrime" spec="util.ESS"/>
|
|
189
327
|
</logger>
|
|
190
328
|
|
|
191
|
-
<logger
|
|
192
|
-
<log
|
|
329
|
+
<logger id="treelog" spec="Logger" fileName="$(filebase).trees" logEvery="1000" mode="tree">
|
|
330
|
+
<log id="TreeWithMetaDataLogger" spec="TreeWithMetaDataLogger" tree="@treeBDMMPrime"/>
|
|
331
|
+
</logger>
|
|
332
|
+
|
|
333
|
+
<logger id="typedTreeLogger" spec="OptionalLogger" enableLogger="true"
|
|
334
|
+
fileName="$(filebase).typed.trees" logEvery="10000" mode="tree">
|
|
335
|
+
<log idref="typeMappedTree"/>
|
|
336
|
+
</logger>
|
|
337
|
+
<logger id="nodeTypedTreeLogger.t:eubdmm_alignment" spec="OptionalLogger" enableLogger="true"
|
|
338
|
+
fileName="$(filebase).typed.node.trees" logEvery="10000" mode="tree">
|
|
339
|
+
<log id="nodeTypedTree" spec="TypedNodeTreeLogger" typedTree="@typeMappedTree"/>
|
|
340
|
+
</logger>
|
|
341
|
+
<logger id="trajLogger" spec="OptionalLogger" enableLogger="true" fileName="$(filebase).traj" logEvery="10000">
|
|
342
|
+
<log id="typedTraj" spec="SampledTrajectory" bdmmDistrib="@BDMMPrime"
|
|
343
|
+
startTypePriorProbs="@typeFrequencies" typeMappedTree="@typeMappedTree" useTauLeaping="true"/>
|
|
193
344
|
</logger>
|
|
194
345
|
|
|
346
|
+
<operatorschedule id="OperatorSchedule" spec="OperatorSchedule"/>
|
|
347
|
+
|
|
195
348
|
</run>
|
|
196
|
-
|
|
349
|
+
|
|
197
350
|
</beast>
|
|
@@ -80,13 +80,12 @@ def run_beast():
|
|
|
80
80
|
cpus=128,
|
|
81
81
|
mem_per_cpu=12000,
|
|
82
82
|
)
|
|
83
|
-
|
|
83
|
+
|
|
84
84
|
os.makedirs(output_dir / "all-predictors-MLP", exist_ok=True)
|
|
85
85
|
job_ids["all-predictors-MLP"] = submit_job(
|
|
86
86
|
" ".join(
|
|
87
87
|
[
|
|
88
88
|
os.environ["BELLA_RUN_BEAST_CMD"],
|
|
89
|
-
f"-D ReDimension='{5 * 7}'",
|
|
90
89
|
f'-D layersRange="0,1,2",nodes="16 8"',
|
|
91
90
|
all_predictors_data,
|
|
92
91
|
f"-prefix {output_dir / 'all-predictors-MLP'}{os.sep}",
|
|
@@ -94,7 +93,8 @@ def run_beast():
|
|
|
94
93
|
]
|
|
95
94
|
),
|
|
96
95
|
base_log_dir / "all-predictors-MLP",
|
|
97
|
-
|
|
96
|
+
cpus=128,
|
|
97
|
+
mem_per_cpu=12000,
|
|
98
98
|
)
|
|
99
99
|
|
|
100
100
|
os.makedirs(output_dir / "flights-MLP", exist_ok=True)
|
|
@@ -102,7 +102,6 @@ def run_beast():
|
|
|
102
102
|
" ".join(
|
|
103
103
|
[
|
|
104
104
|
os.environ["BELLA_RUN_BEAST_CMD"],
|
|
105
|
-
f"-D ReDimension='{5 * 4}'",
|
|
106
105
|
f'-D layersRange="0,1,2",nodes="16 8"',
|
|
107
106
|
flight_predictor_data,
|
|
108
107
|
f"-prefix {output_dir / 'flights-MLP'}{os.sep}",
|
|
@@ -110,9 +109,9 @@ def run_beast():
|
|
|
110
109
|
]
|
|
111
110
|
),
|
|
112
111
|
base_log_dir / "flights-MLP",
|
|
113
|
-
|
|
112
|
+
cpus=128,
|
|
113
|
+
mem_per_cpu=12000,
|
|
114
114
|
)
|
|
115
|
-
"""
|
|
116
115
|
|
|
117
116
|
with open(base_output_dir / "eucovid_job_ids.json", "w") as f:
|
|
118
117
|
json.dump(job_ids, f)
|
bella_companion/utils/slurm.py
CHANGED
|
@@ -19,9 +19,9 @@ def submit_job(
|
|
|
19
19
|
f"-J {log_dir}",
|
|
20
20
|
f"-o {log_dir / 'output.out'}",
|
|
21
21
|
f"-e {log_dir / 'error.err'}",
|
|
22
|
+
f"-c {cpus}",
|
|
22
23
|
f"--time {time}",
|
|
23
|
-
f"--mem-per-cpu
|
|
24
|
-
f"-c={cpus}",
|
|
24
|
+
f"--mem-per-cpu {mem_per_cpu}",
|
|
25
25
|
f"--wrap='{command}'",
|
|
26
26
|
]
|
|
27
27
|
)
|
|
@@ -2,7 +2,7 @@ bella_companion/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
|
|
|
2
2
|
bella_companion/cli.py,sha256=0SwDxkDPqvsp36kGnrBMLPIhAQM8PIpNXrztZayqmDc,2409
|
|
3
3
|
bella_companion/eucovid/__init__.py,sha256=09Ld_G7fZvCDCgEWsmaOyLVQ8pFc9QHAGnXKJ9Zm2AM,81
|
|
4
4
|
bella_companion/eucovid/beast_configs/GLM.xml,sha256=YMvcyeSRIGQOhSSoj7FV0R-5wZHcGWwf9bKxamJ0q9k,20739
|
|
5
|
-
bella_companion/eucovid/beast_configs/MLP.xml,sha256=
|
|
5
|
+
bella_companion/eucovid/beast_configs/MLP.xml,sha256=SGJVUYyi1ULU7zxx8xn9aiKZNQQ3D9ruyYRsDcFjPzo,16139
|
|
6
6
|
bella_companion/eucovid/beast_configs/Nonparametric.xml,sha256=n-t4sUfDS9AzC02tbIk5mx_RDg2l62ELhdR3I3_jjHE,17783
|
|
7
7
|
bella_companion/eucovid/data/case_data.tsv,sha256=XaSzZh5NcEMVt9d_XlQ19T8UuEkHGrjpSFXhe9IycNg,12412
|
|
8
8
|
bella_companion/eucovid/data/change_dates.tsv,sha256=_pmVFYiL4X9Pd79uYVgyz3sKeRap7xVcXk0OjqVhuVQ,227
|
|
@@ -20,7 +20,7 @@ bella_companion/eucovid/data/predictors/all/sharedborders_7e_nt.tsv,sha256=pPVT5
|
|
|
20
20
|
bella_companion/eucovid/data/predictors/changetimes_all_7e.tsv,sha256=hH0xXD2lr_8RPQRqvENv6clPHauAXH22SGQHb3hlfzs,120
|
|
21
21
|
bella_companion/eucovid/data/predictors/changetimes_flights_4e.tsv,sha256=XEepIXKRwcKknJq4-ovKlorvCypGi67B8znuQ5f1LTg,60
|
|
22
22
|
bella_companion/eucovid/data/predictors/flight_pop_x_4e_ls.tsv,sha256=tMR9-tuGtC3rVABXUtNdV9irUX-9aCCVb_fwksHTn8U,1068
|
|
23
|
-
bella_companion/eucovid/run_beast.py,sha256=
|
|
23
|
+
bella_companion/eucovid/run_beast.py,sha256=FYeqqG2_S3o_NrmYqyyll82CR0sbYtI7QuRv5MIrRVY,3748
|
|
24
24
|
bella_companion/platyrrhine/__init__.py,sha256=dIx6exNz-vuKiG5FZumvq74QUWcIEFd3L6ErqnOa83c,274
|
|
25
25
|
bella_companion/platyrrhine/beast_config.xml,sha256=8A6E5iPu9FqDL3UdlsqDbabLFlC6Qhfa4Ta47niRkVA,7090
|
|
26
26
|
bella_companion/platyrrhine/data/change_times.csv,sha256=tedobHbaY7-6M3V6F6HSqGAU9dpeeajR5mu1XGJfp6w,68
|
|
@@ -68,8 +68,8 @@ bella_companion/simulations/summarize_logs.py,sha256=Shf3Dx9k4lTbmO__MSLw-aIA8a8
|
|
|
68
68
|
bella_companion/utils/__init__.py,sha256=UtMwPK9dWf9NAl0ic8CSsgdW7aSm-5J49OqgvD7UpYw,480
|
|
69
69
|
bella_companion/utils/beast.py,sha256=TBa0cLklX1_tXqoQE4LRYvds7mLg_9fS2-6U6OHENHo,2184
|
|
70
70
|
bella_companion/utils/explain.py,sha256=uP7HPyn2YiykAI69BQV3RooDpC6qKoCLXfp3Uibp4zk,1475
|
|
71
|
-
bella_companion/utils/slurm.py,sha256=
|
|
72
|
-
bella_companion-0.0.
|
|
73
|
-
bella_companion-0.0.
|
|
74
|
-
bella_companion-0.0.
|
|
75
|
-
bella_companion-0.0.
|
|
71
|
+
bella_companion/utils/slurm.py,sha256=xEyf-Jxk8fy71t3fko_Ic9WtUFSdLFE3w4tR17gaBPw,1868
|
|
72
|
+
bella_companion-0.0.28.dist-info/METADATA,sha256=f_4at3vdN5Z4FMjq-1C71qUa1raHCBL4TaouU3S0TDw,576
|
|
73
|
+
bella_companion-0.0.28.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
|
|
74
|
+
bella_companion-0.0.28.dist-info/entry_points.txt,sha256=rSeKoAhmjnQqAYFcXBv0gAM2ViJfJe0D8_dD-fWrXeg,50
|
|
75
|
+
bella_companion-0.0.28.dist-info/RECORD,,
|
|
File without changes
|
|
File without changes
|