bella-companion 0.0.14__py3-none-any.whl → 0.0.16__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- bella_companion/fbd_empirical/beast_config.xml +117 -0
- bella_companion/fbd_empirical/data/traits.csv +122 -122
- bella_companion/fbd_empirical/data/trees.nwk +46 -46
- bella_companion/fbd_empirical/results.py +6 -6
- bella_companion/fbd_empirical/run_beast.py +10 -28
- bella_companion/fbd_empirical/summarize_logs.py +2 -2
- bella_companion/simulations/beast_configs/epi-multitype/GLM.xml +81 -0
- bella_companion/simulations/beast_configs/epi-multitype/MLP.xml +81 -0
- bella_companion/simulations/beast_configs/epi-multitype/Nonparametric.xml +65 -0
- bella_companion/simulations/beast_configs/epi-skyline/GLM.xml +71 -0
- bella_companion/simulations/beast_configs/epi-skyline/MLP.xml +73 -0
- bella_companion/simulations/beast_configs/epi-skyline/Nonparametric.xml +57 -0
- bella_companion/simulations/beast_configs/fbd-2traits/GLM.xml +101 -0
- bella_companion/simulations/beast_configs/fbd-2traits/MLP.xml +98 -0
- bella_companion/simulations/beast_configs/fbd-2traits/Nonparametric.xml +70 -0
- bella_companion/simulations/beast_configs/fbd-no-traits/GLM.xml +88 -0
- bella_companion/simulations/beast_configs/fbd-no-traits/MLP.xml +86 -0
- bella_companion/simulations/beast_configs/fbd-no-traits/Nonparametric.xml +62 -0
- bella_companion/simulations/generate_data.py +3 -3
- bella_companion/simulations/metrics.py +0 -4
- bella_companion/simulations/run_beast.py +5 -4
- {bella_companion-0.0.14.dist-info → bella_companion-0.0.16.dist-info}/METADATA +2 -2
- {bella_companion-0.0.14.dist-info → bella_companion-0.0.16.dist-info}/RECORD +25 -12
- {bella_companion-0.0.14.dist-info → bella_companion-0.0.16.dist-info}/WHEEL +0 -0
- {bella_companion-0.0.14.dist-info → bella_companion-0.0.16.dist-info}/entry_points.txt +0 -0
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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.operator.kernel
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:beast.base.inference.parameter
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:beast.base.inference.operator.kernel
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:beast.base.inference
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:beast.base.inference.distribution
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:bdmmprime.distribution
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:bdmmprime.parameterization
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:feast.fileio
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:feast.function
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:feast.expressions"
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version="2.5"
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>
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<map name="Normal">beast.base.inference.distribution.Normal</map>
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<map name="Uniform">beast.base.inference.distribution.Uniform</map>
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<map name="TreeFromNewickFile">feast.fileio.TreeFromNewickFile</map>
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<map name="TaxonSetFromTree">feast.fileio.TaxonSetFromTree</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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<TreeFromNewickFile id="tree" fileName="$(treeFile)" IsLabelledNewick="true" adjustTipHeights='false'/>
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<TaxonSetFromTree id="taxonSet" tree="@tree"/>
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<TraitSetFromTaxonSet id="typeTraitSet" traitname="type" delimiter="|" takeGroup="1" taxa="@taxonSet"/>
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<TypeSet id="typeSet" value="$(types)" typeTraitSet="@typeTraitSet"/>
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<Normal id="weightsPrior" mean="0" sigma="1"/>
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<Uniform id="birthRatePrior" upper="$(birthRateUpper)"/>
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<Uniform id="deathRatePrior" upper="$(deathRateUpper)"/>
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<run spec="MCMC" chainLength="10000000">
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<state id="state">
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<stateNode spec="RealParameter" id="birthRateScaler" value="1"/>
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<stateNode spec="RealParameter" id="deathRateScaler" value="1"/>
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<stateNode spec="RealParameter" id="birthRateW" value="0"/>
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<stateNode spec="RealParameter" id="deathRateW" value="0"/>
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</state>
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<distribution id="posterior" spec="CompoundDistribution">
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<distribution id="likelihood" spec="CompoundDistribution">
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<distribution spec="BirthDeathMigrationDistribution" tree="@tree" typeTraitSet="@typeTraitSet">
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<parameterization spec="CanonicalParameterization" processLength="$(processLength)" typeSet="@typeSet">
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<birthRate id="birthRateSP" spec="SkylineVectorParameter" changeTimes="$(changeTimes)" typeSet="@typeSet">
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<skylineValues id="birthRate" spec="glmprior.util.GLMLogLinear" coefficients="@birthRateW" scaleFactor="@birthRateScaler" transform="false">
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<predictor spec="RealParameter" value="$(timePredictor)"/>
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<predictor spec="RealParameter" value="$(trait1Predictor)"/>
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<predictor spec="RealParameter" value="$(trait2Predictor)"/>
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<predictor spec="RealParameter" value="$(randomPredictor)"/>
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<indicators spec="BooleanParameter" value="1"/>
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</skylineValues>
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</birthRate>
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<deathRate id="deathRateSP" spec="SkylineVectorParameter" changeTimes="$(changeTimes)" typeSet="@typeSet">
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<skylineValues id="deathRate" spec="glmprior.util.GLMLogLinear" coefficients="@deathRateW" scaleFactor="@deathRateScaler" transform="false">
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<predictor spec="RealParameter" value="$(timePredictor)"/>
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<predictor spec="RealParameter" value="$(trait1Predictor)"/>
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<predictor spec="RealParameter" value="$(trait2Predictor)"/>
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<predictor spec="RealParameter" value="$(randomPredictor)"/>
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<indicators spec="BooleanParameter" value="1"/>
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</skylineValues>
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</deathRate>
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<migrationRate spec="SkylineMatrixParameter" skylineValues="$(migrationRate)" typeSet="@typeSet"/>
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<samplingRate spec="SkylineVectorParameter" skylineValues="$(samplingRate)" typeSet="@typeSet"/>
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<removalProb spec="SkylineVectorParameter" skylineValues="0.0" typeSet="@typeSet"/>
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<rhoSampling spec="TimedParameter" values="1" times="$(processLength)" typeSet="@typeSet"/>
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</parameterization>
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<startTypePriorProbs spec="RealParameter" value="$(startTypePriorProbs)"/>
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</distribution>
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</distribution>
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<distribution id="prior" spec="CompoundDistribution">
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<distribution spec="Prior" x="@birthRateScaler" distr="@weightsPrior"/>
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<distribution spec="Prior" x="@deathRateScaler" distr="@weightsPrior"/>
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<distribution spec="Prior" x="@birthRateW" distr="@weightsPrior"/>
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<distribution spec="Prior" x="@deathRateW" distr="@weightsPrior"/>
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<distribution spec="Prior" x="@birthRate" distr="@birthRatePrior"/>
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<distribution spec="Prior" x="@deathRate" distr="@deathRatePrior"/>
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</distribution>
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</distribution>
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<operator spec="BactrianScaleOperator" parameter="@birthRateScaler" weight="30.0"/>
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<operator spec="BactrianScaleOperator" parameter="@deathRateScaler" weight="30.0"/>
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<operator spec="BactrianRandomWalkOperator" parameter="@birthRateW" weight="30.0"/>
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<operator spec="BactrianRandomWalkOperator" parameter="@deathRateW" weight="30.0"/>
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<logger spec="Logger" fileName="$(treeID).log" logEvery="1000" model="@posterior">
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<log idref="posterior"/>
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<log idref="prior"/>
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<log idref="likelihood"/>
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<log idref="birthRateSP"/>
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<log idref="deathRateSP"/>
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<log idref="birthRateW"/>
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<log idref="deathRateW"/>
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<log idref="birthRateScaler"/>
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<log idref="deathRateScaler"/>
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</logger>
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</run>
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</beast>
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<?xml version="1.0"?>
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<beast
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namespace="
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:beast.base.inference.parameter
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:beast.base.inference.operator.kernel
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:beast.base.inference
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:beast.base.inference.distribution
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:bdmmprime.distribution
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:bdmmprime.parameterization
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:feast.fileio
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:feast.function
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:feast.expressions"
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version="2.5"
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>
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<map name="Normal">beast.base.inference.distribution.Normal</map>
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<map name="TreeFromNewickFile">feast.fileio.TreeFromNewickFile</map>
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<map name="TaxonSetFromTree">feast.fileio.TaxonSetFromTree</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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<TreeFromNewickFile id="tree" fileName="$(treeFile)" IsLabelledNewick="true" adjustTipHeights='false'/>
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<TaxonSetFromTree id="taxonSet" tree="@tree"/>
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<TraitSetFromTaxonSet id="typeTraitSet" traitname="type" delimiter="|" takeGroup="1" taxa="@taxonSet"/>
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<TypeSet id="typeSet" value="$(types)" typeTraitSet="@typeTraitSet"/>
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<Normal id="weightsPrior" mean="0" sigma="1"/>
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<run spec="MCMC" chainLength="10000000">
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<state id="state">
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<plate var="n" range="$(layersRange)">
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<stateNode spec="RealParameter" name="stateNode" id="birthRateW$(n)" value="0"/>
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<stateNode spec="RealParameter" name="stateNode" id="deathRateW$(n)" value="0"/>
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</plate>
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</state>
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<distribution id="posterior" spec="CompoundDistribution">
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<distribution id="likelihood" spec="CompoundDistribution">
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<distribution spec="BirthDeathMigrationDistribution" tree="@tree" typeTraitSet="@typeTraitSet">
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<parameterization spec="CanonicalParameterization" processLength="$(processLength)" typeSet="@typeSet">
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<birthRate id="birthRateSP" spec="SkylineVectorParameter" changeTimes="$(changeTimes)" typeSet="@typeSet">
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<skylineValues id="birthRate" spec="bella.BayesMLP" nodes="$(nodes)">
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<predictor spec="RealParameter" value="$(timePredictor)"/>
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<predictor spec="RealParameter" value="$(trait1Predictor)"/>
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<predictor spec="RealParameter" value="$(trait2Predictor)"/>
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<predictor spec="RealParameter" value="$(randomPredictor)"/>
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<plate var="n" range="$(layersRange)">
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<weights idref="birthRateW$(n)"/>
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</plate>
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<activationFunctionsOutput spec="bella.Sigmoid" upper="$(birthRateUpper)"/>
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</skylineValues>
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</birthRate>
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<deathRate id="deathRateSP" spec="SkylineVectorParameter" changeTimes="$(changeTimes)" typeSet="@typeSet">
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<skylineValues id="deathRate" spec="bella.BayesMLP" nodes="$(nodes)">
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<predictor spec="RealParameter" value="$(timePredictor)"/>
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<predictor spec="RealParameter" value="$(trait1Predictor)"/>
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<predictor spec="RealParameter" value="$(trait2Predictor)"/>
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<predictor spec="RealParameter" value="$(randomPredictor)"/>
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<plate var="n" range="$(layersRange)">
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<weights idref="deathRateW$(n)"/>
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</plate>
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<activationFunctionsOutput spec="bella.Sigmoid" upper="$(deathRateUpper)"/>
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</skylineValues>
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</deathRate>
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<migrationRate spec="SkylineMatrixParameter" skylineValues="$(migrationRate)" typeSet="@typeSet"/>
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<samplingRate spec="SkylineVectorParameter" skylineValues="$(samplingRate)" typeSet="@typeSet"/>
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<removalProb spec="SkylineVectorParameter" skylineValues="0.0" typeSet="@typeSet"/>
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<rhoSampling spec="TimedParameter" values="1" times="$(processLength)" typeSet="@typeSet"/>
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</parameterization>
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<startTypePriorProbs spec="RealParameter" value="$(startTypePriorProbs)"/>
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</distribution>
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</distribution>
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<distribution id="prior" spec="CompoundDistribution">
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<plate var="n" range="$(layersRange)">
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<distribution spec="Prior" x="@birthRateW$(n)" distr="@weightsPrior"/>
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<distribution spec="Prior" x="@deathRateW$(n)" distr="@weightsPrior"/>
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</plate>
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</distribution>
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</distribution>
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<plate var="n" range="$(layersRange)">
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<operator spec="BactrianRandomWalkOperator" parameter="@birthRateW$(n)" weight="30.0"/>
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<operator spec="BactrianRandomWalkOperator" parameter="@deathRateW$(n)" weight="30.0"/>
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</plate>
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<logger spec="Logger" fileName="$(treeID).log" logEvery="1000" model="@posterior">
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<log idref="posterior"/>
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<log idref="prior"/>
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<log idref="likelihood"/>
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<log idref="birthRateSP"/>
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<log idref="deathRateSP"/>
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<log idref="birthRate"/>
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<log idref="deathRate"/>
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</logger>
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</run>
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</beast>
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<?xml version="1.0"?>
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<beast
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:beast.base.evolution.operator.kernel
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:beast.base.inference.parameter
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:beast.base.inference.operator.kernel
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:beast.base.inference
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:beast.base.inference.distribution
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:bdmmprime.distribution
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:bdmmprime.parameterization
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:feast.fileio
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:feast.function
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:feast.expressions"
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version="2.5"
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>
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<map name="Uniform">beast.base.inference.distribution.Uniform</map>
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<map name="TreeFromNewickFile">feast.fileio.TreeFromNewickFile</map>
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<map name="TaxonSetFromTree">feast.fileio.TaxonSetFromTree</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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<TreeFromNewickFile id="tree" fileName="$(treeFile)" IsLabelledNewick="true" adjustTipHeights='false'/>
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<TaxonSetFromTree id="taxonSet" tree="@tree"/>
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<TraitSetFromTaxonSet id="typeTraitSet" traitname="type" delimiter="|" takeGroup="1" taxa="@taxonSet"/>
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<TypeSet id="typeSet" value="$(types)" typeTraitSet="@typeTraitSet"/>
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<Uniform id="birthRatePrior" upper="$(birthRateUpper)"/>
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<Uniform id="deathRatePrior" upper="$(deathRateUpper)"/>
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<run spec="MCMC" chainLength="10000000">
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<state id="state">
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<stateNode spec="RealParameter" id="birthRate" value="$(birthRateInit)"/>
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<stateNode spec="RealParameter" id="deathRate" value="$(deathRateInit)"/>
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</state>
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<distribution id="posterior" spec="CompoundDistribution">
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<distribution id="likelihood" spec="CompoundDistribution">
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<distribution spec="BirthDeathMigrationDistribution" tree="@tree" typeTraitSet="@typeTraitSet">
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<parameterization spec="CanonicalParameterization" processLength="$(processLength)" typeSet="@typeSet">
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<birthRate id="birthRateSP" spec="SkylineVectorParameter" skylineValues="@birthRate" changeTimes="$(changeTimes)" typeSet="@typeSet"/>
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<deathRate id="deathRateSP" spec="SkylineVectorParameter" skylineValues="@deathRate" changeTimes="$(changeTimes)" typeSet="@typeSet"/>
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<migrationRate spec="SkylineMatrixParameter" skylineValues="$(migrationRate)" typeSet="@typeSet"/>
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<samplingRate spec="SkylineVectorParameter" skylineValues="$(samplingRate)" typeSet="@typeSet"/>
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<removalProb spec="SkylineVectorParameter" skylineValues="0.0" typeSet="@typeSet"/>
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<rhoSampling spec="TimedParameter" values="1" times="$(processLength)" typeSet="@typeSet"/>
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</parameterization>
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<startTypePriorProbs spec="RealParameter" value="$(startTypePriorProbs)"/>
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<distribution spec="Prior" x="@deathRate" distr="@deathRatePrior"/>
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<?xml version="1.0"?>
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<beast
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namespace="
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:bdmmprime.distribution
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:bdmmprime.parameterization
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:feast.fileio
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:feast.expressions"
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version="2.5"
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>
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<map name="Normal">beast.base.inference.distribution.Normal</map>
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<map name="Uniform">beast.base.inference.distribution.Uniform</map>
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<map name="TreeFromNewickFile">feast.fileio.TreeFromNewickFile</map>
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<TreeFromNewickFile id="tree" fileName="$(treeFile)" IsLabelledNewick="true" adjustTipHeights='false'/>
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<Normal id="weightsPrior" mean="0" sigma="1"/>
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<Uniform id="birthRatePrior" upper="$(birthRateUpper)"/>
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<Uniform id="deathRatePrior" upper="$(deathRateUpper)"/>
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<run spec="MCMC" chainLength="10000000">
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<stateNode spec="RealParameter" id="birthRateScaler" value="1"/>
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<stateNode spec="RealParameter" id="deathRateScaler" value="1"/>
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<stateNode spec="RealParameter" id="birthRateW" value="0"/>
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<stateNode spec="RealParameter" id="deathRateW" value="0"/>
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</state>
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<distribution id="posterior" spec="CompoundDistribution">
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<distribution id="likelihood" spec="CompoundDistribution">
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<distribution spec="BirthDeathMigrationDistribution" tree="@tree">
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<parameterization spec="CanonicalParameterization" processLength="$(processLength)">
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<birthRate id="birthRateSP" spec="SkylineVectorParameter" changeTimes="$(changeTimes)">
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<skylineValues id="birthRate" spec="glmprior.util.GLMLogLinear" coefficients="@birthRateW" scaleFactor="@birthRateScaler" transform="false">
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<predictor spec="RealParameter" value="$(timePredictor)"/>
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<predictor spec="RealParameter" value="$(randomPredictor)"/>
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<indicators spec="BooleanParameter" value="1"/>
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</skylineValues>
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</birthRate>
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<deathRate id="deathRateSP" spec="SkylineVectorParameter" changeTimes="$(changeTimes)">
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<skylineValues id="deathRate" spec="glmprior.util.GLMLogLinear" coefficients="@deathRateW" scaleFactor="@deathRateScaler" transform="false">
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<predictor spec="RealParameter" value="$(timePredictor)"/>
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<predictor spec="RealParameter" value="$(randomPredictor)"/>
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<indicators spec="BooleanParameter" value="1"/>
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</skylineValues>
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</deathRate>
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<samplingRate spec="SkylineVectorParameter" skylineValues="$(samplingRate)"/>
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<removalProb spec="SkylineVectorParameter" skylineValues="0.0"/>
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<rhoSampling spec="TimedParameter" values="1" times="$(processLength)"/>
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<distribution spec="Prior" x="@birthRateScaler" distr="@weightsPrior"/>
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<distribution spec="Prior" x="@deathRateScaler" distr="@weightsPrior"/>
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<distribution spec="Prior" x="@deathRateW" distr="@weightsPrior"/>
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<distribution spec="Prior" x="@birthRate" distr="@birthRatePrior"/>
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<operator spec="BactrianScaleOperator" parameter="@birthRateScaler" weight="30.0"/>
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<operator spec="BactrianScaleOperator" parameter="@deathRateScaler" weight="30.0"/>
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<operator spec="BactrianRandomWalkOperator" parameter="@birthRateW" weight="30.0"/>
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<operator spec="BactrianRandomWalkOperator" parameter="@deathRateW" weight="30.0"/>
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<logger spec="Logger" fileName="$(treeID).log" logEvery="1000" model="@posterior">
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<log idref="posterior"/>
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<log idref="birthRateW"/>
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<log idref="deathRateW"/>
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<log idref="birthRateScaler"/>
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<log idref="deathRateScaler"/>
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</logger>
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</run>
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</beast>
|
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@@ -0,0 +1,86 @@
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<?xml version="1.0"?>
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<beast
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namespace="
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:beast.base.inference.parameter
|
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:beast.base.inference.operator.kernel
|
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:beast.base.inference
|
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:beast.base.inference.distribution
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:bdmmprime.distribution
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:bdmmprime.parameterization
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:feast.fileio
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:feast.function
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:feast.expressions"
|
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version="2.5"
|
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>
|
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<map name="Normal">beast.base.inference.distribution.Normal</map>
|
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<map name="TreeFromNewickFile">feast.fileio.TreeFromNewickFile</map>
|
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|
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<TreeFromNewickFile id="tree" fileName="$(treeFile)" IsLabelledNewick="true" adjustTipHeights='false'/>
|
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<Normal id="weightsPrior" mean="0" sigma="1"/>
|
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|
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<run spec="MCMC" chainLength="10000000">
|
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<state id="state">
|
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<plate var="n" range="$(layersRange)">
|
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<stateNode spec="RealParameter" name="stateNode" id="birthRateW$(n)" value="0"/>
|
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|
+
<stateNode spec="RealParameter" name="stateNode" id="deathRateW$(n)" value="0"/>
|
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|
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</plate>
|
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</state>
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+
|
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<distribution id="posterior" spec="CompoundDistribution">
|
|
32
|
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<distribution id="likelihood" spec="CompoundDistribution">
|
|
33
|
+
<distribution spec="BirthDeathMigrationDistribution" tree="@tree">
|
|
34
|
+
<parameterization spec="CanonicalParameterization" processLength="$(processLength)">
|
|
35
|
+
<birthRate id="birthRateSP" spec="SkylineVectorParameter" changeTimes="$(changeTimes)">
|
|
36
|
+
<skylineValues id="birthRate" spec="bella.BayesMLP" nodes="$(nodes)">
|
|
37
|
+
<predictor spec="RealParameter" value="$(timePredictor)"/>
|
|
38
|
+
<predictor spec="RealParameter" value="$(randomPredictor)"/>
|
|
39
|
+
<plate var="n" range="$(layersRange)">
|
|
40
|
+
<weights idref="birthRateW$(n)"/>
|
|
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|
+
</plate>
|
|
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|
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<activationFunctionsOutput spec="bella.Sigmoid" upper="$(birthRateUpper)"/>
|
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|
+
</skylineValues>
|
|
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|
+
</birthRate>
|
|
45
|
+
<deathRate id="deathRateSP" spec="SkylineVectorParameter" changeTimes="$(changeTimes)">
|
|
46
|
+
<skylineValues id="deathRate" spec="bella.BayesMLP" nodes="$(nodes)">
|
|
47
|
+
<predictor spec="RealParameter" value="$(timePredictor)"/>
|
|
48
|
+
<predictor spec="RealParameter" value="$(randomPredictor)"/>
|
|
49
|
+
<plate var="n" range="$(layersRange)">
|
|
50
|
+
<weights idref="deathRateW$(n)"/>
|
|
51
|
+
</plate>
|
|
52
|
+
<activationFunctionsOutput spec="bella.Sigmoid" upper="$(deathRateUpper)"/>
|
|
53
|
+
</skylineValues>
|
|
54
|
+
</deathRate>
|
|
55
|
+
<samplingRate spec="SkylineVectorParameter" skylineValues="$(samplingRate)"/>
|
|
56
|
+
<removalProb spec="SkylineVectorParameter" skylineValues="0.0"/>
|
|
57
|
+
<rhoSampling spec="TimedParameter" values="1" times="$(processLength)"/>
|
|
58
|
+
</parameterization>
|
|
59
|
+
</distribution>
|
|
60
|
+
</distribution>
|
|
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|
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|
|
62
|
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<distribution id="prior" spec="CompoundDistribution">
|
|
63
|
+
<plate var="n" range="$(layersRange)">
|
|
64
|
+
<distribution spec="Prior" x="@birthRateW$(n)" distr="@weightsPrior"/>
|
|
65
|
+
<distribution spec="Prior" x="@deathRateW$(n)" distr="@weightsPrior"/>
|
|
66
|
+
</plate>
|
|
67
|
+
</distribution>
|
|
68
|
+
</distribution>
|
|
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|
+
|
|
70
|
+
<plate var="n" range="$(layersRange)">
|
|
71
|
+
<operator spec="BactrianRandomWalkOperator" parameter="@birthRateW$(n)" weight="30.0"/>
|
|
72
|
+
<operator spec="BactrianRandomWalkOperator" parameter="@deathRateW$(n)" weight="30.0"/>
|
|
73
|
+
</plate>
|
|
74
|
+
|
|
75
|
+
<logger spec="Logger" fileName="$(treeID).log" logEvery="1000" model="@posterior">
|
|
76
|
+
<log idref="posterior"/>
|
|
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|
+
<log idref="prior"/>
|
|
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|
+
<log idref="likelihood"/>
|
|
79
|
+
<log idref="birthRateSP"/>
|
|
80
|
+
<log idref="deathRateSP"/>
|
|
81
|
+
<log idref="birthRate"/>
|
|
82
|
+
<log idref="deathRate"/>
|
|
83
|
+
</logger>
|
|
84
|
+
</run>
|
|
85
|
+
|
|
86
|
+
</beast>
|
|
@@ -0,0 +1,62 @@
|
|
|
1
|
+
<?xml version="1.0"?>
|
|
2
|
+
<beast
|
|
3
|
+
namespace="
|
|
4
|
+
:beast.base.evolution.operator.kernel
|
|
5
|
+
:beast.base.inference.parameter
|
|
6
|
+
:beast.base.inference.operator.kernel
|
|
7
|
+
:beast.base.inference
|
|
8
|
+
:beast.base.inference.distribution
|
|
9
|
+
:bdmmprime.distribution
|
|
10
|
+
:bdmmprime.parameterization
|
|
11
|
+
:feast.fileio
|
|
12
|
+
:feast.function
|
|
13
|
+
:feast.expressions"
|
|
14
|
+
version="2.5"
|
|
15
|
+
>
|
|
16
|
+
<map name="Uniform">beast.base.inference.distribution.Uniform</map>
|
|
17
|
+
|
|
18
|
+
<map name="TreeFromNewickFile">feast.fileio.TreeFromNewickFile</map>
|
|
19
|
+
|
|
20
|
+
<TreeFromNewickFile id="tree" fileName="$(treeFile)" IsLabelledNewick="true" adjustTipHeights='false'/>
|
|
21
|
+
|
|
22
|
+
<Uniform id="birthRatePrior" upper="$(birthRateUpper)"/>
|
|
23
|
+
<Uniform id="deathRatePrior" upper="$(deathRateUpper)"/>
|
|
24
|
+
|
|
25
|
+
<run spec="MCMC" chainLength="10000000">
|
|
26
|
+
<state id="state">
|
|
27
|
+
<stateNode spec="RealParameter" id="birthRate" value="$(birthRateInit)"/>
|
|
28
|
+
<stateNode spec="RealParameter" id="deathRate" value="$(deathRateInit)"/>
|
|
29
|
+
</state>
|
|
30
|
+
|
|
31
|
+
<distribution id="posterior" spec="CompoundDistribution">
|
|
32
|
+
<distribution id="likelihood" spec="CompoundDistribution">
|
|
33
|
+
<distribution spec="BirthDeathMigrationDistribution" tree="@tree">
|
|
34
|
+
<parameterization spec="CanonicalParameterization" processLength="$(processLength)">
|
|
35
|
+
<birthRate id="birthRateSP" spec="SkylineVectorParameter" skylineValues="@birthRate" changeTimes="$(changeTimes)"/>
|
|
36
|
+
<deathRate id="deathRateSP" spec="SkylineVectorParameter" skylineValues="@deathRate" changeTimes="$(changeTimes)"/>
|
|
37
|
+
<samplingRate spec="SkylineVectorParameter" skylineValues="$(samplingRate)"/>
|
|
38
|
+
<removalProb spec="SkylineVectorParameter" skylineValues="0.0"/>
|
|
39
|
+
<rhoSampling spec="TimedParameter" values="1" times="$(processLength)"/>
|
|
40
|
+
</parameterization>
|
|
41
|
+
</distribution>
|
|
42
|
+
</distribution>
|
|
43
|
+
|
|
44
|
+
<distribution id="prior" spec="CompoundDistribution">
|
|
45
|
+
<distribution spec="Prior" x="@birthRate" distr="@birthRatePrior"/>
|
|
46
|
+
<distribution spec="Prior" x="@deathRate" distr="@deathRatePrior"/>
|
|
47
|
+
</distribution>
|
|
48
|
+
</distribution>
|
|
49
|
+
|
|
50
|
+
<operator spec="BactrianScaleOperator" parameter="@birthRate" weight="30.0"/>
|
|
51
|
+
<operator spec="BactrianScaleOperator" parameter="@deathRate" weight="30.0"/>
|
|
52
|
+
|
|
53
|
+
<logger spec="Logger" fileName="$(treeID).log" logEvery="1000" model="@posterior">
|
|
54
|
+
<log idref="posterior"/>
|
|
55
|
+
<log idref="prior"/>
|
|
56
|
+
<log idref="likelihood"/>
|
|
57
|
+
<log idref="birthRateSP"/>
|
|
58
|
+
<log idref="deathRateSP"/>
|
|
59
|
+
</logger>
|
|
60
|
+
</run>
|
|
61
|
+
|
|
62
|
+
</beast>
|
|
@@ -20,8 +20,8 @@ def generate_data():
|
|
|
20
20
|
init_state=scenario.init_state,
|
|
21
21
|
sampling_probability_at_present=int(scenario.type == ScenarioType.FBD),
|
|
22
22
|
max_time=scenario.max_time,
|
|
23
|
-
min_tips=MIN_TIPS,
|
|
24
|
-
max_tips=MAX_TIPS,
|
|
25
23
|
seed=42,
|
|
26
|
-
|
|
24
|
+
acceptance_criterion=lambda t: MIN_TIPS
|
|
25
|
+
<= sum(1 for l in t.get_leaves() if l.branch_length > 0) # pyright: ignore
|
|
26
|
+
<= MAX_TIPS,
|
|
27
27
|
)
|
|
@@ -5,8 +5,7 @@ from glob import glob
|
|
|
5
5
|
from pathlib import Path
|
|
6
6
|
|
|
7
7
|
from numpy.random import default_rng
|
|
8
|
-
from phylogenie import Tree, load_newick
|
|
9
|
-
from phylogenie.utils import get_node_depths
|
|
8
|
+
from phylogenie import Tree, get_node_depths, load_newick
|
|
10
9
|
from tqdm import tqdm
|
|
11
10
|
|
|
12
11
|
from bella_companion.simulations.scenarios import SCENARIOS, ScenarioType
|
|
@@ -22,8 +21,10 @@ def run_beast():
|
|
|
22
21
|
for scenario_name, scenario in SCENARIOS.items():
|
|
23
22
|
job_ids[scenario_name] = defaultdict(dict)
|
|
24
23
|
data_dir = base_data_dir / scenario_name
|
|
25
|
-
inference_configs_dir =
|
|
26
|
-
|
|
24
|
+
inference_configs_dir = (
|
|
25
|
+
Path(__file__).parent
|
|
26
|
+
/ "beast_configs"
|
|
27
|
+
/ (scenario_name.split("_")[0] if "_" in scenario_name else scenario_name)
|
|
27
28
|
)
|
|
28
29
|
log_dir = Path(os.environ["BELLA_SBATCH_LOG_DIR"]) / scenario_name
|
|
29
30
|
for tree_file in tqdm(
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
Metadata-Version: 2.1
|
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Name: bella-companion
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Version: 0.0.
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Version: 0.0.16
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Summary:
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Author: gabriele-marino
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Author-email: gabmarino.8601@gmail.com
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Requires-Dist: arviz (>=0.22.0,<0.23.0)
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Requires-Dist: bella-lumiere (>=0.0.14,<0.0.15)
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Requires-Dist: dotenv (>=0.9.9,<0.10.0)
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Requires-Dist: phylogenie (>=
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Requires-Dist: phylogenie (>=3.1.1,<4.0.0)
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Requires-Dist: seaborn (>=0.13.2,<0.14.0)
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bella_companion/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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bella_companion/cli.py,sha256=D-kQuj0I-g5Vm5-mXdOZoio68mhOBpJ3jVG8B2Kwvn4,2190
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bella_companion/fbd_empirical/__init__.py,sha256=FgzjaEpwZImvBsJs17ghF0ltZvhFmgmkTGGF3HgdsGo,284
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bella_companion/fbd_empirical/beast_config.xml,sha256=McImvRgzYflbfCLQdo6sqTgvJcSDc8CQiRjDhgUWkFI,7075
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bella_companion/fbd_empirical/data/change_times.csv,sha256=tedobHbaY7-6M3V6F6HSqGAU9dpeeajR5mu1XGJfp6w,68
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bella_companion/fbd_empirical/data/traits.csv,sha256=
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bella_companion/fbd_empirical/data/trees.nwk,sha256=
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bella_companion/fbd_empirical/results.py,sha256=
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bella_companion/fbd_empirical/run_beast.py,sha256=
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bella_companion/fbd_empirical/summarize_logs.py,sha256=
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bella_companion/fbd_empirical/data/traits.csv,sha256=N_mCnaM9Gy0Qot7-l_mK0vMvr7e_5BZ4bgUHpcoG9UM,3949
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bella_companion/fbd_empirical/data/trees.nwk,sha256=Y5ro7vQ8vz2Cp3kpNtOTRBfOdQAT-eJUwkb75x79bHE,539477
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bella_companion/fbd_empirical/results.py,sha256=skf7PsdWZuOVkMeGgKsSCKDfho6tVWT7bUVFWTthxag,3114
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bella_companion/fbd_empirical/run_beast.py,sha256=60t8tbqlgdv86JwBk_DvUQ8i7TpThz0EmwEv-OkBAQM,2560
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bella_companion/fbd_empirical/summarize_logs.py,sha256=f3NgdyrCmbD5eHDHYwiA8ggh4b3rZ63SrlfDt0FAZmc,955
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bella_companion/simulations/__init__.py,sha256=ShYRdp1iSjnS_SzcsH-8jbqXz6P1nyRQZqAtPZJCMVE,454
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bella_companion/simulations/beast_configs/epi-multitype/GLM.xml,sha256=VymAYsaZVuB3EPE0DCQSXpKepVq8pPjKaB5yhEpaVkE,4334
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bella_companion/simulations/beast_configs/epi-multitype/MLP.xml,sha256=J-OVblMRmk4XRhz9DHhLpMwaIzqSqYZ7Yq7dTMvQW1s,4094
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bella_companion/simulations/beast_configs/epi-multitype/Nonparametric.xml,sha256=DfCMcLM53b-XP9oIiQ9wJWOVTEP3GnoZaL5BMzLLfIQ,3208
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bella_companion/simulations/beast_configs/epi-skyline/GLM.xml,sha256=7LtJhU7o7aQsnWK7ZIKj-mzmHgCn_RjxvKKbLIlp1Go,3619
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bella_companion/simulations/beast_configs/epi-skyline/MLP.xml,sha256=ovjFleUnTgyrT8T1uaKboUsL-ZFLCaQN5mk4HadFPU0,3443
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bella_companion/simulations/beast_configs/epi-skyline/Nonparametric.xml,sha256=LTiatqeAMiFfdD1leQ5TrGaJhsYwlkbMDpxqhVFOgUQ,2561
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bella_companion/simulations/beast_configs/fbd-2traits/GLM.xml,sha256=Iff0eAShKLeOnlTmNu6044Wljtla3yckqo2LZ7mP6LY,5897
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bella_companion/simulations/beast_configs/fbd-2traits/MLP.xml,sha256=E8sgfOAJI4rkbCVhGYa-HwM44ItwxVs4pIXkQOGNTtY,5462
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bella_companion/simulations/beast_configs/fbd-2traits/Nonparametric.xml,sha256=ev6ZfMeCwMyK54G_4O8g-tbgoxoD3asxt71x91Cb1QY,3618
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bella_companion/simulations/beast_configs/fbd-no-traits/GLM.xml,sha256=Caq7Gxqx-wYAu3_YkMikVqni3DjBv1Wt00sc1Upo1X8,4743
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bella_companion/simulations/beast_configs/fbd-no-traits/MLP.xml,sha256=_EzDVPrU6Y5ZfzkVn---Sp62KeBZuRCZfoYqxblLq8I,4309
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bella_companion/simulations/beast_configs/fbd-no-traits/Nonparametric.xml,sha256=m2xaHZwskCFInvVY1QH1fwQqH6p_fgESlPX2BbBeUhk,2822
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bella_companion/simulations/features.py,sha256=DZOBpJGlQ0UinqUZYbEtoemZ2eQGVLV_i-DfpW31qJI,104
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bella_companion/simulations/figures/__init__.py,sha256=aBYbJntH4egFmkSSWiVMYDEApXPYxJD7eA3TCPNNegM,658
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bella_companion/simulations/figures/epi_multitype_results.py,sha256=j85WgvN5AyAtX-CalMegr2lwlAZBmzyJxkikBPXRjCc,2629
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bella_companion/simulations/figures/fbd_no_traits_results.py,sha256=fLsgpV3IbLLtxQEFNOL9K4jEEJrG324ziUM0rxIv7_k,1962
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bella_companion/simulations/figures/scenarios.py,sha256=gbMz1TUxxT2RSIq2kQlFioNdgSHk-gQY2OQuf6-7Fww,2817
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bella_companion/simulations/figures/utils.py,sha256=0M5OrxaEuqcj9rR2uAc_O7utQvhEceZGH0sKrGRWaWs,3129
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bella_companion/simulations/generate_data.py,sha256=
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bella_companion/simulations/generate_data.py,sha256=edfhXrs76hl30i_xizup4z6qgzXZyaDzX_PVC62Ytpw,849
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bella_companion/simulations/generate_figures.py,sha256=layMgoj3Bfl78Ceb1oE7YirAQ8zhjDyD9IrxDRXf6go,657
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bella_companion/simulations/metrics.py,sha256=
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bella_companion/simulations/run_beast.py,sha256=
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bella_companion/simulations/metrics.py,sha256=duIkPb8cCXmIzjKA2yk9HLf4Y9eFIB_hRWaH05uIDws,1876
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bella_companion/simulations/run_beast.py,sha256=qniy326i-vDCeHzzHpQRrSnY2ULqNNrO0z3GEsWx4Mc,3208
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bella_companion/simulations/scenarios/__init__.py,sha256=3Kl1lKcFpfb3vLX64DmSW4XCF5kXU1ZoHtstFH-ZIzU,876
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bella_companion/simulations/scenarios/common.py,sha256=_ddaSuTvEVdttGkXB4HPc2B7IB1F_GBOCW3cVOPZ-ZM,807
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bella_companion/simulations/scenarios/epi_multitype.py,sha256=fTkFeGHxyV_1f2nX3g_Oyr_e6wkorhXEicJjIAgeZKA,2439
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bella_companion/utils/beast.py,sha256=TBa0cLklX1_tXqoQE4LRYvds7mLg_9fS2-6U6OHENHo,2184
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bella_companion/utils/explain.py,sha256=uP7HPyn2YiykAI69BQV3RooDpC6qKoCLXfp3Uibp4zk,1475
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bella_companion/utils/slurm.py,sha256=v5DaG7YHVyK8KRFptgGDC6I8jxEhyJuMVK9N08pZSAI,1812
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bella_companion-0.0.
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bella_companion-0.0.16.dist-info/METADATA,sha256=Kd_M6fOFsQ9v3Ph7_saJZp3_GGZHfGC88-0Uk3UPJS8,576
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bella_companion-0.0.16.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
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bella_companion-0.0.16.dist-info/entry_points.txt,sha256=rSeKoAhmjnQqAYFcXBv0gAM2ViJfJe0D8_dD-fWrXeg,50
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bella_companion-0.0.16.dist-info/RECORD,,
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