PyPI - bella-companion - Versions diffs - 0.0.27__py3-none-any.whl → 0.0.29__py3-none-any.whl - Mend

bella-companion 0.0.27py3-none-any.whl → 0.0.29py3-none-any.whl

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bella_companion/eucovid/beast_configs/GLM.xml CHANGED Viewed

@@ -1,450 +1,169 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<beast namespace="beast.base.inference
-    :beast.base.inference.parameter
-    :beast.base.evolution.branchratemodel
-    :beast.base.evolution.substitutionmodel
-    :beast.base.evolution.sitemodel
-    :beast.base.evolution.tree.coalescent
-    :beast.base.evolution.tree
-    :beast.base.evolution.likelihood
-    :beast.base.evolution.alignment
-    :beast.base.evolution.operator
-    :beast.base.evolution.operator.kernel
-    :beast.base.inference.operator.kernel
-    :beast.base.inference.operator
-    :beast.base.math.distributions
-    :beast.base.evolution
-    :bdmmprime.util.operators
-    :bdmmprime.util.priors
-    :bdmmprime.distribution
-    :bdmmprime.parameterization
-    :bdmmprime.mapping
-    :bdmmprime.util
-    :bdmmprime.trajectories
-    :feast
-    :feast.parameter
-    :feast.fileio
-    :feast.function
-    :feast.expressions
-    :glmprior.util"
-    required="BEAST.base v2.7.7:BDMM-Prime v2.2.2" version="2.7">
-<!-- Map elements -->
-    <map name="Uniform" >beast.base.inference.distribution.Uniform</map>
-    <map name="Exponential" >beast.base.inference.distribution.Exponential</map>
-    <map name="LogNormal" >beast.base.inference.distribution.LogNormalDistributionModel</map>
-    <map name="Normal" >beast.base.inference.distribution.Normal</map>
-    <map name="Poisson" >beast.base.inference.distribution.Poisson</map>
-    <map name="prior" >beast.base.inference.distribution.Prior</map>
-<!-- Adapted from https://github.com/SarahNadeau/cov-europe-bdmm/blob/master/analyses/with_hubei_migration_decrease/with_hubei_migration_decrease_scrubbed.xml -->
-<!-- Sequence data loaded from GISAID with the gisaid EPI ISLs -->
-<!-- Alignment -->
-    <alignment id="alignment" spec= "AlignmentFromFasta"
-        fileName = "$(aligned_fasta)"/>
-    <typeSet id="typeSetBDMMPrime" spec="TypeSet">
-        <typeTraitSet id="typeTraitSet" spec="TraitSetFromTaxonSet"
-            traitname="type"
-            delimiter="|"
-            takeGroup="1">
-        <taxa spec="TaxonSet" alignment="@alignment"/>
-        </typeTraitSet>
-    </typeSet>
-    <trait id="dateTrait" spec="TraitSetFromTaxonSet"
-           traitname="date"
-           dateFormat="yyyy-M-dd"
-           delimiter= "|"
-           everythingAfterLast="true">
-        <taxa spec="TaxonSet" alignment="@alignment"/>
-    </trait>
- <!-- BDMMPrime Population Model -->
-    <processLength id="originBDMMPrime" spec="RealParameter">10.0</processLength>
-    <Re id="ReSV" spec="SkylineVectorParameter"
-        timesAreAges="true" processLength="@originBDMMPrime" typeSet="@typeSetBDMMPrime">
-        <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>
-         <changeTimes id="ReRateChangeTimes" spec="RealParameter">0.123</changeTimes>
-    </Re>
-    <samplingProportion id="samplingProportionSV" spec="SkylineVectorParameter"
-                        timesAreAges="true" processLength="@originBDMMPrime" typeSet="@typeSetBDMMPrime">
-        <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>
-        <changeTimes id="samplingProportionChangeTimes" spec="RealParameter">0.123 0.205</changeTimes>
-    </samplingProportion>
-    <becomeUninfectiousRate id="becomeUninfectiousRateSV" spec="SkylineVectorParameter"
-                            typeSet="@typeSetBDMMPrime">
-        <skylineValues id="becomeUninfectiousValues" spec="RealParameter">36.5</skylineValues>
-    </becomeUninfectiousRate>
-    <migrationRate id="migrationRateSM" spec="SkylineMatrixParameter"
-                   timesAreAges="true"  processLength="@originBDMMPrime" typeSet="@typeSetBDMMPrime">
-        <skylineValues id="migrationRateValues" spec="glmprior.util.GLMLogLinear" transform="false">
-            <plate var="predictor" range="$(GLMpredictor_files)">
-                <predictor spec="RealParameterFromXSV" id="$(predictor)" fileName="$(predictor)"/>
-            </plate>
-            <parameter id="coefficientsGLM" spec="RealParameter" name="coefficients" value="0.1"/>
-            <parameter id="scaleFactorGLM" spec="RealParameter" name="scaleFactor" value="1"/>
-            <parameter id="indicatorGLM" spec="BooleanParameter" name="indicators" value="1"/>
-            <!-- <parameter id="errorTermGLM" spec="RealParameter" name="error" value="0.01" dimension="30"/> -->
-        </skylineValues>
-        <changeTimes id="migrationRateChangeTimes" spec="RealParameterFromXSV"
-                     fileName="$(GLMpredictor_changetimes)"/>
-    </migrationRate>
-    <removalProb id="removalProbSV" spec="SkylineVectorParameter" skylineValues="1.0"
-        processLength="@originBDMMPrime" typeSet="@typeSetBDMMPrime"/>
-    <startTypePriorProbs id="typeFrequencies" spec="RealParameter"
-        estimate="false" lower="0.0" upper="1.0">1.0 0.0 0.0 0.0 0.0</startTypePriorProbs>
-<!-- Site Model -->
-    <siteModel id="siteModel" spec="SiteModel" gammaCategoryCount="4">
-        <parameter id="gammaShape" name="shape" value="1.0"/>
-        <parameter name="mutationRate"  estimate="false" value="1.0"/>
-        <parameter name="proportionInvariant" estimate="false" value="0.0"/>
-        <substModel spec="HKY">
-            <kappa id="kappa" spec="RealParameter" value="2.0"/>
-            <frequencies id="empiricalFreqs" spec="Frequencies" data="@alignment"/>
-        </substModel>
-    </siteModel>
-<!-- Branch rate Model -->
-    <branchRateModel id="branchRateModel" spec="StrictClockModel">
-        <parameter id="clockRate" name="clock.rate"  estimate="false">8.0E-4</parameter>
-    </branchRateModel>
-<!-- Population Model for Tree initialiser -->
-    <popFunc id="popFunc" spec="ConstantPopulation">
-        <popSize spec="RealParameter" value="0.1"/>
-    </popFunc>
-<!-- MCMC -->
-    <run id="mcmc" spec="MCMC" chainLength="10000000" numInitializationAttempts="100">
-    <!-- State -->
+<?xml version="1.0"?>
+<beast
+    namespace="
+        :beast.base.evolution
+        :beast.base.evolution.alignment
+        :beast.base.evolution.branchratemodel
+        :beast.base.evolution.likelihood
+        :beast.base.evolution.operator
+        :beast.base.evolution.operator.kernel
+        :beast.base.evolution.sitemodel
+        :beast.base.evolution.substitutionmodel
+        :beast.base.evolution.tree
+        :beast.base.evolution.tree.coalescent
+        :beast.base.inference
+        :beast.base.inference.parameter
+        :beast.base.inference.operator.kernel
+        :bdmmprime.distribution
+        :bdmmprime.mapping
+        :bdmmprime.trajectories
+        :bdmmprime.parameterization
+        :bdmmprime.util
+        :bdmmprime.util.operators
+        :bdmmprime.util.priors
+        :feast.fileio"
+    version="2.7"
+>
+    <map name="Uniform">beast.base.inference.distribution.Uniform</map>
+    <map name="Exponential">beast.base.inference.distribution.Exponential</map>
+    <map name="LogNormal">beast.base.inference.distribution.LogNormalDistributionModel</map>
+    <map name="Normal">beast.base.inference.distribution.Normal</map>
+    <map name="prior">beast.base.inference.distribution.Prior</map>
+    <map name="AlignmentFromFasta">feast.fileio.AlignmentFromFasta</map>
+    <map name="TaxonSet">beast.base.evolution.alignment.TaxonSet</map>
+    <map name="TraitSetFromTaxonSet">feast.fileio.TraitSetFromTaxonSet</map>
+    <map name="TypeSet">bdmmprime.parameterization.TypeSet</map>
+    <map name="TypeMappedTree">bdmmprime.mapping.TypeMappedTree</map>
+    <AlignmentFromFasta id="alignment" fileName="$(msa_file)"/>
+    <TaxonSet id="taxonSet" alignment="@alignment"/>
+    <TraitSetFromTaxonSet id="typeTraitSet" traitname="type" delimiter="|" takeGroup="1" taxa="@taxonSet"/>
+    <TypeSet id="typeSet" typeTraitSet="@typeTraitSet"/>
+    <TraitSetFromTaxonSet id="dateTrait" traitname="date" dateFormat="yyyy-M-dd" delimiter="|" everythingAfterLast="true" taxa="@taxonSet"/>
+    <TypeMappedTree id="typeMappedTree" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@startTypePriorProbs" mapOnInit="false" remapOnLog="true" typeLabel="type" typeTraitSet="@typeTraitSet" untypedTree="@tree"/>
+    <run spec="MCMC" chainLength="10000000">
         <state id="state" spec="State">
-            <stateNode id="treeBDMMPrime" spec="RandomTree"
-                       taxa="@alignment"
-                       populationModel="@popFunc"
-                       trait="@dateTrait">
+            <stateNode id="tree" spec="RandomTree" taxa="@alignment" trait="@dateTrait">
+                <populationModel spec="ConstantPopulation" popSize="0.1"/>
             </stateNode>
-            <stateNode idref="originBDMMPrime"/>
-            <stateNode idref="ReValues"/>
-            <stateNode idref="samplingProportionValues"/>
-            <stateNode idref="coefficientsGLM"/>
-            <stateNode idref="scaleFactorGLM"/>
-            <stateNode idref="indicatorGLM"/>
-            <stateNode idref="kappa"/>
-            <stateNode idref="gammaShape"/>
+            <stateNode id="Re" spec="RealParameter" value="1.0 1.1 1.2 1.3 1.4 1.01 1.1 1.2 1.3 1.4"/>
+            <stateNode id="samplingProportion" spec="RealParameter" value="1.11E-5 1.2E-5 1.3E-5 1.4E-5 1.5E-5 1.1E-5 1.2E-5 1.3E-5 1.4E-5 1.5E-5 0.0 0.0 0.0 0.0 0.0"/>
+            <stateNode id="migrationRateW" spec="RealParameter" value="0"/>
+            <stateNode id="migrationRateScaler" spec="RealParameter" value="0.1"/>
+            <stateNode id="processLength" spec="RealParameter" value="10.0"/>
+            <stateNode id="gammaShape" spec="RealParameter" value="1.0"/>
+            <stateNode id="kappa" spec="RealParameter" value="2.0"/>
         </state>
-    <!-- Posterior Distribution -->
         <distribution id="posterior" spec="CompoundDistribution">
-             <!-- Tree Likelihood -->
             <distribution id="likelihood" spec="CompoundDistribution" useThreads="true">
-                <distribution id="treeLikelihood" spec="ThreadedTreeLikelihood"
-                              data="@alignment"
-                              tree="@treeBDMMPrime"
-                              siteModel="@siteModel"
-                              branchRateModel="@branchRateModel"/>
+                <distribution id="treeLikelihood" spec="ThreadedTreeLikelihood" data="@alignment" tree="@tree">
+                    <siteModel spec="SiteModel" gammaCategoryCount="4" shape="@gammaShape" mutationRate="1.0">
+                        <substModel spec="HKY" kappa="@kappa">
+                            <frequencies spec="Frequencies" data="@alignment"/>
+                        </substModel>
+                    </siteModel>
+                    <branchRateModel spec="StrictClockModel" clock.rate="8.0E-4"/>
+                </distribution>
             </distribution>
-            <!-- Prior distribution -->
             <distribution id="prior" spec="CompoundDistribution">
+                <distribution id="BDMMPrime" spec="BirthDeathMigrationDistribution" tree="@tree" conditionOnSurvival="true" typeTraitSet="@typeTraitSet">
+                    <parameterization id="EpiBDMMPrimeParameterization" spec="EpiParameterization" processLength="@processLength" typeSet="@typeSet">
+                        <Re id="ReSP" spec="SkylineVectorParameter" skylineValues="@Re" changeTimes="0.123" timesAreAges="true" processLength="@processLength" typeSet="@typeSet"/>
+                        <samplingProportion id="samplingProportionSP" spec="SkylineVectorParameter" skylineValues="@samplingProportion" changeTimes="0.123 0.205" timesAreAges="true" processLength="@processLength" typeSet="@typeSet"/>
+                        <becomeUninfectiousRate spec="SkylineVectorParameter" skylineValues="36.5" typeSet="@typeSet"/>
+                        <migrationRate id="migrationRateSP" spec="SkylineMatrixParameter" timesAreAges="true" processLength="@processLength" typeSet="@typeSet">
+                            <skylineValues spec="glmprior.util.GLMLogLinear" coefficients="@migrationRateW" scaleFactor="@migrationRateScaler" transform="false">
+                                <plate var="predictorFile" range="$(predictorFiles)">
+                                    <predictor spec="RealParameterFromXSV" fileName="$(predictorFile)"/>
+                                </plate>
+                                <indicators spec="BooleanParameter" value="1"/>
+                            </skylineValues>
+                            <changeTimes spec="RealParameterFromXSV" fileName="$(changeTimesFile)"/>
+                        </migrationRate>
+                        <removalProb spec="SkylineVectorParameter" skylineValues="1.0" typeSet="@typeSet"/>
+                    </parameterization>
+                    <startTypePriorProbs id="startTypePriorProbs" spec="RealParameter" value="1.0 0.0 0.0 0.0 0.0"/>
+                </distribution>
-                <!-- BDMM-Prime tree prior distribution -->
-                <distribution id="BDMMPrime" spec="BirthDeathMigrationDistribution"
-                              tree="@treeBDMMPrime"
-                              conditionOnSurvival="true"
-                              finalSampleOffset="0.0"
-                              typeTraitSet="@typeTraitSet"
-                              startTypePriorProbs="@typeFrequencies">
-                    <!-- Parameterization BDMM-Prime -->
-                    <parameterization id="EpiBDMMPrimeParameterization" spec="EpiParameterization"
-                                      processLength="@originBDMMPrime"
-                                      Re="@ReSV"
-                                      samplingProportion="@samplingProportionSV"
-                                      becomeUninfectiousRate="@becomeUninfectiousRateSV"
-                                      migrationRate="@migrationRateSM"
-                                      removalProb="@removalProbSV"
-                                      typeSet="@typeSetBDMMPrime"/>
-                </distribution>
-            <!-- Priors on parameters -->
-            <!-- BDMMPrime parameters priors -->
-                <prior id="originBDMMPrimePrior" name="distribution" x="@originBDMMPrime">
+                <prior name="distribution" x="@processLength">
                     <LogNormal name="distr" M="-1.0" S="0.2"/>
                 </prior>
-                <!-- Reproductive number Prior -->
-                <distribution id="RePrior" spec="SmartZeroExcludingPrior" x="@ReValues">
+                <distribution spec="SmartZeroExcludingPrior" x="@Re">
                     <LogNormal name="distr" M="0.8" S="0.5"/>
                 </distribution>
-                <!-- Prior for sampling proportion for China -->
-                <distribution id="spChinaE2Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
-                    classesToExclude="1.2E-5 1.3E-5 1.4E-5 1.5E-5">
+                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.2E-5 1.3E-5 1.4E-5 1.5E-5">
                     <Uniform name="distr" lower="0" upper="0.15"/>
                 </distribution>
-                 <!-- Prior for sampling proportion for France -->
-                <distribution id="spFranceE1Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
-                    classesToExclude="1.1E-5 1.3E-5 1.4E-5 1.5E-5">
+                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.3E-5 1.4E-5 1.5E-5">
                     <Uniform name="distr" lower="0" upper="0.093"/>
                 </distribution>
-                <!-- Prior for sampling proportion for Germany Epoch -->
-                <distribution id="spGermanyE1Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
-                    classesToExclude="1.1E-5 1.2E-5 1.4E-5 1.5E-5">
+                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.4E-5 1.5E-5">
                     <Uniform name="distr" lower="0" upper="0.10"/>
                 </distribution>
-                <!-- Prior for sampling proportion for Italy -->
-                <distribution id="spItalyE1Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
-                    classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.5E-5">
+                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.5E-5">
                     <Uniform name="distr" lower="0" upper="0.005"/>
                 </distribution>
-                <!-- Prior for sampling proportion for OtherEuropean -->
-                <distribution id="spOEE1Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
-                    classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.4E-5">
+                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.4E-5">
                     <Uniform name="distr" lower="0" upper="0.057"/>
                 </distribution>
-            <!-- Migration rate GLM Prior -->
-                <!-- <prior id="migRatePrior" name="distribution" x="@migrationRateValues">
-                    <Uniform id="Uniform.migRate" name="distr" lower="0.0" upper="50.0"/>
-                </prior>  -->
-<!--                  <prior id="migRatePrior" name="distribution" x="@migrationRateValues">
-                    <LogNormal name="distr" M="0" S="1.5"/>
-                </prior> -->
-                <prior id="coefficientsPrior" name="distribution" x="@coefficientsGLM">
-                    <Normal name="distr">
-                        <parameter spec="RealParameter" estimate="false" name="mean">0.0</parameter>
-                        <parameter spec="RealParameter" estimate="false" name="sigma">1.0</parameter>
-                    </Normal>
-                </prior>
-                <prior id="scaleFactorPrior" name="distribution" x="@scaleFactorGLM">
-                    <LogNormal name="distr">
-                        <parameter spec="RealParameter" estimate="false" name="M">0.0</parameter>
-                        <parameter spec="RealParameter" estimate="false" name="S">0.8</parameter>
-                    </LogNormal>
+                <plate var="n" range="$(layersRange)">
+                    <prior name="distribution" x="@migrationW$(n)">
+                        <Normal name="distr" mean="0.0" sigma="1.0"/>
+                    </prior>
+                </plate>
+                <prior name="distribution" x="@gammaShape">
+                    <Exponential name="distr" mean="0.5"/>
                 </prior>
-        <!--         <prior id="nonZeroIndicatorGLMPrior" name="distribution">
-                    <x id="indicatorSumGLM" spec="Sum" arg="@indicatorGLM"/>
-                    <Poisson name="distr" lambda='0.693'/>
-                </prior> -->
-            <!-- Substitution model parameter priors -->
-                <prior id="GammaShapePrior" name="distribution" x="@gammaShape">
-                    <Exponential name="distr">
-                        <parameter spec="RealParameter" estimate="false" name="mean">0.5</parameter>
-                    </Exponential>
-                </prior>
                 <prior id="KappaPrior" name="distribution" x="@kappa">
-                    <LogNormal name="distr">
-                        <parameter spec="RealParameter" estimate="false" name="M">1.0</parameter>
-                        <parameter spec="RealParameter" estimate="false" name="S">1.25</parameter>
-                    </LogNormal>
+                    <LogNormal name="distr" M="1.0" S="1.25"/>
                 </prior>
             </distribution>
         </distribution>
-    <!-- Operators -->
-        <!-- Tree operators -->
-        <operator id="BDMMPrimeTreeRootScaler" spec="BactrianScaleOperator" tree="@treeBDMMPrime"
-            rootOnly="true" scaleFactor="0.25"  weight="5.0"/>
-        <operator id="BDMMPrimeUniformOperator" spec="BactrianNodeOperator" tree="@treeBDMMPrime"
-            weight="30.0"/>
-        <operator id="BDMMPrimeSubtreeSlideScaler" spec="BactrianSubtreeSlide" tree="@treeBDMMPrime"
-            weight="15.0"/>
-        <operator id="BDMMPrimeNarrow" spec="Exchange" tree="@treeBDMMPrime"
-            weight="15.0"/>
-        <operator id="BDMMPrimeWide" spec="Exchange" tree="@treeBDMMPrime"
-            isNarrow="false" weight="3.0"/>
-        <operator id="BDMMPrimeWilsonBalding" spec="WilsonBalding" tree="@treeBDMMPrime"
-            weight="3.0"/>
-        <operator id="BDMMPrimeBICEPSEpochTop" spec="EpochFlexOperator" tree="@treeBDMMPrime"
-            scaleFactor="0.1" weight="2.0"/>
-        <operator id="BDMMPrimeBICEPSEpochAll" spec="EpochFlexOperator" tree="@treeBDMMPrime"
-            fromOldestTipOnly="false" scaleFactor="0.1" weight="2.0"/>
-        <operator id="BDMMPrimeBICEPSTreeFlex" spec="TreeStretchOperator" tree="@treeBDMMPrime"
-            scaleFactor="0.01" weight="2.0"/>
-        <!-- Population model operators -->
-        <operator id="originBDMMPrimeScaler" spec="BactrianScaleOperator" parameter="@originBDMMPrime"
-            scaleFactor="0.25" weight="3.0" />
-        <operator id="ReScaler" spec="SmartScaleOperator" parameter="@ReValues" scaleFactor="0.25"
-                weight="10.0" />
-<!--         <operator id="ReScalerAll" spec="BactrianScaleOperator" parameter="@ReValues" scaleFactor="0.25"
-                weight="3.0" scaleAll="true" /> -->
-        <operator id="samplingProportionScaler" spec="SmartScaleOperator" parameter="@samplingProportionValues"
-                weight="3.0" />
-        <!-- <operator id="scaleFactorGLMScaler" spec="BactrianScaleOperator" parameter="@scaleFactorGLM" scaleFactor="0.25" weight="3.0" /> -->
-        <operator id="coefficientsGLMScaler" spec="BactrianRandomWalkOperator" parameter="@coefficientsGLM"
-            weight="5.0" scaleFactor="0.1"/>
-         <operator id="AVNMOperator" spec="beast.base.evolution.operator.kernel.AdaptableVarianceMultivariateNormalOperator" weight="5.0"
-            coefficient="1.0"
-            scaleFactor="0.5"
-            beta="0.05"
-            initial="800"
-            burnin="400"
-            every="1">
-            <transformations spec="beast.base.inference.operator.kernel.Transform$NoTransform">
-                <f idref="coefficientsGLM"/>
-            </transformations>
+        <operator spec="BactrianScaleOperator" tree="@tree" rootOnly="true" scaleFactor="0.25"  weight="5.0"/>
+        <operator spec="BactrianNodeOperator" tree="@tree" weight="30.0"/>
+        <operator spec="BactrianSubtreeSlide" tree="@tree" weight="15.0"/>
+        <operator spec="Exchange" tree="@tree" weight="15.0"/>
+        <operator spec="Exchange" tree="@tree" isNarrow="false" weight="3.0"/>
+        <operator spec="WilsonBalding" tree="@tree" weight="3.0"/>
+        <operator spec="EpochFlexOperator" tree="@tree" scaleFactor="0.1" weight="2.0"/>
+        <operator spec="EpochFlexOperator" tree="@tree" fromOldestTipOnly="false" scaleFactor="0.1" weight="2.0"/>
+        <operator spec="TreeStretchOperator" tree="@tree" scaleFactor="0.01" weight="2.0"/>
+        <operator spec="BactrianScaleOperator" parameter="@processLength" scaleFactor="0.25" weight="3.0"/>
+        <operator spec="SmartScaleOperator" parameter="@Re" scaleFactor="0.25" weight="10.0"/>
+        <operator spec="SmartScaleOperator" parameter="@samplingProportion" weight="3.0"/>
+        <operator spec="BactrianRandomWalkOperator" parameter="@migrationRateW" weight="5.0" scaleFactor="0.1"/>
+        <operator spec="AdaptableVarianceMultivariateNormalOperator" weight="5.0" coefficient="1.0" scaleFactor="0.5" beta="0.05" initial="800" burnin="400" every="1">
+            <transformations spec="Transform$NoTransform" f="@migrationRateW"/>
         </operator>
+        <operator spec="BactrianScaleOperator" parameter="@gammaShape" weight="1.0"/>
+        <operator spec="BactrianScaleOperator" parameter="@kappa" weight="1.0"/>
-       <!--  <operator id="indicatorParamGLMFlip" spec="BitFlipOperator" parameter="@indicatorGLM"
-            weight="10.0" uniform="false" />
-        <operator id="indicatorSwap" spec="glmprior.operator.ExtendedSwapOperator" boolparameter="@indicatorGLM" weight="5.0" />
-        <operator id="indicatorParamGLMPick" spec="glmprior.operator.PickIndicatorOperator"
-         parameter="@indicatorGLM" weight="3.0" />
-        <operator id="BSSVSGLMoperator" spec="glmprior.operator.BitFlipBSSVSOperator" indicator="@indicatorGLM" mu="@scaleFactorGLM" weight="10"/>
-        <operator id="multiSwapOperator" spec="glmprior.operator.MultiSwapOperator" boolparameter="@indicatorGLM" parameter="@coefficientsGLM" weight="10.0" />
-        <operator id="JointSwapGLM1" spec="JointOperator" weight="3.0">
-            <operator idref="indicatorSwap"/>
-            <operator idref="AVNMOperator"/>
-        </operator>
-        <operator id="JointSwapGLM2" spec="JointOperator" weight="3.0">
-            <operator idref="coefficientsGLMScaler"/>
-            <operator idref="scaleFactorGLMScaler"/>
-        </operator>
- -->
-        <!-- <operator id="errorTermGLMScaler" spec="BactrianScaleOperator" parameter="@errorTermGLM"
-            weight="5.0" upper="20.0"/> -->
-        <!-- Substitution model operators -->
-        <operator id="gammaShapeScaler" spec="BactrianScaleOperator" parameter="@gammaShape"
-             weight="1.0"/>
-        <operator id="KappaScaler" spec="BactrianScaleOperator" parameter="@kappa"
-             weight="1.0"/>
-    <!-- Loggers -->
-        <logger id="tracelog" spec="Logger" fileName="$(filebase).log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
+        <logger spec="Logger" fileName="MCMC.log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
             <log idref="posterior"/>
             <log idref="likelihood"/>
             <log idref="prior"/>
-            <log idref="treeLikelihood"/>
-            <log idref="gammaShape"/>
-            <log idref="kappa"/>
-            <log id="TreeHeight" spec="TreeStatLogger" tree="@treeBDMMPrime"/>
-            <log id="typedTreeStats" spec="TypedTreeStatsLogger" includeRootEdge="true"
-                typeLabel="type" typeSet="@typeSetBDMMPrime">
-                <typedTree id="typeMappedTree" spec="TypeMappedTree" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@typeFrequencies" mapOnInit="false" remapOnLog="true" typeLabel="type" typeTraitSet="@typeTraitSet" untypedTree="@treeBDMMPrime"/>
-            </log>
-            <log idref="originBDMMPrime"/>
-            <log idref="ReSV"/>
-            <log idref="becomeUninfectiousRateSV"/>
-            <log idref="samplingProportionSV"/>
-            <log idref="migrationRateSM"/>
-            <log idref="coefficientsGLM"/>
-            <log idref="scaleFactorGLM"/>
-            <log idref="indicatorGLM"/>
-            <log id="coefbyindGLM" spec="ExpCalculator" value="coefficientsGLM*indicatorGLM" useCaching="false">
-                <arg idref="coefficientsGLM"/>
-                <arg idref="indicatorGLM"/>
-            </log>
-            <plate var="predictor" range="$(GLMpredictor_files)">
-                <log idref="$(predictor)"/>
-            </plate>
-            <!-- <log idref="errorTermGLM"/> -->
-            <log idref="removalProbSV"/>
-            <log idref="typeFrequencies"/>
-        </logger>
-        <logger id="screenlog" spec="Logger" logEvery="1000">
-            <log idref="posterior"/>
-            <log arg="@posterior" id="ESS_posterior" spec="util.ESS"/>
-            <log idref="likelihood"/>
-            <log arg="@likelihood" id="ESS_likelihood" spec="util.ESS"/>
-            <log idref="prior"/>
-            <log arg="@prior" id="ESS_prior" spec="util.ESS"/>
             <log idref="BDMMPrime"/>
-            <log arg="@BDMMPrime" id="ESS_BDMMPrime" spec="util.ESS"/>
-        </logger>
-        <logger id="treelog" spec="Logger" fileName="$(filebase).trees" logEvery="1000" mode="tree">
-            <log id="TreeWithMetaDataLogger" spec="TreeWithMetaDataLogger" tree="@treeBDMMPrime"/>
+            <log idref="gammaShape"/>
+            <log idref="kappa"/>
+            <log idref="processLength"/>
+            <log idref="ReSP"/>
+            <log idref="samplingProportionSP"/>
+            <log idref="migrationRateSP"/>
+            <log idref="migrationRateW"/>
+            <log idref="migrationRateScaler"/>
         </logger>
-        <logger id="typedTreeLogger" spec="OptionalLogger" enableLogger="true"
-            fileName="$(filebase).typed.trees" logEvery="10000" mode="tree">
+        <logger spec="Logger" fileName="typedTrees.trees" logEvery="10000" mode="tree">
             <log idref="typeMappedTree"/>
         </logger>
-        <logger id="nodeTypedTreeLogger.t:eubdmm_alignment" spec="OptionalLogger" enableLogger="true"
-            fileName="$(filebase).typed.node.trees" logEvery="10000" mode="tree">
-            <log id="nodeTypedTree" spec="TypedNodeTreeLogger" typedTree="@typeMappedTree"/>
+        <logger spec="Logger" fileName="TypedNodeTrees.trees" logEvery="10000" mode="tree">
+            <log spec="TypedNodeTreeLogger" typedTree="@typeMappedTree"/>
         </logger>
-        <logger id="trajLogger" spec="OptionalLogger" enableLogger="true" fileName="$(filebase).traj" logEvery="10000">
-            <log id="typedTraj" spec="SampledTrajectory" bdmmDistrib="@BDMMPrime"
-                startTypePriorProbs="@typeFrequencies" typeMappedTree="@typeMappedTree" useTauLeaping="true"/>
+        <logger spec="Logger" fileName="trajectories.csv" logEvery="10000">
+            <log spec="SampledTrajectory" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@startTypePriorProbs" typeMappedTree="@typeMappedTree" useTauLeaping="true"/>
         </logger>
-        <operatorschedule id="OperatorSchedule" spec="OperatorSchedule"/>
     </run>
 </beast>

bella_companion/eucovid/beast_configs/MLP.xml CHANGED Viewed

@@ -1,34 +1,27 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<beast
+<?xml version="1.0"?>
+<beast
     namespace="
-        beast.base.inference
-        :beast.base.inference.parameter
+        :beast.base.evolution
+        :beast.base.evolution.alignment
         :beast.base.evolution.branchratemodel
-        :beast.base.evolution.substitutionmodel
-        :beast.base.evolution.sitemodel
-        :beast.base.evolution.tree.coalescent
-        :beast.base.evolution.tree
         :beast.base.evolution.likelihood
-        :beast.base.evolution.alignment
         :beast.base.evolution.operator
         :beast.base.evolution.operator.kernel
+        :beast.base.evolution.sitemodel
+        :beast.base.evolution.substitutionmodel
+        :beast.base.evolution.tree
+        :beast.base.evolution.tree.coalescent
+        :beast.base.inference
+        :beast.base.inference.parameter
         :beast.base.inference.operator.kernel
-        :beast.base.inference.operator
-        :beast.base.math.distributions
-        :beast.base.evolution
-        :bdmmprime.util.operators
-        :bdmmprime.util.priors
         :bdmmprime.distribution
-        :bdmmprime.parameterization
         :bdmmprime.mapping
-        :bdmmprime.util
         :bdmmprime.trajectories
-        :feast
-        :feast.parameter
-        :feast.fileio
-        :feast.function
-        :feast.expressions"
-    required="BEAST.base v2.7.7:BDMM-Prime v2.2.2"
+        :bdmmprime.parameterization
+        :bdmmprime.util
+        :bdmmprime.util.operators
+        :bdmmprime.util.priors
+        :feast.fileio"
     version="2.7"
 >
     <map name="Uniform">beast.base.inference.distribution.Uniform</map>
@@ -36,81 +29,67 @@
     <map name="LogNormal">beast.base.inference.distribution.LogNormalDistributionModel</map>
     <map name="Normal">beast.base.inference.distribution.Normal</map>
     <map name="prior">beast.base.inference.distribution.Prior</map>
     <map name="AlignmentFromFasta">feast.fileio.AlignmentFromFasta</map>
-	<map name="TraitSetFromTaxonSet">feast.fileio.TraitSetFromTaxonSet</map>
-	<map name="TypeSet">bdmmprime.parameterization.TypeSet</map>
-    <alignment id="alignment" spec="AlignmentFromFasta" fileName="$(msa_file)"/>
-    <TaxonSet id="TaxonSet" spec="TaxonSet" alignment="@alignment"/>
-    <TraitSetFromTaxonSet id="typeTraitSet" traitname="type" delimiter="|" takeGroup="1" taxa="@TaxonSet"/>
-    <TraitSetFromTaxonSet id="dateTraitSet" traitname="date" dateFormat="yyyy-M-dd" delimiter= "|" everythingAfterLast="true" taxa="@TaxonSet"/>
-    <typeSet id="typeSet" spec="TypeSet" typeTraitSet="@typeTraitSet"/>
-    <parameter id="processLength" spec="RealParameter" value="1.0"/>
-    <Re id="ReSP" spec="SkylineVectorParameter" timesAreAges="true" processLength="@processLength" typeSet="@typeSet">
-        <skylineValues id="Re" spec="RealParameter" dimension="$(ReDimension)" value="1.0"/>
-        <changeTimes spec="RealParameterFromXSV" fileName="$(changeTimesFile)"/>
-    </Re>
-    <samplingProportion id="samplingProportionSP" spec="SkylineVectorParameter" timesAreAges="true" processLength="@processLength" typeSet="@typeSet" changeTimes="0.123 0.205">
-        <skylineValues id="samplingProportion" spec="RealParameter" value="1.11E-5 1.2E-5 1.3E-5 1.4E-5 1.5E-5 1.1E-5 1.2E-5 1.3E-5 1.4E-5 1.5E-5 0.0 0.0 0.0 0.0 0.0"/>
-    </samplingProportion>
-    <becomeUninfectiousRate id="becomeUninfectiousRateSP" spec="SkylineVectorParameter" typeSet="@typeSet" skylineValues="36.5"/>
-    <migrationRate id="migrationRateSP" spec="SkylineMatrixParameter" timesAreAges="true" processLength="@processLength" typeSet="@typeSet">
-        <skylineValues id="migrationRate" spec="bella.BayesMLP" nodes="$(nodes)">
-            <plate var="predictorFile" range="$(predictorFiles)">
-                <predictor spec="RealParameterFromXSV" fileName="$(predictorFile)"/>
-            </plate>
+    <map name="TaxonSet">beast.base.evolution.alignment.TaxonSet</map>
+    <map name="TraitSetFromTaxonSet">feast.fileio.TraitSetFromTaxonSet</map>
+    <map name="TypeSet">bdmmprime.parameterization.TypeSet</map>
+    <map name="TypeMappedTree">bdmmprime.mapping.TypeMappedTree</map>
+    <AlignmentFromFasta id="alignment" fileName="$(msa_file)"/>
+    <TaxonSet id="taxonSet" alignment="@alignment"/>
+    <TraitSetFromTaxonSet id="typeTraitSet" traitname="type" delimiter="|" takeGroup="1" taxa="@taxonSet"/>
+    <TypeSet id="typeSet" typeTraitSet="@typeTraitSet"/>
+    <TraitSetFromTaxonSet id="dateTrait" traitname="date" dateFormat="yyyy-M-dd" delimiter="|" everythingAfterLast="true" taxa="@taxonSet"/>
+    <TypeMappedTree id="typeMappedTree" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@startTypePriorProbs" mapOnInit="false" remapOnLog="true" typeLabel="type" typeTraitSet="@typeTraitSet" untypedTree="@tree"/>
+    <run spec="MCMC" chainLength="10000000">
+        <state id="state" spec="State">
+            <stateNode id="tree" spec="RandomTree" taxa="@alignment" trait="@dateTrait">
+                <populationModel spec="ConstantPopulation" popSize="0.1"/>
+            </stateNode>
+            <stateNode id="Re" spec="RealParameter" value="1.0 1.1 1.2 1.3 1.4 1.01 1.1 1.2 1.3 1.4"/>
+            <stateNode id="samplingProportion" spec="RealParameter" value="1.11E-5 1.2E-5 1.3E-5 1.4E-5 1.5E-5 1.1E-5 1.2E-5 1.3E-5 1.4E-5 1.5E-5 0.0 0.0 0.0 0.0 0.0"/>
             <plate var="n" range="$(layersRange)">
-                <weights idref="migrationW$(n)"/>
+                <stateNode spec="RealParameter" id="migrationRateW$(n)" value="0"/>
             </plate>
-        </skylineValues>
-        <changeTimes spec="RealParameterFromXSV" fileName="$(changeTimesFile)"/>
-    </migrationRate>
-    <removalProb id="removalProbSP" spec="SkylineVectorParameter" skylineValues="1.0" processLength="@processLength" typeSet="@typeSet"/>
-    <startTypePriorProbs id="typeFrequencies" spec="RealParameter" value="1.0 0.0 0.0 0.0 0.0"/>
-    <siteModel id="siteModel" spec="SiteModel" gammaCategoryCount="4" proportionInvariant="0.0">
-        <parameter id="gammaShape" name="shape" value="1.0"/>
-        <substModel spec="HKY">
-            <kappa id="kappa" spec="RealParameter" value="2.0"/>
-            <frequencies id="empiricalFreqs" spec="Frequencies" data="@alignment"/>
-        </substModel>
-    </siteModel>
-    <branchRateModel id="branchRateModel" spec="StrictClockModel" clock.rate="8.0E-4"/>
-    <popFunc id="popFunc" spec="ConstantPopulation" popSize="0.1"/>
-    <run spec="MCMC" chainLength="10000000" numInitializationAttempts="100">
-        <state spec="State" storeEvery="5000">
-            <stateNode id="treeBDMMPrime" spec="RandomTree" taxa="@alignment" populationModel="@popFunc" trait="@dateTraitSet"/>
-            <stateNode idref="processLength"/>
-            <stateNode idref="Re"/>
-            <stateNode idref="samplingProportion"/>
-            <plate var="n" range="$(layersRange)">
-                <stateNode spec="RealParameter" id="migrationW$(n)" value="0"/>
-            </plate>
-            <stateNode idref="kappa"/>
-            <stateNode idref="gammaShape"/>
+            <stateNode id="processLength" spec="RealParameter" value="10.0"/>
+            <stateNode id="gammaShape" spec="RealParameter" value="1.0"/>
+            <stateNode id="kappa" spec="RealParameter" value="2.0"/>
         </state>
         <distribution id="posterior" spec="CompoundDistribution">
             <distribution id="likelihood" spec="CompoundDistribution" useThreads="true">
-                <distribution id="treeLikelihood" spec="ThreadedTreeLikelihood" data="@alignment" tree="@treeBDMMPrime" siteModel="@siteModel" branchRateModel="@branchRateModel"/>
+                <distribution id="treeLikelihood" spec="ThreadedTreeLikelihood" data="@alignment" tree="@tree">
+                    <siteModel spec="SiteModel" gammaCategoryCount="4" shape="@gammaShape" mutationRate="1.0">
+                        <substModel spec="HKY" kappa="@kappa">
+                            <frequencies spec="Frequencies" data="@alignment"/>
+                        </substModel>
+                    </siteModel>
+                    <branchRateModel spec="StrictClockModel" clock.rate="8.0E-4"/>
+                </distribution>
             </distribution>
             <distribution id="prior" spec="CompoundDistribution">
-                <distribution id="BDMMPrime" spec="BirthDeathMigrationDistribution" tree="@treeBDMMPrime" conditionOnSurvival="true" finalSampleOffset="0.0" typeTraitSet="@typeTraitSet" startTypePriorProbs="@typeFrequencies">
-                    <parameterization id="EpiBDMMPrimeParameterization" spec="EpiParameterization" processLength="@processLength" Re="@ReSP" samplingProportion="@samplingProportionSP" becomeUninfectiousRate="@becomeUninfectiousRateSP" migrationRate="@migrationRateSP" removalProb="@removalProbSP" typeSet="@typeSet"/>
-                </distribution>
+                <distribution id="BDMMPrime" spec="BirthDeathMigrationDistribution" tree="@tree" conditionOnSurvival="true" typeTraitSet="@typeTraitSet">
+                    <parameterization id="EpiBDMMPrimeParameterization" spec="EpiParameterization" processLength="@processLength" typeSet="@typeSet">
+                        <Re id="ReSP" spec="SkylineVectorParameter" skylineValues="@Re" changeTimes="0.123" timesAreAges="true" processLength="@processLength" typeSet="@typeSet" />
+                        <samplingProportion id="samplingProportionSP" spec="SkylineVectorParameter" skylineValues="@samplingProportion" changeTimes="0.123 0.205" timesAreAges="true" processLength="@processLength" typeSet="@typeSet"/>
+                        <becomeUninfectiousRate spec="SkylineVectorParameter" skylineValues="36.5" typeSet="@typeSet"/>
+                        <migrationRate id="migrationRateSP" spec="SkylineMatrixParameter" timesAreAges="true" processLength="@processLength" typeSet="@typeSet">
+                            <skylineValues id="migrationRate" spec="bella.BayesMLP" nodes="$(nodes)">
+                                <plate var="predictorFile" range="$(predictorFiles)">
+                                    <predictor spec="RealParameterFromXSV" fileName="$(predictorFile)"/>
+                                </plate>
+                                <plate var="n" range="$(layersRange)">
+                                    <weights idref="migrationRateW$(n)"/>
+                                </plate>
+                            </skylineValues>
+                            <changeTimes spec="RealParameterFromXSV" fileName="$(changeTimesFile)"/>
+                        </migrationRate>
+                        <removalProb spec="SkylineVectorParameter" skylineValues="1.0" typeSet="@typeSet"/>
+                    </parameterization>
+                    <startTypePriorProbs id="startTypePriorProbs" spec="RealParameter" value="1.0 0.0 0.0 0.0 0.0"/>
+                </distribution>
                 <prior name="distribution" x="@processLength">
                     <LogNormal name="distr" M="-1.0" S="0.2"/>
@@ -134,64 +113,58 @@
                     <Uniform name="distr" lower="0" upper="0.057"/>
                 </distribution>
                 <plate var="n" range="$(layersRange)">
-                    <prior name="distribution" x="@migrationW$(n)">
+                    <prior name="distribution" x="@migrationRateW$(n)">
                         <Normal name="distr" mean="0.0" sigma="1.0"/>
                     </prior>
                 </plate>
                 <prior name="distribution" x="@gammaShape">
                     <Exponential name="distr" mean="0.5"/>
                 </prior>
-                <prior name="distribution" x="@kappa">
+                <prior id="KappaPrior" name="distribution" x="@kappa">
                     <LogNormal name="distr" M="1.0" S="1.25"/>
                 </prior>
             </distribution>
         </distribution>
-        <operator spec="BactrianScaleOperator" tree="@treeBDMMPrime" rootOnly="true" scaleFactor="0.25"  weight="5.0"/>
-        <operator spec="BactrianNodeOperator" tree="@treeBDMMPrime" weight="30.0"/>
-        <operator spec="BactrianSubtreeSlide" tree="@treeBDMMPrime" weight="15.0"/>
-        <operator spec="Exchange" tree="@treeBDMMPrime" weight="15.0"/>
-        <operator spec="Exchange" tree="@treeBDMMPrime" isNarrow="false" weight="3.0"/>
-        <operator spec="WilsonBalding" tree="@treeBDMMPrime" weight="3.0"/>
-        <operator spec="EpochFlexOperator" tree="@treeBDMMPrime" scaleFactor="0.1" weight="2.0"/>
-        <operator spec="EpochFlexOperator" tree="@treeBDMMPrime" fromOldestTipOnly="false" scaleFactor="0.1" weight="2.0"/>
-        <operator spec="TreeStretchOperator" tree="@treeBDMMPrime" scaleFactor="0.01" weight="2.0"/>
-        <operator spec="BactrianScaleOperator" parameter="@processLength" scaleFactor="0.25" weight="3.0" />
-        <operator spec="BactrianScaleOperator" parameter="@Re" scaleFactor="0.25" weight="10.0"/>
-        <operator spec="SmartScaleOperator" parameter="@samplingProportion" weight="3.0" />
+        <operator spec="BactrianScaleOperator" tree="@tree" rootOnly="true" scaleFactor="0.25"  weight="5.0"/>
+        <operator spec="BactrianNodeOperator" tree="@tree" weight="30.0"/>
+        <operator spec="BactrianSubtreeSlide" tree="@tree" weight="15.0"/>
+        <operator spec="Exchange" tree="@tree" weight="15.0"/>
+        <operator spec="Exchange" tree="@tree" isNarrow="false" weight="3.0"/>
+        <operator spec="WilsonBalding" tree="@tree" weight="3.0"/>
+        <operator spec="EpochFlexOperator" tree="@tree" scaleFactor="0.1" weight="2.0"/>
+        <operator spec="EpochFlexOperator" tree="@tree" fromOldestTipOnly="false" scaleFactor="0.1" weight="2.0"/>
+        <operator spec="TreeStretchOperator" tree="@tree" scaleFactor="0.01" weight="2.0"/>
+        <operator spec="BactrianScaleOperator" parameter="@processLength" scaleFactor="0.25" weight="3.0"/>
+        <operator spec="SmartScaleOperator" parameter="@Re" scaleFactor="0.25" weight="10.0"/>
+        <operator spec="SmartScaleOperator" parameter="@samplingProportion" weight="3.0"/>
         <plate var="n" range="$(layersRange)">
-            <operator spec="BactrianRandomWalkOperator" parameter="@migrationW$(n)" weight="5.0"/>
+            <operator spec="BactrianRandomWalkOperator" parameter="@migrationRateW$(n)" weight="5.0"/>
         </plate>
-        <operator id="gammaShapeScaler" spec="BactrianScaleOperator" parameter="@gammaShape" weight="1.0"/>
-        <operator id="KappaScaler" spec="BactrianScaleOperator" parameter="@kappa" weight="1.0"/>
-        <operatorschedule spec="OperatorSchedule"/>
+        <operator spec="BactrianScaleOperator" parameter="@gammaShape" weight="1.0"/>
+        <operator spec="BactrianScaleOperator" parameter="@kappa" weight="1.0"/>
         <logger spec="Logger" fileName="MCMC.log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
             <log idref="posterior"/>
             <log idref="likelihood"/>
             <log idref="prior"/>
             <log idref="BDMMPrime"/>
+            <log idref="gammaShape"/>
+            <log idref="kappa"/>
+            <log idref="processLength"/>
             <log idref="ReSP"/>
             <log idref="samplingProportionSP"/>
             <log idref="migrationRateSP"/>
             <log idref="migrationRate"/>
-            <log spec="TypedTreeStatsLogger" includeRootEdge="true" typeLabel="type" typeSet="@typeSet">
-                <typedTree id="typeMappedTree" spec="TypeMappedTree" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@typeFrequencies" mapOnInit="false" remapOnLog="true" typeLabel="type" typeTraitSet="@typeTraitSet" untypedTree="@treeBDMMPrime"/>
-            </log>
         </logger>
-        <logger spec="OptionalLogger" enableLogger="true" fileName="TypedTree.trees" logEvery="10000" mode="tree">
+        <logger spec="Logger" fileName="typedTrees.trees" logEvery="100000" mode="tree">
             <log idref="typeMappedTree"/>
         </logger>
-        <logger spec="OptionalLogger" enableLogger="true" fileName="TypedNodeTree.trees" logEvery="10000" mode="tree">
+        <logger spec="Logger" fileName="TypedNodeTrees.trees" logEvery="100000" mode="tree">
             <log spec="TypedNodeTreeLogger" typedTree="@typeMappedTree"/>
         </logger>
-        <logger spec="OptionalLogger" enableLogger="true" fileName="trajectory.traj" logEvery="10000">
-            <log spec="SampledTrajectory" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@typeFrequencies" typeMappedTree="@typeMappedTree" useTauLeaping="true"/>
+        <logger spec="Logger" fileName="trajectories.csv" logEvery="100000">
+            <log spec="SampledTrajectory" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@startTypePriorProbs" typeMappedTree="@typeMappedTree" useTauLeaping="true"/>
         </logger>
     </run>
 </beast>

bella_companion/eucovid/run_beast.py CHANGED Viewed

@@ -21,16 +21,16 @@ def run_beast():
     all_predictor_files = ",".join(glob(str(predictors_dir / "all" / "*.tsv")))
     all_predictors_data = " ".join(
         [
-            f"-D aligned_fasta={msa_file}",
-            f"-D GLMpredictor_changetimes={predictors_dir / 'changetimes_all_7e.tsv'}",
-            f"-D GLMpredictor_files={all_predictor_files}",
+            f"-D msa_file={msa_file}",
+            f"-D changeTimesFile={predictors_dir / 'changetimes_all_7e.tsv'}",
+            f"-D predictorFiles={all_predictor_files}",
         ]
     )
     flight_predictor_data = " ".join(
         [
-            f"-D aligned_fasta={msa_file}",
-            f"-D GLMpredictor_changetimes={predictors_dir / 'changetimes_flights_4e.tsv'}",
-            f"-D GLMpredictor_files={predictors_dir / 'flight_pop_x_4e_ls.tsv'}",
+            f"-D msa_file={msa_file}",
+            f"-D changeTimesFile={predictors_dir / 'changetimes_flights_4e.tsv'}",
+            f"-D predictorFiles={predictors_dir / 'flight_pop_x_4e_ls.tsv'}",
         ]
     )
@@ -80,13 +80,12 @@ def run_beast():
         cpus=128,
         mem_per_cpu=12000,
     )
-    """
     os.makedirs(output_dir / "all-predictors-MLP", exist_ok=True)
     job_ids["all-predictors-MLP"] = submit_job(
         " ".join(
             [
                 os.environ["BELLA_RUN_BEAST_CMD"],
-                f"-D ReDimension='{5 * 7}'",
                 f'-D layersRange="0,1,2",nodes="16 8"',
                 all_predictors_data,
                 f"-prefix {output_dir / 'all-predictors-MLP'}{os.sep}",
@@ -94,7 +93,8 @@ def run_beast():
             ]
         ),
         base_log_dir / "all-predictors-MLP",
-        mem_per_cpu="256000",
+        cpus=128,
+        mem_per_cpu=12000,
     )
     os.makedirs(output_dir / "flights-MLP", exist_ok=True)
@@ -102,7 +102,6 @@ def run_beast():
         " ".join(
             [
                 os.environ["BELLA_RUN_BEAST_CMD"],
-                f"-D ReDimension='{5 * 4}'",
                 f'-D layersRange="0,1,2",nodes="16 8"',
                 flight_predictor_data,
                 f"-prefix {output_dir / 'flights-MLP'}{os.sep}",
@@ -110,9 +109,9 @@ def run_beast():
             ]
         ),
         base_log_dir / "flights-MLP",
-        mem_per_cpu="256000",
+        cpus=128,
+        mem_per_cpu=12000,
     )
-    """
     with open(base_output_dir / "eucovid_job_ids.json", "w") as f:
         json.dump(job_ids, f)

bella_companion/platyrrhine/beast_config.xml CHANGED Viewed

@@ -36,8 +36,8 @@
     <run spec="MCMC" chainLength="10000000">
         <state id="state">
             <plate var="n" range="$(layersRange)">
-                <stateNode spec="RealParameter" name="stateNode" id="birthRateW$(n)" value="0"/>
-                <stateNode spec="RealParameter" name="stateNode" id="deathRateW$(n)" value="0"/>
+                <stateNode spec="RealParameter" id="birthRateW$(n)" value="0"/>
+                <stateNode spec="RealParameter" id="deathRateW$(n)" value="0"/>
             </plate>
             <stateNode spec="RealParameter" id="samplingRate" value="$(samplingRateInit)"/>
             <stateNode spec="RealParameter" id="migrationRate" value="$(migrationRateInit)"/>

bella_companion/platyrrhine/run_beast.py CHANGED Viewed

@@ -34,7 +34,9 @@ def run_beast():
     log10BM_predictor = " ".join(types * T)
     job_ids = {}
-    for i, tree in enumerate(tqdm(trees)):
+    for i, tree in enumerate(
+        tqdm(trees, desc="Submitting BEAST jobs for platyrrhine datasets")
+    ):
         process_length = max(get_node_depths(tree).values())
         command = " ".join(
             [

bella_companion/simulations/beast_configs/epi-multitype/MLP.xml CHANGED Viewed

@@ -31,7 +31,7 @@
     <run spec="MCMC" chainLength="10000000">
         <state id="state">
             <plate var="n" range="$(layersRange)">
-                <stateNode spec="RealParameter" name="stateNode" id="migrationRateW$(n)" value="0"/>
+                <stateNode spec="RealParameter" id="migrationRateW$(n)" value="0"/>
             </plate>
         </state>

bella_companion/simulations/beast_configs/epi-skyline/MLP.xml CHANGED Viewed

@@ -25,7 +25,7 @@
     <run spec="MCMC" chainLength="10000000">
         <state id="state">
             <plate var="n" range="$(layersRange)">
-                <stateNode spec="RealParameter" name="stateNode" id="reproductionNumberW$(n)" value="0"/>
+                <stateNode spec="RealParameter" id="reproductionNumberW$(n)" value="0"/>
             </plate>
         </state>

bella_companion/simulations/beast_configs/fbd-2traits/MLP.xml CHANGED Viewed

@@ -29,8 +29,8 @@
     <run spec="MCMC" chainLength="10000000">
         <state id="state">
             <plate var="n" range="$(layersRange)">
-                <stateNode spec="RealParameter" name="stateNode" id="birthRateW$(n)" value="0"/>
-                <stateNode spec="RealParameter" name="stateNode" id="deathRateW$(n)" value="0"/>
+                <stateNode spec="RealParameter" id="birthRateW$(n)" value="0"/>
+                <stateNode spec="RealParameter" id="deathRateW$(n)" value="0"/>
             </plate>
         </state>

bella_companion/simulations/beast_configs/fbd-no-traits/MLP.xml CHANGED Viewed

@@ -23,8 +23,8 @@
     <run spec="MCMC" chainLength="10000000">
         <state id="state">
             <plate var="n" range="$(layersRange)">
-                <stateNode spec="RealParameter" name="stateNode" id="birthRateW$(n)" value="0"/>
-                <stateNode spec="RealParameter" name="stateNode" id="deathRateW$(n)" value="0"/>
+                <stateNode spec="RealParameter" id="birthRateW$(n)" value="0"/>
+                <stateNode spec="RealParameter" id="deathRateW$(n)" value="0"/>
             </plate>
         </state>

{bella_companion-0.0.27.dist-info → bella_companion-0.0.29.dist-info}/METADATA RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bella-companion
-Version: 0.0.27
+Version: 0.0.29
 Summary:
 Author: gabriele-marino
 Author-email: gabmarino.8601@gmail.com

{bella_companion-0.0.27.dist-info → bella_companion-0.0.29.dist-info}/RECORD RENAMED Viewed

@@ -1,8 +1,8 @@
 bella_companion/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bella_companion/cli.py,sha256=0SwDxkDPqvsp36kGnrBMLPIhAQM8PIpNXrztZayqmDc,2409
 bella_companion/eucovid/__init__.py,sha256=09Ld_G7fZvCDCgEWsmaOyLVQ8pFc9QHAGnXKJ9Zm2AM,81
-bella_companion/eucovid/beast_configs/GLM.xml,sha256=YMvcyeSRIGQOhSSoj7FV0R-5wZHcGWwf9bKxamJ0q9k,20739
-bella_companion/eucovid/beast_configs/MLP.xml,sha256=qLvfP3qEIa_XEDigXrPGbegKDLddifRvoZjNmoDDmFo,11268
+bella_companion/eucovid/beast_configs/GLM.xml,sha256=_pqs2-ADRGSmaBxCmMepuVMWiNEyce3azgE-qD6FNrs,10828
+bella_companion/eucovid/beast_configs/MLP.xml,sha256=M0_B6t0bZpjCAQqAmjrFshW96pt9sNREcoLUjwchX6Q,10616
 bella_companion/eucovid/beast_configs/Nonparametric.xml,sha256=n-t4sUfDS9AzC02tbIk5mx_RDg2l62ELhdR3I3_jjHE,17783
 bella_companion/eucovid/data/case_data.tsv,sha256=XaSzZh5NcEMVt9d_XlQ19T8UuEkHGrjpSFXhe9IycNg,12412
 bella_companion/eucovid/data/change_dates.tsv,sha256=_pmVFYiL4X9Pd79uYVgyz3sKeRap7xVcXk0OjqVhuVQ,227
@@ -20,27 +20,27 @@ bella_companion/eucovid/data/predictors/all/sharedborders_7e_nt.tsv,sha256=pPVT5
 bella_companion/eucovid/data/predictors/changetimes_all_7e.tsv,sha256=hH0xXD2lr_8RPQRqvENv6clPHauAXH22SGQHb3hlfzs,120
 bella_companion/eucovid/data/predictors/changetimes_flights_4e.tsv,sha256=XEepIXKRwcKknJq4-ovKlorvCypGi67B8znuQ5f1LTg,60
 bella_companion/eucovid/data/predictors/flight_pop_x_4e_ls.tsv,sha256=tMR9-tuGtC3rVABXUtNdV9irUX-9aCCVb_fwksHTn8U,1068
-bella_companion/eucovid/run_beast.py,sha256=Rj_Cf38TtyljP0JRyMn7G5Nt5Jv9T4CM5eJsKKfoy4E,3823
+bella_companion/eucovid/run_beast.py,sha256=DU3T0xVVQ6y0ZClyFyouMd939V7sf5KGfadEzTDQf6I,3712
 bella_companion/platyrrhine/__init__.py,sha256=dIx6exNz-vuKiG5FZumvq74QUWcIEFd3L6ErqnOa83c,274
-bella_companion/platyrrhine/beast_config.xml,sha256=8A6E5iPu9FqDL3UdlsqDbabLFlC6Qhfa4Ta47niRkVA,7090
+bella_companion/platyrrhine/beast_config.xml,sha256=bLzavt-Zd8cmSgQQnlCBfZ9KyM7d1inOGx12VNjPFb4,7056
 bella_companion/platyrrhine/data/change_times.csv,sha256=tedobHbaY7-6M3V6F6HSqGAU9dpeeajR5mu1XGJfp6w,68
 bella_companion/platyrrhine/data/traits.csv,sha256=N_mCnaM9Gy0Qot7-l_mK0vMvr7e_5BZ4bgUHpcoG9UM,3949
 bella_companion/platyrrhine/data/trees.nwk,sha256=lpSiGUG5s3zE--IKPOyWrJ5vpJb_xAPnfxychs3YNIs,488232
 bella_companion/platyrrhine/results.py,sha256=qosxqstTy7uadHARRt1WqmxZzxnQ3hiTjtw6V-YWKGA,2556
-bella_companion/platyrrhine/run_beast.py,sha256=xYpK_QS5Qr-8jvq3_s-uXBW5yGsxE3c8AvHd12N6PFY,2552
+bella_companion/platyrrhine/run_beast.py,sha256=fnUmpJue3o0vZn9GWmwlmV0z2HIzXc4t_U2LFIKOq_I,2621
 bella_companion/platyrrhine/summarize_logs.py,sha256=82N7rcmLthCyQqmP4Yub4KUsIjNzQl9vEuFLMvIv03o,951
 bella_companion/simulations/__init__.py,sha256=ShYRdp1iSjnS_SzcsH-8jbqXz6P1nyRQZqAtPZJCMVE,454
 bella_companion/simulations/beast_configs/epi-multitype/GLM.xml,sha256=VymAYsaZVuB3EPE0DCQSXpKepVq8pPjKaB5yhEpaVkE,4334
-bella_companion/simulations/beast_configs/epi-multitype/MLP.xml,sha256=J-OVblMRmk4XRhz9DHhLpMwaIzqSqYZ7Yq7dTMvQW1s,4094
+bella_companion/simulations/beast_configs/epi-multitype/MLP.xml,sha256=AoJyjvVcwKtut64d7sB2gnnenx5sXyuTTNCivykUyqU,4077
 bella_companion/simulations/beast_configs/epi-multitype/Nonparametric.xml,sha256=DfCMcLM53b-XP9oIiQ9wJWOVTEP3GnoZaL5BMzLLfIQ,3208
 bella_companion/simulations/beast_configs/epi-skyline/GLM.xml,sha256=7LtJhU7o7aQsnWK7ZIKj-mzmHgCn_RjxvKKbLIlp1Go,3619
-bella_companion/simulations/beast_configs/epi-skyline/MLP.xml,sha256=ovjFleUnTgyrT8T1uaKboUsL-ZFLCaQN5mk4HadFPU0,3443
+bella_companion/simulations/beast_configs/epi-skyline/MLP.xml,sha256=ptoLM0FLDp54bUSxPm12qIvOYWyBkWR1e9VWVWjgU8E,3426
 bella_companion/simulations/beast_configs/epi-skyline/Nonparametric.xml,sha256=LTiatqeAMiFfdD1leQ5TrGaJhsYwlkbMDpxqhVFOgUQ,2561
 bella_companion/simulations/beast_configs/fbd-2traits/GLM.xml,sha256=Iff0eAShKLeOnlTmNu6044Wljtla3yckqo2LZ7mP6LY,5897
-bella_companion/simulations/beast_configs/fbd-2traits/MLP.xml,sha256=E8sgfOAJI4rkbCVhGYa-HwM44ItwxVs4pIXkQOGNTtY,5462
+bella_companion/simulations/beast_configs/fbd-2traits/MLP.xml,sha256=RvF70fcnvoBcJxjyT4nELlFm94atSZpKm9d1aS-cJZ4,5428
 bella_companion/simulations/beast_configs/fbd-2traits/Nonparametric.xml,sha256=ev6ZfMeCwMyK54G_4O8g-tbgoxoD3asxt71x91Cb1QY,3618
 bella_companion/simulations/beast_configs/fbd-no-traits/GLM.xml,sha256=Caq7Gxqx-wYAu3_YkMikVqni3DjBv1Wt00sc1Upo1X8,4743
-bella_companion/simulations/beast_configs/fbd-no-traits/MLP.xml,sha256=_EzDVPrU6Y5ZfzkVn---Sp62KeBZuRCZfoYqxblLq8I,4309
+bella_companion/simulations/beast_configs/fbd-no-traits/MLP.xml,sha256=JE_cGh2DW5yPAXyXXr0D3DlovmV-aIbze7qrhENHK3w,4275
 bella_companion/simulations/beast_configs/fbd-no-traits/Nonparametric.xml,sha256=m2xaHZwskCFInvVY1QH1fwQqH6p_fgESlPX2BbBeUhk,2822
 bella_companion/simulations/features.py,sha256=DZOBpJGlQ0UinqUZYbEtoemZ2eQGVLV_i-DfpW31qJI,104
 bella_companion/simulations/figures/__init__.py,sha256=aBYbJntH4egFmkSSWiVMYDEApXPYxJD7eA3TCPNNegM,658
@@ -69,7 +69,7 @@ bella_companion/utils/__init__.py,sha256=UtMwPK9dWf9NAl0ic8CSsgdW7aSm-5J49OqgvD7
 bella_companion/utils/beast.py,sha256=TBa0cLklX1_tXqoQE4LRYvds7mLg_9fS2-6U6OHENHo,2184
 bella_companion/utils/explain.py,sha256=uP7HPyn2YiykAI69BQV3RooDpC6qKoCLXfp3Uibp4zk,1475
 bella_companion/utils/slurm.py,sha256=xEyf-Jxk8fy71t3fko_Ic9WtUFSdLFE3w4tR17gaBPw,1868
-bella_companion-0.0.27.dist-info/METADATA,sha256=Sl37hKYlQ0qIq5NxxA1wNCmF-Mj109HazWo8EDq_pkk,576
-bella_companion-0.0.27.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-bella_companion-0.0.27.dist-info/entry_points.txt,sha256=rSeKoAhmjnQqAYFcXBv0gAM2ViJfJe0D8_dD-fWrXeg,50
-bella_companion-0.0.27.dist-info/RECORD,,
+bella_companion-0.0.29.dist-info/METADATA,sha256=GfkFvoMcKT2VpMWy3vrbyeKPMoR8xEo7UlZtLcVEon0,576
+bella_companion-0.0.29.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+bella_companion-0.0.29.dist-info/entry_points.txt,sha256=rSeKoAhmjnQqAYFcXBv0gAM2ViJfJe0D8_dD-fWrXeg,50
+bella_companion-0.0.29.dist-info/RECORD,,

{bella_companion-0.0.27.dist-info → bella_companion-0.0.29.dist-info}/WHEEL RENAMED Viewed

File without changes

{bella_companion-0.0.27.dist-info → bella_companion-0.0.29.dist-info}/entry_points.txt RENAMED Viewed

File without changes

bella-companion 0.0.27__py3-none-any.whl → 0.0.29__py3-none-any.whl

Potentially problematic release.

bella-companion 0.0.27py3-none-any.whl → 0.0.29py3-none-any.whl