bella-companion 0.0.27__tar.gz → 0.0.28__tar.gz

{bella_companion-0.0.27 → bella_companion-0.0.28}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bella-companion
-Version: 0.0.27
+Version: 0.0.28
 Summary: 
 Author: gabriele-marino
 Author-email: gabmarino.8601@gmail.com

bella_companion-0.0.28/bella_companion/eucovid/beast_configs/MLP.xml

@@ -0,0 +1,350 @@
+<?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 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>
+
+    <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>
+
+    <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="bella.BayesMLP" nodes="$(nodes)">
+            <plate var="predictor" range="$(GLMpredictor_files)">
+                <predictor spec="RealParameterFromXSV" id="$(predictor)" fileName="$(predictor)"/>
+            </plate>
+
+            <plate var="n" range="$(layersRange)">
+                <weights idref="migrationW$(n)"/>
+            </plate>
+
+        </skylineValues>
+
+        <changeTimes id="migrationRateChangeTimes" spec="RealParameterFromXSV" 
+                     fileName="$(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 -->
+        <state id="state" spec="State">
+            
+            <stateNode id="treeBDMMPrime" spec="RandomTree" 
+                       taxa="@alignment" 
+                       populationModel="@popFunc"
+                       trait="@dateTrait">
+            </stateNode>
+            
+            <stateNode idref="originBDMMPrime"/>
+            <stateNode idref="ReValues"/>
+            <stateNode idref="samplingProportionValues"/>
+            <plate var="n" range="$(layersRange)">
+                <stateNode spec="RealParameter" id="migrationW$(n)" value="0"/>
+            </plate>
+
+            <stateNode idref="kappa"/>
+            <stateNode idref="gammaShape"/>
+
+        </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>
+
+            <!-- Prior distribution -->
+            <distribution id="prior" spec="CompoundDistribution">
+
+                <!-- 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">
+                    <LogNormal name="distr" M="-1.0" S="0.2"/>
+                </prior>
+
+                <!-- Reproductive number Prior -->
+                <distribution id="RePrior" spec="SmartZeroExcludingPrior" x="@ReValues">
+                    <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">
+                    <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">
+                    <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">
+                    <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">
+                    <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">
+                    <Uniform name="distr" lower="0" upper="0.057"/>
+                </distribution>
+
+                <plate var="n" range="$(layersRange)">
+                    <prior name="distribution" x="@migrationW$(n)">
+                        <Normal name="distr" mean="0.0" sigma="1.0"/>
+                    </prior>
+                </plate>
+
+                <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>
+                </prior>
+
+            </distribution>
+        </distribution>
+
+
+        <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"/>
+
+        <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="samplingProportionScaler" spec="SmartScaleOperator" parameter="@samplingProportionValues" 
+                weight="3.0" />
+
+        <plate var="n" range="$(layersRange)">
+            <operator spec="BactrianRandomWalkOperator" parameter="@migrationW$(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"/>
+
+
+    <!-- Loggers -->
+        <logger id="tracelog" spec="Logger" fileName="$(filebase).log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
+            <log idref="posterior"/>
+            <log idref="likelihood"/>
+            <log idref="prior"/>
+            <log idref="treeLikelihood"/>
+            <log idref="gammaShape"/>   
+            <log idref="kappa"/>
+            <log id="TreeHeight" spec="TreeStatLogger" tree="@treeBDMMPrime"/>
+            <log id="typedTreeStats" spec="TypedTreeStatsLogger" includeRootEdge="true" 
+                typeLabel="type" typeSet="@typeSetBDMMPrime">
+                <typedTree id="typeMappedTree" spec="TypeMappedTree" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@typeFrequencies" mapOnInit="false" remapOnLog="true" typeLabel="type" typeTraitSet="@typeTraitSet" untypedTree="@treeBDMMPrime"/>
+            </log>
+            <log idref="originBDMMPrime"/>
+            <log idref="ReSV"/>
+            <log idref="becomeUninfectiousRateSV"/>
+            <log idref="samplingProportionSV"/>
+            <log idref="migrationRateSM"/>
+
+            <log idref="removalProbSV"/>
+            <log idref="typeFrequencies"/>
+        </logger>
+
+        <logger id="screenlog" spec="Logger" logEvery="1000">
+            <log idref="posterior"/>
+            <log arg="@posterior" id="ESS_posterior" spec="util.ESS"/>
+            <log idref="likelihood"/>
+            <log arg="@likelihood" id="ESS_likelihood" spec="util.ESS"/>
+            <log idref="prior"/>
+            <log arg="@prior" id="ESS_prior" spec="util.ESS"/>
+            <log idref="BDMMPrime"/>
+            <log arg="@BDMMPrime" id="ESS_BDMMPrime" spec="util.ESS"/>
+        </logger>
+
+        <logger id="treelog" spec="Logger" fileName="$(filebase).trees" logEvery="1000" mode="tree">
+            <log id="TreeWithMetaDataLogger" spec="TreeWithMetaDataLogger" tree="@treeBDMMPrime"/>
+        </logger>
+ 
+        <logger id="typedTreeLogger" spec="OptionalLogger" enableLogger="true" 
+            fileName="$(filebase).typed.trees" logEvery="10000" mode="tree">
+            <log idref="typeMappedTree"/>
+        </logger>
+        <logger id="nodeTypedTreeLogger.t:eubdmm_alignment" spec="OptionalLogger" enableLogger="true" 
+            fileName="$(filebase).typed.node.trees" logEvery="10000" mode="tree">
+            <log id="nodeTypedTree" spec="TypedNodeTreeLogger" typedTree="@typeMappedTree"/>
+        </logger>
+        <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>
+
+        <operatorschedule id="OperatorSchedule" spec="OperatorSchedule"/>
+
+    </run>
+
+</beast>

{bella_companion-0.0.27 → bella_companion-0.0.28}/bella_companion/eucovid/run_beast.py

@@ -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-0.0.27 → bella_companion-0.0.28}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "bella-companion"
-version = "0.0.27"
+version = "0.0.28"
 description = ""
 authors = ["gabriele-marino <gabmarino.8601@gmail.com>"]
 

bella_companion-0.0.27/bella_companion/eucovid/beast_configs/MLP.xml

@@ -1,197 +0,0 @@
-<?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"
-    required="BEAST.base v2.7.7:BDMM-Prime v2.2.2"
-    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="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>
-            <plate var="n" range="$(layersRange)">
-                <weights idref="migrationW$(n)"/>
-            </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"/>
-        </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>
-
-            <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> 
-
-                <prior name="distribution" x="@processLength">
-                    <LogNormal name="distr" M="-1.0" S="0.2"/>
-                </prior>
-                <distribution spec="SmartZeroExcludingPrior" x="@Re">
-                    <LogNormal name="distr" M="0.8" S="0.5"/>
-                </distribution>
-                <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>
-                <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>
-                <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>
-                <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>
-                <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>
-                <plate var="n" range="$(layersRange)">
-                    <prior name="distribution" x="@migrationW$(n)">
-                        <Normal name="distr" mean="0.0" sigma="1.0"/>
-                    </prior>
-                </plate>
-                <prior name="distribution" x="@gammaShape">
-                    <Exponential name="distr" mean="0.5"/>
-                </prior>
-                <prior name="distribution" x="@kappa">
-                    <LogNormal name="distr" M="1.0" S="1.25"/>
-                </prior>
-            </distribution>
-        </distribution>
-
-        <operator spec="BactrianScaleOperator" tree="@treeBDMMPrime" rootOnly="true" scaleFactor="0.25"  weight="5.0"/>
-        <operator spec="BactrianNodeOperator" tree="@treeBDMMPrime" weight="30.0"/>
-        <operator spec="BactrianSubtreeSlide" tree="@treeBDMMPrime" weight="15.0"/>
-        <operator spec="Exchange" tree="@treeBDMMPrime" weight="15.0"/>
-        <operator spec="Exchange" tree="@treeBDMMPrime" isNarrow="false" weight="3.0"/>
-        <operator spec="WilsonBalding" tree="@treeBDMMPrime" weight="3.0"/>
-        <operator spec="EpochFlexOperator" tree="@treeBDMMPrime" scaleFactor="0.1" weight="2.0"/>
-        <operator spec="EpochFlexOperator" tree="@treeBDMMPrime" fromOldestTipOnly="false" scaleFactor="0.1" weight="2.0"/>
-        <operator spec="TreeStretchOperator" tree="@treeBDMMPrime" scaleFactor="0.01" weight="2.0"/>
-        <operator spec="BactrianScaleOperator" parameter="@processLength" scaleFactor="0.25" weight="3.0" />
-        <operator spec="BactrianScaleOperator" parameter="@Re" scaleFactor="0.25" weight="10.0"/>
-        <operator spec="SmartScaleOperator" parameter="@samplingProportion" weight="3.0" />
-        <plate var="n" range="$(layersRange)">
-            <operator spec="BactrianRandomWalkOperator" parameter="@migrationW$(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"/>
-
-        <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="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">
-            <log idref="typeMappedTree"/>
-        </logger>
-
-        <logger spec="OptionalLogger" enableLogger="true" fileName="TypedNodeTree.trees" logEvery="10000" 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>
-
-    </run>
-    
-</beast>