bella-companion 0.0.30__tar.gz → 0.0.33__tar.gz

bella_companion-0.0.33/PKG-INFO

@@ -0,0 +1,12 @@
+Metadata-Version: 2.4
+Name: bella-companion
+Version: 0.0.33
+Summary: Add your description here
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: arviz>=0.22.0
+Requires-Dist: bella-lumiere>=0.0.14
+Requires-Dist: dotenv>=0.9.9
+Requires-Dist: phylogenie>=3.1.2
+Requires-Dist: poetry>=2.2.1
+Requires-Dist: seaborn>=0.13.2

bella_companion-0.0.33/bella_companion.egg-info/PKG-INFO

@@ -0,0 +1,12 @@
+Metadata-Version: 2.4
+Name: bella-companion
+Version: 0.0.33
+Summary: Add your description here
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: arviz>=0.22.0
+Requires-Dist: bella-lumiere>=0.0.14
+Requires-Dist: dotenv>=0.9.9
+Requires-Dist: phylogenie>=3.1.2
+Requires-Dist: poetry>=2.2.1
+Requires-Dist: seaborn>=0.13.2

bella_companion-0.0.33/bella_companion.egg-info/SOURCES.txt

@@ -0,0 +1,44 @@
+README.md
+pyproject.toml
+bella_companion/__init__.py
+bella_companion/cli.py
+bella_companion.egg-info/PKG-INFO
+bella_companion.egg-info/SOURCES.txt
+bella_companion.egg-info/dependency_links.txt
+bella_companion.egg-info/entry_points.txt
+bella_companion.egg-info/requires.txt
+bella_companion.egg-info/top_level.txt
+bella_companion/eucovid/__init__.py
+bella_companion/eucovid/run_beast.py
+bella_companion/platyrrhine/__init__.py
+bella_companion/platyrrhine/results.py
+bella_companion/platyrrhine/run_beast.py
+bella_companion/platyrrhine/summarize_logs.py
+bella_companion/simulations/__init__.py
+bella_companion/simulations/features.py
+bella_companion/simulations/generate_data.py
+bella_companion/simulations/generate_figures.py
+bella_companion/simulations/metrics.py
+bella_companion/simulations/run_beast.py
+bella_companion/simulations/summarize_logs.py
+bella_companion/simulations/figures/__init__.py
+bella_companion/simulations/figures/epi_multitype_results.py
+bella_companion/simulations/figures/epi_skyline_results.py
+bella_companion/simulations/figures/fbd_2traits_results.py
+bella_companion/simulations/figures/fbd_no_traits_results.py
+bella_companion/simulations/figures/scenarios.py
+bella_companion/simulations/figures/utils.py
+bella_companion/simulations/figures/explain/__init__.py
+bella_companion/simulations/figures/explain/pdp.py
+bella_companion/simulations/figures/explain/shap.py
+bella_companion/simulations/scenarios/__init__.py
+bella_companion/simulations/scenarios/common.py
+bella_companion/simulations/scenarios/epi_multitype.py
+bella_companion/simulations/scenarios/epi_skyline.py
+bella_companion/simulations/scenarios/fbd_2traits.py
+bella_companion/simulations/scenarios/fbd_no_traits.py
+bella_companion/simulations/scenarios/scenario.py
+bella_companion/utils/__init__.py
+bella_companion/utils/beast.py
+bella_companion/utils/explain.py
+bella_companion/utils/slurm.py

bella_companion-0.0.33/bella_companion.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

bella_companion-0.0.33/bella_companion.egg-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+bella = bella_companion.cli:main

bella_companion-0.0.33/bella_companion.egg-info/requires.txt

@@ -0,0 +1,6 @@
+arviz>=0.22.0
+bella-lumiere>=0.0.14
+dotenv>=0.9.9
+phylogenie>=3.1.2
+poetry>=2.2.1
+seaborn>=0.13.2

bella_companion-0.0.33/bella_companion.egg-info/top_level.txt

@@ -0,0 +1 @@
+bella_companion

bella_companion-0.0.33/pyproject.toml

@@ -0,0 +1,29 @@
+[project]
+name = "bella-companion"
+version = "0.0.33"
+description = "Add your description here"
+readme = "README.md"
+requires-python = ">=3.10"
+dependencies = [
+    "arviz>=0.22.0",
+    "bella-lumiere>=0.0.14",
+    "dotenv>=0.9.9",
+    "phylogenie>=3.1.2",
+    "poetry>=2.2.1",
+    "seaborn>=0.13.2",
+]
+
+[dependency-groups]
+dev = [
+    "joblib-stubs>=1.5.2.0.20250831",
+]
+
+[tool.pyright]
+typeCheckingMode = "strict"
+
+[project.scripts]
+bella = "bella_companion.cli:main"
+
+[build-system]
+requires = ["setuptools>=42"]
+build-backend = "setuptools.build_meta"

bella_companion-0.0.33/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

bella_companion-0.0.30/PKG-INFO

@@ -1,16 +0,0 @@
-Metadata-Version: 2.1
-Name: bella-companion
-Version: 0.0.30
-Summary: 
-Author: gabriele-marino
-Author-email: gabmarino.8601@gmail.com
-Requires-Python: >=3.10,<4.0
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Requires-Dist: arviz (>=0.22.0,<0.23.0)
-Requires-Dist: bella-lumiere (>=0.0.14,<0.0.15)
-Requires-Dist: dotenv (>=0.9.9,<0.10.0)
-Requires-Dist: phylogenie (>=3.1.2,<4.0.0)
-Requires-Dist: seaborn (>=0.13.2,<0.14.0)

bella_companion-0.0.30/bella_companion/eucovid/beast_configs/GLM.xml

@@ -1,170 +0,0 @@
-<?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="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"/>
-            <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>
-    
-        <distribution id="posterior" spec="CompoundDistribution">
-            <distribution id="likelihood" spec="CompoundDistribution" useThreads="true">
-                <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="@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>
-
-                <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>
-                <prior name="distribution" x="@migrationRateW">
-                    <Normal name="distr" mean="0.0" sigma="1.0"/>
-                </prior>
-                <prior name="distribution" x="@migrationRateScaler">
-                    <LogNormal name="distr" M="0.0" S="0.8"/>
-                </prior>
-                <prior name="distribution" x="@gammaShape">
-                    <Exponential name="distr" mean="0.5"/>
-                </prior>
-                <prior id="KappaPrior" name="distribution" x="@kappa">
-                    <LogNormal name="distr" M="1.0" S="1.25"/>
-                </prior>
-            </distribution>
-        </distribution>
-
-        <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"/>
-
-        <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="migrationRateW"/>
-            <log idref="migrationRateScaler"/>
-        </logger>
-        <logger spec="Logger" fileName="typedTrees.trees" logEvery="10000" mode="tree">
-            <log idref="typeMappedTree"/>
-        </logger>
-        <logger spec="Logger" fileName="TypedNodeTrees.trees" logEvery="10000" mode="tree">
-            <log spec="TypedNodeTreeLogger" typedTree="@typeMappedTree"/>
-        </logger>
-        <logger spec="Logger" fileName="trajectories.csv" logEvery="10000">
-            <log spec="SampledTrajectory" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@startTypePriorProbs" typeMappedTree="@typeMappedTree" useTauLeaping="true"/>
-        </logger>
-    </run>
-</beast>

bella_companion-0.0.30/bella_companion/eucovid/beast_configs/MLP.xml

@@ -1,170 +0,0 @@
-<?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="$(msa_file)"/>
-    <TaxonSet id="taxonSet" alignment="@alignment"/>
-    <TraitSetFromTaxonSet id="typeTraitSet" traitname="type" delimiter="|" takeGroup="1" taxa="@taxonSet"/>
-    <TypeSet id="typeSet" typeTraitSet="@typeTraitSet"/>
-    <TraitSetFromTaxonSet id="dateTrait" traitname="date" dateFormat="yyyy-M-dd" delimiter="|" everythingAfterLast="true" taxa="@taxonSet"/>
-    <TypeMappedTree id="typeMappedTree" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@startTypePriorProbs" mapOnInit="false" remapOnLog="true" typeLabel="type" typeTraitSet="@typeTraitSet" untypedTree="@tree"/>
-
-    <run spec="MCMC" chainLength="10000000">
-        <state id="state" spec="State">
-            <stateNode id="tree" spec="RandomTree" taxa="@alignment" trait="@dateTrait">
-                <populationModel spec="ConstantPopulation" popSize="0.1"/>
-            </stateNode>
-            <stateNode id="Re" spec="RealParameter" value="1.0 1.1 1.2 1.3 1.4 1.01 1.1 1.2 1.3 1.4"/>
-            <stateNode id="samplingProportion" spec="RealParameter" value="1.11E-5 1.2E-5 1.3E-5 1.4E-5 1.5E-5 1.1E-5 1.2E-5 1.3E-5 1.4E-5 1.5E-5 0.0 0.0 0.0 0.0 0.0"/>
-            <plate var="n" range="$(layersRange)">
-                <stateNode spec="RealParameter" id="migrationRateW$(n)" value="0"/>
-            </plate>
-            <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="@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="@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="$(changeTimesFile)"/>
-                        </migrationRate> 
-                        <removalProb spec="SkylineVectorParameter" skylineValues="1.0" typeSet="@typeSet"/>
-                    </parameterization>
-                    <startTypePriorProbs id="startTypePriorProbs" spec="RealParameter" value="1.0 0.0 0.0 0.0 0.0"/>
-                </distribution>
-
-                <prior name="distribution" x="@processLength">
-                    <LogNormal name="distr" M="-1.0" S="0.2"/>
-                </prior>
-                <distribution spec="SmartZeroExcludingPrior" x="@Re">
-                    <LogNormal name="distr" M="0.8" S="0.5"/>
-                </distribution>
-                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.2E-5 1.3E-5 1.4E-5 1.5E-5">
-                    <Uniform name="distr" lower="0" upper="0.15"/>
-                </distribution>
-                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.3E-5 1.4E-5 1.5E-5">
-                    <Uniform name="distr" lower="0" upper="0.093"/>
-                </distribution>
-                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.4E-5 1.5E-5">
-                    <Uniform name="distr" lower="0" upper="0.10"/>
-                </distribution>
-                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.5E-5">
-                    <Uniform name="distr" lower="0" upper="0.005"/>
-                </distribution>
-                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.4E-5">
-                    <Uniform name="distr" lower="0" upper="0.057"/>
-                </distribution>
-                <plate var="n" range="$(layersRange)">
-                    <prior name="distribution" x="@migrationRateW$(n)">
-                        <Normal name="distr" mean="0.0" sigma="1.0"/>
-                    </prior>
-                </plate>
-                <prior name="distribution" x="@gammaShape">
-                    <Exponential name="distr" mean="0.5"/>
-                </prior>
-                <prior id="KappaPrior" name="distribution" x="@kappa">
-                    <LogNormal name="distr" M="1.0" S="1.25"/>
-                </prior>
-            </distribution>
-        </distribution>
-
-        <operator spec="BactrianScaleOperator" tree="@tree" rootOnly="true" scaleFactor="0.25"  weight="5.0"/>
-        <operator spec="BactrianNodeOperator" tree="@tree" weight="30.0"/>
-        <operator spec="BactrianSubtreeSlide" tree="@tree" weight="15.0"/>
-        <operator spec="Exchange" tree="@tree" weight="15.0"/>
-        <operator spec="Exchange" tree="@tree" isNarrow="false" weight="3.0"/>
-        <operator spec="WilsonBalding" tree="@tree" weight="3.0"/>
-        <operator spec="EpochFlexOperator" tree="@tree" scaleFactor="0.1" weight="2.0"/>
-        <operator spec="EpochFlexOperator" tree="@tree" fromOldestTipOnly="false" scaleFactor="0.1" weight="2.0"/>
-        <operator spec="TreeStretchOperator" tree="@tree" scaleFactor="0.01" weight="2.0"/>
-        <operator spec="BactrianScaleOperator" parameter="@processLength" scaleFactor="0.25" weight="3.0"/>
-        <operator spec="SmartScaleOperator" parameter="@Re" scaleFactor="0.25" weight="10.0"/>
-        <operator spec="SmartScaleOperator" parameter="@samplingProportion" weight="3.0"/>
-        <plate var="n" range="$(layersRange)">
-            <operator spec="BactrianRandomWalkOperator" parameter="@migrationRateW$(n)" weight="5.0"/>
-        </plate>
-        <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"/>
-        </logger>
-        <logger spec="Logger" fileName="typedTrees.trees" logEvery="100000" mode="tree">
-            <log idref="typeMappedTree"/>
-        </logger>
-        <logger spec="Logger" fileName="TypedNodeTrees.trees" logEvery="100000" mode="tree">
-            <log spec="TypedNodeTreeLogger" typedTree="@typeMappedTree"/>
-        </logger>
-        <logger spec="Logger" fileName="trajectories.csv" logEvery="100000">
-            <log spec="SampledTrajectory" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@startTypePriorProbs" typeMappedTree="@typeMappedTree" useTauLeaping="true"/>
-        </logger>
-    </run>
-</beast>