bella-companion 0.0.48__py3-none-any.whl → 0.1.2__py3-none-any.whl

bella_companion/eucovid/beast_configs/Nonparametric.xml

@@ -1,399 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<beast namespace="beast.base.inference
-    :beast.base.inference.parameter
-    :beast.base.inference.distribution
-    :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.kernel
-    :beast.base.inference.operator.kernel
-    :beast.base.inference.operator
-    :beast.base.math.distributions
-    :beast.base.evolution
-    :beast.base.evolution.operator
-    :bdmmprime.util
-    :bdmmprime.util.operators
-    :bdmmprime.util.priors
-    :bdmmprime.distribution
-    :bdmmprime.parameterization
-    :bdmmprime.mapping
-    :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="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">1.0</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">0.12 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_scaled" name="skylineValues" spec="feast.expressions.ExpCalculator">
-                            <![CDATA[
-                            migrationRateValues *
-                            {  f,f,f,f,
-                             f,  1,1,1,
-                             f,1,  1,1,
-                             f,1,1,  1,
-                             f,1,1,1,
-
-                               1,1,1,1,
-                             1,  1,1,1,
-                             1,1,  1,1,
-                             1,1,1,  1,
-                             1,1,1,1  }
-                            ]]>
-            <arg id="migrationRateValues" spec="RealParameter" dimension="40">
-                0.11 0.15 0.2 0.24 
-            0.0      0.14 0.18 0.22 
-            0.0 0.1       0.19 0.23 
-            0.0 0.12 0.16      0.25 
-            0.0 0.13 0.17 0.21 
-            
-                0.11 0.15 0.2 0.24 
-            0.0      0.14 0.18 0.22 
-            0.0 0.1       0.19 0.23 
-            0.0 0.12 0.16      0.25 
-            0.0 0.13 0.17 0.21
-        </arg>
-            <arg id="f" spec="RealParameter">0.5</arg>
-        </skylineValues>
-
-        <changeTimes id="migrationRateChangeTimes" spec="RealParameter">0.123</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" storeEvery="5000">
-            
-            <stateNode id="treeBDMMPrime" spec="RandomTree" 
-                       taxa="@alignment" 
-                       populationModel="@popFunc"
-                       trait="@dateTrait">
-            </stateNode>
-            
-            <stateNode idref="originBDMMPrime"/>
-            <stateNode idref="ReValues"/>
-            <stateNode idref="samplingProportionValues"/>
-            <stateNode idref="migrationRateValues"/>
-            <stateNode idref="f"/>
-
-            <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>
-
-                <!-- Migration rate  Prior -->
-                <distribution id="migRatePrior" name="distribution" spec="SmartZeroExcludingPrior" x="@migrationRateValues">
-                    <LogNormal name="distr" M="0.0" S="1.0"/>
-                </distribution> 
-
-                <distribution id="fPrior" name="distribution" spec="ZeroExcludingPrior" x="@f">
-                    <Uniform name="distr" lower="0.0" upper="1.0"/>
-                </distribution>
-
-            <!-- 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>
-                </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="5.0" />
-
-<!--         <operator id="ReScaler" spec="BactrianScaleOperator" parameter="@ReValues" 
-                weight="5.0" />
-        <operator id="ReScalerAll" spec="BactrianScaleOperator" parameter="@ReValues" 
-                weight="5.0" scaleAll="true" /> -->
-
-        <operator id="ReScaler" spec="SmartScaleOperator" parameter="@ReValues" 
-        weight="5.0" />
-
-        <operator id="samplingProportionScaler" spec="SmartScaleOperator" parameter="@samplingProportionValues" 
-                weight="3.0" />
-
-        <operator id="migrationRateScaler" spec="SmartScaleOperator" parameter="@migrationRateValues" 
-                weight="5.0" />
-        <operator id="fScaler" spec="BactrianScaleOperator" parameter="@f" 
-             weight="5.0"/>
-
-        <!-- 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">
-            <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="migrationRateValues"/>
-            <log idref="f"/>
-            <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>