bella-companion 0.0.24__tar.gz → 0.0.26__tar.gz

{bella_companion-0.0.24 → bella_companion-0.0.26}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bella-companion
-Version: 0.0.24
+Version: 0.0.26
 Summary: 
 Author: gabriele-marino
 Author-email: gabmarino.8601@gmail.com

bella_companion-0.0.26/bella_companion/eucovid/beast_configs/GLM.xml

@@ -0,0 +1,450 @@
+<?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 -->
+        <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"/>
+            <stateNode idref="coefficientsGLM"/>
+            <stateNode idref="scaleFactorGLM"/>
+            <stateNode idref="indicatorGLM"/>
+
+            <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 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>
+                </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>
+                </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>
+
+       <!--  <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="$(filebase).log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
+            <log idref="posterior"/>
+            <log idref="likelihood"/>
+            <log idref="prior"/>
+            <log idref="treeLikelihood"/>
+            <log idref="gammaShape"/>   
+            <log idref="kappa"/>
+            <log id="TreeHeight" spec="TreeStatLogger" tree="@treeBDMMPrime"/>
+            <log id="typedTreeStats" spec="TypedTreeStatsLogger" includeRootEdge="true" 
+                typeLabel="type" typeSet="@typeSetBDMMPrime">
+                <typedTree id="typeMappedTree" spec="TypeMappedTree" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@typeFrequencies" mapOnInit="false" remapOnLog="true" typeLabel="type" typeTraitSet="@typeTraitSet" untypedTree="@treeBDMMPrime"/>
+            </log>
+            <log idref="originBDMMPrime"/>
+            <log idref="ReSV"/>
+            <log idref="becomeUninfectiousRateSV"/>
+            <log idref="samplingProportionSV"/>
+            <log idref="migrationRateSM"/>
+            <log idref="coefficientsGLM"/>
+            <log idref="scaleFactorGLM"/>
+            <log idref="indicatorGLM"/>
+            <log id="coefbyindGLM" spec="ExpCalculator" value="coefficientsGLM*indicatorGLM" useCaching="false">
+                <arg idref="coefficientsGLM"/>
+                <arg idref="indicatorGLM"/>
+            </log>
+            <plate var="predictor" range="$(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"/>
+        </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>