blob: 68a198f09bfe67441fae608af088fde74ca6a985 [file] [log] [blame]
<?xml version="1.0" encoding="UTF-8"?>
<ecore:EPackage xmi:version="2.0"
xmlns:xmi="http://www.omg.org/XMI" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:ecore="http://www.eclipse.org/emf/2002/Ecore" name="standard"
nsURI="http:///org/eclipse/stem/diseasemodels/standard.ecore" nsPrefix="org.eclipse.stem.diseasemodels.standard">
<eClassifiers xsi:type="ecore:EClass" name="DeterministicSEIRDiseaseModel" eSuperTypes="#//SEIR"/>
<eClassifiers xsi:type="ecore:EClass" name="DeterministicSIDiseaseModel" eSuperTypes="#//SI"/>
<eClassifiers xsi:type="ecore:EClass" name="DeterministicSIRDiseaseModel" eSuperTypes="#//SIR"/>
<eClassifiers xsi:type="ecore:EClass" name="DiseaseModel" abstract="true" eSuperTypes="../../org.eclipse.stem.core/model/model.ecore#//NodeDecorator #//SanityChecker ../../org.eclipse.stem.core/model/modifier.ecore#//Modifiable">
<eOperations name="getAdjustedBackgroundMortalityRate" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble">
<eParameters name="timeDelta" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//ELong"/>
</eOperations>
<eOperations name="createDiseaseModelLabel" eType="#//DiseaseModelLabel"/>
<eOperations name="createDiseaseModelLabelValue" eType="#//DiseaseModelLabelValue"/>
<eOperations name="createDiseaseModelState" eType="#//DiseaseModelState"/>
<eOperations name="initializeDiseaseState" eType="#//DiseaseModelState">
<eParameters name="diseaseModelState" eType="#//DiseaseModelState"/>
<eParameters name="diseaseModelLabel" eType="#//DiseaseModelLabel"/>
</eOperations>
<eOperations name="initializeDiseaseState">
<eParameters name="diseaseModelLabel" eType="#//DiseaseModelLabel"/>
</eOperations>
<eOperations name="createInfector" eType="#//Infector"/>
<eOperations name="getAdjustedBackgroundBirthRate" eType="ecore:EDataType platform:/plugin/org.eclipse.emf.ecore/model/Ecore.ecore#//EDouble">
<eParameters name="timeDelta" eType="ecore:EDataType platform:/plugin/org.eclipse.emf.ecore/model/Ecore.ecore#//ELong"/>
</eOperations>
<eStructuralFeatures xsi:type="ecore:EAttribute" name="backgroundMortalityRate"
eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble" defaultValueLiteral="5.5E-5"/>
<eStructuralFeatures xsi:type="ecore:EAttribute" name="populationIdentifier" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EString"
defaultValueLiteral="human"/>
<eStructuralFeatures xsi:type="ecore:EAttribute" name="timePeriod" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//ELong"
defaultValueLiteral="86400000"/>
<eStructuralFeatures xsi:type="ecore:EAttribute" name="diseaseName" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EString"/>
<eStructuralFeatures xsi:type="ecore:EAttribute" name="relativeTolerance" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble"
defaultValueLiteral="1E-9"/>
<eStructuralFeatures xsi:type="ecore:EAttribute" name="finiteDifference" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EBoolean"
defaultValueLiteral="true"/>
<eStructuralFeatures xsi:type="ecore:EAttribute" name="frequencyDependent" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EBoolean"
defaultValueLiteral="true"/>
<eStructuralFeatures xsi:type="ecore:EAttribute" name="backgroundBirthRate" eType="ecore:EDataType platform:/plugin/org.eclipse.emf.ecore/model/Ecore.ecore#//EDouble"
defaultValueLiteral="5.5E-5"/>
</eClassifiers>
<eClassifiers xsi:type="ecore:EClass" name="DiseaseModelLabel" abstract="true" eSuperTypes="../../org.eclipse.stem.core/model/graph.ecore#//DynamicNodeLabel">
<eStructuralFeatures xsi:type="ecore:EReference" name="populationLabel" eType="ecore:EClass ../../org.eclipse.stem.definitions/model/labels.ecore#//PopulationLabel"/>
<eStructuralFeatures xsi:type="ecore:EReference" name="diseaseModelState" eType="#//DiseaseModelState"
containment="true" resolveProxies="false" eOpposite="#//DiseaseModelState/label"/>
<eStructuralFeatures xsi:type="ecore:EReference" name="populationModelLabel" eType="ecore:EClass ../../org.eclipse.stem.populationmodels/model/standard.ecore#//PopulationModelLabel"/>
</eClassifiers>
<eClassifiers xsi:type="ecore:EClass" name="DiseaseModelLabelValue" abstract="true"
eSuperTypes="../../org.eclipse.stem.core/model/graph.ecore#//LabelValue #//IntegrationLabelValue">
<eOperations name="set" eType="#//DiseaseModelLabelValue">
<eParameters name="value" eType="#//DiseaseModelLabelValue"/>
</eOperations>
<eOperations name="add" eType="#//DiseaseModelLabelValue">
<eParameters name="value" eType="#//DiseaseModelLabelValue"/>
</eOperations>
<eOperations name="sub" eType="#//DiseaseModelLabelValue">
<eParameters name="value" eType="#//DiseaseModelLabelValue"/>
</eOperations>
<eOperations name="scale" eType="#//DiseaseModelLabelValue">
<eParameters name="scaleFactor" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble"/>
</eOperations>
<eOperations name="zeroOutPopulationCount"/>
<eOperations name="getAdditions" eType="ecore:EDataType platform:/plugin/org.eclipse.emf.ecore/model/Ecore.ecore#//EDouble"/>
<eOperations name="getSubstractions" eType="ecore:EDataType platform:/plugin/org.eclipse.emf.ecore/model/Ecore.ecore#//EDouble"/>
<eStructuralFeatures xsi:type="ecore:EAttribute" name="diseaseDeaths" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble"
defaultValueLiteral="0"/>
<eStructuralFeatures xsi:type="ecore:EAttribute" name="populationCount" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble"
changeable="false" volatile="true" transient="true"/>
<eStructuralFeatures xsi:type="ecore:EAttribute" name="incidence" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble"/>
</eClassifiers>
<eClassifiers xsi:type="ecore:EClass" name="DiseaseModelState" abstract="true">
<eStructuralFeatures xsi:type="ecore:EReference" name="label" eType="#//DiseaseModelLabel"
eOpposite="#//DiseaseModelLabel/diseaseModelState"/>
</eClassifiers>
<eClassifiers xsi:type="ecore:EClass" name="Infector" abstract="true" eSuperTypes="../../org.eclipse.stem.core/model/model.ecore#//NodeDecorator ../../org.eclipse.stem.core/model/modifier.ecore#//Modifiable">
<eStructuralFeatures xsi:type="ecore:EReference" name="diseaseModel" eType="#//StandardDiseaseModel"/>
<eStructuralFeatures xsi:type="ecore:EAttribute" name="targetURI" eType="#//URI"/>
<eStructuralFeatures xsi:type="ecore:EAttribute" name="diseaseName" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EString"/>
<eStructuralFeatures xsi:type="ecore:EAttribute" name="targetISOKey" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EString"/>
<eStructuralFeatures xsi:type="ecore:EReference" name="labelsToInfect" upperBound="-1"
eType="#//DiseaseModelLabel"/>
<eStructuralFeatures xsi:type="ecore:EAttribute" name="populationIdentifier" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EString"/>
</eClassifiers>
<eClassifiers xsi:type="ecore:EClass" name="SEIR" abstract="true" eSuperTypes="#//SIR">
<eOperations name="getAdjustedIncubationRate" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble">
<eParameters name="timeDelta" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//ELong"/>
</eOperations>
<eStructuralFeatures xsi:type="ecore:EAttribute" name="incubationRate" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble"
defaultValueLiteral="0.0"/>
</eClassifiers>
<eClassifiers xsi:type="ecore:EClass" name="SEIRLabel" eSuperTypes="#//StandardDiseaseModelLabel">
<eStructuralFeatures xsi:type="ecore:EReference" name="deltaValue" eType="#//SEIRLabelValue"/>
<eStructuralFeatures xsi:type="ecore:EReference" name="probeValue" eType="#//SEIRLabelValue"/>
<eStructuralFeatures xsi:type="ecore:EReference" name="tempValue" eType="#//SEIRLabelValue"/>
<eStructuralFeatures xsi:type="ecore:EReference" name="originalValue" eType="#//SEIRLabelValue"/>
<eStructuralFeatures xsi:type="ecore:EReference" name="errorScale" eType="#//SEIRLabelValue"/>
</eClassifiers>
<eClassifiers xsi:type="ecore:EClass" name="SEIRLabelValue" eSuperTypes="#//SIRLabelValue">
<eStructuralFeatures xsi:type="ecore:EAttribute" name="e" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble"/>
</eClassifiers>
<eClassifiers xsi:type="ecore:EClass" name="SI" abstract="true" eSuperTypes="#//StandardDiseaseModel">
<eOperations name="getAdjustedInfectiousMortalityRate" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble">
<eParameters name="timeDelta" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//ELong"/>
</eOperations>
<eOperations name="getAdjustedTransmissionRate" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble">
<eParameters name="timeDelta" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//ELong"/>
</eOperations>
<eOperations name="getAdjustedRecoveryRate" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble">
<eParameters name="timeDelta" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//ELong"/>
</eOperations>
<eOperations name="getEffectiveInfectious" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble">
<eParameters name="node" eType="ecore:EClass ../../org.eclipse.stem.core/model/graph.ecore#//Node"/>
<eParameters name="diseaseLabel" eType="#//StandardDiseaseModelLabel"/>
<eParameters name="onsiteInfectious" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble"/>
</eOperations>
<eOperations name="getNormalizedEffectiveInfectious" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble">
<eParameters name="node" eType="ecore:EClass ../../org.eclipse.stem.core/model/graph.ecore#//Node"/>
<eParameters name="diseaseLabel" eType="#//StandardDiseaseModelLabel"/>
<eParameters name="onsiteInfectious" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble"/>
</eOperations>
<eStructuralFeatures xsi:type="ecore:EAttribute" name="transmissionRate" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble"
defaultValueLiteral="0.0"/>
<eStructuralFeatures xsi:type="ecore:EAttribute" name="nonLinearityCoefficient"
eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble" defaultValueLiteral="1.0"/>
<eStructuralFeatures xsi:type="ecore:EAttribute" name="recoveryRate" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble"
defaultValueLiteral="0.0"/>
<eStructuralFeatures xsi:type="ecore:EAttribute" name="infectiousMortalityRate"
eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble" defaultValueLiteral="0.0"/>
<eStructuralFeatures xsi:type="ecore:EAttribute" name="physicallyAdjacentInfectiousProportion"
eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble" defaultValueLiteral="0.05"/>
<eStructuralFeatures xsi:type="ecore:EAttribute" name="roadNetworkInfectiousProportion"
eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble" defaultValueLiteral="0.01"/>
<eStructuralFeatures xsi:type="ecore:EAttribute" name="infectiousMortality" eType="ecore:EDataType platform:/plugin/org.eclipse.emf.ecore/model/Ecore.ecore#//EDouble"/>
</eClassifiers>
<eClassifiers xsi:type="ecore:EClass" name="SIDiseaseModelState" eSuperTypes="#//StandardDiseaseModelState"/>
<eClassifiers xsi:type="ecore:EClass" name="SIInfector" eSuperTypes="#//StandardInfector">
<eStructuralFeatures xsi:type="ecore:EAttribute" name="infectiousCount" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble"
defaultValueLiteral="1"/>
</eClassifiers>
<eClassifiers xsi:type="ecore:EClass" name="SILabel" eSuperTypes="#//StandardDiseaseModelLabel">
<eStructuralFeatures xsi:type="ecore:EReference" name="deltaValue" eType="#//SILabelValue"/>
<eStructuralFeatures xsi:type="ecore:EReference" name="probeValue" eType="#//SILabelValue"/>
<eStructuralFeatures xsi:type="ecore:EReference" name="tempValue" eType="#//SILabelValue"/>
<eStructuralFeatures xsi:type="ecore:EReference" name="originalValue" eType="#//SILabelValue"/>
<eStructuralFeatures xsi:type="ecore:EReference" name="errorScale" eType="#//SILabelValue"/>
</eClassifiers>
<eClassifiers xsi:type="ecore:EClass" name="SILabelValue" eSuperTypes="#//StandardDiseaseModelLabelValue">
<eStructuralFeatures xsi:type="ecore:EAttribute" name="i" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble"/>
</eClassifiers>
<eClassifiers xsi:type="ecore:EClass" name="SIR" abstract="true" eSuperTypes="#//SI">
<eOperations name="getAdjustedImmunityLossRate" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble">
<eParameters name="timeDelta" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//ELong"/>
</eOperations>
<eStructuralFeatures xsi:type="ecore:EAttribute" name="immunityLossRate" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble"
defaultValueLiteral="0.0"/>
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<eClassifiers xsi:type="ecore:EClass" name="SIRLabel" eSuperTypes="#//StandardDiseaseModelLabel">
<eStructuralFeatures xsi:type="ecore:EReference" name="deltaValue" eType="#//SIRLabelValue"/>
<eStructuralFeatures xsi:type="ecore:EReference" name="probeValue" eType="#//SIRLabelValue"/>
<eStructuralFeatures xsi:type="ecore:EReference" name="tempValue" eType="#//SIRLabelValue"/>
<eStructuralFeatures xsi:type="ecore:EReference" name="originalValue" eType="#//SIRLabelValue"/>
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<eClassifiers xsi:type="ecore:EClass" name="SIRLabelValue" eSuperTypes="#//SILabelValue">
<eStructuralFeatures xsi:type="ecore:EAttribute" name="r" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble"/>
</eClassifiers>
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eSuperTypes="#//DiseaseModel #//IntegrationDecorator">
<eOperations name="addToTotalPopulationCount">
<eParameters name="populationCount" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble"/>
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<eOperations name="computeTotalPopulationCountReciprocal" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble"/>
<eOperations name="addToTotalArea">
<eParameters name="area" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble"/>
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<eOperations name="calculateDelta">
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<eParameters name="labels">
<eGenericType eClassifier="ecore:EDataType platform:/plugin/org.eclipse.emf.ecore/model/Ecore.ecore#//EEList">
<eTypeArguments eClassifier="ecore:EClass ../../org.eclipse.stem.core/model/graph.ecore#//DynamicLabel"/>
</eGenericType>
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<eOperations name="doModelSpecificAdjustments">
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<eStructuralFeatures xsi:type="ecore:EAttribute" name="totalPopulationCountReciprocal"
eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble" changeable="false"/>
<eStructuralFeatures xsi:type="ecore:EAttribute" name="totalArea" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble"
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<eStructuralFeatures xsi:type="ecore:EAttribute" name="referencePopulationDensity"
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</eClassifiers>
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eSuperTypes="#//DiseaseModelLabel #//IntegrationLabel"/>
<eClassifiers xsi:type="ecore:EClass" name="StandardDiseaseModelLabelValue" abstract="true"
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</eClassifiers>
<eClassifiers xsi:type="ecore:EClass" name="StandardInfector" abstract="true" eSuperTypes="#//Infector"/>
<eClassifiers xsi:type="ecore:EClass" name="StochasticSEIRDiseaseModel" eSuperTypes="#//SEIR #//StandardStochasticDiseaseModel"/>
<eClassifiers xsi:type="ecore:EClass" name="StochasticSIDiseaseModel" eSuperTypes="#//SI #//StandardStochasticDiseaseModel"/>
<eClassifiers xsi:type="ecore:EClass" name="StochasticSIRDiseaseModel" eSuperTypes="#//SIR #//StandardStochasticDiseaseModel"/>
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abstract="true" interface="true"/>
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<eClassifiers xsi:type="ecore:EClass" name="IntegrationDecorator" instanceClassName="org.eclipse.stem.core.model.IntegrationDecorator"
abstract="true" interface="true">
<eOperations name="isDeterministic" eType="ecore:EDataType platform:/plugin/org.eclipse.emf.ecore/model/Ecore.ecore#//EBoolean"/>
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<eStructuralFeatures xsi:type="ecore:EReference" name="childrensLabels" upperBound="-1"
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</eClassifiers>
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<eClassifiers xsi:type="ecore:EClass" name="AggregatingSIRDiseaseModel" eSuperTypes="#//AggregatingSIDiseaseModel"/>
<eClassifiers xsi:type="ecore:EClass" name="StochasticDiseaseModel" abstract="true"
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defaultValueLiteral="0"/>
<eStructuralFeatures xsi:type="ecore:EAttribute" name="randomGenerator" eType="#//Random"
changeable="false" defaultValueLiteral="0"/>
</eClassifiers>
<eClassifiers xsi:type="ecore:EClass" name="StandardStochasticDiseaseModel" abstract="true"
eSuperTypes="#//StochasticDiseaseModel">
<eOperations name="computeNoise" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble"/>
<eStructuralFeatures xsi:type="ecore:EAttribute" name="gain" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble"
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<eClassifiers xsi:type="ecore:EClass" name="SIRInoculator" eSuperTypes="#//SIInfector">
<eStructuralFeatures xsi:type="ecore:EAttribute" name="inoculatedPercentage" eType="ecore:EDataType http://www.eclipse.org/emf/2002/Ecore#//EDouble"
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<eClassifiers xsi:type="ecore:EDataType" name="URI" instanceClassName="org.eclipse.emf.common.util.URI"/>
<eClassifiers xsi:type="ecore:EDataType" name="EList" instanceClassName="org.eclipse.emf.common.util.EList"/>
<eClassifiers xsi:type="ecore:EDataType" name="Random" instanceClassName="java.util.Random"/>
<eClassifiers xsi:type="ecore:EClass" name="StochasticPoissonSIDiseaseModel" eSuperTypes="#//SI"/>
<eClassifiers xsi:type="ecore:EClass" name="StochasticPoissonSIRDiseaseModel" eSuperTypes="#//SIR"/>
<eClassifiers xsi:type="ecore:EClass" name="StochasticPoissonSEIRDiseaseModel" eSuperTypes="#//SEIR"/>
</ecore:EPackage>