models/epidemiology/org.eclipse.stem.diseasemodels.multipopulation/src/org/eclipse/stem/diseasemodels/multipopulation/impl/MultiPopulationSEIRDiseaseModelImpl.java - stem/org.eclipse.stem - Git at Google

 /*******************************************************************************
  * Copyright (c) 2009,2010 IBM Corporation and others.
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
  * which accompanies this distribution, and is available at
  * http://www.eclipse.org/legal/epl-v10.html
  *
  * Contributors:
  *     IBM Corporation - initial API and implementation
  *******************************************************************************/
 package org.eclipse.stem.diseasemodels.multipopulation.impl;

 import org.eclipse.emf.common.notify.Notification;
 import org.eclipse.emf.common.notify.NotificationChain;
 import org.eclipse.emf.common.util.EList;
 import org.eclipse.emf.ecore.EClass;
 import org.eclipse.emf.ecore.InternalEObject;
 import org.eclipse.emf.ecore.impl.ENotificationImpl;
 import org.eclipse.stem.core.common.DoubleValue;
 import org.eclipse.stem.core.common.DoubleValueList;
 import org.eclipse.stem.core.common.StringValue;
 import org.eclipse.stem.core.graph.Node;
 import org.eclipse.stem.core.graph.NodeLabel;
 import org.eclipse.stem.core.model.STEMTime;
 import org.eclipse.stem.diseasemodels.multipopulation.MultiPopulationSEIRDiseaseModel;
 import org.eclipse.stem.diseasemodels.multipopulation.MultipopulationPackage;
 import org.eclipse.stem.diseasemodels.standard.DiseaseModelLabel;
 import org.eclipse.stem.diseasemodels.standard.DiseaseModelLabelValue;
 import org.eclipse.stem.diseasemodels.standard.SEIRLabel;
 import org.eclipse.stem.diseasemodels.standard.SEIRLabelValue;
 import org.eclipse.stem.diseasemodels.standard.StandardDiseaseModelLabel;
 import org.eclipse.stem.diseasemodels.standard.StandardDiseaseModelLabelValue;
 import org.eclipse.stem.diseasemodels.standard.StandardFactory;
 import org.eclipse.stem.diseasemodels.standard.StandardPackage;
 import org.eclipse.stem.diseasemodels.standard.impl.SEIRLabelValueImpl;

 /**
  * <!-- begin-user-doc -->
  * An implementation of the model object '<em><b>Multi Population SEIR Disease Model</b></em>'.
  * <!-- end-user-doc -->
  * <p>
  * The following features are implemented:
  * <ul>
  *   <li>{@link org.eclipse.stem.diseasemodels.multipopulation.impl.MultiPopulationSEIRDiseaseModelImpl#getIncubationRate <em>Incubation Rate</em>}</li>
  * </ul>
  * </p>
  *
  * @generated
  */
 public class MultiPopulationSEIRDiseaseModelImpl extends MultiPopulationSIRDiseaseModelImpl implements MultiPopulationSEIRDiseaseModel {
 	/**
 	 * The cached value of the '{@link #getIncubationRate() <em>Incubation Rate</em>}' containment reference.
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @see #getIncubationRate()
 	 * @generated
 	 * @ordered
 	 */
 	protected DoubleValueList incubationRate;

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated NOT
 	 */
 	public MultiPopulationSEIRDiseaseModelImpl() {
 		super();
 	}

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	@Override
 	protected EClass eStaticClass() {
 		return MultipopulationPackage.Literals.MULTI_POPULATION_SEIR_DISEASE_MODEL;
 	}

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	public DoubleValueList getIncubationRate() {
 		return incubationRate;
 	}

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	public NotificationChain basicSetIncubationRate(DoubleValueList newIncubationRate, NotificationChain msgs) {
 		DoubleValueList oldIncubationRate = incubationRate;
 		incubationRate = newIncubationRate;
 		if (eNotificationRequired()) {
 			ENotificationImpl notification = new ENotificationImpl(this, Notification.SET, MultipopulationPackage.MULTI_POPULATION_SEIR_DISEASE_MODEL__INCUBATION_RATE, oldIncubationRate, newIncubationRate);
 			if (msgs == null) msgs = notification; else msgs.add(notification);
 		}
 		return msgs;
 	}

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	public void setIncubationRate(DoubleValueList newIncubationRate) {
 		if (newIncubationRate != incubationRate) {
 			NotificationChain msgs = null;
 			if (incubationRate != null)
 				msgs = ((InternalEObject)incubationRate).eInverseRemove(this, EOPPOSITE_FEATURE_BASE - MultipopulationPackage.MULTI_POPULATION_SEIR_DISEASE_MODEL__INCUBATION_RATE, null, msgs);
 			if (newIncubationRate != null)
 				msgs = ((InternalEObject)newIncubationRate).eInverseAdd(this, EOPPOSITE_FEATURE_BASE - MultipopulationPackage.MULTI_POPULATION_SEIR_DISEASE_MODEL__INCUBATION_RATE, null, msgs);
 			msgs = basicSetIncubationRate(newIncubationRate, msgs);
 			if (msgs != null) msgs.dispatch();
 		}
 		else if (eNotificationRequired())
 			eNotify(new ENotificationImpl(this, Notification.SET, MultipopulationPackage.MULTI_POPULATION_SEIR_DISEASE_MODEL__INCUBATION_RATE, newIncubationRate, newIncubationRate));
 	}

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	@Override
 	public NotificationChain eInverseRemove(InternalEObject otherEnd, int featureID, NotificationChain msgs) {
 		switch (featureID) {
 			case MultipopulationPackage.MULTI_POPULATION_SEIR_DISEASE_MODEL__INCUBATION_RATE:
 				return basicSetIncubationRate(null, msgs);
 		}
 		return super.eInverseRemove(otherEnd, featureID, msgs);
 	}

 	@Override
 	public StandardDiseaseModelLabelValue computeDiseaseDeltas(STEMTime time,
 			StandardDiseaseModelLabelValue currentState,
 			StandardDiseaseModelLabel diseaseLabel, long timeDelta,
 			DiseaseModelLabelValue returnValue) {

 		// THIS method gets called multiple times, once for each population identifier
 		// in the population model.
 		// which population is "this"....
 		final SEIRLabelValue currentSEIR = (SEIRLabelValue) currentState;
 		String thisPopulation = diseaseLabel.getPopulationModelLabel().getPopulationIdentifier();

 		// Compute deaths
 		final double adjustedInfectiousMortalityRate = getAdjustedInfectiousMortalityRate(timeDelta, thisPopulation);
 		final double diseaseDeaths = adjustedInfectiousMortalityRate
 				* currentSEIR.getI();

 		// next get it's INDEX in the model
 		int populationIndex = this.getPopulationIndex(thisPopulation);

 		// now we know the index of the current population being integrated.
 		// Get the correct transmission rate list from the MATRIX
 		EList<DoubleValue> transmissionVector = getTransmissionRate().getValueLists().get(populationIndex).getValues();

 		// ALL the other disease parameters are also DoubleValueLists. We now iterate through all populations
 		// get the specific rate parameters from EACH list based on this population index
 		double thisRecoveryRate = 0.0;
 		if(getRecoveryRate() != null) thisRecoveryRate = getRecoveryRate().getValues().get(populationIndex).getValue();
 		double thisImmunityLossRate = 0.0;
 		if(getImmunityLossRate() != null)
 			thisImmunityLossRate = getImmunityLossRate().getValues().get(populationIndex).getValue();
 		double thisIncubationRate = 0.0;
 		if(getIncubationRate() != null)
 			thisIncubationRate = getIncubationRate().getValues().get(populationIndex).getValue();

 		//  NOW iterate over every population (including this one) to compute new infections
 		//  this includes infections within a population group
 		//  and all the cross terms
 		double numberOfSusceptibleToExposed = 0.0;
 		double numberSusceptible = currentSEIR.getS();
 		Node thisNode = diseaseLabel.getNode();

 		EList<StringValue> groupList = getPopulationGroups().getValues();

 		for(int i = 0; i< transmissionVector.size(); i ++) {
 			// We need to get the identifier of the ith population model
 			String nextPop = groupList.get(i).getValue();

             //////////////////
 			// 1. compute BETA for transmission from the ith population to this population
 			 double specificTransmission = transmissionVector.get(i).getValue();
 			 double adjustedTransmission = getAdjustedTransmissionRate(specificTransmission, timeDelta);
 			 if(!this.isFrequencyDependent()) adjustedTransmission *= getTransmissionRateScaleFactor(diseaseLabel);


 			// we need to get the disease label for the ith population as well.
 			// to get the on site number of infectios individuals of type i
 			EList<NodeLabel> nodeLabels = thisNode.getLabels();
 			for(int j = 0; j < nodeLabels.size(); j ++) {
 				NodeLabel label = nodeLabels.get(j);
 				if(label instanceof SEIRLabel) {
 					if (this == ((SEIRLabel)label).getDecorator()) {
 						StandardDiseaseModelLabel otherDiseaseLabel = (StandardDiseaseModelLabel) label;
 						// now check the popualtion type
 						String otherPopulation = otherDiseaseLabel.getPopulationModelLabel().getPopulationIdentifier();
 						if(otherPopulation.equals(nextPop)) {
 							// Yes?
 							// then we found the label for the correct next population


 							// for this population we need to get the EFFECTIVE Infectious including
 							// ALL neighboring nodes
 							double onsiteInfectious = ((SEIRLabelValue) otherDiseaseLabel.getTempValue()).getI();
 							final double effectiveInfectious = getNormalizedEffectiveInfectious(
 									thisNode, otherDiseaseLabel, onsiteInfectious,
 									StandardPackage.Literals.SI_LABEL_VALUE__I);

 						    // ADD up the new incidence
 							numberOfSusceptibleToExposed += adjustedTransmission * numberSusceptible * effectiveInfectious;
 						}
 					}
 				}// if it's an SI label
 			}//for all labels in THIS node
 		}// For all population in the model

 		double numberOfInfectedToRecovered = getAdjustedRecoveryRate(thisRecoveryRate, timeDelta) * currentSEIR.getI();
 		double numberOfRecoveredToSusceptible = getAdjustedImmunityLossRate(thisImmunityLossRate, timeDelta) * currentSEIR.getR();
 		double numberOfExposedToInfected = getAdjustedIncubationRate(thisIncubationRate, timeDelta) * currentSEIR.getE();

 		// Determine delta S
 		final double deltaS = - numberOfSusceptibleToExposed + numberOfRecoveredToSusceptible;
 		// Delta E
 		final double deltaE = numberOfSusceptibleToExposed - numberOfExposedToInfected;
 		// Determine delta I
 		final double deltaI = numberOfExposedToInfected - numberOfInfectedToRecovered - diseaseDeaths;
 		// Determine delta R
 		final double deltaR = numberOfInfectedToRecovered - numberOfRecoveredToSusceptible;

 		SEIRLabelValueImpl ret = (SEIRLabelValueImpl)returnValue;
 		ret.setS(deltaS);
 		ret.setE(deltaE);
 		ret.setI(deltaI);
 		ret.setR(deltaR);
 		ret.setIncidence(numberOfSusceptibleToExposed);
 		ret.setDiseaseDeaths(diseaseDeaths);
 		return ret;

 	}

 	public double getAdjustedIncubationRate(double specificIncRate, long timeDelta) {
 		return (specificIncRate * ((double) timeDelta / (double) getTimePeriod()) );
 	} // getAdjustedIncubationRate

 	@Override
 	public DiseaseModelLabel createDiseaseModelLabel(String populationIdentifier) {
 		return StandardFactory.eINSTANCE.createSEIRLabel();
 	}

 	@Override
 	public DiseaseModelLabelValue createDiseaseModelLabelValue(String populationIdentifier) {
 		return StandardFactory.eINSTANCE.createSEIRLabelValue();
 	}


 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	@Override
 	public Object eGet(int featureID, boolean resolve, boolean coreType) {
 		switch (featureID) {
 			case MultipopulationPackage.MULTI_POPULATION_SEIR_DISEASE_MODEL__INCUBATION_RATE:
 				return getIncubationRate();
 		}
 		return super.eGet(featureID, resolve, coreType);
 	}

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	@Override
 	public void eSet(int featureID, Object newValue) {
 		switch (featureID) {
 			case MultipopulationPackage.MULTI_POPULATION_SEIR_DISEASE_MODEL__INCUBATION_RATE:
 				setIncubationRate((DoubleValueList)newValue);
 				return;
 		}
 		super.eSet(featureID, newValue);
 	}

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	@Override
 	public void eUnset(int featureID) {
 		switch (featureID) {
 			case MultipopulationPackage.MULTI_POPULATION_SEIR_DISEASE_MODEL__INCUBATION_RATE:
 				setIncubationRate((DoubleValueList)null);
 				return;
 		}
 		super.eUnset(featureID);
 	}

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	@Override
 	public boolean eIsSet(int featureID) {
 		switch (featureID) {
 			case MultipopulationPackage.MULTI_POPULATION_SEIR_DISEASE_MODEL__INCUBATION_RATE:
 				return incubationRate != null;
 		}
 		return super.eIsSet(featureID);
 	}

 } //MultiPopulationSEIRDiseaseModelImpl
	/*******************************************************************************
	* Copyright (c) 2009,2010 IBM Corporation and others.
	* All rights reserved. This program and the accompanying materials
	* are made available under the terms of the Eclipse Public License v1.0
	* which accompanies this distribution, and is available at
	* http://www.eclipse.org/legal/epl-v10.html
	*
	* Contributors:
	* IBM Corporation - initial API and implementation
	*******************************************************************************/
	package org.eclipse.stem.diseasemodels.multipopulation.impl;

	import org.eclipse.emf.common.notify.Notification;
	import org.eclipse.emf.common.notify.NotificationChain;
	import org.eclipse.emf.common.util.EList;
	import org.eclipse.emf.ecore.EClass;
	import org.eclipse.emf.ecore.InternalEObject;
	import org.eclipse.emf.ecore.impl.ENotificationImpl;
	import org.eclipse.stem.core.common.DoubleValue;
	import org.eclipse.stem.core.common.DoubleValueList;
	import org.eclipse.stem.core.common.StringValue;
	import org.eclipse.stem.core.graph.Node;
	import org.eclipse.stem.core.graph.NodeLabel;
	import org.eclipse.stem.core.model.STEMTime;
	import org.eclipse.stem.diseasemodels.multipopulation.MultiPopulationSEIRDiseaseModel;
	import org.eclipse.stem.diseasemodels.multipopulation.MultipopulationPackage;
	import org.eclipse.stem.diseasemodels.standard.DiseaseModelLabel;
	import org.eclipse.stem.diseasemodels.standard.DiseaseModelLabelValue;
	import org.eclipse.stem.diseasemodels.standard.SEIRLabel;
	import org.eclipse.stem.diseasemodels.standard.SEIRLabelValue;
	import org.eclipse.stem.diseasemodels.standard.StandardDiseaseModelLabel;
	import org.eclipse.stem.diseasemodels.standard.StandardDiseaseModelLabelValue;
	import org.eclipse.stem.diseasemodels.standard.StandardFactory;
	import org.eclipse.stem.diseasemodels.standard.StandardPackage;
	import org.eclipse.stem.diseasemodels.standard.impl.SEIRLabelValueImpl;

	/**
	* <!-- begin-user-doc -->
	* An implementation of the model object '<em><b>Multi Population SEIR Disease Model</b></em>'.
	* <!-- end-user-doc -->
	* <p>
	* The following features are implemented:
	* <ul>
	* <li>{@link org.eclipse.stem.diseasemodels.multipopulation.impl.MultiPopulationSEIRDiseaseModelImpl#getIncubationRate <em>Incubation Rate</em>}</li>
	* </ul>
	* </p>
	*
	* @generated
	*/
	public class MultiPopulationSEIRDiseaseModelImpl extends MultiPopulationSIRDiseaseModelImpl implements MultiPopulationSEIRDiseaseModel {
	/**
	* The cached value of the '{@link #getIncubationRate() <em>Incubation Rate</em>}' containment reference.
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @see #getIncubationRate()
	* @generated
	* @ordered
	*/
	protected DoubleValueList incubationRate;

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated NOT
	*/
	public MultiPopulationSEIRDiseaseModelImpl() {
	super();
	}

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	@Override
	protected EClass eStaticClass() {
	return MultipopulationPackage.Literals.MULTI_POPULATION_SEIR_DISEASE_MODEL;
	}

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	public DoubleValueList getIncubationRate() {
	return incubationRate;
	}

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	public NotificationChain basicSetIncubationRate(DoubleValueList newIncubationRate, NotificationChain msgs) {
	DoubleValueList oldIncubationRate = incubationRate;
	incubationRate = newIncubationRate;
	if (eNotificationRequired()) {
	ENotificationImpl notification = new ENotificationImpl(this, Notification.SET, MultipopulationPackage.MULTI_POPULATION_SEIR_DISEASE_MODEL__INCUBATION_RATE, oldIncubationRate, newIncubationRate);
	if (msgs == null) msgs = notification; else msgs.add(notification);
	}
	return msgs;
	}

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	public void setIncubationRate(DoubleValueList newIncubationRate) {
	if (newIncubationRate != incubationRate) {
	NotificationChain msgs = null;
	if (incubationRate != null)
	msgs = ((InternalEObject)incubationRate).eInverseRemove(this, EOPPOSITE_FEATURE_BASE - MultipopulationPackage.MULTI_POPULATION_SEIR_DISEASE_MODEL__INCUBATION_RATE, null, msgs);
	if (newIncubationRate != null)
	msgs = ((InternalEObject)newIncubationRate).eInverseAdd(this, EOPPOSITE_FEATURE_BASE - MultipopulationPackage.MULTI_POPULATION_SEIR_DISEASE_MODEL__INCUBATION_RATE, null, msgs);
	msgs = basicSetIncubationRate(newIncubationRate, msgs);
	if (msgs != null) msgs.dispatch();
	}
	else if (eNotificationRequired())
	eNotify(new ENotificationImpl(this, Notification.SET, MultipopulationPackage.MULTI_POPULATION_SEIR_DISEASE_MODEL__INCUBATION_RATE, newIncubationRate, newIncubationRate));
	}

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	@Override
	public NotificationChain eInverseRemove(InternalEObject otherEnd, int featureID, NotificationChain msgs) {
	switch (featureID) {
	case MultipopulationPackage.MULTI_POPULATION_SEIR_DISEASE_MODEL__INCUBATION_RATE:
	return basicSetIncubationRate(null, msgs);
	}
	return super.eInverseRemove(otherEnd, featureID, msgs);
	}

	@Override
	public StandardDiseaseModelLabelValue computeDiseaseDeltas(STEMTime time,
	StandardDiseaseModelLabelValue currentState,
	StandardDiseaseModelLabel diseaseLabel, long timeDelta,
	DiseaseModelLabelValue returnValue) {

	// THIS method gets called multiple times, once for each population identifier
	// in the population model.
	// which population is "this"....
	final SEIRLabelValue currentSEIR = (SEIRLabelValue) currentState;
	String thisPopulation = diseaseLabel.getPopulationModelLabel().getPopulationIdentifier();

	// Compute deaths
	final double adjustedInfectiousMortalityRate = getAdjustedInfectiousMortalityRate(timeDelta, thisPopulation);
	final double diseaseDeaths = adjustedInfectiousMortalityRate
	* currentSEIR.getI();

	// next get it's INDEX in the model
	int populationIndex = this.getPopulationIndex(thisPopulation);

	// now we know the index of the current population being integrated.
	// Get the correct transmission rate list from the MATRIX
	EList<DoubleValue> transmissionVector = getTransmissionRate().getValueLists().get(populationIndex).getValues();

	// ALL the other disease parameters are also DoubleValueLists. We now iterate through all populations
	// get the specific rate parameters from EACH list based on this population index
	double thisRecoveryRate = 0.0;
	if(getRecoveryRate() != null) thisRecoveryRate = getRecoveryRate().getValues().get(populationIndex).getValue();
	double thisImmunityLossRate = 0.0;
	if(getImmunityLossRate() != null)
	thisImmunityLossRate = getImmunityLossRate().getValues().get(populationIndex).getValue();
	double thisIncubationRate = 0.0;
	if(getIncubationRate() != null)
	thisIncubationRate = getIncubationRate().getValues().get(populationIndex).getValue();

	// NOW iterate over every population (including this one) to compute new infections
	// this includes infections within a population group
	// and all the cross terms
	double numberOfSusceptibleToExposed = 0.0;
	double numberSusceptible = currentSEIR.getS();
	Node thisNode = diseaseLabel.getNode();

	EList<StringValue> groupList = getPopulationGroups().getValues();

	for(int i = 0; i< transmissionVector.size(); i ++) {
	// We need to get the identifier of the ith population model
	String nextPop = groupList.get(i).getValue();

	//////////////////
	// 1. compute BETA for transmission from the ith population to this population
	double specificTransmission = transmissionVector.get(i).getValue();
	double adjustedTransmission = getAdjustedTransmissionRate(specificTransmission, timeDelta);
	if(!this.isFrequencyDependent()) adjustedTransmission *= getTransmissionRateScaleFactor(diseaseLabel);


	// we need to get the disease label for the ith population as well.
	// to get the on site number of infectios individuals of type i
	EList<NodeLabel> nodeLabels = thisNode.getLabels();
	for(int j = 0; j < nodeLabels.size(); j ++) {
	NodeLabel label = nodeLabels.get(j);
	if(label instanceof SEIRLabel) {
	if (this == ((SEIRLabel)label).getDecorator()) {
	StandardDiseaseModelLabel otherDiseaseLabel = (StandardDiseaseModelLabel) label;
	// now check the popualtion type
	String otherPopulation = otherDiseaseLabel.getPopulationModelLabel().getPopulationIdentifier();
	if(otherPopulation.equals(nextPop)) {
	// Yes?
	// then we found the label for the correct next population


	// for this population we need to get the EFFECTIVE Infectious including
	// ALL neighboring nodes
	double onsiteInfectious = ((SEIRLabelValue) otherDiseaseLabel.getTempValue()).getI();
	final double effectiveInfectious = getNormalizedEffectiveInfectious(
	thisNode, otherDiseaseLabel, onsiteInfectious,
	StandardPackage.Literals.SI_LABEL_VALUE__I);

	// ADD up the new incidence
	numberOfSusceptibleToExposed += adjustedTransmission * numberSusceptible * effectiveInfectious;
	}
	}
	}// if it's an SI label
	}//for all labels in THIS node
	}// For all population in the model

	double numberOfInfectedToRecovered = getAdjustedRecoveryRate(thisRecoveryRate, timeDelta) * currentSEIR.getI();
	double numberOfRecoveredToSusceptible = getAdjustedImmunityLossRate(thisImmunityLossRate, timeDelta) * currentSEIR.getR();
	double numberOfExposedToInfected = getAdjustedIncubationRate(thisIncubationRate, timeDelta) * currentSEIR.getE();

	// Determine delta S
	final double deltaS = - numberOfSusceptibleToExposed + numberOfRecoveredToSusceptible;
	// Delta E
	final double deltaE = numberOfSusceptibleToExposed - numberOfExposedToInfected;
	// Determine delta I
	final double deltaI = numberOfExposedToInfected - numberOfInfectedToRecovered - diseaseDeaths;
	// Determine delta R
	final double deltaR = numberOfInfectedToRecovered - numberOfRecoveredToSusceptible;

	SEIRLabelValueImpl ret = (SEIRLabelValueImpl)returnValue;
	ret.setS(deltaS);
	ret.setE(deltaE);
	ret.setI(deltaI);
	ret.setR(deltaR);
	ret.setIncidence(numberOfSusceptibleToExposed);
	ret.setDiseaseDeaths(diseaseDeaths);
	return ret;

	}

	public double getAdjustedIncubationRate(double specificIncRate, long timeDelta) {
	return (specificIncRate * ((double) timeDelta / (double) getTimePeriod()) );
	} // getAdjustedIncubationRate

	@Override
	public DiseaseModelLabel createDiseaseModelLabel(String populationIdentifier) {
	return StandardFactory.eINSTANCE.createSEIRLabel();
	}

	@Override
	public DiseaseModelLabelValue createDiseaseModelLabelValue(String populationIdentifier) {
	return StandardFactory.eINSTANCE.createSEIRLabelValue();
	}



	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	@Override
	public Object eGet(int featureID, boolean resolve, boolean coreType) {
	switch (featureID) {
	case MultipopulationPackage.MULTI_POPULATION_SEIR_DISEASE_MODEL__INCUBATION_RATE:
	return getIncubationRate();
	}
	return super.eGet(featureID, resolve, coreType);
	}

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	@Override
	public void eSet(int featureID, Object newValue) {
	switch (featureID) {
	case MultipopulationPackage.MULTI_POPULATION_SEIR_DISEASE_MODEL__INCUBATION_RATE:
	setIncubationRate((DoubleValueList)newValue);
	return;
	}
	super.eSet(featureID, newValue);
	}

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	@Override
	public void eUnset(int featureID) {
	switch (featureID) {
	case MultipopulationPackage.MULTI_POPULATION_SEIR_DISEASE_MODEL__INCUBATION_RATE:
	setIncubationRate((DoubleValueList)null);
	return;
	}
	super.eUnset(featureID);
	}

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated
	*/
	@Override
	public boolean eIsSet(int featureID) {
	switch (featureID) {
	case MultipopulationPackage.MULTI_POPULATION_SEIR_DISEASE_MODEL__INCUBATION_RATE:
	return incubationRate != null;
	}
	return super.eIsSet(featureID);
	}

	} //MultiPopulationSEIRDiseaseModelImpl