models/epidemiology/org.eclipse.stem.diseasemodels/src/org/eclipse/stem/diseasemodels/standard/impl/SEIRImpl.java - stem/org.eclipse.stem - Git at Google

 package org.eclipse.stem.diseasemodels.standard.impl;

 /*******************************************************************************
  * Copyright (c) 2006 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
  *******************************************************************************/

 import org.eclipse.emf.common.notify.Notification;
 import org.eclipse.emf.ecore.EClass;
 import org.eclipse.emf.ecore.impl.ENotificationImpl;
 import org.eclipse.stem.core.graph.Node;
 import org.eclipse.stem.core.model.STEMTime;
 import org.eclipse.stem.diseasemodels.standard.DiseaseModelLabel;
 import org.eclipse.stem.diseasemodels.standard.DiseaseModelLabelValue;
 import org.eclipse.stem.diseasemodels.standard.SEIR;
 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.interventions.StandardInterventionLabel;
 import org.eclipse.stem.interventions.StandardInterventionLabelValue;

 /**
  * <!-- begin-user-doc --> An implementation of the model object '<em><b>SEIR</b></em>'.
  * <!-- end-user-doc -->
  * <p>
  * The following features are implemented:
  * <ul>
  *   <li>{@link org.eclipse.stem.diseasemodels.standard.impl.SEIRImpl#getIncubationRate <em>Incubation Rate</em>}</li>
  * </ul>
  * </p>
  *
  * @generated
  */
 public abstract class SEIRImpl extends SIRImpl implements SEIR {

 	/**
 	 * The default value of the '{@link #getIncubationRate() <em>Incubation Rate</em>}' attribute.
 	 * <!-- begin-user-doc --> <!-- end-user-doc -->
 	 * @see #getIncubationRate()
 	 * @generated
 	 * @ordered
 	 */
 	protected static final double INCUBATION_RATE_EDEFAULT = 0.0;

 	/**
 	 * The cached value of the '{@link #getIncubationRate() <em>Incubation Rate</em>}' attribute.
 	 * <!-- begin-user-doc --> <!-- end-user-doc -->
 	 * @see #getIncubationRate()
 	 * @generated
 	 * @ordered
 	 */
 	protected double incubationRate = INCUBATION_RATE_EDEFAULT;

 	/**
 	 * <!-- begin-user-doc --> <!-- end-user-doc -->
 	 * @generated
 	 */
 	protected SEIRImpl() {
 		super();
 	}

 	/**
 	 * @see org.eclipse.stem.diseasemodels.standard.impl.SIImpl#computeDiseaseDeltas(StandardDiseaseModelLabelValue,
 	 *      StandardDiseaseModelLabel, long)
 	 */
 	@Override
 	public StandardDiseaseModelLabelValue computeDiseaseDeltas(
 			final STEMTime time,
 			final StandardDiseaseModelLabelValue currentState,
 			final StandardDiseaseModelLabel diseaseLabel, final long timeDelta, DiseaseModelLabelValue returnValue) {
 		final SEIRLabelValue currentSEIR = (SEIRLabelValue) currentState;

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

 		// This is beta*
 		double transmissionRate = getAdjustedTransmissionRate(timeDelta);

 		if(!this.isFrequencyDependent()) transmissionRate *= getTransmissionRateScaleFactor(diseaseLabel);


 		// The effective Infectious population  is a dimensionles number normalize by total
 		// population used in teh computation of bets*S*i where i = Ieffective/Pop.
 		// This includes a correction to the current
 		// infectious population (Ieffective) based on the conserved exchange of people (circulation)
 		// between regions. Note that this is no the "arrivals" and "departures" which are
 		// a different process.
 		final double effectiveInfectious = getNormalizedEffectiveInfectious(diseaseLabel.getNode(), diseaseLabel, currentSEIR.getI(), StandardPackage.Literals.SI_LABEL_VALUE__I);

 		/*
 		 * Compute state transitions
 		 *
 		 * Regarding computing the number of transitions from Susceptible to Exposed:
 		 * In a linear model the "effective" number of infectious people is just
 		 * the number of infectious people In a nonlinear model we have a
 		 * nonLinearity exponent that is > 1 this models the effect of immune
 		 * system saturation when Susceptible people are exposed to large
 		 * numbers of infectious people. then the "effective" number of
 		 * infectious people is I^nonLinearity exponent to allow for either
 		 * linear or nonlinear models we always calculate I^nonLinearity
 		 * exponent and allow nonLinearity exponent >= 1.0
 		 */
 		double numberOfInfectedToRecovered = getAdjustedRecoveryRate(timeDelta)
 		* currentSEIR.getI();
 		double numberOfRecoveredToSusceptible = getAdjustedImmunityLossRate(timeDelta)
 		* currentSEIR.getR();
 		// Need to checked what do do here. If non linear coefficient is not 1 and
 		// the effective infectious is negative (which is possible), what do do?
 		// Let's fall back on the linear method for now.
 		double numberOfSusceptibleToExposed = 0.0;
 		if(getNonLinearityCoefficient() != 1.0 && effectiveInfectious >=0.0)
 			numberOfSusceptibleToExposed = transmissionRate
 			* currentSEIR.getS()* Math.pow(effectiveInfectious, getNonLinearityCoefficient());
 		else
 			numberOfSusceptibleToExposed = transmissionRate
 			* currentSEIR.getS()* effectiveInfectious;
 		double numberOfExposedToInfectious = getAdjustedIncubationRate(timeDelta)
 		* currentSEIR.getE();


 		// Determine delta S
 		double deltaS = numberOfRecoveredToSusceptible - numberOfSusceptibleToExposed;
 		// Determine delta E
 		double deltaE = numberOfSusceptibleToExposed - numberOfExposedToInfectious;
 		// Determine delta I
 		double deltaI = numberOfExposedToInfectious - numberOfInfectedToRecovered - diseaseDeaths;
 		// Determine delta R
 		double deltaR = numberOfInfectedToRecovered - numberOfRecoveredToSusceptible;

 		StandardInterventionLabel scl = findInterventionLabel((Node)diseaseLabel.getIdentifiable());
 		if(scl != null) {
 			double vaccinations = ((StandardInterventionLabelValue)scl.getCurrentValue()).getVaccinations();
 			double isolations = ((StandardInterventionLabelValue)scl.getCurrentValue()).getIsolations();
 			vaccinations *= ((double) timeDelta / (double) getTimePeriod());
 			isolations *= ((double) timeDelta / (double) getTimePeriod());
 			if(currentSEIR.getS() < vaccinations) vaccinations = currentSEIR.getS();
 			if(currentSEIR.getI() < isolations) isolations = currentSEIR.getI();

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

 	} // computeDiseaseDeltas

 	/**
 	 * @see org.eclipse.stem.diseasemodels.standard.impl.DiseaseModelImpl#createDiseaseModelLabel()
 	 */
 	@Override
 	public DiseaseModelLabel createDiseaseModelLabel(String populationIdentifier) {
 		return StandardFactory.eINSTANCE.createSEIRLabel();
 	} // createDiseaseModelLabel

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


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

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

 	/**
 	 * <!-- begin-user-doc -->
 	 *
 	 * @param newIncubationRate
 	 *
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	public void setIncubationRate(double newIncubationRate) {
 		double oldIncubationRate = incubationRate;
 		incubationRate = newIncubationRate;
 		if (eNotificationRequired())
 			eNotify(new ENotificationImpl(this, Notification.SET, StandardPackage.SEIR__INCUBATION_RATE, oldIncubationRate, incubationRate));
 	}

 	/**
 	 * <!-- begin-user-doc -->
 	 *
 	 * @param timeDelta
 	 *            the time period to adjust the rate to
 	 * @return the adjusted rate
 	 *
 	 * <!-- end-user-doc -->
 	 * @generated NOT
 	 */
 	public double getAdjustedIncubationRate(long timeDelta) {
 		return getIncubationRate()
 				* ((double) timeDelta / (double) getTimePeriod());
 	} // getAdjustedIncubationRate


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

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

 	/**
 	 * <!-- begin-user-doc -->
 	 *
 	 * @param featureID
 	 *
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	@Override
 	public void eUnset(int featureID) {
 		switch (featureID) {
 			case StandardPackage.SEIR__INCUBATION_RATE:
 				setIncubationRate(INCUBATION_RATE_EDEFAULT);
 				return;
 		}
 		super.eUnset(featureID);
 	}

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

 	/**
 	 * <!-- begin-user-doc -->
 	 *
 	 * @return
 	 *
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	@Override
 	public String toString() {
 		if (eIsProxy()) return super.toString();

 		StringBuffer result = new StringBuffer(super.toString());
 		result.append(" (incubationRate: "); //$NON-NLS-1$
 		result.append(incubationRate);
 		result.append(')');
 		return result.toString();
 	}

 	/**
 	 * @see org.eclipse.stem.core.model.impl.NodeDecoratorImpl#sane()
 	 */
 	@Override
 	public boolean sane() {
 		boolean retValue = super.sane();

 		retValue = retValue && getIncubationRate() >= INCUBATION_RATE_EDEFAULT;
 		assert retValue;

 		retValue = retValue && !Double.isInfinite(getIncubationRate());
 		assert retValue;

 		retValue = retValue && !Double.isNaN(getIncubationRate());
 		assert retValue;

 		return retValue;
 	} // sane

 } // SEIRImpl
	package org.eclipse.stem.diseasemodels.standard.impl;

	/*******************************************************************************
	* Copyright (c) 2006 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
	*******************************************************************************/

	import org.eclipse.emf.common.notify.Notification;
	import org.eclipse.emf.ecore.EClass;
	import org.eclipse.emf.ecore.impl.ENotificationImpl;
	import org.eclipse.stem.core.graph.Node;
	import org.eclipse.stem.core.model.STEMTime;
	import org.eclipse.stem.diseasemodels.standard.DiseaseModelLabel;
	import org.eclipse.stem.diseasemodels.standard.DiseaseModelLabelValue;
	import org.eclipse.stem.diseasemodels.standard.SEIR;
	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.interventions.StandardInterventionLabel;
	import org.eclipse.stem.interventions.StandardInterventionLabelValue;

	/**
	* <!-- begin-user-doc --> An implementation of the model object '<em><b>SEIR</b></em>'.
	* <!-- end-user-doc -->
	* <p>
	* The following features are implemented:
	* <ul>
	* <li>{@link org.eclipse.stem.diseasemodels.standard.impl.SEIRImpl#getIncubationRate <em>Incubation Rate</em>}</li>
	* </ul>
	* </p>
	*
	* @generated
	*/
	public abstract class SEIRImpl extends SIRImpl implements SEIR {

	/**
	* The default value of the '{@link #getIncubationRate() <em>Incubation Rate</em>}' attribute.
	* <!-- begin-user-doc --> <!-- end-user-doc -->
	* @see #getIncubationRate()
	* @generated
	* @ordered
	*/
	protected static final double INCUBATION_RATE_EDEFAULT = 0.0;

	/**
	* The cached value of the '{@link #getIncubationRate() <em>Incubation Rate</em>}' attribute.
	* <!-- begin-user-doc --> <!-- end-user-doc -->
	* @see #getIncubationRate()
	* @generated
	* @ordered
	*/
	protected double incubationRate = INCUBATION_RATE_EDEFAULT;

	/**
	* <!-- begin-user-doc --> <!-- end-user-doc -->
	* @generated
	*/
	protected SEIRImpl() {
	super();
	}

	/**
	* @see org.eclipse.stem.diseasemodels.standard.impl.SIImpl#computeDiseaseDeltas(StandardDiseaseModelLabelValue,
	* StandardDiseaseModelLabel, long)
	*/
	@Override
	public StandardDiseaseModelLabelValue computeDiseaseDeltas(
	final STEMTime time,
	final StandardDiseaseModelLabelValue currentState,
	final StandardDiseaseModelLabel diseaseLabel, final long timeDelta, DiseaseModelLabelValue returnValue) {
	final SEIRLabelValue currentSEIR = (SEIRLabelValue) currentState;

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

	// This is beta*
	double transmissionRate = getAdjustedTransmissionRate(timeDelta);

	if(!this.isFrequencyDependent()) transmissionRate *= getTransmissionRateScaleFactor(diseaseLabel);


	// The effective Infectious population is a dimensionles number normalize by total
	// population used in teh computation of betsSi where i = Ieffective/Pop.
	// This includes a correction to the current
	// infectious population (Ieffective) based on the conserved exchange of people (circulation)
	// between regions. Note that this is no the "arrivals" and "departures" which are
	// a different process.
	final double effectiveInfectious = getNormalizedEffectiveInfectious(diseaseLabel.getNode(), diseaseLabel, currentSEIR.getI(), StandardPackage.Literals.SI_LABEL_VALUE__I);

	/*
	* Compute state transitions
	*
	* Regarding computing the number of transitions from Susceptible to Exposed:
	* In a linear model the "effective" number of infectious people is just
	* the number of infectious people In a nonlinear model we have a
	* nonLinearity exponent that is > 1 this models the effect of immune
	* system saturation when Susceptible people are exposed to large
	* numbers of infectious people. then the "effective" number of
	* infectious people is I^nonLinearity exponent to allow for either
	* linear or nonlinear models we always calculate I^nonLinearity
	* exponent and allow nonLinearity exponent >= 1.0
	*/
	double numberOfInfectedToRecovered = getAdjustedRecoveryRate(timeDelta)
	* currentSEIR.getI();
	double numberOfRecoveredToSusceptible = getAdjustedImmunityLossRate(timeDelta)
	* currentSEIR.getR();
	// Need to checked what do do here. If non linear coefficient is not 1 and
	// the effective infectious is negative (which is possible), what do do?
	// Let's fall back on the linear method for now.
	double numberOfSusceptibleToExposed = 0.0;
	if(getNonLinearityCoefficient() != 1.0 && effectiveInfectious >=0.0)
	numberOfSusceptibleToExposed = transmissionRate
	* currentSEIR.getS()* Math.pow(effectiveInfectious, getNonLinearityCoefficient());
	else
	numberOfSusceptibleToExposed = transmissionRate
	* currentSEIR.getS()* effectiveInfectious;
	double numberOfExposedToInfectious = getAdjustedIncubationRate(timeDelta)
	* currentSEIR.getE();


	// Determine delta S
	double deltaS = numberOfRecoveredToSusceptible - numberOfSusceptibleToExposed;
	// Determine delta E
	double deltaE = numberOfSusceptibleToExposed - numberOfExposedToInfectious;
	// Determine delta I
	double deltaI = numberOfExposedToInfectious - numberOfInfectedToRecovered - diseaseDeaths;
	// Determine delta R
	double deltaR = numberOfInfectedToRecovered - numberOfRecoveredToSusceptible;

	StandardInterventionLabel scl = findInterventionLabel((Node)diseaseLabel.getIdentifiable());
	if(scl != null) {
	double vaccinations = ((StandardInterventionLabelValue)scl.getCurrentValue()).getVaccinations();
	double isolations = ((StandardInterventionLabelValue)scl.getCurrentValue()).getIsolations();
	vaccinations *= ((double) timeDelta / (double) getTimePeriod());
	isolations *= ((double) timeDelta / (double) getTimePeriod());
	if(currentSEIR.getS() < vaccinations) vaccinations = currentSEIR.getS();
	if(currentSEIR.getI() < isolations) isolations = currentSEIR.getI();

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

	} // computeDiseaseDeltas

	/**
	* @see org.eclipse.stem.diseasemodels.standard.impl.DiseaseModelImpl#createDiseaseModelLabel()
	*/
	@Override
	public DiseaseModelLabel createDiseaseModelLabel(String populationIdentifier) {
	return StandardFactory.eINSTANCE.createSEIRLabel();
	} // createDiseaseModelLabel

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


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

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

	/**
	* <!-- begin-user-doc -->
	*
	* @param newIncubationRate
	*
	* <!-- end-user-doc -->
	* @generated
	*/
	public void setIncubationRate(double newIncubationRate) {
	double oldIncubationRate = incubationRate;
	incubationRate = newIncubationRate;
	if (eNotificationRequired())
	eNotify(new ENotificationImpl(this, Notification.SET, StandardPackage.SEIR__INCUBATION_RATE, oldIncubationRate, incubationRate));
	}

	/**
	* <!-- begin-user-doc -->
	*
	* @param timeDelta
	* the time period to adjust the rate to
	* @return the adjusted rate
	*
	* <!-- end-user-doc -->
	* @generated NOT
	*/
	public double getAdjustedIncubationRate(long timeDelta) {
	return getIncubationRate()
	* ((double) timeDelta / (double) getTimePeriod());
	} // getAdjustedIncubationRate


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

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

	/**
	* <!-- begin-user-doc -->
	*
	* @param featureID
	*
	* <!-- end-user-doc -->
	* @generated
	*/
	@Override
	public void eUnset(int featureID) {
	switch (featureID) {
	case StandardPackage.SEIR__INCUBATION_RATE:
	setIncubationRate(INCUBATION_RATE_EDEFAULT);
	return;
	}
	super.eUnset(featureID);
	}

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

	/**
	* <!-- begin-user-doc -->
	*
	* @return
	*
	* <!-- end-user-doc -->
	* @generated
	*/
	@Override
	public String toString() {
	if (eIsProxy()) return super.toString();

	StringBuffer result = new StringBuffer(super.toString());
	result.append(" (incubationRate: "); //$NON-NLS-1$
	result.append(incubationRate);
	result.append(')');
	return result.toString();
	}

	/**
	* @see org.eclipse.stem.core.model.impl.NodeDecoratorImpl#sane()
	*/
	@Override
	public boolean sane() {
	boolean retValue = super.sane();

	retValue = retValue && getIncubationRate() >= INCUBATION_RATE_EDEFAULT;
	assert retValue;

	retValue = retValue && !Double.isInfinite(getIncubationRate());
	assert retValue;

	retValue = retValue && !Double.isNaN(getIncubationRate());
	assert retValue;

	return retValue;
	} // sane

	} // SEIRImpl