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

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

 /*******************************************************************************
  * Copyright (c) 2006, 2008 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.model.STEMTime;
 import org.eclipse.stem.diseasemodels.standard.DiseaseModelLabel;
 import org.eclipse.stem.diseasemodels.standard.DiseaseModelLabelValue;
 import org.eclipse.stem.diseasemodels.standard.Infector;
 import org.eclipse.stem.diseasemodels.standard.SI;
 import org.eclipse.stem.diseasemodels.standard.SIInfector;
 import org.eclipse.stem.diseasemodels.standard.SILabelValue;
 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;

 /**
  * <!-- begin-user-doc --> An implementation of the model object '<em><b>SI</b></em>'.
  * <!-- end-user-doc -->
  * <p>
  * The following features are implemented:
  * <ul>
  *   <li>{@link org.eclipse.stem.diseasemodels.standard.impl.SIImpl#getTransmissionRate <em>Transmission Rate</em>}</li>
  *   <li>{@link org.eclipse.stem.diseasemodels.standard.impl.SIImpl#getNonLinearityCoefficient <em>Non Linearity Coefficient</em>}</li>
  *   <li>{@link org.eclipse.stem.diseasemodels.standard.impl.SIImpl#getRecoveryRate <em>Recovery Rate</em>}</li>
  *   <li>{@link org.eclipse.stem.diseasemodels.standard.impl.SIImpl#getInfectiousMortalityRate <em>Infectious Mortality Rate</em>}</li>
  * </ul>
  * </p>
  *
  * @generated
  */
 public abstract class SIImpl extends StandardDiseaseModelImpl implements SI {
 	/**
 	 * The default value of the '{@link #getTransmissionRate() <em>Transmission Rate</em>}' attribute.
 	 * <!-- begin-user-doc --> <!-- end-user-doc -->
 	 * @see #getTransmissionRate()
 	 * @generated
 	 * @ordered
 	 */
 	protected static final double TRANSMISSION_RATE_EDEFAULT = 0.0;

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

 	/**
 	 * The default value of the '{@link #getNonLinearityCoefficient() <em>Non Linearity Coefficient</em>}' attribute.
 	 * <!-- begin-user-doc --> <!-- end-user-doc -->
 	 * @see #getNonLinearityCoefficient()
 	 * @generated
 	 * @ordered
 	 */
 	protected static final double NON_LINEARITY_COEFFICIENT_EDEFAULT = 1.0;

 	/**
 	 * The cached value of the '{@link #getNonLinearityCoefficient() <em>Non Linearity Coefficient</em>}' attribute.
 	 * <!-- begin-user-doc --> <!-- end-user-doc -->
 	 * @see #getNonLinearityCoefficient()
 	 * @generated
 	 * @ordered
 	 */
 	protected double nonLinearityCoefficient = NON_LINEARITY_COEFFICIENT_EDEFAULT;

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

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

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

 	/**
 	 * The cached value of the '{@link #getInfectiousMortalityRate() <em>Infectious Mortality Rate</em>}' attribute.
 	 * <!-- begin-user-doc --> <!-- end-user-doc -->
 	 * @see #getInfectiousMortalityRate()
 	 * @generated
 	 * @ordered
 	 */
 	protected double infectiousMortalityRate = INFECTIOUS_MORTALITY_RATE_EDEFAULT;

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

 	/**
 	 * @see org.eclipse.stem.diseasemodels.standard.impl.StandardDiseaseModelImpl#computeTransitions(org.eclipse.stem.diseasemodels.standard.StandardDiseaseModelLabelValue,
 	 *      long, double, long)
 	 */
 	@Override
 	public StandardDiseaseModelLabelValue computeDiseaseDeltas(
 			final STEMTime time, double t,
 			final StandardDiseaseModelLabelValue currentState,
 			final StandardDiseaseModelLabel diseaseLabel, final long timeDelta, DiseaseModelLabelValue returnValue) {

 		final SILabelValue currentSI = (SILabelValue) currentState;

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

 		// 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 numberOfSusceptibleToInfected = 0.0;
 		if(getNonLinearityCoefficient() != 1.0 && effectiveInfectious >= 0.0)
 			numberOfSusceptibleToInfected = transmissionRate
 			* currentSI.getS()* Math.pow(effectiveInfectious, getNonLinearityCoefficient());
 		else
 			numberOfSusceptibleToInfected = transmissionRate
 			* currentSI.getS()* effectiveInfectious;

 		double numberOfInfectedToSusceptible = getAdjustedRecoveryRate(timeDelta)
 				* currentSI.getI();


 		// Determine delta S
 		final double deltaS = - numberOfSusceptibleToInfected + numberOfInfectedToSusceptible;
 		// Determine delta I
 		final double deltaI = numberOfSusceptibleToInfected - numberOfInfectedToSusceptible - diseaseDeaths;

 		SILabelValueImpl ret = (SILabelValueImpl)returnValue;
 		ret.setS(deltaS);
 		ret.setI(deltaI);
 		ret.setIncidence(numberOfSusceptibleToInfected);
 		ret.setDiseaseDeaths(diseaseDeaths);
 		return ret;
 	} // computeDiseaseDeltas


 	/**
 	 * This method is used to scale the transmission rate.
  	 * it returns the local density divided by a "reference" density
 	 * @param diseaseLabel the label being processed
 	 * @return the transmission rate scale factor for the label being processed
 	 */
 	public double getTransmissionRateScaleFactor(
 			StandardDiseaseModelLabel diseaseLabel) {
 		//final StandardDiseaseModelState sdms = (StandardDiseaseModelState) diseaseLabel
 		//		.getDiseaseModelState();

 		double referenceDensity = getReferencePopulationDensity();
 		// assert(referenceDensity > 0);
 		// need editor check so ref density always >1. Default is 100.
 		assert getArea(diseaseLabel.getPopulationLabel()) > 0.0;
 		double localDensity = ((StandardDiseaseModelLabelValue)diseaseLabel.getTempValue()).getPopulationCount()/getArea(diseaseLabel.getPopulationLabel());
 		return localDensity/referenceDensity;
 	} // getTransmissionRateScaleFactor


 	/**
 	 * The <em>infectious mortality rate</em> is the rate at which
 	 * <em>Infectious</em> population members die. Basically, that rate is
 	 * simply the proportional fraction of the flow into the <em>Infectious</em>
 	 * state.
 	 *
 	 * @param infectiousInputRate
 	 *            the rate at which population members enter the infectious
 	 *            state (&beta;)
 	 * @param infectiousMortality
 	 *            the proportion of population members that die from the disease
 	 *            (x)
 	 * @return the rate at which population members die from the disease
 	 */
 //	public double computeInfectiousMortalityRate(
 //			final double infectiousInputRate, final double infectiousMortality) {
 //		return infectiousMortality * infectiousInputRate;
 //	} // computeInfectiousMortalityRate


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

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


 	/**
 	 * @see org.eclipse.stem.diseasemodels.standard.impl.DiseaseModelImpl#createInfector()
 	 */
 	@Override
 	public Infector createInfector() {
 		SIInfector retValue = StandardFactory.eINSTANCE.createSIInfector();
 		retValue.setDiseaseName(this.getDiseaseName());
 		retValue.setPopulationIdentifier(getPopulationIdentifier());
 		return retValue;
 	} // createInfector

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

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

 	/**
 	 * <!-- begin-user-doc -->
 	 *
 	 * @param newTransmissionRate
 	 *
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	public void setTransmissionRate(double newTransmissionRate) {
 		double oldTransmissionRate = transmissionRate;
 		transmissionRate = newTransmissionRate;
 		if (eNotificationRequired())
 			eNotify(new ENotificationImpl(this, Notification.SET, StandardPackage.SI__TRANSMISSION_RATE, oldTransmissionRate, transmissionRate));
 	}

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

 	/**
 	 * <!-- begin-user-doc -->
 	 *
 	 * @param newRecoveryRate
 	 *
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	public void setRecoveryRate(double newRecoveryRate) {
 		double oldRecoveryRate = recoveryRate;
 		recoveryRate = newRecoveryRate;
 		if (eNotificationRequired())
 			eNotify(new ENotificationImpl(this, Notification.SET, StandardPackage.SI__RECOVERY_RATE, oldRecoveryRate, recoveryRate));
 	}

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

 	/**
 	 * <!-- begin-user-doc --> <!-- end-user-doc -->
 	 * @generated
 	 */
 	public void setInfectiousMortalityRate(double newInfectiousMortalityRate) {
 		double oldInfectiousMortalityRate = infectiousMortalityRate;
 		infectiousMortalityRate = newInfectiousMortalityRate;
 		if (eNotificationRequired())
 			eNotify(new ENotificationImpl(this, Notification.SET, StandardPackage.SI__INFECTIOUS_MORTALITY_RATE, oldInfectiousMortalityRate, infectiousMortalityRate));
 	}

 	/**
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @generated NOT
 	 */
 	public double getAdjustedInfectiousMortalityRate(long timeDelta) {
 		// TODO this division can be eliminated if timeDelta==getTimePeriod
 		return getInfectiousMortalityRate()
 		* ((double) timeDelta / (double) getTimePeriod());
 	} // getAdjustedInfectiousMortalityRate

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

 	/**
 	 * <!-- begin-user-doc -->
 	 *
 	 * @param newNonLinearityCoefficient
 	 *
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	public void setNonLinearityCoefficient(double newNonLinearityCoefficient) {
 		double oldNonLinearityCoefficient = nonLinearityCoefficient;
 		nonLinearityCoefficient = newNonLinearityCoefficient;
 		if (eNotificationRequired())
 			eNotify(new ENotificationImpl(this, Notification.SET, StandardPackage.SI__NON_LINEARITY_COEFFICIENT, oldNonLinearityCoefficient, nonLinearityCoefficient));
 	}

 	/**
 	 * <!-- begin-user-doc -->
 	 * Returns the time interval deltaT divided by the initial time period
 	 * @param timeDelta
 	 *
 	 * @return
 	 *
 	 * <!-- end-user-doc -->
 	 *
 	 * @generated NOT
 	 */
 	public double getAdjustedTransmissionRate(long timeDelta) {
 		return getTransmissionRate()
 				* ((double) timeDelta / (double) getTimePeriod());
 	} // getAdjustedTransmissionRate

 	/**
 	 * <!-- begin-user-doc -->
 	 *
 	 * @param timeDelta
 	 *
 	 * @return
 	 *
 	 * <!-- end-user-doc -->
 	 *
 	 * @generated NOT
 	 */
 	public double getAdjustedRecoveryRate(long timeDelta) {
 		return getRecoveryRate()
 				* ((double) timeDelta / (double) getTimePeriod());
 	} // getAdjustedRecoveryRate

 	/**
 	 * <!-- 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.SI__TRANSMISSION_RATE:
 				return getTransmissionRate();
 			case StandardPackage.SI__NON_LINEARITY_COEFFICIENT:
 				return getNonLinearityCoefficient();
 			case StandardPackage.SI__RECOVERY_RATE:
 				return getRecoveryRate();
 			case StandardPackage.SI__INFECTIOUS_MORTALITY_RATE:
 				return getInfectiousMortalityRate();
 		}
 		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.SI__TRANSMISSION_RATE:
 				setTransmissionRate((Double)newValue);
 				return;
 			case StandardPackage.SI__NON_LINEARITY_COEFFICIENT:
 				setNonLinearityCoefficient((Double)newValue);
 				return;
 			case StandardPackage.SI__RECOVERY_RATE:
 				setRecoveryRate((Double)newValue);
 				return;
 			case StandardPackage.SI__INFECTIOUS_MORTALITY_RATE:
 				setInfectiousMortalityRate((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.SI__TRANSMISSION_RATE:
 				setTransmissionRate(TRANSMISSION_RATE_EDEFAULT);
 				return;
 			case StandardPackage.SI__NON_LINEARITY_COEFFICIENT:
 				setNonLinearityCoefficient(NON_LINEARITY_COEFFICIENT_EDEFAULT);
 				return;
 			case StandardPackage.SI__RECOVERY_RATE:
 				setRecoveryRate(RECOVERY_RATE_EDEFAULT);
 				return;
 			case StandardPackage.SI__INFECTIOUS_MORTALITY_RATE:
 				setInfectiousMortalityRate(INFECTIOUS_MORTALITY_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.SI__TRANSMISSION_RATE:
 				return transmissionRate != TRANSMISSION_RATE_EDEFAULT;
 			case StandardPackage.SI__NON_LINEARITY_COEFFICIENT:
 				return nonLinearityCoefficient != NON_LINEARITY_COEFFICIENT_EDEFAULT;
 			case StandardPackage.SI__RECOVERY_RATE:
 				return recoveryRate != RECOVERY_RATE_EDEFAULT;
 			case StandardPackage.SI__INFECTIOUS_MORTALITY_RATE:
 				return infectiousMortalityRate != INFECTIOUS_MORTALITY_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(" (transmissionRate: "); //$NON-NLS-1$
 		result.append(transmissionRate);
 		result.append(", nonLinearityCoefficient: "); //$NON-NLS-1$
 		result.append(nonLinearityCoefficient);
 		result.append(", recoveryRate: "); //$NON-NLS-1$
 		result.append(recoveryRate);
 		result.append(", infectiousMortalityRate: "); //$NON-NLS-1$
 		result.append(infectiousMortalityRate);
 		result.append(')');
 		return result.toString();
 	}

 	/**
 	 * @see org.eclipse.stem.diseasemodels.standard.impl.StandardDiseaseModelImpl#sane()
 	 */
 	@Override
 	public boolean sane() {
 		boolean retValue = super.sane();

 		// transmissionRate
 		retValue = retValue && getTransmissionRate() >= TRANSMISSION_RATE_EDEFAULT;
 		assert retValue;

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

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

 		// recoveryRate
 		retValue = retValue && getRecoveryRate() >= RECOVERY_RATE_EDEFAULT;
 		assert retValue;

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

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

 		// nonLinearityCoefficient
 		retValue = retValue
 				&& getNonLinearityCoefficient() >= 0.0;
 		assert retValue;

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

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

 		return retValue;
 	} // sane

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

	/*******************************************************************************
	* Copyright (c) 2006, 2008 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.model.STEMTime;
	import org.eclipse.stem.diseasemodels.standard.DiseaseModelLabel;
	import org.eclipse.stem.diseasemodels.standard.DiseaseModelLabelValue;
	import org.eclipse.stem.diseasemodels.standard.Infector;
	import org.eclipse.stem.diseasemodels.standard.SI;
	import org.eclipse.stem.diseasemodels.standard.SIInfector;
	import org.eclipse.stem.diseasemodels.standard.SILabelValue;
	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;

	/**
	* <!-- begin-user-doc --> An implementation of the model object '<em><b>SI</b></em>'.
	* <!-- end-user-doc -->
	* <p>
	* The following features are implemented:
	* <ul>
	* <li>{@link org.eclipse.stem.diseasemodels.standard.impl.SIImpl#getTransmissionRate <em>Transmission Rate</em>}</li>
	* <li>{@link org.eclipse.stem.diseasemodels.standard.impl.SIImpl#getNonLinearityCoefficient <em>Non Linearity Coefficient</em>}</li>
	* <li>{@link org.eclipse.stem.diseasemodels.standard.impl.SIImpl#getRecoveryRate <em>Recovery Rate</em>}</li>
	* <li>{@link org.eclipse.stem.diseasemodels.standard.impl.SIImpl#getInfectiousMortalityRate <em>Infectious Mortality Rate</em>}</li>
	* </ul>
	* </p>
	*
	* @generated
	*/
	public abstract class SIImpl extends StandardDiseaseModelImpl implements SI {
	/**
	* The default value of the '{@link #getTransmissionRate() <em>Transmission Rate</em>}' attribute.
	* <!-- begin-user-doc --> <!-- end-user-doc -->
	* @see #getTransmissionRate()
	* @generated
	* @ordered
	*/
	protected static final double TRANSMISSION_RATE_EDEFAULT = 0.0;

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

	/**
	* The default value of the '{@link #getNonLinearityCoefficient() <em>Non Linearity Coefficient</em>}' attribute.
	* <!-- begin-user-doc --> <!-- end-user-doc -->
	* @see #getNonLinearityCoefficient()
	* @generated
	* @ordered
	*/
	protected static final double NON_LINEARITY_COEFFICIENT_EDEFAULT = 1.0;

	/**
	* The cached value of the '{@link #getNonLinearityCoefficient() <em>Non Linearity Coefficient</em>}' attribute.
	* <!-- begin-user-doc --> <!-- end-user-doc -->
	* @see #getNonLinearityCoefficient()
	* @generated
	* @ordered
	*/
	protected double nonLinearityCoefficient = NON_LINEARITY_COEFFICIENT_EDEFAULT;

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

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

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

	/**
	* The cached value of the '{@link #getInfectiousMortalityRate() <em>Infectious Mortality Rate</em>}' attribute.
	* <!-- begin-user-doc --> <!-- end-user-doc -->
	* @see #getInfectiousMortalityRate()
	* @generated
	* @ordered
	*/
	protected double infectiousMortalityRate = INFECTIOUS_MORTALITY_RATE_EDEFAULT;

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

	/**
	* @see org.eclipse.stem.diseasemodels.standard.impl.StandardDiseaseModelImpl#computeTransitions(org.eclipse.stem.diseasemodels.standard.StandardDiseaseModelLabelValue,
	* long, double, long)
	*/
	@Override
	public StandardDiseaseModelLabelValue computeDiseaseDeltas(
	final STEMTime time, double t,
	final StandardDiseaseModelLabelValue currentState,
	final StandardDiseaseModelLabel diseaseLabel, final long timeDelta, DiseaseModelLabelValue returnValue) {

	final SILabelValue currentSI = (SILabelValue) currentState;

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

	// 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 numberOfSusceptibleToInfected = 0.0;
	if(getNonLinearityCoefficient() != 1.0 && effectiveInfectious >= 0.0)
	numberOfSusceptibleToInfected = transmissionRate
	* currentSI.getS()* Math.pow(effectiveInfectious, getNonLinearityCoefficient());
	else
	numberOfSusceptibleToInfected = transmissionRate
	* currentSI.getS()* effectiveInfectious;

	double numberOfInfectedToSusceptible = getAdjustedRecoveryRate(timeDelta)
	* currentSI.getI();


	// Determine delta S
	final double deltaS = - numberOfSusceptibleToInfected + numberOfInfectedToSusceptible;
	// Determine delta I
	final double deltaI = numberOfSusceptibleToInfected - numberOfInfectedToSusceptible - diseaseDeaths;

	SILabelValueImpl ret = (SILabelValueImpl)returnValue;
	ret.setS(deltaS);
	ret.setI(deltaI);
	ret.setIncidence(numberOfSusceptibleToInfected);
	ret.setDiseaseDeaths(diseaseDeaths);
	return ret;
	} // computeDiseaseDeltas


	/**
	* This method is used to scale the transmission rate.
	* it returns the local density divided by a "reference" density
	* @param diseaseLabel the label being processed
	* @return the transmission rate scale factor for the label being processed
	*/
	public double getTransmissionRateScaleFactor(
	StandardDiseaseModelLabel diseaseLabel) {
	//final StandardDiseaseModelState sdms = (StandardDiseaseModelState) diseaseLabel
	// .getDiseaseModelState();

	double referenceDensity = getReferencePopulationDensity();
	// assert(referenceDensity > 0);
	// need editor check so ref density always >1. Default is 100.
	assert getArea(diseaseLabel.getPopulationLabel()) > 0.0;
	double localDensity = ((StandardDiseaseModelLabelValue)diseaseLabel.getTempValue()).getPopulationCount()/getArea(diseaseLabel.getPopulationLabel());
	return localDensity/referenceDensity;
	} // getTransmissionRateScaleFactor


	/**
	* The <em>infectious mortality rate</em> is the rate at which
	* <em>Infectious</em> population members die. Basically, that rate is
	* simply the proportional fraction of the flow into the <em>Infectious</em>
	* state.
	*
	* @param infectiousInputRate
	* the rate at which population members enter the infectious
	* state (β)
	* @param infectiousMortality
	* the proportion of population members that die from the disease
	* (x)
	* @return the rate at which population members die from the disease
	*/
	// public double computeInfectiousMortalityRate(
	// final double infectiousInputRate, final double infectiousMortality) {
	// return infectiousMortality * infectiousInputRate;
	// } // computeInfectiousMortalityRate


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

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


	/**
	* @see org.eclipse.stem.diseasemodels.standard.impl.DiseaseModelImpl#createInfector()
	*/
	@Override
	public Infector createInfector() {
	SIInfector retValue = StandardFactory.eINSTANCE.createSIInfector();
	retValue.setDiseaseName(this.getDiseaseName());
	retValue.setPopulationIdentifier(getPopulationIdentifier());
	return retValue;
	} // createInfector

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

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

	/**
	* <!-- begin-user-doc -->
	*
	* @param newTransmissionRate
	*
	* <!-- end-user-doc -->
	* @generated
	*/
	public void setTransmissionRate(double newTransmissionRate) {
	double oldTransmissionRate = transmissionRate;
	transmissionRate = newTransmissionRate;
	if (eNotificationRequired())
	eNotify(new ENotificationImpl(this, Notification.SET, StandardPackage.SI__TRANSMISSION_RATE, oldTransmissionRate, transmissionRate));
	}

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

	/**
	* <!-- begin-user-doc -->
	*
	* @param newRecoveryRate
	*
	* <!-- end-user-doc -->
	* @generated
	*/
	public void setRecoveryRate(double newRecoveryRate) {
	double oldRecoveryRate = recoveryRate;
	recoveryRate = newRecoveryRate;
	if (eNotificationRequired())
	eNotify(new ENotificationImpl(this, Notification.SET, StandardPackage.SI__RECOVERY_RATE, oldRecoveryRate, recoveryRate));
	}

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

	/**
	* <!-- begin-user-doc --> <!-- end-user-doc -->
	* @generated
	*/
	public void setInfectiousMortalityRate(double newInfectiousMortalityRate) {
	double oldInfectiousMortalityRate = infectiousMortalityRate;
	infectiousMortalityRate = newInfectiousMortalityRate;
	if (eNotificationRequired())
	eNotify(new ENotificationImpl(this, Notification.SET, StandardPackage.SI__INFECTIOUS_MORTALITY_RATE, oldInfectiousMortalityRate, infectiousMortalityRate));
	}

	/**
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @generated NOT
	*/
	public double getAdjustedInfectiousMortalityRate(long timeDelta) {
	// TODO this division can be eliminated if timeDelta==getTimePeriod
	return getInfectiousMortalityRate()
	* ((double) timeDelta / (double) getTimePeriod());
	} // getAdjustedInfectiousMortalityRate

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

	/**
	* <!-- begin-user-doc -->
	*
	* @param newNonLinearityCoefficient
	*
	* <!-- end-user-doc -->
	* @generated
	*/
	public void setNonLinearityCoefficient(double newNonLinearityCoefficient) {
	double oldNonLinearityCoefficient = nonLinearityCoefficient;
	nonLinearityCoefficient = newNonLinearityCoefficient;
	if (eNotificationRequired())
	eNotify(new ENotificationImpl(this, Notification.SET, StandardPackage.SI__NON_LINEARITY_COEFFICIENT, oldNonLinearityCoefficient, nonLinearityCoefficient));
	}

	/**
	* <!-- begin-user-doc -->
	* Returns the time interval deltaT divided by the initial time period
	* @param timeDelta
	*
	* @return
	*
	* <!-- end-user-doc -->
	*
	* @generated NOT
	*/
	public double getAdjustedTransmissionRate(long timeDelta) {
	return getTransmissionRate()
	* ((double) timeDelta / (double) getTimePeriod());
	} // getAdjustedTransmissionRate

	/**
	* <!-- begin-user-doc -->
	*
	* @param timeDelta
	*
	* @return
	*
	* <!-- end-user-doc -->
	*
	* @generated NOT
	*/
	public double getAdjustedRecoveryRate(long timeDelta) {
	return getRecoveryRate()
	* ((double) timeDelta / (double) getTimePeriod());
	} // getAdjustedRecoveryRate

	/**
	* <!-- 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.SI__TRANSMISSION_RATE:
	return getTransmissionRate();
	case StandardPackage.SI__NON_LINEARITY_COEFFICIENT:
	return getNonLinearityCoefficient();
	case StandardPackage.SI__RECOVERY_RATE:
	return getRecoveryRate();
	case StandardPackage.SI__INFECTIOUS_MORTALITY_RATE:
	return getInfectiousMortalityRate();
	}
	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.SI__TRANSMISSION_RATE:
	setTransmissionRate((Double)newValue);
	return;
	case StandardPackage.SI__NON_LINEARITY_COEFFICIENT:
	setNonLinearityCoefficient((Double)newValue);
	return;
	case StandardPackage.SI__RECOVERY_RATE:
	setRecoveryRate((Double)newValue);
	return;
	case StandardPackage.SI__INFECTIOUS_MORTALITY_RATE:
	setInfectiousMortalityRate((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.SI__TRANSMISSION_RATE:
	setTransmissionRate(TRANSMISSION_RATE_EDEFAULT);
	return;
	case StandardPackage.SI__NON_LINEARITY_COEFFICIENT:
	setNonLinearityCoefficient(NON_LINEARITY_COEFFICIENT_EDEFAULT);
	return;
	case StandardPackage.SI__RECOVERY_RATE:
	setRecoveryRate(RECOVERY_RATE_EDEFAULT);
	return;
	case StandardPackage.SI__INFECTIOUS_MORTALITY_RATE:
	setInfectiousMortalityRate(INFECTIOUS_MORTALITY_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.SI__TRANSMISSION_RATE:
	return transmissionRate != TRANSMISSION_RATE_EDEFAULT;
	case StandardPackage.SI__NON_LINEARITY_COEFFICIENT:
	return nonLinearityCoefficient != NON_LINEARITY_COEFFICIENT_EDEFAULT;
	case StandardPackage.SI__RECOVERY_RATE:
	return recoveryRate != RECOVERY_RATE_EDEFAULT;
	case StandardPackage.SI__INFECTIOUS_MORTALITY_RATE:
	return infectiousMortalityRate != INFECTIOUS_MORTALITY_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(" (transmissionRate: "); //$NON-NLS-1$
	result.append(transmissionRate);
	result.append(", nonLinearityCoefficient: "); //$NON-NLS-1$
	result.append(nonLinearityCoefficient);
	result.append(", recoveryRate: "); //$NON-NLS-1$
	result.append(recoveryRate);
	result.append(", infectiousMortalityRate: "); //$NON-NLS-1$
	result.append(infectiousMortalityRate);
	result.append(')');
	return result.toString();
	}

	/**
	* @see org.eclipse.stem.diseasemodels.standard.impl.StandardDiseaseModelImpl#sane()
	*/
	@Override
	public boolean sane() {
	boolean retValue = super.sane();

	// transmissionRate
	retValue = retValue && getTransmissionRate() >= TRANSMISSION_RATE_EDEFAULT;
	assert retValue;

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

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

	// recoveryRate
	retValue = retValue && getRecoveryRate() >= RECOVERY_RATE_EDEFAULT;
	assert retValue;

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

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

	// nonLinearityCoefficient
	retValue = retValue
	&& getNonLinearityCoefficient() >= 0.0;
	assert retValue;

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

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

	return retValue;
	} // sane

	} // SIImpl