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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.SIR;
import org.eclipse.stem.diseasemodels.standard.SIRLabelValue;
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>SIR</b></em>'.
* <!-- end-user-doc -->
* <p>
* The following features are implemented:
* <ul>
* <li>{@link org.eclipse.stem.diseasemodels.standard.impl.SIRImpl#getImmunityLossRate <em>Immunity Loss Rate</em>}</li>
* </ul>
* </p>
*
* @generated
*/
public abstract class SIRImpl extends SIImpl implements SIR {
/**
* The default value of the '{@link #getImmunityLossRate() <em>Immunity Loss Rate</em>}' attribute.
* <!-- begin-user-doc --> <!-- end-user-doc -->
* @see #getImmunityLossRate()
* @generated
* @ordered
*/
protected static final double IMMUNITY_LOSS_RATE_EDEFAULT = 0.0;
/**
* The cached value of the '{@link #getImmunityLossRate() <em>Immunity Loss Rate</em>}' attribute.
* <!-- begin-user-doc --> <!-- end-user-doc -->
* @see #getImmunityLossRate()
* @generated
* @ordered
*/
protected double immunityLossRate = IMMUNITY_LOSS_RATE_EDEFAULT;
/**
* <!-- begin-user-doc --> <!-- end-user-doc -->
* @generated
*/
protected SIRImpl() {
super();
}
/**
* @see org.eclipse.stem.diseasemodels.standard.impl.DiseaseModelImpl#createDiseaseModelLabel()
*/
@Override
public DiseaseModelLabel createDiseaseModelLabel(String populationIdentifier) {
return StandardFactory.eINSTANCE.createSIRLabel();
} // createDiseaseModelLabel
@Override
public DiseaseModelLabelValue createDiseaseModelLabelValue(String populationIdentifier) {
return StandardFactory.eINSTANCE.createSIRLabelValue();
} // createDiseaseModelLabelValue
/**
* @see org.eclipse.stem.diseasemodels.standard.impl.SIImpl#computeTransitions(StandardDiseaseModelLabelValue,
* StandardDiseaseModelLabel, long)
*/
@Override
public StandardDiseaseModelLabelValue computeDiseaseDeltas(
final STEMTime time,
final StandardDiseaseModelLabelValue currentState,
final StandardDiseaseModelLabel diseaseLabel, final long timeDelta, DiseaseModelLabelValue returnValue) {
final SIRLabelValue currentSIR = (SIRLabelValue) currentState;
// Compute deaths
final double adjustedInfectiousMortalityRate = getAdjustedInfectiousMortalityRate(timeDelta);
final double diseaseDeaths = adjustedInfectiousMortalityRate
* currentSIR.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, currentSIR.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)
* currentSIR.getI();
double numberOfRecoveredToSusceptible = getAdjustedImmunityLossRate(timeDelta)
* currentSIR.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 numberOfSusceptibleToInfected = 0.0;
if(getNonLinearityCoefficient() != 1.0 && effectiveInfectious >= 0.0)
numberOfSusceptibleToInfected = transmissionRate
* currentSIR.getS()* Math.pow(effectiveInfectious, getNonLinearityCoefficient());
else
numberOfSusceptibleToInfected = transmissionRate
* currentSIR.getS()* effectiveInfectious;
// Determine delta S
double deltaS = numberOfRecoveredToSusceptible - numberOfSusceptibleToInfected;
// Determine delta I
double deltaI = numberOfSusceptibleToInfected- numberOfInfectedToRecovered - diseaseDeaths;
// Determine delta R
double deltaR = numberOfInfectedToRecovered - numberOfRecoveredToSusceptible;
// If there is a control label attached to the region, we need to adjust for any interventions in effect.
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(currentSIR.getS() < vaccinations) vaccinations = currentSIR.getS();
if(currentSIR.getI() < isolations) isolations = currentSIR.getI();
deltaS -= vaccinations;
deltaR += vaccinations;
deltaI -= isolations;
deltaR += isolations;
}
SIRLabelValueImpl ret = (SIRLabelValueImpl)returnValue;
ret.setS(deltaS);
ret.setI(deltaI);
ret.setIncidence(numberOfInfectedToRecovered);
ret.setR(deltaR);
ret.setDiseaseDeaths(diseaseDeaths);
return ret;
} // computeTransitions
/**
* <!-- begin-user-doc --> <!-- end-user-doc -->
* @generated
*/
@Override
protected EClass eStaticClass() {
return StandardPackage.Literals.SIR;
}
/**
* <!-- begin-user-doc -->
*
* @return
*
* <!-- end-user-doc -->
* @generated
*/
public double getImmunityLossRate() {
return immunityLossRate;
}
/**
* <!-- begin-user-doc -->
*
* @param newImmunityLossRate
*
* <!-- end-user-doc -->
* @generated
*/
public void setImmunityLossRate(double newImmunityLossRate) {
double oldImmunityLossRate = immunityLossRate;
immunityLossRate = newImmunityLossRate;
if (eNotificationRequired())
eNotify(new ENotificationImpl(this, Notification.SET, StandardPackage.SIR__IMMUNITY_LOSS_RATE, oldImmunityLossRate, immunityLossRate));
}
/**
* <!-- begin-user-doc -->
*
* @param timeDelta
* @return
*
* <!-- end-user-doc -->
* @generated NOT
*/
public double getAdjustedImmunityLossRate(long timeDelta) {
return getImmunityLossRate()
* ((double) timeDelta / (double) getTimePeriod());
} // getAdjustedImmunityRate
/**
* <!-- 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.SIR__IMMUNITY_LOSS_RATE:
return getImmunityLossRate();
}
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.SIR__IMMUNITY_LOSS_RATE:
setImmunityLossRate((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.SIR__IMMUNITY_LOSS_RATE:
setImmunityLossRate(IMMUNITY_LOSS_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.SIR__IMMUNITY_LOSS_RATE:
return immunityLossRate != IMMUNITY_LOSS_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(" (immunityLossRate: "); //$NON-NLS-1$
result.append(immunityLossRate);
result.append(')');
return result.toString();
}
/**
* @see org.eclipse.stem.diseasemodels.standard.impl.SIImpl#sane()
*/
@Override
public boolean sane() {
boolean retValue = super.sane();
retValue = retValue && getImmunityLossRate() >= IMMUNITY_LOSS_RATE_EDEFAULT;
assert retValue;
retValue = retValue && !Double.isInfinite(getImmunityLossRate());
assert retValue;
retValue = retValue && !Double.isNaN(getImmunityLossRate());
assert retValue;
return retValue;
} // sane
} // SIRImpl