| package org.eclipse.stem.diseasemodels.forcing.impl; |
| /******************************************************************************* |
| * Copyright (c) 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 |
| *******************************************************************************/ |
| |
| import java.io.FileWriter; |
| import java.util.ArrayList; |
| import java.util.Calendar; |
| |
| 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.forcing.ForcingPackage; |
| import org.eclipse.stem.diseasemodels.forcing.Gaussian2ForcingDiseaseModel; |
| import org.eclipse.stem.diseasemodels.standard.DiseaseModelLabelValue; |
| import org.eclipse.stem.diseasemodels.standard.SILabelValue; |
| 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.StandardPackage; |
| import org.eclipse.stem.diseasemodels.standard.impl.SIRLabelValueImpl; |
| |
| /** |
| * <!-- begin-user-doc --> |
| * An implementation of the model object '<em><b>Gaussian2 Forcing Disease Model</b></em>'. |
| * <!-- end-user-doc --> |
| * <p> |
| * The following features are implemented: |
| * <ul> |
| * <li>{@link org.eclipse.stem.diseasemodels.forcing.impl.Gaussian2ForcingDiseaseModelImpl#getSigma2_2 <em>Sigma2 2</em>}</li> |
| * <li>{@link org.eclipse.stem.diseasemodels.forcing.impl.Gaussian2ForcingDiseaseModelImpl#getAtt1 <em>Att1</em>}</li> |
| * <li>{@link org.eclipse.stem.diseasemodels.forcing.impl.Gaussian2ForcingDiseaseModelImpl#getAtt2 <em>Att2</em>}</li> |
| * <li>{@link org.eclipse.stem.diseasemodels.forcing.impl.Gaussian2ForcingDiseaseModelImpl#getAtt3 <em>Att3</em>}</li> |
| * <li>{@link org.eclipse.stem.diseasemodels.forcing.impl.Gaussian2ForcingDiseaseModelImpl#getAtt4 <em>Att4</em>}</li> |
| * </ul> |
| * </p> |
| * |
| * @generated |
| */ |
| public class Gaussian2ForcingDiseaseModelImpl extends GaussianForcingDiseaseModelImpl implements Gaussian2ForcingDiseaseModel { |
| /** |
| * The default value of the '{@link #getSigma2_2() <em>Sigma2 2</em>}' attribute. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @see #getSigma2_2() |
| * @generated |
| * @ordered |
| */ |
| protected static final double SIGMA2_2_EDEFAULT = 100.0; |
| |
| /** |
| * The cached value of the '{@link #getSigma2_2() <em>Sigma2 2</em>}' attribute. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @see #getSigma2_2() |
| * @generated |
| * @ordered |
| */ |
| protected double sigma2_2 = SIGMA2_2_EDEFAULT; |
| |
| /** |
| * The default value of the '{@link #getAtt1() <em>Att1</em>}' attribute. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @see #getAtt1() |
| * @generated |
| * @ordered |
| */ |
| protected static final double ATT1_EDEFAULT = 1.0; |
| |
| /** |
| * The cached value of the '{@link #getAtt1() <em>Att1</em>}' attribute. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @see #getAtt1() |
| * @generated |
| * @ordered |
| */ |
| protected double att1 = ATT1_EDEFAULT; |
| |
| /** |
| * The default value of the '{@link #getAtt2() <em>Att2</em>}' attribute. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @see #getAtt2() |
| * @generated |
| * @ordered |
| */ |
| protected static final double ATT2_EDEFAULT = 1.0; |
| |
| /** |
| * The cached value of the '{@link #getAtt2() <em>Att2</em>}' attribute. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @see #getAtt2() |
| * @generated |
| * @ordered |
| */ |
| protected double att2 = ATT2_EDEFAULT; |
| |
| /** |
| * The default value of the '{@link #getAtt3() <em>Att3</em>}' attribute. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @see #getAtt3() |
| * @generated |
| * @ordered |
| */ |
| protected static final double ATT3_EDEFAULT = 1.0; |
| |
| /** |
| * The cached value of the '{@link #getAtt3() <em>Att3</em>}' attribute. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @see #getAtt3() |
| * @generated |
| * @ordered |
| */ |
| protected double att3 = ATT3_EDEFAULT; |
| |
| /** |
| * The default value of the '{@link #getAtt4() <em>Att4</em>}' attribute. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @see #getAtt4() |
| * @generated |
| * @ordered |
| */ |
| protected static final double ATT4_EDEFAULT = 1.0; |
| |
| /** |
| * The cached value of the '{@link #getAtt4() <em>Att4</em>}' attribute. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @see #getAtt4() |
| * @generated |
| * @ordered |
| */ |
| protected double att4 = ATT4_EDEFAULT; |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated NOT |
| */ |
| public Gaussian2ForcingDiseaseModelImpl() { |
| super(); |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| @Override |
| protected EClass eStaticClass() { |
| return ForcingPackage.Literals.GAUSSIAN2_FORCING_DISEASE_MODEL; |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public double getSigma2_2() { |
| return sigma2_2; |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public void setSigma2_2(double newSigma2_2) { |
| double oldSigma2_2 = sigma2_2; |
| sigma2_2 = newSigma2_2; |
| if (eNotificationRequired()) |
| eNotify(new ENotificationImpl(this, Notification.SET, ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__SIGMA2_2, oldSigma2_2, sigma2_2)); |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public double getAtt1() { |
| return att1; |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public void setAtt1(double newAtt1) { |
| double oldAtt1 = att1; |
| att1 = newAtt1; |
| if (eNotificationRequired()) |
| eNotify(new ENotificationImpl(this, Notification.SET, ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT1, oldAtt1, att1)); |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public double getAtt2() { |
| return att2; |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public void setAtt2(double newAtt2) { |
| double oldAtt2 = att2; |
| att2 = newAtt2; |
| if (eNotificationRequired()) |
| eNotify(new ENotificationImpl(this, Notification.SET, ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT2, oldAtt2, att2)); |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public double getAtt3() { |
| return att3; |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public void setAtt3(double newAtt3) { |
| double oldAtt3 = att3; |
| att3 = newAtt3; |
| if (eNotificationRequired()) |
| eNotify(new ENotificationImpl(this, Notification.SET, ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT3, oldAtt3, att3)); |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public double getAtt4() { |
| return att4; |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| public void setAtt4(double newAtt4) { |
| double oldAtt4 = att4; |
| att4 = newAtt4; |
| if (eNotificationRequired()) |
| eNotify(new ENotificationImpl(this, Notification.SET, ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT4, oldAtt4, att4)); |
| } |
| |
| private Long firstTime = new Long(Long.MAX_VALUE); |
| private Calendar calendar = Calendar.getInstance(); |
| private Calendar calendar2 = Calendar.getInstance(); |
| private static final double MILLIS_PER_DAY = 1000.0*60.0*60.0*24.0; |
| |
| private ArrayList<Long> writtedTimes = new ArrayList<Long>(); |
| private FileWriter fw; |
| @Override |
| public StandardDiseaseModelLabelValue computeDiseaseDeltas( |
| final STEMTime time, |
| final StandardDiseaseModelLabelValue currentState, |
| final StandardDiseaseModelLabel diseaseLabel, final long timeDelta, DiseaseModelLabelValue returnValue) { |
| final SIRLabelValue currentSIR = (SIRLabelValue) currentState; |
| |
| long currentMillis = time.getTime().getTime(); |
| double seasonalModulationFloor = getModulationFloor(); |
| double modulationPeriod = getModulationPeriod(); |
| double phase = getModulationPhaseShift(); |
| double sigma2 = getSigma2(); |
| double sigma2_2 = getSigma2_2(); |
| |
| synchronized(this) { |
| if(firstTime.longValue() == Long.MAX_VALUE) |
| firstTime = Long.valueOf(time.getTime().getTime()); |
| } |
| |
| // Get the day from time and adjust for the phase |
| double day=0; |
| // Shared calendar object not thread safe |
| synchronized(calendar) { |
| calendar.setTimeInMillis(currentMillis); |
| calendar2.setTimeInMillis(firstTime.longValue()); |
| day = (calendar.getTimeInMillis() - calendar2.getTimeInMillis())/MILLIS_PER_DAY; |
| } |
| |
| |
| double mu1 = phase; |
| double mu2 = phase + modulationPeriod; |
| |
| double modulation1 = (1/Math.sqrt(2*Math.PI*sigma2))*Math.exp(-(Math.pow(day-mu1,2))/(2*sigma2)); |
| double modulation2 = (1/Math.sqrt(2*Math.PI*sigma2_2))*Math.exp(-(Math.pow(day-mu2,2))/(2*sigma2_2)); |
| |
| // This is beta* |
| double transmissionRate = seasonalModulationFloor + (getAdjustedTransmissionRate(timeDelta)) * (modulation1+modulation2); |
| |
| if(day >= 116 && day <= 119) // April 24 - 27 |
| transmissionRate = transmissionRate * this.getAtt1(); |
| else if(day >= 120 && day <= 127) // April 28 - May 5 |
| transmissionRate = transmissionRate * this.getAtt2(); |
| else if(day >= 128 && day <= 132) // May 6 - May 10 |
| transmissionRate = transmissionRate * this.getAtt3(); |
| |
| synchronized(writtedTimes) { |
| if(!writtedTimes.contains(time.getTime().getTime())) { |
| try { |
| if(fw == null) fw = new FileWriter("beta.csv"); |
| fw.write(time.getTime().getTime()+","+transmissionRate+"\n"); |
| } catch(Exception e) { |
| e.printStackTrace(); |
| } |
| writtedTimes.add(time.getTime().getTime()); |
| } |
| } |
| |
| 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 |
| final double deltaS = numberOfRecoveredToSusceptible - numberOfSusceptibleToInfected; |
| // Determine delta I |
| final double deltaI = numberOfSusceptibleToInfected- numberOfInfectedToRecovered; |
| // Determine delta R |
| final double deltaR = numberOfInfectedToRecovered - numberOfRecoveredToSusceptible; |
| |
| SIRLabelValueImpl ret = (SIRLabelValueImpl)returnValue; |
| ret.setS(deltaS); |
| ret.setI(deltaI); |
| ret.setIncidence(numberOfInfectedToRecovered); |
| ret.setR(deltaR); |
| ret.setDiseaseDeaths(0); |
| return ret; |
| } // computeTransitions |
| |
| /** |
| * ModelSpecificAdjustments for a Stochastic model adds noise to or adjusts |
| * the disease state transition values by multiplying |
| * the additions by a random variable r ~ (1+/-x) with x small. |
| * The requirements that no more individuals can be moved from a state than are |
| * already in that state is still enforced. |
| * |
| */ |
| @Override |
| public void doModelSpecificAdjustments( |
| final StandardDiseaseModelLabelValue state) { |
| final SILabelValue currentSI = (SILabelValue) state; |
| double oldI = currentSI.getI(); |
| double Inoisy = currentSI.getI()* computeNoise(); |
| double change = oldI-Inoisy; |
| currentSI.setI(Inoisy); |
| double newS = currentSI.getS() + change; |
| if(newS < 0.0) { |
| // Need to rescale |
| double scale = (currentSI.getS() + newS) / currentSI.getS(); |
| currentSI.setI(Inoisy*scale); |
| } else currentSI.setS(newS); |
| return; |
| } // doModelSpecificAdjustments |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| @Override |
| public Object eGet(int featureID, boolean resolve, boolean coreType) { |
| switch (featureID) { |
| case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__SIGMA2_2: |
| return getSigma2_2(); |
| case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT1: |
| return getAtt1(); |
| case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT2: |
| return getAtt2(); |
| case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT3: |
| return getAtt3(); |
| case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT4: |
| return getAtt4(); |
| } |
| return super.eGet(featureID, resolve, coreType); |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| @Override |
| public void eSet(int featureID, Object newValue) { |
| switch (featureID) { |
| case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__SIGMA2_2: |
| setSigma2_2((Double)newValue); |
| return; |
| case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT1: |
| setAtt1((Double)newValue); |
| return; |
| case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT2: |
| setAtt2((Double)newValue); |
| return; |
| case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT3: |
| setAtt3((Double)newValue); |
| return; |
| case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT4: |
| setAtt4((Double)newValue); |
| return; |
| } |
| super.eSet(featureID, newValue); |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| @Override |
| public void eUnset(int featureID) { |
| switch (featureID) { |
| case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__SIGMA2_2: |
| setSigma2_2(SIGMA2_2_EDEFAULT); |
| return; |
| case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT1: |
| setAtt1(ATT1_EDEFAULT); |
| return; |
| case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT2: |
| setAtt2(ATT2_EDEFAULT); |
| return; |
| case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT3: |
| setAtt3(ATT3_EDEFAULT); |
| return; |
| case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT4: |
| setAtt4(ATT4_EDEFAULT); |
| return; |
| } |
| super.eUnset(featureID); |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| @Override |
| public boolean eIsSet(int featureID) { |
| switch (featureID) { |
| case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__SIGMA2_2: |
| return sigma2_2 != SIGMA2_2_EDEFAULT; |
| case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT1: |
| return att1 != ATT1_EDEFAULT; |
| case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT2: |
| return att2 != ATT2_EDEFAULT; |
| case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT3: |
| return att3 != ATT3_EDEFAULT; |
| case ForcingPackage.GAUSSIAN2_FORCING_DISEASE_MODEL__ATT4: |
| return att4 != ATT4_EDEFAULT; |
| } |
| return super.eIsSet(featureID); |
| } |
| |
| /** |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @generated |
| */ |
| @Override |
| public String toString() { |
| if (eIsProxy()) return super.toString(); |
| |
| StringBuffer result = new StringBuffer(super.toString()); |
| result.append(" (sigma2_2: "); //$NON-NLS-1$ |
| result.append(sigma2_2); |
| result.append(", att1: "); //$NON-NLS-1$ |
| result.append(att1); |
| result.append(", att2: "); //$NON-NLS-1$ |
| result.append(att2); |
| result.append(", att3: "); //$NON-NLS-1$ |
| result.append(att3); |
| result.append(", att4: "); //$NON-NLS-1$ |
| result.append(att4); |
| result.append(')'); |
| return result.toString(); |
| } |
| |
| } //Gaussian2ForcingDiseaseModelImpl |
