| package org.eclipse.stem.runtime.execute.compactjava; |
| |
| |
| import java.util.ArrayList; |
| import java.util.List; |
| |
| import org.apache.commons.math.ode.DerivativeException; |
| import org.eclipse.stem.runtime.compactjava.RuntimeDecorator; |
| import org.eclipse.stem.runtime.compactjava.RuntimeLabel; |
| import org.eclipse.stem.runtime.compactjava.RuntimeNode; |
| import org.eclipse.stem.runtime.compactjava.RuntimeScenario; |
| |
| public class DengueModel extends RuntimeDiffEquation { |
| |
| short hostLabelTypeId; |
| short vectorLabelTypeId; |
| |
| double bitingRateSV; |
| double bitingRateIV; |
| double hostInfectivity1; |
| double hostInfectivity2; |
| double hostInfectivity3; |
| double hostInfectivity4; |
| double hostPrimaryIncubationRate1; |
| double hostPrimaryIncubationRate2; |
| double hostPrimaryIncubationRate3; |
| double hostPrimaryIncubationRate4; |
| double hostPrimaryRecoveryRate1; |
| double hostPrimaryRecoveryRate2; |
| double hostPrimaryRecoveryRate3; |
| double hostPrimaryRecoveryRate4; |
| double hostPrimaryImmunityLossRate1; |
| double hostPrimaryImmunityLossRate2; |
| double hostPrimaryImmunityLossRate3; |
| double hostPrimaryImmunityLossRate4; |
| double hostPrimaryDiseaseDeathRate1; |
| double hostPrimaryDiseaseDeathRate2; |
| double hostPrimaryDiseaseDeathRate3; |
| double hostPrimaryDiseaseDeathRate4; |
| double hostADE12; |
| double hostADE13; |
| double hostADE14; |
| double hostADE21; |
| double hostADE23; |
| double hostADE24; |
| double hostADE31; |
| double hostADE32; |
| double hostADE34; |
| double hostADE41; |
| double hostADE42; |
| double hostADE43; |
| double hostSecondaryDiseaseDeathRate12; |
| double hostSecondaryDiseaseDeathRate13; |
| double hostSecondaryDiseaseDeathRate14; |
| double hostSecondaryDiseaseDeathRate21; |
| double hostSecondaryDiseaseDeathRate23; |
| double hostSecondaryDiseaseDeathRate24; |
| double hostSecondaryDiseaseDeathRate31; |
| double hostSecondaryDiseaseDeathRate32; |
| double hostSecondaryDiseaseDeathRate34; |
| double hostSecondaryDiseaseDeathRate41; |
| double hostSecondaryDiseaseDeathRate42; |
| double hostSecondaryDiseaseDeathRate43; |
| double hostSecondaryRecoveryRate12; |
| double hostSecondaryRecoveryRate13; |
| double hostSecondaryRecoveryRate14; |
| double hostSecondaryRecoveryRate21; |
| double hostSecondaryRecoveryRate23; |
| double hostSecondaryRecoveryRate24; |
| double hostSecondaryRecoveryRate31; |
| double hostSecondaryRecoveryRate32; |
| double hostSecondaryRecoveryRate34; |
| double hostSecondaryRecoveryRate41; |
| double hostSecondaryRecoveryRate42; |
| double hostSecondaryRecoveryRate43; |
| double hostSecondaryIncubationRate12; |
| double hostSecondaryIncubationRate13; |
| double hostSecondaryIncubationRate14; |
| double hostSecondaryIncubationRate21; |
| double hostSecondaryIncubationRate23; |
| double hostSecondaryIncubationRate24; |
| double hostSecondaryIncubationRate31; |
| double hostSecondaryIncubationRate32; |
| double hostSecondaryIncubationRate34; |
| double hostSecondaryIncubationRate41; |
| double hostSecondaryIncubationRate42; |
| double hostSecondaryIncubationRate43; |
| double vectorInfectivity1; |
| double vectorInfectivity2; |
| double vectorInfectivity3; |
| double vectorInfectivity4; |
| double vectorADE1; |
| double vectorADE2; |
| double vectorADE3; |
| double vectorADE4; |
| double vectorIncubationRate1; |
| double vectorIncubationRate2; |
| double vectorIncubationRate3; |
| double vectorIncubationRate4; |
| double episilon1; |
| double episilon2; |
| double episilon3; |
| double episilon4; |
| long timePeriod; |
| |
| double characteristicMixingDistance; |
| double roadNetworkInfectiousProportion; |
| |
| String hostPopulationIdentifier; |
| String vectorPopulationIdentifier; |
| |
| public DengueModel(RuntimeScenario s, RuntimeDecorator rd, Integer d) { |
| super(s, rd, d); |
| timePeriod = (Long)runtimeDecorator.getAttributeValue(runtimeDecorator.getRuntimeType().getAttributeIndex("timePeriod")); |
| double adjustFactor = runtimeScenario.getRuntimeSequencer().getStepSize()/(((double)timePeriod)/86400000.0); |
| |
| bitingRateSV= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("bitingRateSV"))*adjustFactor; |
| bitingRateIV= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("bitingRateIV"))*adjustFactor; |
| hostInfectivity1= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostInfectivity1"))*adjustFactor; |
| hostInfectivity2= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostInfectivity2"))*adjustFactor; |
| hostInfectivity3= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostInfectivity3"))*adjustFactor; |
| hostInfectivity4= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostInfectivity4"))*adjustFactor; |
| hostPrimaryIncubationRate1= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostPrimaryIncubationRate1"))*adjustFactor; |
| hostPrimaryIncubationRate2= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostPrimaryIncubationRate2"))*adjustFactor; |
| hostPrimaryIncubationRate3= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostPrimaryIncubationRate3"))*adjustFactor; |
| hostPrimaryIncubationRate4= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostPrimaryIncubationRate4"))*adjustFactor; |
| hostPrimaryRecoveryRate1= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostPrimaryRecoveryRate1"))*adjustFactor; |
| hostPrimaryRecoveryRate2= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostPrimaryRecoveryRate2"))*adjustFactor; |
| hostPrimaryRecoveryRate3= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostPrimaryRecoveryRate3"))*adjustFactor; |
| hostPrimaryRecoveryRate4= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostPrimaryRecoveryRate4"))*adjustFactor; |
| hostPrimaryImmunityLossRate1= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostPrimaryImmunityLossRate1"))*adjustFactor; |
| hostPrimaryImmunityLossRate2= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostPrimaryImmunityLossRate2"))*adjustFactor; |
| hostPrimaryImmunityLossRate3= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostPrimaryImmunityLossRate3"))*adjustFactor; |
| hostPrimaryImmunityLossRate4= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostPrimaryImmunityLossRate4"))*adjustFactor; |
| hostPrimaryDiseaseDeathRate1= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostPrimaryDiseaseDeathRate1"))*adjustFactor; |
| hostPrimaryDiseaseDeathRate2= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostPrimaryDiseaseDeathRate2"))*adjustFactor; |
| hostPrimaryDiseaseDeathRate3= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostPrimaryDiseaseDeathRate3"))*adjustFactor; |
| hostPrimaryDiseaseDeathRate4= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostPrimaryDiseaseDeathRate4"))*adjustFactor; |
| hostADE12= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostADE12"))*adjustFactor; |
| hostADE13= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostADE13"))*adjustFactor; |
| hostADE14= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostADE14"))*adjustFactor; |
| hostADE21= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostADE21"))*adjustFactor; |
| hostADE23= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostADE23"))*adjustFactor; |
| hostADE24= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostADE24"))*adjustFactor; |
| hostADE31= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostADE31"))*adjustFactor; |
| hostADE32= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostADE32"))*adjustFactor; |
| hostADE34= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostADE34"))*adjustFactor; |
| hostADE41= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostADE41"))*adjustFactor; |
| hostADE42= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostADE42"))*adjustFactor; |
| hostADE43= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostADE43"))*adjustFactor; |
| hostSecondaryDiseaseDeathRate12= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryDiseaseDeathRate12"))*adjustFactor; |
| hostSecondaryDiseaseDeathRate13= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryDiseaseDeathRate13"))*adjustFactor; |
| hostSecondaryDiseaseDeathRate14= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryDiseaseDeathRate14"))*adjustFactor; |
| hostSecondaryDiseaseDeathRate21= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryDiseaseDeathRate21"))*adjustFactor; |
| hostSecondaryDiseaseDeathRate23= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryDiseaseDeathRate23"))*adjustFactor; |
| hostSecondaryDiseaseDeathRate24= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryDiseaseDeathRate24"))*adjustFactor; |
| hostSecondaryDiseaseDeathRate31= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryDiseaseDeathRate31"))*adjustFactor; |
| hostSecondaryDiseaseDeathRate32= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryDiseaseDeathRate32"))*adjustFactor; |
| hostSecondaryDiseaseDeathRate34= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryDiseaseDeathRate34"))*adjustFactor; |
| hostSecondaryDiseaseDeathRate41= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryDiseaseDeathRate41"))*adjustFactor; |
| hostSecondaryDiseaseDeathRate42= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryDiseaseDeathRate42"))*adjustFactor; |
| hostSecondaryDiseaseDeathRate43= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryDiseaseDeathRate43"))*adjustFactor; |
| hostSecondaryRecoveryRate12= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryRecoveryRate12"))*adjustFactor; |
| hostSecondaryRecoveryRate13= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryRecoveryRate13"))*adjustFactor; |
| hostSecondaryRecoveryRate13= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryRecoveryRate14"))*adjustFactor; |
| hostSecondaryRecoveryRate21= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryRecoveryRate21"))*adjustFactor; |
| hostSecondaryRecoveryRate21= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryRecoveryRate23"))*adjustFactor; |
| hostSecondaryRecoveryRate24= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryRecoveryRate24"))*adjustFactor; |
| hostSecondaryRecoveryRate31= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryRecoveryRate31"))*adjustFactor; |
| hostSecondaryRecoveryRate32= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryRecoveryRate32"))*adjustFactor; |
| hostSecondaryRecoveryRate34= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryRecoveryRate34"))*adjustFactor; |
| hostSecondaryRecoveryRate41= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryRecoveryRate41"))*adjustFactor; |
| hostSecondaryRecoveryRate42= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryRecoveryRate42"))*adjustFactor; |
| hostSecondaryRecoveryRate43= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryRecoveryRate43"))*adjustFactor; |
| hostSecondaryIncubationRate12= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryIncubationRate12"))*adjustFactor; |
| hostSecondaryIncubationRate13= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryIncubationRate13"))*adjustFactor; |
| hostSecondaryIncubationRate14= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryIncubationRate14"))*adjustFactor; |
| hostSecondaryIncubationRate21= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryIncubationRate21"))*adjustFactor; |
| hostSecondaryIncubationRate23= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryIncubationRate23"))*adjustFactor; |
| hostSecondaryIncubationRate23= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryIncubationRate24"))*adjustFactor; |
| hostSecondaryIncubationRate31= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryIncubationRate31"))*adjustFactor; |
| hostSecondaryIncubationRate32= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryIncubationRate32"))*adjustFactor; |
| hostSecondaryIncubationRate34= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryIncubationRate34"))*adjustFactor; |
| hostSecondaryIncubationRate41= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryIncubationRate41"))*adjustFactor; |
| hostSecondaryIncubationRate42= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryIncubationRate42"))*adjustFactor; |
| hostSecondaryIncubationRate43= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("hostSecondaryIncubationRate43"))*adjustFactor; |
| vectorInfectivity1= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("vectorInfectivity1"))*adjustFactor; |
| vectorInfectivity2= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("vectorInfectivity2"))*adjustFactor; |
| vectorInfectivity3= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("vectorInfectivity3"))*adjustFactor; |
| vectorInfectivity3= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("vectorInfectivity4"))*adjustFactor; |
| vectorInfectivity3= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("vectorADE1"))*adjustFactor; |
| vectorADE2= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("vectorADE2"))*adjustFactor; |
| vectorADE3= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("vectorADE3"))*adjustFactor; |
| vectorADE4= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("vectorADE4"))*adjustFactor; |
| vectorIncubationRate1= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("vectorIncubationRate1"))*adjustFactor; |
| vectorIncubationRate2= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("vectorIncubationRate2"))*adjustFactor; |
| vectorIncubationRate3= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("vectorIncubationRate3"))*adjustFactor; |
| vectorIncubationRate4= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("vectorIncubationRate4"))*adjustFactor; |
| vectorIncubationRate4= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("episilon1"))*adjustFactor; |
| vectorIncubationRate4= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("episilon2"))*adjustFactor; |
| vectorIncubationRate4= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("episilon3"))*adjustFactor; |
| episilon4= runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("episilon4"))*adjustFactor; |
| |
| characteristicMixingDistance = runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("characteristicMixingDistance")); |
| roadNetworkInfectiousProportion = runtimeDecorator.getDoubleAttributeValue(runtimeDecorator.getRuntimeType().getDoubleAttributeIndex("roadNetworkInfectiousProportion")); |
| |
| |
| hostPopulationIdentifier = (String)runtimeDecorator.getAttributeValue(runtimeDecorator.getRuntimeType().getAttributeIndex("populationIdentifier")); |
| vectorPopulationIdentifier = (String)runtimeDecorator.getAttributeValue(runtimeDecorator.getRuntimeType().getAttributeIndex("vectorPopulationIdentifier")); |
| // Find the type ids for the two type of labels the model use |
| |
| hostLabelTypeId = runtimeScenario.getLabelTypeSystem().findTypeId("DengueModelHostLabel"); |
| vectorLabelTypeId = runtimeScenario.getLabelTypeSystem().findTypeId("DengueModelVectorLabel"); |
| } |
| |
| /** |
| * Remember the positions of the variables we need for fast access below |
| * @param y |
| */ |
| public void initialize(double [] y) { |
| super.initialize(y); |
| String [] vars = { |
| "s", |
| "E1", |
| "E2", |
| "E3", |
| "E4", |
| "I1", |
| "I2", |
| "I3", |
| "I4", |
| "T1", |
| "T2", |
| "T3", |
| "T4", |
| "R1", |
| "R2", |
| "R3", |
| "R4", |
| "E12", |
| "E13", |
| "E14", |
| "E21", |
| "E23", |
| "E24", |
| "E31", |
| "E32", |
| "E34", |
| "E41", |
| "E42", |
| "E43", |
| "I12", |
| "I13", |
| "I14", |
| "I21", |
| "I23", |
| "I24", |
| "I31", |
| "I32", |
| "I34", |
| "I41", |
| "I42", |
| "I43", |
| "R", |
| "incidence", |
| "incidence1", |
| "incidence2", |
| "incidence3", |
| "incidence4", |
| "incidence12", |
| "incidence21", |
| "incidence31", |
| "incidence41", |
| "incidence13", |
| "incidence23", |
| "incidence32", |
| "incidence42", |
| "incidence14", |
| "incidence24", |
| "incidence34", |
| "incidence43", |
| "diseaseDeaths", |
| "diseaseDeaths1", |
| "diseaseDeaths2", |
| "diseaseDeaths3", |
| "diseaseDeaths4", |
| "diseaseDeaths12", |
| "diseaseDeaths21", |
| "diseaseDeaths31", |
| "diseaseDeaths41", |
| "diseaseDeaths13", |
| "diseaseDeaths23", |
| "diseaseDeaths32", |
| "diseaseDeaths42", |
| "diseaseDeaths14", |
| "diseaseDeaths24", |
| "diseaseDeaths34", |
| "diseaseDeaths43" |
| }; |
| |
| extractVariablePositions(vars); |
| } |
| |
| @Override |
| public int getDimension() { |
| return dimensions; |
| } |
| |
| // For performance |
| private short IDENTIFIER_ATTR_INDEX=-1; |
| private short IDENTIFIER_HOST_ATTR_INDEX=-1; |
| private short I1_ATTR_INDEX=-1; |
| private short I2_ATTR_INDEX=-1; |
| private short I3_ATTR_INDEX=-1; |
| private short I4_ATTR_INDEX=-1; |
| String [] allComps = {"s", "E1", "E2", "E3", "E4", "I1", "I2", "I3", "I4", "T1", "T2", "T3", "T4", "R1", "R2", "R3", "R4", "E12", "E13", "E14", "E21", "E23", "E24", "E31", "E32", "E34", "E41", "E42", "E43", |
| "I12", "I13", "I14", "I21", "I23", "I24", "I31", "I32", "I34", "I41", "I42", "I43"}; |
| |
| String [] infComps = {"I1", "I2", "I3", "I4", "I12", "I13", "I14", "I21", "I23", "I24", "I31", "I32", "I34", "I41", "I42", "I43"}; |
| |
| @Override |
| public void computeDerivatives(double t, double[] y, double[] yDot) |
| throws DerivativeException { |
| |
| int index = 0; |
| int labelIndex = 0; |
| for(Integer rLabelId:runtimeDecorator.getLabelsToUpdate()) { |
| RuntimeLabel rLabel = runtimeScenario.getGraph().findLabel(rLabelId); |
| RuntimeNode rNode = runtimeScenario.getGraph().findNode(rLabel.getNodeId()); |
| |
| if (rLabel.getRuntimeType().getName().equals("DengueModelHostLabel")) { |
| double s = y[index+variable_position_offsets.get("s")[labelIndex]]; |
| double e1 = y[index+variable_position_offsets.get("E1")[labelIndex]]; |
| double e2 = y[index+variable_position_offsets.get("E2")[labelIndex]]; |
| double e3 = y[index+variable_position_offsets.get("E3")[labelIndex]]; |
| double e4 = y[index+variable_position_offsets.get("E4")[labelIndex]]; |
| double i1 = y[index+variable_position_offsets.get("I1")[labelIndex]]; |
| double i2 = y[index+variable_position_offsets.get("I2")[labelIndex]]; |
| double i3 = y[index+variable_position_offsets.get("I3")[labelIndex]]; |
| double i4 = y[index+variable_position_offsets.get("I4")[labelIndex]]; |
| double t1 = y[index+variable_position_offsets.get("T1")[labelIndex]]; |
| double t2 = y[index+variable_position_offsets.get("T2")[labelIndex]]; |
| double t3 = y[index+variable_position_offsets.get("T3")[labelIndex]]; |
| double t4 = y[index+variable_position_offsets.get("T4")[labelIndex]]; |
| double r1 = y[index+variable_position_offsets.get("R1")[labelIndex]]; |
| double r2 = y[index+variable_position_offsets.get("R2")[labelIndex]]; |
| double r3 = y[index+variable_position_offsets.get("R3")[labelIndex]]; |
| double r4 = y[index+variable_position_offsets.get("R4")[labelIndex]]; |
| double e12 = y[index+variable_position_offsets.get("E12")[labelIndex]]; |
| double e13 = y[index+variable_position_offsets.get("E13")[labelIndex]]; |
| double e14 = y[index+variable_position_offsets.get("E14")[labelIndex]]; |
| double e21 = y[index+variable_position_offsets.get("E21")[labelIndex]]; |
| double e23 = y[index+variable_position_offsets.get("E23")[labelIndex]]; |
| double e24 = y[index+variable_position_offsets.get("E24")[labelIndex]]; |
| double e31 = y[index+variable_position_offsets.get("E31")[labelIndex]]; |
| double e32 = y[index+variable_position_offsets.get("E32")[labelIndex]]; |
| double e34 = y[index+variable_position_offsets.get("E34")[labelIndex]]; |
| double e41 = y[index+variable_position_offsets.get("E41")[labelIndex]]; |
| double e42 = y[index+variable_position_offsets.get("E42")[labelIndex]]; |
| double e43 = y[index+variable_position_offsets.get("E43")[labelIndex]]; |
| double i12 = y[index+variable_position_offsets.get("I12")[labelIndex]]; |
| double i13 = y[index+variable_position_offsets.get("I13")[labelIndex]]; |
| double i14 = y[index+variable_position_offsets.get("I14")[labelIndex]]; |
| double i21 = y[index+variable_position_offsets.get("I21")[labelIndex]]; |
| double i23 = y[index+variable_position_offsets.get("I23")[labelIndex]]; |
| double i24 = y[index+variable_position_offsets.get("I24")[labelIndex]]; |
| double i31 = y[index+variable_position_offsets.get("I31")[labelIndex]]; |
| double i32 = y[index+variable_position_offsets.get("I32")[labelIndex]]; |
| double i34 = y[index+variable_position_offsets.get("I34")[labelIndex]]; |
| double i41 = y[index+variable_position_offsets.get("I41")[labelIndex]]; |
| double i42 = y[index+variable_position_offsets.get("I42")[labelIndex]]; |
| double i43 = y[index+variable_position_offsets.get("I43")[labelIndex]]; |
| double r = y[index+variable_position_offsets.get("R")[labelIndex]]; |
| double hostPopulationCount = s+e1+e2+e3+e4+i1+i2+i3+i4+t1+t2+t3+t4+r1+r2+r3+r4+e12+e13+e14+e21+e23+e24+e31+e32+e34+e41+e42+e43+i12+i13+i14+i21+i23+i24+i31+i32+i34+i41+i42+i43+r; |
| |
| if (hostPopulationCount == 0.0) { |
| continue; |
| } |
| |
| RuntimeLabel vectorRLabel = null; |
| List<RuntimeLabel> allLabels = rNode.getLabels(vectorLabelTypeId); |
| |
| if(allLabels == null) { |
| System.err.println("Cannot find vector label"); |
| continue; |
| } |
| |
| for (RuntimeLabel label : allLabels) { |
| if(IDENTIFIER_ATTR_INDEX == -1) |
| IDENTIFIER_ATTR_INDEX = label.getRuntimeType().getAttributeIndex(Names.IDENTIFIER); |
| if(label.getAttributeValue(IDENTIFIER_ATTR_INDEX).equals(vectorPopulationIdentifier)) |
| {vectorRLabel = label;break;} |
| } |
| if(vectorRLabel == null) { |
| System.err.println("Cannot find vector label"); |
| continue; |
| } |
| |
| int vectorLabelIndex =labelSequenceNumberMap.get(vectorRLabel); |
| int vectorLabelStartPosition = labelVectorPositions[vectorLabelIndex]; |
| double vector_i1 = y[vectorLabelStartPosition+variable_position_offsets.get("I1")[vectorLabelIndex]]; |
| double vector_i2 = y[vectorLabelStartPosition+variable_position_offsets.get("I2")[vectorLabelIndex]]; |
| double vector_i3 = y[vectorLabelStartPosition+variable_position_offsets.get("I3")[vectorLabelIndex]]; |
| double vector_i4 = y[vectorLabelStartPosition+variable_position_offsets.get("I4")[vectorLabelIndex]]; |
| |
| |
| // define the transition between the compartments |
| double toE1 = hostInfectivity1 * bitingRateIV |
| * vector_i1 * s / hostPopulationCount; |
| double toE2 = hostInfectivity2 * bitingRateIV |
| * vector_i2 * s / hostPopulationCount; |
| double toE3 = hostInfectivity3 * bitingRateIV |
| * vector_i3 * s / hostPopulationCount; |
| double toE4 = hostInfectivity4 * bitingRateIV |
| * vector_i4 * s / hostPopulationCount; |
| |
| double toI1 = hostPrimaryIncubationRate1 * e1; |
| double toI2 = hostPrimaryIncubationRate2 * e2; |
| double toI3 = hostPrimaryIncubationRate3 * e3; |
| double toI4 = hostPrimaryIncubationRate4 * e4; |
| |
| double toT1 = episilon1 * hostPrimaryRecoveryRate1 * i1; |
| double toT2 = episilon2 * hostPrimaryRecoveryRate2 * i2; |
| double toT3 = episilon3 * hostPrimaryRecoveryRate3 * i3; |
| double toT4 = episilon4 * hostPrimaryRecoveryRate4 * i4; |
| |
| //imperfect cross immunity - 20110818 |
| double fromI1toR1 = (1 - episilon1) * hostPrimaryRecoveryRate1 * i1; |
| double fromI2toR2 = (1 - episilon2) * hostPrimaryRecoveryRate2 * i2; |
| double fromI3toR3 = (1 - episilon3) * hostPrimaryRecoveryRate3 * i3; |
| double fromI4toR4 = (1 - episilon4) * hostPrimaryRecoveryRate4 * i4; |
| |
| double toR1 = hostPrimaryImmunityLossRate1 * t1; |
| double toR2 = hostPrimaryImmunityLossRate2 * t2; |
| double toR3 = hostPrimaryImmunityLossRate3 * t3; |
| double toR4 = hostPrimaryImmunityLossRate4 * t3; |
| |
| if(I1_ATTR_INDEX == -1) { |
| I1_ATTR_INDEX = vectorRLabel.getRuntimeType().getDoubleAttributeIndex("I1"); |
| I2_ATTR_INDEX = vectorRLabel.getRuntimeType().getDoubleAttributeIndex("I2"); |
| I3_ATTR_INDEX = vectorRLabel.getRuntimeType().getDoubleAttributeIndex("I3"); |
| I4_ATTR_INDEX = vectorRLabel.getRuntimeType().getDoubleAttributeIndex("I4"); |
| |
| } |
| //the formula is revised due to the wrong definition - 20110818 |
| |
| double toE12 = vectorADE2 * hostInfectivity2 * bitingRateIV |
| * vectorRLabel.getDoubleAttributeValue(I2_ATTR_INDEX) * r1 / hostPopulationCount; |
| double toE13 = vectorADE3 * hostInfectivity3 * bitingRateIV |
| * vectorRLabel.getDoubleAttributeValue(I3_ATTR_INDEX) * r1 / hostPopulationCount; |
| double toE14 = vectorADE4 * hostInfectivity4 * bitingRateIV |
| * vectorRLabel.getDoubleAttributeValue(I4_ATTR_INDEX) * r1 / hostPopulationCount; |
| double toE21 = vectorADE1 * hostInfectivity1 * bitingRateIV |
| * vectorRLabel.getDoubleAttributeValue(I1_ATTR_INDEX) * r2 / hostPopulationCount; |
| double toE23 = vectorADE3 * hostInfectivity3 * bitingRateIV |
| * vectorRLabel.getDoubleAttributeValue(I3_ATTR_INDEX) * r2 / hostPopulationCount; |
| double toE24 = vectorADE4 * hostInfectivity4 * bitingRateIV |
| * vectorRLabel.getDoubleAttributeValue(I4_ATTR_INDEX) * r2 / hostPopulationCount; |
| double toE31 = vectorADE1 * hostInfectivity1 * bitingRateIV |
| * vectorRLabel.getDoubleAttributeValue(I1_ATTR_INDEX) * r3 / hostPopulationCount; |
| double toE32 = vectorADE2 * hostInfectivity2 * bitingRateIV |
| * vectorRLabel.getDoubleAttributeValue(I2_ATTR_INDEX) * r3 / hostPopulationCount; |
| double toE34 = vectorADE4 * hostInfectivity4 * bitingRateIV |
| * vectorRLabel.getDoubleAttributeValue(I4_ATTR_INDEX) * r3 / hostPopulationCount; |
| double toE41 = vectorADE1 * hostInfectivity1 * bitingRateIV |
| * vectorRLabel.getDoubleAttributeValue(I1_ATTR_INDEX) * r4 / hostPopulationCount; |
| double toE42 = vectorADE2 * hostInfectivity2 * bitingRateIV |
| * vectorRLabel.getDoubleAttributeValue(I2_ATTR_INDEX) * r4 / hostPopulationCount; |
| double toE43 = vectorADE3 * hostInfectivity3 * bitingRateIV |
| * vectorRLabel.getDoubleAttributeValue(I3_ATTR_INDEX) * r4 / hostPopulationCount; |
| |
| double toI12 = hostSecondaryIncubationRate12 |
| * e12; |
| double toI13 = hostSecondaryIncubationRate13 |
| * e13; |
| double toI14 = hostSecondaryIncubationRate14 |
| * e14; |
| double toI21 = hostSecondaryIncubationRate21 |
| * e21; |
| double toI23 = hostSecondaryIncubationRate23 |
| * e23; |
| double toI24 = hostSecondaryIncubationRate24 |
| * e24; |
| double toI31 = hostSecondaryIncubationRate31 |
| * e31; |
| double toI32 = hostSecondaryIncubationRate32 |
| * e32; |
| double toI34 = hostSecondaryIncubationRate34 |
| * e34; |
| double toI41 = hostSecondaryIncubationRate41 |
| * e41; |
| double toI42 = hostSecondaryIncubationRate42 |
| * e42; |
| double toI43 = hostSecondaryIncubationRate43 |
| * e43; |
| |
| double toR12 = hostSecondaryRecoveryRate12 * i12; |
| double toR13 = hostSecondaryRecoveryRate13 * i13; |
| double toR14 = hostSecondaryRecoveryRate14 * i14; |
| double toR21 = hostSecondaryRecoveryRate21 * i21; |
| double toR23 = hostSecondaryRecoveryRate23 * i23; |
| double toR24 = hostSecondaryRecoveryRate24 * i24; |
| double toR31 = hostSecondaryRecoveryRate31 * i31; |
| double toR32 = hostSecondaryRecoveryRate32 * i32; |
| double toR34 = hostSecondaryRecoveryRate34 * i34; |
| double toR41 = hostSecondaryRecoveryRate41 * i41; |
| double toR42 = hostSecondaryRecoveryRate42 * i42; |
| double toR43 = hostSecondaryRecoveryRate43 * i43; |
| |
| double deathsI1 = hostPrimaryDiseaseDeathRate1 |
| * i1; |
| double deathsI2 = hostPrimaryDiseaseDeathRate2 |
| * i2; |
| double deathsI3 = hostPrimaryDiseaseDeathRate3 |
| * i3; |
| double deathsI4 = hostPrimaryDiseaseDeathRate4 |
| * i4; |
| |
| double deathsI12 = hostSecondaryDiseaseDeathRate12 |
| * i12; |
| double deathsI13 = hostSecondaryDiseaseDeathRate13 |
| * i13; |
| double deathsI14 = hostSecondaryDiseaseDeathRate14 |
| * i14; |
| double deathsI21 = hostSecondaryDiseaseDeathRate21 |
| * i21; |
| double deathsI23 = hostSecondaryDiseaseDeathRate23 |
| * i23; |
| double deathsI24 = hostSecondaryDiseaseDeathRate24 |
| * i24; |
| double deathsI31 = hostSecondaryDiseaseDeathRate31 |
| * i31; |
| double deathsI32 = hostSecondaryDiseaseDeathRate32 |
| * i32; |
| double deathsI34 = hostSecondaryDiseaseDeathRate34 |
| * i34; |
| double deathsI41 = hostSecondaryDiseaseDeathRate41 |
| * i41; |
| double deathsI42 = hostSecondaryDiseaseDeathRate42 |
| * i42; |
| double deathsI43 = hostSecondaryDiseaseDeathRate43 |
| * i43; |
| |
| double deltaS =-toE1 - toE2 - toE3 - toE4; |
| yDot[index+variable_position_offsets.get("s")[labelIndex]] = deltaS; |
| double deltaE1 =toE1 - toI1; |
| yDot[index+variable_position_offsets.get("E1")[labelIndex]] = deltaE1; |
| double deltaE2 =toE2 - toI2; |
| yDot[index+variable_position_offsets.get("E2")[labelIndex]] = deltaE2; |
| double deltaE3 = toE3 - toI3; |
| yDot[index+variable_position_offsets.get("E3")[labelIndex]] = deltaE3; |
| double deltaE4 = toE4 - toI4; |
| yDot[index+variable_position_offsets.get("E4")[labelIndex]] = deltaE4; |
| |
| double deltaI1 =(toI1 - toT1 - deathsI1 - fromI1toR1); |
| yDot[index+variable_position_offsets.get("I1")[labelIndex]] = deltaI1; |
| double deltaI2 =(toI2 - toT2 - deathsI2 - fromI2toR2); |
| yDot[index+variable_position_offsets.get("I2")[labelIndex]] = deltaI2; |
| double deltaI3 =(toI3 - toT3 - deathsI3 - fromI3toR3); |
| yDot[index+variable_position_offsets.get("I3")[labelIndex]] = deltaI3; |
| double deltaI4 =(toI4 - toT4 - deathsI4 - fromI4toR4); |
| yDot[index+variable_position_offsets.get("I4")[labelIndex]] = deltaI4; |
| |
| double deltaT1 =(toT1 - toR1); |
| yDot[index+variable_position_offsets.get("T1")[labelIndex]] = deltaT1; |
| double deltaT2 =(toT2 - toR2); |
| yDot[index+variable_position_offsets.get("T2")[labelIndex]] = deltaT2; |
| double deltaT3 =(toT3 - toR3); |
| yDot[index+variable_position_offsets.get("T3")[labelIndex]] = deltaT3; |
| double deltaT4 =(toT4 - toR4); |
| yDot[index+variable_position_offsets.get("T4")[labelIndex]] = deltaT4; |
| |
| double deltaR1 =(fromI1toR1 + toR1 - toE12 - toE13 - toE14); |
| yDot[index+variable_position_offsets.get("R1")[labelIndex]] = deltaR1; |
| double deltaR2 =(fromI2toR2 + toR2 - toE21 - toE23 - toE24); |
| yDot[index+variable_position_offsets.get("R2")[labelIndex]] = deltaR2; |
| double deltaR3 =(fromI3toR3 + toR3 - toE31 - toE32 - toE34); |
| yDot[index+variable_position_offsets.get("E3")[labelIndex]] = deltaR3; |
| double deltaR4 =(fromI4toR4 + toR4 - toE41 - toE42 - toE43); |
| yDot[index+variable_position_offsets.get("R4")[labelIndex]] = deltaR4; |
| |
| double deltaE12 =(toE12 - toI12); |
| yDot[index+variable_position_offsets.get("E12")[labelIndex]] = deltaE12; |
| double deltaE13 =(toE13 - toI13); |
| yDot[index+variable_position_offsets.get("E13")[labelIndex]] = deltaE13; |
| double deltaE14 =(toE14 - toI14); |
| yDot[index+variable_position_offsets.get("E14")[labelIndex]] = deltaE14; |
| double deltaE21 =(toE21 - toI21); |
| yDot[index+variable_position_offsets.get("E21")[labelIndex]] = deltaE21; |
| double deltaE23 =(toE23 - toI23); |
| yDot[index+variable_position_offsets.get("E23")[labelIndex]] = deltaE23; |
| double deltaE24 =(toE24 - toI24); |
| yDot[index+variable_position_offsets.get("E24")[labelIndex]] = deltaE24; |
| double deltaE31 =(toE31 - toI31); |
| yDot[index+variable_position_offsets.get("E31")[labelIndex]] = deltaE31; |
| double deltaE32 =(toE32 - toI32); |
| yDot[index+variable_position_offsets.get("E32")[labelIndex]] = deltaE32; |
| double deltaE34 =(toE34 - toI34); |
| yDot[index+variable_position_offsets.get("E34")[labelIndex]] = deltaE34; |
| double deltaE41 =(toE41 - toI41); |
| yDot[index+variable_position_offsets.get("E41")[labelIndex]] = deltaE41; |
| double deltaE42 =(toE42 - toI42); |
| yDot[index+variable_position_offsets.get("E42")[labelIndex]] = deltaE42; |
| double deltaE43 =(toE43 - toI43); |
| yDot[index+variable_position_offsets.get("E43")[labelIndex]] = deltaE43; |
| |
| double deltaI12 =(toI12 - toR12); |
| yDot[index+variable_position_offsets.get("I12")[labelIndex]] = deltaI12; |
| double deltaI13 =(toI13 - toR13); |
| yDot[index+variable_position_offsets.get("I13")[labelIndex]] = deltaI13; |
| double deltaI14 =(toI14 - toR14); |
| yDot[index+variable_position_offsets.get("I14")[labelIndex]] = deltaI14; |
| double deltaI21 =(toI21 - toR21); |
| yDot[index+variable_position_offsets.get("I21")[labelIndex]] = deltaI21; |
| double deltaI23 =(toI23 - toR23); |
| yDot[index+variable_position_offsets.get("I23")[labelIndex]] = deltaI23; |
| double deltaI24 =(toI24 - toR24); |
| yDot[index+variable_position_offsets.get("I24")[labelIndex]] = deltaI24; |
| double deltaI31 =(toI31 - toR31); |
| yDot[index+variable_position_offsets.get("I31")[labelIndex]] = deltaI31; |
| double deltaI32 =(toI32 - toR32); |
| yDot[index+variable_position_offsets.get("I32")[labelIndex]] = deltaI32; |
| double deltaI34 =(toI34 - toR34); |
| yDot[index+variable_position_offsets.get("I34")[labelIndex]] = deltaI34; |
| double deltaI41 =(toI41 - toR41); |
| yDot[index+variable_position_offsets.get("I41")[labelIndex]] = deltaI41; |
| double deltaI42 =(toI42 - toR42); |
| yDot[index+variable_position_offsets.get("I42")[labelIndex]] = deltaI42; |
| double deltaI43 =(toI43 - toR43); |
| yDot[index+variable_position_offsets.get("I43")[labelIndex]] = deltaI43; |
| |
| double deltaR =(toR12 + toR13 + toR14 + toR21 + toR23 + toR24 |
| + toR31 + toR32 + toR34 + toR41 + toR42 + toR43); |
| yDot[index+variable_position_offsets.get("R")[labelIndex]] = deltaR; |
| |
| double newIncidence1 = (toE1); |
| yDot[index+variable_position_offsets.get("incidence1")[labelIndex]] = newIncidence1; |
| double newIncidence2 = (toE2); |
| yDot[index+variable_position_offsets.get("incidence2")[labelIndex]] = newIncidence2; |
| double newIncidence3 = (toE3); |
| yDot[index+variable_position_offsets.get("incidence3")[labelIndex]] = newIncidence3; |
| double newIncidence4 = (toE4); |
| yDot[index+variable_position_offsets.get("incidence4")[labelIndex]] = newIncidence4; |
| |
| double newIncidence12 = (toE12); |
| yDot[index+variable_position_offsets.get("incidence12")[labelIndex]] = newIncidence12; |
| double newIncidence13 = (toE13); |
| yDot[index+variable_position_offsets.get("incidence13")[labelIndex]] = newIncidence13; |
| double newIncidence14 = (toE14); |
| yDot[index+variable_position_offsets.get("incidence14")[labelIndex]] = newIncidence14; |
| double newIncidence21 = (toE21); |
| yDot[index+variable_position_offsets.get("incidence21")[labelIndex]] = newIncidence21; |
| double newIncidence23 = (toE23); |
| yDot[index+variable_position_offsets.get("incidence23")[labelIndex]] = newIncidence23; |
| double newIncidence24 = (toE24); |
| yDot[index+variable_position_offsets.get("incidence24")[labelIndex]] = newIncidence24; |
| double newIncidence31 = (toE31); |
| yDot[index+variable_position_offsets.get("incidence31")[labelIndex]] = newIncidence31; |
| double newIncidence32 = (toE32); |
| yDot[index+variable_position_offsets.get("incidence32")[labelIndex]] = newIncidence32; |
| double newIncidence34 = (toE34); |
| yDot[index+variable_position_offsets.get("incidence34")[labelIndex]] = newIncidence34; |
| double newIncidence41 = (toE41); |
| yDot[index+variable_position_offsets.get("incidence41")[labelIndex]] = newIncidence41; |
| double newIncidence42 = (toE42); |
| yDot[index+variable_position_offsets.get("incidence42")[labelIndex]] = newIncidence42; |
| double newIncidence43 = (toE43); |
| yDot[index+variable_position_offsets.get("incidence43")[labelIndex]] = newIncidence43; |
| |
| double newIncidence = (toE1 + toE2 + toE3 + toE4 + toE12 + toE13 |
| + toE14 + toE21 + toE23 + toE24 + toE31 + toE32 + toE34 |
| + toE41 + toE42 + toE43); |
| |
| yDot[index+variable_position_offsets.get("incidence")[labelIndex]] = newIncidence; |
| double newDiseaseDeaths1 = (deathsI1); |
| yDot[index+variable_position_offsets.get("diseaseDeaths1")[labelIndex]] = newDiseaseDeaths1; |
| double newDiseaseDeaths2 = (deathsI2); |
| yDot[index+variable_position_offsets.get("diseaseDeaths2")[labelIndex]] = newDiseaseDeaths2; |
| double newDiseaseDeaths3 = (deathsI3); |
| yDot[index+variable_position_offsets.get("diseaseDeaths3")[labelIndex]] = newDiseaseDeaths3; |
| double newDiseaseDeaths4 = (deathsI4); |
| yDot[index+variable_position_offsets.get("diseaseDeaths4")[labelIndex]] = newDiseaseDeaths4; |
| |
| double newDiseaseDeaths12 = (deathsI12); |
| yDot[index+variable_position_offsets.get("diseaseDeaths12")[labelIndex]] = newDiseaseDeaths12; |
| double newDiseaseDeaths13 = (deathsI13); |
| yDot[index+variable_position_offsets.get("diseaseDeaths13")[labelIndex]] = newDiseaseDeaths13; |
| double newDiseaseDeaths14 = (deathsI14); |
| yDot[index+variable_position_offsets.get("diseaseDeaths14")[labelIndex]] = newDiseaseDeaths14; |
| double newDiseaseDeaths21 = (deathsI21); |
| yDot[index+variable_position_offsets.get("diseaseDeaths21")[labelIndex]] = newDiseaseDeaths21; |
| double newDiseaseDeaths23 = (deathsI23); |
| yDot[index+variable_position_offsets.get("diseaseDeaths23")[labelIndex]] = newDiseaseDeaths23; |
| double newDiseaseDeaths24 = (deathsI24); |
| yDot[index+variable_position_offsets.get("diseaseDeaths24")[labelIndex]] = newDiseaseDeaths24; |
| double newDiseaseDeaths31 = (deathsI31); |
| yDot[index+variable_position_offsets.get("diseaseDeaths31")[labelIndex]] = newDiseaseDeaths31; |
| double newDiseaseDeaths32 = (deathsI32); |
| yDot[index+variable_position_offsets.get("diseaseDeaths32")[labelIndex]] = newDiseaseDeaths32; |
| double newDiseaseDeaths34 = (deathsI34); |
| yDot[index+variable_position_offsets.get("diseaseDeaths34")[labelIndex]] = newDiseaseDeaths34; |
| double newDiseaseDeaths41 = (deathsI41); |
| yDot[index+variable_position_offsets.get("diseaseDeaths41")[labelIndex]] = newDiseaseDeaths41; |
| double newDiseaseDeaths42 = (deathsI42); |
| yDot[index+variable_position_offsets.get("diseaseDeaths42")[labelIndex]] = newDiseaseDeaths42; |
| double newDiseaseDeaths43 = (deathsI43); |
| yDot[index+variable_position_offsets.get("diseaseDeaths43")[labelIndex]] = newDiseaseDeaths43; |
| |
| double newDiseaseDeaths = (deathsI1 + deathsI2 + deathsI3 |
| + deathsI4 + deathsI12 + deathsI13 + deathsI14 + deathsI21 |
| + deathsI23 + deathsI24 + deathsI31 + deathsI32 + deathsI34 |
| + deathsI41 + deathsI42 + deathsI43); |
| yDot[index+variable_position_offsets.get("diseaseDeaths")[labelIndex]] = newDiseaseDeaths; |
| } |
| // else if the current population is vector population |
| else if (rLabel.getRuntimeType().getName().equals("DengueModelVectorLabel")) { |
| |
| double s = y[index+variable_position_offsets.get("s")[labelIndex]]; |
| double e1 = y[index+variable_position_offsets.get("E1")[labelIndex]]; |
| double e2 = y[index+variable_position_offsets.get("E2")[labelIndex]]; |
| double e3 = y[index+variable_position_offsets.get("E3")[labelIndex]]; |
| double e4 = y[index+variable_position_offsets.get("E4")[labelIndex]]; |
| double i1 = y[index+variable_position_offsets.get("I1")[labelIndex]]; |
| double i2 = y[index+variable_position_offsets.get("I2")[labelIndex]]; |
| double i3 = y[index+variable_position_offsets.get("I3")[labelIndex]]; |
| double i4 = y[index+variable_position_offsets.get("I4")[labelIndex]]; |
| double vectorPopulationCount = s+e1+e2+e3+e4+i1+i2+i3+i4; |
| |
| |
| if (vectorPopulationCount == 0.0) { |
| continue; |
| } |
| |
| RuntimeLabel hostRLabel = null; |
| List<RuntimeLabel> allLabels = rNode.getLabels(hostLabelTypeId); |
| |
| for (RuntimeLabel label : allLabels) { |
| if(IDENTIFIER_HOST_ATTR_INDEX == -1) |
| IDENTIFIER_HOST_ATTR_INDEX = label.getRuntimeType().getAttributeIndex("identifier"); |
| if(label.getAttributeValue(IDENTIFIER_HOST_ATTR_INDEX).equals(hostPopulationIdentifier)) |
| {hostRLabel = label;break;} |
| } |
| if(hostRLabel == null) { |
| System.err.println("Cannot find host label"); |
| continue; |
| } |
| |
| |
| double toE1 = 0.0; |
| double toE2 = 0.0; |
| double toE3 = 0.0; |
| double toE4 = 0.0; |
| |
| int hostLabelIndex = runtimeDecorator.getLabelsToUpdate().indexOf(hostRLabel.getId()); // expensive? |
| int hostLabelStartPosition = labelVectorPositions[hostLabelIndex]; |
| double host_s = y[hostLabelStartPosition+variable_position_offsets.get("s")[labelIndex]]; |
| double host_e1 = y[hostLabelStartPosition+variable_position_offsets.get("E1")[labelIndex]]; |
| double host_e2 = y[hostLabelStartPosition+variable_position_offsets.get("E2")[labelIndex]]; |
| double host_e3 = y[hostLabelStartPosition+variable_position_offsets.get("E3")[labelIndex]]; |
| double host_e4 = y[hostLabelStartPosition+variable_position_offsets.get("E4")[labelIndex]]; |
| double host_i1 = y[hostLabelStartPosition+variable_position_offsets.get("I1")[labelIndex]]; |
| double host_i2 = y[hostLabelStartPosition+variable_position_offsets.get("I2")[labelIndex]]; |
| double host_i3 = y[hostLabelStartPosition+variable_position_offsets.get("I3")[labelIndex]]; |
| double host_i4 = y[hostLabelStartPosition+variable_position_offsets.get("I4")[labelIndex]]; |
| double host_t1 = y[hostLabelStartPosition+variable_position_offsets.get("T1")[labelIndex]]; |
| double host_t2 = y[hostLabelStartPosition+variable_position_offsets.get("T2")[labelIndex]]; |
| double host_t3 = y[hostLabelStartPosition+variable_position_offsets.get("T3")[labelIndex]]; |
| double host_t4 = y[hostLabelStartPosition+variable_position_offsets.get("T4")[labelIndex]]; |
| double host_r1 = y[hostLabelStartPosition+variable_position_offsets.get("R1")[labelIndex]]; |
| double host_r2 = y[hostLabelStartPosition+variable_position_offsets.get("R2")[labelIndex]]; |
| double host_r3 = y[hostLabelStartPosition+variable_position_offsets.get("R3")[labelIndex]]; |
| double host_r4 = y[hostLabelStartPosition+variable_position_offsets.get("R4")[labelIndex]]; |
| double host_e12 = y[hostLabelStartPosition+variable_position_offsets.get("E12")[labelIndex]]; |
| double host_e13 = y[hostLabelStartPosition+variable_position_offsets.get("E13")[labelIndex]]; |
| double host_e14 = y[hostLabelStartPosition+variable_position_offsets.get("E14")[labelIndex]]; |
| double host_e21 = y[hostLabelStartPosition+variable_position_offsets.get("E21")[labelIndex]]; |
| double host_e23 = y[hostLabelStartPosition+variable_position_offsets.get("E23")[labelIndex]]; |
| double host_e24 = y[hostLabelStartPosition+variable_position_offsets.get("E24")[labelIndex]]; |
| double host_e31 = y[hostLabelStartPosition+variable_position_offsets.get("E31")[labelIndex]]; |
| double host_e32 = y[hostLabelStartPosition+variable_position_offsets.get("E32")[labelIndex]]; |
| double host_e34 = y[hostLabelStartPosition+variable_position_offsets.get("E34")[labelIndex]]; |
| double host_e41 = y[hostLabelStartPosition+variable_position_offsets.get("E41")[labelIndex]]; |
| double host_e42 = y[hostLabelStartPosition+variable_position_offsets.get("E42")[labelIndex]]; |
| double host_e43 = y[hostLabelStartPosition+variable_position_offsets.get("E43")[labelIndex]]; |
| double host_i12 = y[hostLabelStartPosition+variable_position_offsets.get("I12")[labelIndex]]; |
| double host_i13 = y[hostLabelStartPosition+variable_position_offsets.get("I13")[labelIndex]]; |
| double host_i14 = y[hostLabelStartPosition+variable_position_offsets.get("I14")[labelIndex]]; |
| double host_i21 = y[hostLabelStartPosition+variable_position_offsets.get("I21")[labelIndex]]; |
| double host_i23 = y[hostLabelStartPosition+variable_position_offsets.get("I23")[labelIndex]]; |
| double host_i24 = y[hostLabelStartPosition+variable_position_offsets.get("I24")[labelIndex]]; |
| double host_i31 = y[hostLabelStartPosition+variable_position_offsets.get("I31")[labelIndex]]; |
| double host_i32 = y[hostLabelStartPosition+variable_position_offsets.get("I32")[labelIndex]]; |
| double host_i34 = y[hostLabelStartPosition+variable_position_offsets.get("I34")[labelIndex]]; |
| double host_i41 = y[hostLabelStartPosition+variable_position_offsets.get("I41")[labelIndex]]; |
| double host_i42 = y[hostLabelStartPosition+variable_position_offsets.get("I42")[labelIndex]]; |
| double host_i43 = y[hostLabelStartPosition+variable_position_offsets.get("I43")[labelIndex]]; |
| double host_r = y[hostLabelStartPosition+variable_position_offsets.get("R")[labelIndex]]; |
| double hostPopulationCount = host_s+host_e1+host_e2+host_e3+host_e4+host_i1+host_i2+host_i3+host_i4+host_t1+host_t2+host_t3+host_t4+host_r1+host_r2+host_r3+host_r4+host_e12+host_e13+host_e14+host_e21+host_e23+host_e24+host_e31+host_e32+host_e34+host_e41+host_e42+host_e43+host_i12+host_i13+host_i14+host_i21+host_i23+host_i24+host_i31+host_i32+host_i34+host_i41+host_i42+host_i43+host_r; |
| |
| if(hostPopulationCount == 0) continue; |
| |
| |
| double [] localInf = {host_i1, host_i2, host_i3, host_i4, host_i12, host_i13, host_i14, host_i21, host_i23, host_i24, host_i31, host_i32, host_i34, host_i41, host_i42, host_i43}; |
| |
| double effectiveI1; |
| double effectiveI2; |
| double effectiveI3; |
| double effectiveI4; |
| double effectiveI12; |
| double effectiveI13; |
| double effectiveI14; |
| double effectiveI21; |
| double effectiveI23; |
| double effectiveI24; |
| double effectiveI31; |
| double effectiveI32; |
| double effectiveI34; |
| double effectiveI41; |
| double effectiveI42; |
| double effectiveI43; |
| |
| double [] effectives; |
| if (characteristicMixingDistance != 0.0 || roadNetworkInfectiousProportion != 0) { |
| effectives = RuntimeUtilities.getEffectiveInfectious(this.runtimeScenario, rLabel, localInf, hostPopulationCount, y, allComps, |
| infComps, characteristicMixingDistance, roadNetworkInfectiousProportion, |
| variable_position_offsets, labelVectorPositions, labelSequenceNumberMap); |
| effectiveI1 = effectives[0]; |
| effectiveI2 = effectives[1]; |
| effectiveI3 = effectives[2]; |
| effectiveI4 = effectives[3]; |
| effectiveI12 = effectives[4]; |
| effectiveI13 = effectives[5]; |
| effectiveI14 = effectives[6]; |
| effectiveI21 = effectives[7]; |
| effectiveI23 = effectives[8]; |
| effectiveI24 = effectives[9]; |
| effectiveI31 = effectives[10]; |
| effectiveI32 = effectives[11]; |
| effectiveI34 = effectives[12]; |
| effectiveI41 = effectives[13]; |
| effectiveI42 = effectives[14]; |
| effectiveI43 = effectives[15]; |
| } |
| else { |
| effectiveI1 = host_i1/hostPopulationCount; |
| effectiveI2 = host_i2/hostPopulationCount; |
| effectiveI3 = host_i3/hostPopulationCount; |
| effectiveI4 = host_i4/hostPopulationCount; |
| effectiveI12 = host_i12/hostPopulationCount; |
| effectiveI13 = host_i13/hostPopulationCount; |
| effectiveI14 = host_i14/hostPopulationCount; |
| effectiveI21 = host_i21/hostPopulationCount; |
| effectiveI23 = host_i23/hostPopulationCount; |
| effectiveI24 = host_i24/hostPopulationCount; |
| effectiveI31 = host_i31/hostPopulationCount; |
| effectiveI32 = host_i32/hostPopulationCount; |
| effectiveI34 = host_i34/hostPopulationCount; |
| effectiveI41 = host_i41/hostPopulationCount; |
| effectiveI42 = host_i42/hostPopulationCount; |
| effectiveI43 = host_i43/hostPopulationCount; |
| } |
| |
| // include all primary and secondary infectious compartments of host |
| |
| |
| toE1 = vectorInfectivity1 * bitingRateSV * effectiveI1 |
| * s; |
| toE1 += vectorInfectivity1 * bitingRateSV |
| * (hostADE21 * effectiveI21 + hostADE31 * effectiveI31 + hostADE41 * effectiveI41) |
| * s; |
| toE2 = vectorInfectivity2 * bitingRateSV * effectiveI2 |
| * s; |
| toE2 += vectorInfectivity2 * bitingRateSV |
| * (hostADE12 * effectiveI12 + hostADE32 * effectiveI32 + hostADE42 * effectiveI42) |
| * s; |
| toE3 = vectorInfectivity3 * bitingRateSV * effectiveI3 |
| * s; |
| toE3 += vectorInfectivity3 * bitingRateSV |
| * (hostADE13 * effectiveI13 + hostADE23 * effectiveI23 + hostADE43 * effectiveI43) |
| * s; |
| toE4 = vectorInfectivity4 * bitingRateSV * effectiveI4 |
| * s; |
| toE4 += vectorInfectivity4 * bitingRateSV |
| * (hostADE14 * effectiveI14 + hostADE24 * effectiveI24 + hostADE34 * effectiveI34) |
| * s; |
| |
| |
| double toI1 = vectorIncubationRate1 * e1; |
| double toI2 = vectorIncubationRate2 * e2; |
| double toI3 = vectorIncubationRate3 * e3; |
| double toI4 = vectorIncubationRate4 * e4; |
| |
| double deltaS =(-toE1 - toE2 - toE3 - toE4); |
| yDot[index+variable_position_offsets.get("s")[labelIndex]] = deltaS; |
| |
| double deltaE1 = (toE1 - toI1); |
| yDot[index+variable_position_offsets.get("E1")[labelIndex]] = deltaE1; |
| double deltaE2 = (toE2 - toI2); |
| yDot[index+variable_position_offsets.get("E2")[labelIndex]] = deltaE2; |
| double deltaE3 = (toE3 - toI3); |
| yDot[index+variable_position_offsets.get("E3")[labelIndex]] = deltaE3; |
| double deltaE4 = (toE4 - toI4); |
| yDot[index+variable_position_offsets.get("E3")[labelIndex]] = deltaE4; |
| |
| double deltaI1=(toI1); |
| yDot[index+variable_position_offsets.get("I1")[labelIndex]] = deltaI1; |
| double deltaI2=(toI2); |
| yDot[index+variable_position_offsets.get("I2")[labelIndex]] = deltaI2; |
| double deltaI3=(toI3); |
| yDot[index+variable_position_offsets.get("I3")[labelIndex]] = deltaI3; |
| double deltaI4=(toI4); |
| yDot[index+variable_position_offsets.get("I4")[labelIndex]] = deltaI4; |
| |
| double incidence1=(toE1); |
| yDot[index+variable_position_offsets.get("incidence1")[labelIndex]] = incidence1; |
| double incidence2=(toE2); |
| yDot[index+variable_position_offsets.get("incidence2")[labelIndex]] = incidence2; |
| double incidence3=(toE3); |
| yDot[index+variable_position_offsets.get("incidence3")[labelIndex]] = incidence3; |
| double incidence4=(toE4); |
| yDot[index+variable_position_offsets.get("incidence4")[labelIndex]] = incidence4; |
| |
| double incidence = (toE1 + toE2 + toE3 + toE4); |
| yDot[index+variable_position_offsets.get("incidence")[labelIndex]] = incidence; |
| double diseaseDeaths = 0.0; |
| yDot[index+variable_position_offsets.get("diseaseDeaths")[labelIndex]] = diseaseDeaths; |
| |
| } |
| |
| int sz = rLabel.getNumDoubleAttributes(); |
| index += sz; |
| ++labelIndex; |
| } |
| } |
| |
| |
| } |
