org.eclipse.ohf.stem.diseasemodels.standard
Interface SIR

All Superinterfaces:
Decorator, DiseaseModel, org.eclipse.emf.ecore.EObject, Identifiable, NodeDecorator, org.eclipse.emf.common.notify.Notifier, SanityChecker, SI, StandardDiseaseModel
All Known Subinterfaces:
DeterministicSEIRDiseaseModel, DeterministicSIRDiseaseModel, SEIR, StochasticSEIRDiseaseModel, StochasticSIRDiseaseModel
All Known Implementing Classes:
DeterministicSEIRDiseaseModelImpl, DeterministicSIRDiseaseModelImpl, SEIRImpl, SIRImpl, StochasticSEIRDiseaseModelImpl, StochasticSIRDiseaseModelImpl

public interface SIR
extends SI

A DiseaseModel with three states Susceptible, Infectious and Recovered(SIR).

The basic SIR (Susceptible, Infectious, Recovered) disease model assumes a uniform population at a single location and that the population members are well "mixed", meaning that they are equally likely to meet and infect each other. This model, for a normalized population, is defined by the three equations below:

Where:

Following basically the same derivation as outlined in SI for the SI model, these become:

Let

Thus, we now have two types of Infectious population members, those that will eventually recover at rate σ, and those that will eventually die at rate μi (of course, members in all three states still die at the background rate μ).

Let

We modify our model to include these additional states and rates.

Spatial Adaptation

Let Sl = s Pl be the number of Susceptible population members at location l. Similarly, let Il = i Pl be the number of population members at location l that are Infectious (both states combined), and let r Pl be the Recovered population. For readability, we drop the l subscript and substitute.

Substituting

Continuing with i = I/Pl, we have: Letting β* = βl/Pl = β (dl/(APD * Pl)) gives: TSF

Neighboring Infectious Populations

Specific statistics on the total number of births, deaths and deaths due to the disease can be computed by adding the appropriate terms of the equations above.

See Also:
SI, SIRLabel, SIRLabelValue, SEIR, SEIRLabel, SEIRLabelValue

Field Summary
static org.eclipse.emf.common.util.URI URI_TYPE_STANDARD_SIR_DISEASE_MODEL
          The Type URI for the standard SIR disease model
static java.lang.String URI_TYPE_STANDARD_SIR_DISEASE_MODEL_SEGMENT
          This is the segment of the type URI that prefixes all other segments in a standard disease model type URI.
 
Fields inherited from interface org.eclipse.ohf.stem.diseasemodels.standard.SI
URI_TYPE_STANDARD_SI_DISEASE_MODEL_SEGMENT
 
Fields inherited from interface org.eclipse.ohf.stem.diseasemodels.standard.StandardDiseaseModel
URI_TYPE_STANDARD_DISEASEMODEL_SEGMENT
 
Fields inherited from interface org.eclipse.ohf.stem.diseasemodels.standard.DiseaseModel
URI_TYPE_DISEASEMODEL_SEGMENT
 
Method Summary
 double getAdjustedImmunityLossRate(long timeDelta)
          Compute the immunity rate adjusted for a time delta potentially different from the time period specified for the rate.
 double getImmunityLossRate()
          This coefficient determines the number of population members that lose their immunity to a disease and become Susceptible to the disease per population member in the Recovered state.
 void setImmunityLossRate(double value)
          Sets the value of the 'Immunity Loss Rate' attribute.
 
Methods inherited from interface org.eclipse.ohf.stem.diseasemodels.standard.SI
getAdjustedInfectiousMortalityRate, getAdjustedRecoveryRate, getAdjustedTransmissionRate, getInfectiousMortality, getInfectiousMortalityRate, getNonLinearityCoefficient, getPhysicallyAdjacentInfectious, getPhysicallyAdjacentInfectiousProportion, getRecoveryRate, getTransmissionRate, setInfectiousMortality, setInfectiousMortalityRate, setNonLinearityCoefficient, setPhysicallyAdjacentInfectiousProportion, setRecoveryRate, setTransmissionRate
 
Methods inherited from interface org.eclipse.ohf.stem.diseasemodels.standard.StandardDiseaseModel
addToTotalArea, addToTotalPopulationCount, computeTotalPopulationCountReciprocal, getTotalArea, getTotalPopulationCount, getTotalPopulationCountReciprocal, setTotalArea, setTotalPopulationCount
 
Methods inherited from interface org.eclipse.ohf.stem.diseasemodels.standard.DiseaseModel
createDiseaseModelLabel, createDiseaseModelLabelValue, createDiseaseModelState, createInfector, getAdjustedBackgroundMortalityRate, getBackgroundMortalityRate, getDiseaseName, getPopulationIdentifier, getTimePeriod, initializeDiseaseState, initializeDiseaseState, setBackgroundMortalityRate, setDiseaseName, setPopulationIdentifier, setTimePeriod
 
Methods inherited from interface org.eclipse.ohf.stem.core.model.Decorator
decorateGraph, getGraph, getLabelsToUpdate, resetLabels, setGraph, updateLabels
 
Methods inherited from interface org.eclipse.ohf.stem.core.common.Identifiable
getDublinCore, getTypeURI, getURI, sane, setDublinCore, setTypeURI, setURI
 
Methods inherited from interface org.eclipse.emf.ecore.EObject
eAllContents, eClass, eContainer, eContainingFeature, eContainmentFeature, eContents, eCrossReferences, eGet, eGet, eIsProxy, eIsSet, eResource, eSet, eUnset
 
Methods inherited from interface org.eclipse.emf.common.notify.Notifier
eAdapters, eDeliver, eNotify, eSetDeliver
 

Field Detail

URI_TYPE_STANDARD_SIR_DISEASE_MODEL_SEGMENT

static final java.lang.String URI_TYPE_STANDARD_SIR_DISEASE_MODEL_SEGMENT
This is the segment of the type URI that prefixes all other segments in a standard disease model type URI.

See Also:
Constant Field Values

URI_TYPE_STANDARD_SIR_DISEASE_MODEL

static final org.eclipse.emf.common.util.URI URI_TYPE_STANDARD_SIR_DISEASE_MODEL
The Type URI for the standard SIR disease model

Method Detail

getImmunityLossRate

double getImmunityLossRate()
This coefficient determines the number of population members that lose their immunity to a disease and become Susceptible to the disease per population member in the Recovered state. A value of zero (0.0), the default, means the population members never lose their immunity. This is γ.

Returns:
the proportion of Recovered population members that lose their immunity per time period.

setImmunityLossRate

void setImmunityLossRate(double value)
Sets the value of the 'Immunity Loss Rate' attribute.

Parameters:
value - the new value of the 'Immunity Loss Rate' attribute.
See Also:
getImmunityLossRate()

getAdjustedImmunityLossRate

double getAdjustedImmunityLossRate(long timeDelta)
Compute the immunity rate adjusted for a time delta potentially different from the time period specified for the rate.

Parameters:
timeDelta - the time period (milliseconds) to which the rate is to be adjusted.
Returns:
the adjusted rate