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

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

public interface SEIR
extends SIR

A DiseaseModel with four states Susceptible, Exposed, Infectious and Recovered(SEIR).

The basic SEIR (Susceptible, Exposed, 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 for the SI and SIR models, these become:

Let

Thus, we now have two types of Infectious population members, those that will eventally 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:
SIR, SIRLabel, SIRLabelValue, SEIRLabel, SEIRLabelValue

Field Summary
static org.eclipse.emf.common.util.URI URI_TYPE_STANDARD_SEIR_DISEASE_MODEL
          The Type URI for the standard SEIR disease model
static java.lang.String URI_TYPE_STANDARD_SEIR_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.SIR
URI_TYPE_STANDARD_SIR_DISEASE_MODEL, URI_TYPE_STANDARD_SIR_DISEASE_MODEL_SEGMENT
 
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 getAdjustedIncubationRate(long timeDelta)
          Compute the incubation rate adjusted for a time delta potentially different from the time period specified for the rate.
 double getIncubationRate()
           
 void setIncubationRate(double value)
          Sets the value of the 'Incubation Rate' attribute.
 
Methods inherited from interface org.eclipse.ohf.stem.diseasemodels.standard.SIR
getAdjustedImmunityLossRate, getImmunityLossRate, setImmunityLossRate
 
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_SEIR_DISEASE_MODEL_SEGMENT

static final java.lang.String URI_TYPE_STANDARD_SEIR_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_SEIR_DISEASE_MODEL

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

Method Detail

getIncubationRate

double getIncubationRate()
Returns:
the number of population members in the Exposed state that move to the infectious state, per time period.

setIncubationRate

void setIncubationRate(double value)
Sets the value of the 'Incubation Rate' attribute.

Parameters:
value - the new value of the 'Incubation Rate' attribute.
See Also:
getIncubationRate()

getAdjustedIncubationRate

double getAdjustedIncubationRate(long timeDelta)
Compute the incubation 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