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java.lang.Objectorg.ascape.model.AscapeObject
org.ascape.model.Agent
org.ascape.model.LocatedAgent
org.ascape.model.Cell
org.ascape.model.CellOccupant
org.ascape.model.Scape
name.milesparker.epi.plague.Epidemic
public class Epidemic
Epidemic Java Implementation. A simple model of epidemic dynamics. We define individual agents with different disease states. The progression of disease moves from succeptible to exposed to infectious (either symptomatic or asymptomatic) to some outcome state. Agents can transmit infection to their immediate neighbors. For some background on the general approach, see Joshua M. Epstein. "Generative Social Science". 2006. Princeton. Copyright 2009, Miles Parker. Released under Eclipse Public License. All uses should be attributed. Generated by AMF for model: EpidemicPlague.metaabm in project: org.eclipse.amp.amf.examples.escape
Nested Class Summary |
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Nested classes/interfaces inherited from class org.ascape.model.Scape |
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Scape.ConditionalIterator, Scape.DrawFeatureObservable |
Field Summary |
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Fields inherited from class org.ascape.model.Scape |
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AGENT_ORDER, agentsPerIteration, ALL_AGENTS, CLEAR_STATS_RULE, COLLECT_STATS_RULE, COMPARE_ORDERED_QUALIFIERS, COMPLETE_TOUR, copyrightAndCredits, CREATE_GRAPHIC_VIEW_RULE, CREATE_RULE, CREATE_SCAPE_RULE, CREATE_VIEW_RULE, EXECUTE_RULES_RULE, INITIAL_RULES_RULE, initialRules, prototypeAgent, REPEATED_DRAW, RULE_ORDER, version |
Fields inherited from class org.ascape.model.CellOccupant |
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PLAY_HOST_RULE, RANDOM_WALK_AVAILABLE_RULE |
Fields inherited from class org.ascape.model.Cell |
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CALCULATE_NEIGHBORS_RULE, neighbors, PLAY_NEIGHBORS_RULE, PLAY_RANDOM_NEIGHBOR_RULE |
Fields inherited from class org.ascape.model.LocatedAgent |
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agentSize, coordinate, MOVE_RANDOM_LOCATION_RULE, RANDOM_WALK_RULE, thisUpdate |
Fields inherited from class org.ascape.model.Agent |
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DEATH_RULE, FISSIONING_RULE, FORCE_DIE_RULE, FORCE_FISSION_RULE, FORCE_MOVE_RULE, INITIALIZE_RULE, ITERATE_AND_UPDATE_RULE, ITERATE_RULE, METABOLISM_RULE, MOVEMENT_RULE, PLAY_OTHER, UPDATE_RULE |
Fields inherited from class org.ascape.model.AscapeObject |
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ARBITRARY_SEED, name, PLATFORM_DEFAULT_COLOR, scape |
Constructor Summary | |
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Epidemic()
Constructs a new Epidemic. |
Method Summary | |
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void |
calculateTimeStep(int timeStep)
A simple model of epidemic dynamics. |
java.lang.Object |
clone()
Clones the agent, ensuring that a unique id is assigned. |
protected void |
create2DViews()
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protected void |
createChartViews()
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protected Flea |
createFleaPrototype()
Create an instance of Flea that will be used to populate the fleaScape. |
void |
createGraphicViews()
Creates UI views for Epidemic. |
protected void |
createGraphViews()
|
protected Individual |
createIndividualPrototype()
Create an instance of Individual that will be used to populate the individualScape. |
protected Rat |
createRatPrototype()
Create an instance of Rat that will be used to populate the ratScape. |
void |
createScape()
Creates the members of Epidemic. |
double |
getCaseMortalityRate()
Gets the Case Mortality Rate property for Epidemic. |
java.util.List<IAgentChild> |
getChildren()
|
Scape |
getCity()
Gets the City property for Epidemic. |
int[] |
getCityDimensions()
Gets the Dimensions property for City. |
int |
getCityHeight()
Gets the Height property for City. |
int |
getCityWidth()
Gets the Width property for City. |
int |
getFleaCount()
Gets the Flea Count property for Epidemic. |
int |
getFleaRange()
Gets the Flea Range property for Epidemic. |
Scape |
getFleaScape()
Returns the Scape containing Fleas. |
IGraphicsAdapter |
getGraphicsAdapter()
|
int |
getIndividualCount()
Gets the Individual Count property for Epidemic. |
Scape |
getIndividualScape()
Returns the Scape containing Individuals. |
double |
getInitialInfectionProbability()
Gets the Initial Infection Probability property for Epidemic. |
double |
getMaxContactTransmissionProbability()
Gets the Max Contact Transmission Probability property for Epidemic. |
int |
getMaxPeriodAsymptomInfection()
Gets the Max Period Asymptom Infection property for Epidemic. |
int |
getMaxPeriodExposure()
Gets the Max Period Exposure property for Epidemic. |
int |
getMaxPeriodSymptomInfection()
Gets the Max Period Symptom Infection property for Epidemic. |
double |
getMinContactTransmissionProbability()
Gets the Min Contact Transmission Probability property for Epidemic. |
int |
getMinPeriodAsymptomInfection()
Gets the Min Period Asymptom Infection property for Epidemic. |
int |
getMinPeriodExposure()
Gets the Min Period Exposure property for Epidemic. |
int |
getMinPeriodSymptomInfection()
Gets the Min Period Symptom Infection property for Epidemic. |
double |
getMovementProbability()
Gets the Movement Probability property for Epidemic. |
java.lang.String |
getName()
|
int |
getPeriodsperDay()
Gets the Periods per Day property for Epidemic. |
int |
getRatCount()
Gets the Rat Count property for Epidemic. |
Scape |
getRatScape()
Returns the Scape containing Rats. |
long |
getUID()
|
static void |
main(java.lang.String[] args)
|
void |
scapeSetup(ScapeEvent scapeEvent)
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void |
setCaseMortalityRate(double _caseMortalityRate)
Sets the Case Mortality Rate property for Epidemic. |
void |
setCity(Scape _city)
Sets the City property for Epidemic. |
void |
setCityDimensions(int[] _cityDimensions)
Sets the Dimensions property for City. |
void |
setCityHeight(int _cityHeight)
Sets the Height property for City. |
void |
setCityWidth(int _cityWidth)
Sets the Width property for City. |
void |
setFleaCount(int _fleaCount)
Sets the Flea Count property for Epidemic. |
void |
setFleaRange(int _fleaRange)
Sets the Flea Range property for Epidemic. |
void |
setIndividualCount(int _individualCount)
Sets the Individual Count property for Epidemic. |
void |
setInitialInfectionProbability(double _initialInfectionProbability)
Sets the Initial Infection Probability property for Epidemic. |
void |
setMaxContactTransmissionProbability(double _maxContactTransmissionProbability)
Sets the Max Contact Transmission Probability property for Epidemic. |
void |
setMaxPeriodAsymptomInfection(int _maxPeriodAsymptomInfection)
Sets the Max Period Asymptom Infection property for Epidemic. |
void |
setMaxPeriodExposure(int _maxPeriodExposure)
Sets the Max Period Exposure property for Epidemic. |
void |
setMaxPeriodSymptomInfection(int _maxPeriodSymptomInfection)
Sets the Max Period Symptom Infection property for Epidemic. |
void |
setMinContactTransmissionProbability(double _minContactTransmissionProbability)
Sets the Min Contact Transmission Probability property for Epidemic. |
void |
setMinPeriodAsymptomInfection(int _minPeriodAsymptomInfection)
Sets the Min Period Asymptom Infection property for Epidemic. |
void |
setMinPeriodExposure(int _minPeriodExposure)
Sets the Min Period Exposure property for Epidemic. |
void |
setMinPeriodSymptomInfection(int _minPeriodSymptomInfection)
Sets the Min Period Symptom Infection property for Epidemic. |
void |
setMovementProbability(double _movementProbability)
Sets the Movement Probability property for Epidemic. |
void |
setPeriodsperDay(int _periodsperDay)
Sets the Periods per Day property for Epidemic. |
void |
setRatCount(int _ratCount)
Sets the Rat Count property for Epidemic. |
void |
startSimulationAgentChild(int timeStep)
A simple model of epidemic dynamics. |
Methods inherited from class org.ascape.model.CellOccupant |
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die, findAvailableNeighbors, findNearest, findNearest, findNearest, findNearest, findNearest, findNeighbors, findNeighborsOnHost, findRandomAvailableNeighbor, findRandomNeighbor, findRandomNeighborOnHost, findWithin, findWithin, findWithin, getCoordinate, getHostCell, getHostScape, leave, moveAway, moveTo, moveToRandomLocation, moveToward, playNeighbors, playRandomNeighbor, randomWalk, randomWalkAvailable, setHostCell, setHostScape |
Methods inherited from class org.ascape.model.Cell |
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calculateNeighbors, countNeighbors, findOccupants, findRelative, getDistance, getNeighbors, getNeighbors, getNetwork, getOccupant, hostedCondition, isAvailable, removeOccupant, setNeighbors, setNeighborsList, setNetwork, setOccupant |
Methods inherited from class org.ascape.model.LocatedAgent |
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calculateDistance, calculateDistance, countWithin, countWithin, countWithin, findMaximumWithin, findWithin, getAgentSize, hasWithin, hasWithin, hasWithin, isUpdateNeeded, moveAway, moveAway, moveTo, moveToward, moveToward, requestUpdate, requestUpdateNext, setAgentSize, setCoordinate |
Methods inherited from class org.ascape.model.Agent |
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clearDeleteMarker, death, deathCondition, execute, execute, fission, fissionCondition, fissioning, getColor, getColor, getImage, getImage, getPlatformColor, isDelete, isInitialized, iterate, markForDeletion, metabolism, move, movement, movementCondition, play, scapeCreated, setInitialized, setScape, update |
Methods inherited from class org.ascape.model.AscapeObject |
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diffDeep, diffDeep, diffDeepBFS, diffDeepDFS, diffDeepValidate, diffDeepVisit, equalsDeep, equalsDeep, equalsDeep, getComparisonStream, getRandom, getRandomSeed, getScape, randomInRange, randomInRange, randomIs, randomToLimit, reseed, setComparisonStream, setName, setRandom, setRandomSeed |
Methods inherited from class java.lang.Object |
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equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface java.util.Collection |
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equals, hashCode |
Methods inherited from interface org.ascape.model.event.ScapeListener |
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getScape |
Methods inherited from interface org.ascape.model.space.Location |
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clearDeleteMarker, isDelete, markForDeletion, setCoordinate |
Constructor Detail |
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public Epidemic()
Method Detail |
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public java.util.List<IAgentChild> getChildren()
public long getUID()
public java.lang.Object clone()
clone
in interface ScapeListener
clone
in interface Location
clone
in class Scape
protected Individual createIndividualPrototype()
protected Flea createFleaPrototype()
protected Rat createRatPrototype()
public void createScape()
createScape
in class Scape
Scape.setPopulateOnCreate(boolean)
public void createGraphicViews()
createGraphicViews
in class Scape
public void scapeSetup(ScapeEvent scapeEvent)
scapeSetup
in interface ScapeListener
scapeSetup
in class Scape
scapeEvent
- the associated scape eventpublic Scape getIndividualScape()
public Scape getFleaScape()
public Scape getRatScape()
protected void createChartViews()
protected void create2DViews()
protected void createGraphViews()
public IGraphicsAdapter getGraphicsAdapter()
getGraphicsAdapter
in interface IGraphicsAdapted
public static void main(java.lang.String[] args)
public void startSimulationAgentChild(int timeStep)
public void calculateTimeStep(int timeStep)
public int getIndividualCount()
public void setIndividualCount(int _individualCount)
_individualCount
- the new Individual Count value
public double getInitialInfectionProbability()
public void setInitialInfectionProbability(double _initialInfectionProbability)
_initialInfectionProbability
- the new Initial Infection Probability value
public double getMinContactTransmissionProbability()
public void setMinContactTransmissionProbability(double _minContactTransmissionProbability)
_minContactTransmissionProbability
- the new Min Contact Transmission Probability value
public double getMaxContactTransmissionProbability()
public void setMaxContactTransmissionProbability(double _maxContactTransmissionProbability)
_maxContactTransmissionProbability
- the new Max Contact Transmission Probability value
public double getCaseMortalityRate()
public void setCaseMortalityRate(double _caseMortalityRate)
_caseMortalityRate
- the new Case Mortality Rate value
public int getPeriodsperDay()
public void setPeriodsperDay(int _periodsperDay)
_periodsperDay
- the new Periods per Day value
public int getMinPeriodExposure()
public void setMinPeriodExposure(int _minPeriodExposure)
_minPeriodExposure
- the new Min Period Exposure value
public int getMaxPeriodExposure()
public void setMaxPeriodExposure(int _maxPeriodExposure)
_maxPeriodExposure
- the new Max Period Exposure value
public int getMinPeriodAsymptomInfection()
public void setMinPeriodAsymptomInfection(int _minPeriodAsymptomInfection)
_minPeriodAsymptomInfection
- the new Min Period Asymptom Infection value
public int getMaxPeriodAsymptomInfection()
public void setMaxPeriodAsymptomInfection(int _maxPeriodAsymptomInfection)
_maxPeriodAsymptomInfection
- the new Max Period Asymptom Infection value
public int getMinPeriodSymptomInfection()
public void setMinPeriodSymptomInfection(int _minPeriodSymptomInfection)
_minPeriodSymptomInfection
- the new Min Period Symptom Infection value
public int getMaxPeriodSymptomInfection()
public void setMaxPeriodSymptomInfection(int _maxPeriodSymptomInfection)
_maxPeriodSymptomInfection
- the new Max Period Symptom Infection value
public double getMovementProbability()
public void setMovementProbability(double _movementProbability)
_movementProbability
- the new Movement Probability value
public int getFleaCount()
public void setFleaCount(int _fleaCount)
_fleaCount
- the new Flea Count value
public int getRatCount()
public void setRatCount(int _ratCount)
_ratCount
- the new Rat Count value
public int getFleaRange()
public void setFleaRange(int _fleaRange)
_fleaRange
- the new Flea Range value
public int[] getCityDimensions()
public void setCityDimensions(int[] _cityDimensions)
_cityDimensions
- the new Dimensions value
public int getCityWidth()
public void setCityWidth(int _cityWidth)
_cityWidth
- the new Width value
public int getCityHeight()
public void setCityHeight(int _cityHeight)
_cityHeight
- the new Height value
public Scape getCity()
public void setCity(Scape _city)
_city
- the new City value
public java.lang.String getName()
getName
in interface SpaceContext
getName
in interface HasName
getName
in class Scape
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SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |