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org.mrd.models.cagn
Class CagnModel  

java.lang.Object
  SimModelImpl
      org.mrd.models.cagn.CagnModel

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public class CagnModel

extends SimModelImpl

The CAGN Model.

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Nested Class Summary
class	CagnModel.PairFactory           PairFactor is a place to store instances of the Pair object, this way we don't need to keep createing and destroying them, which can be an expensive task.

 

Field Summary
protected  double[]	ageReproductionTable           Holds value of property ageReproductionTable.
protected  double[]	ageSurvivalTable           Holds value of property ageSurvivalTable.
protected  double	currentIterationSurvival           Holds value of property currentIterationSurvival.
protected  RandomElement	disp_generator           Used in all the pairs to determine their dispersal distance.
private  org.mrd.analysis.RunningBasicStatistics	dispersalStatistics
protected  java.lang.String	habitatSpaceFile           Holds the location of the PGM file used to load the landscape
protected  Beta	iteration_survivial_distribution           Used to generate the currentIterationSurvival probability.
private  double	iterationDispersalSurvival           Holds value of property iterationDispersalSurvival.
protected  double	iterationSurvivalMean           Holds value of property iterationSurvivalMean.
protected  double	iterationSurvivalStd           Holds value of property iterationSurvivalStd.
protected  double[]	landReproductionTable           Holds value of property landReproductionTable.
protected  Landscape	landscape           the landscape encapsulates agentList and grid datastructures.
protected  double[]	landSurvivalTable           Holds value of property landSurvivalTable.
protected  org.apache.commons.logging.Log	log           logging is always good to do, learn to use it.
protected  double	maxIterations           Holds value of property maxIterations, stop is scheduled using this.
protected  int	modelInitialPairs           Holds value of property modelInitialPairs.
protected  int	pairClutchSize           Holds value of property pairClutchSize.
protected  int	pairDispersalSeed           Holds value of property pairDispersalSeed.
protected  double	pairMeanDispersalDistance           Holds value of property pairMeanDispersalDistance.
protected  int	pairReproductionSeed           Holds value of property pairReproductionSeed.
protected  int	pairSearchTime           Holds value of property pairSearchTime.
protected  int	pairSurvivalSeed           Holds value of property pairSurvivalSeed.
protected  org.apache.commons.pool.ObjectPool	pool           Holds value of property maxIterations, stop is scheduled using this.
protected  RandomElement	rep_generator           Used in the Bernoulli trials of all the pairs to determine reproduction roll.
protected  Schedule	schedule           Every model must have a schedule
protected  RandomElement	survival_generator           Used in the Bernoulli trials of all the pairs to determine their survival roll.

 

Constructor Summary

CagnModel()

 

Method Summary
void	begin()           Model begins from this method.
java.lang.String	getAgeReproductionTable()           Getter for property survivalTable.
java.lang.String	getAgeSurvivalTable()           Getter for property survivalTable.
double	getCurrentIterationSurvival()           Getter for property currentIterationSurvival.
org.mrd.analysis.RunningBasicStatistics	getDispersalStatistics()
java.lang.String	getHabitatSpaceFile()           Getter for property habitatSpace.
java.lang.String[]	getInitParam()           Used by the GUI to expose the Parameters that can be Manipulated.
double	getIterationDispersalSurvival()
double	getIterationSurvivalMean()           Getter for property iterationSurvivalMean.
double	getIterationSurvivalStd()           Getter for property iterationSurvivalStd.
java.lang.String	getLandReproductionTable()           Getter for property landReproductionTable.
Landscape	getLandscape()           Getter for property landscape.
java.lang.String	getLandSurvivalTable()           Getter for property landSurvivalTable.
double	getMaxIterations()           Getter for property maxIterations.
int	getModelInitialPairs()           Getter for property modelInitialPairs.
java.lang.String	getName()           a required method - displayed on the Controller toolbar.
int	getPairClutchSize()           Getter for property pairClutchSize.
int	getPairDispersalSeed()           Getter for property pairDispersalSeed.
int	getPairMaxAge()           Getter for property maxAge.
double	getPairMeanDispersalDistance()           Getter for property pairMeanDispersalDistance.
int	getPairReproductionSeed()           Getter for property pairReproductionSeed.
int	getPairSearchTime()           Getter for property pairSearchTime.
int	getPairSurvivalSeed()           Getter for property pairSurvivalSeed.
Schedule	getSchedule()           Getter for property schedule.
void	setAgeReproductionTable(java.lang.String table)           Setter for property survivalTable.
void	setAgeSurvivalTable(java.lang.String table)           Setter for property survivalTable.
void	setHabitatSpaceFile(java.lang.String habitatSpaceFile)           Setter for property habitatSpace.
void	setIterationSurvivalMean(double iterationSurvivalMean)           Setter for property iterationSurvivalMean.
void	setIterationSurvivalStd(double iterationSurvivalStd)           Setter for property iterationSurvivalStd.
void	setLandReproductionTable(java.lang.String table)           Setter for property landReproductionTable.
void	setLandSurvivalTable(java.lang.String table)           Setter for property landSurvivalTable.
void	setMaxIterations(double maxIterations)           Setter for property maxIterations.
void	setModelInitialPairs(int modelInitialPairs)           Setter for property modelInitialPairs.
void	setPairClutchSize(int pairClutchSize)           Setter for property pairClutchSize.
void	setPairDispersalSeed(int pairDispersalSeed)           Setter for property pairDispersalSeed.
void	setPairMeanDispersalDistance(double pairMeanDispersalDistance)           Setter for property pairMeanDispersalDistance.
void	setPairReproductionSeed(int pairReproductionSeed)           Setter for property pairReproductionSeed.
void	setPairSearchTime(int pairSearchTime)           Setter for property pairSearchTime.
void	setPairSurvivalSeed(int pairSurvivalSeed)           Setter for property pairSurvivalSeed.
void	setSchedule(Schedule schedule)           Setter for property schedule.
void	setup()           Model is setup from this method.
void	step()           This method is defined in the stepable interface, it is scheduled from with the begin method.

 

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

 

Field Detail

log

protected org.apache.commons.logging.Log log

logging is always good to do, learn to use it.

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schedule

protected Schedule schedule

Every model must have a schedule

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maxIterations

protected double maxIterations

Holds value of property maxIterations, stop is scheduled using this.

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pool

protected org.apache.commons.pool.ObjectPool pool

Holds value of property maxIterations, stop is scheduled using this.

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landscape

protected Landscape landscape

the landscape encapsulates agentList and grid datastructures.

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habitatSpaceFile

protected java.lang.String habitatSpaceFile

Holds the location of the PGM file used to load the landscape

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iteration_survivial_distribution

protected Beta iteration_survivial_distribution

Used to generate the currentIterationSurvival probability. This is later used by the pairs in calculating thier survival

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survival_generator

protected RandomElement survival_generator

Used in the Bernoulli trials of all the pairs to determine their survival roll.

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rep_generator

protected RandomElement rep_generator

Used in the Bernoulli trials of all the pairs to determine reproduction roll.

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disp_generator

protected RandomElement disp_generator

Used in all the pairs to determine their dispersal distance.

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pairClutchSize

protected int pairClutchSize

Holds value of property pairClutchSize.

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pairSearchTime

protected int pairSearchTime

Holds value of property pairSearchTime.

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pairMeanDispersalDistance

protected double pairMeanDispersalDistance

Holds value of property pairMeanDispersalDistance.

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modelInitialPairs

protected int modelInitialPairs

Holds value of property modelInitialPairs.

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pairSurvivalSeed

protected int pairSurvivalSeed

Holds value of property pairSurvivalSeed.

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pairReproductionSeed

protected int pairReproductionSeed

Holds value of property pairReproductionSeed.

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pairDispersalSeed

protected int pairDispersalSeed

Holds value of property pairDispersalSeed.

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ageSurvivalTable

protected double[] ageSurvivalTable

Holds value of property ageSurvivalTable.

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ageReproductionTable

protected double[] ageReproductionTable

Holds value of property ageReproductionTable.

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landReproductionTable

protected double[] landReproductionTable

Holds value of property landReproductionTable.

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landSurvivalTable

protected double[] landSurvivalTable

Holds value of property landSurvivalTable.

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iterationSurvivalMean

protected double iterationSurvivalMean

Holds value of property iterationSurvivalMean.

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iterationSurvivalStd

protected double iterationSurvivalStd

Holds value of property iterationSurvivalStd.

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currentIterationSurvival

protected double currentIterationSurvival

Holds value of property currentIterationSurvival.

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iterationDispersalSurvival

private double iterationDispersalSurvival

Holds value of property iterationDispersalSurvival.

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dispersalStatistics

private org.mrd.analysis.RunningBasicStatistics dispersalStatistics

Constructor Detail

CagnModel

public CagnModel()

Method Detail

setup

public void setup()

Model is setup from this method. Runs first.

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begin

public void begin()

Model begins from this method. Executes second.

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step

public void step()

This method is defined in the stepable interface, it is scheduled from with the begin method. Any code added here will be executed when the scheduled event occurs (currently once each iteration).

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getName

public java.lang.String getName()

a required method - displayed on the Controller toolbar.

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getInitParam

public java.lang.String[] getInitParam()

Used by the GUI to expose the Parameters that can be Manipulated.

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getPairClutchSize

public int getPairClutchSize()

Getter for property pairClutchSize.

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setPairClutchSize

public void setPairClutchSize(int pairClutchSize)

Setter for property pairClutchSize.

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getPairSearchTime

public int getPairSearchTime()

Getter for property pairSearchTime.

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setPairSearchTime

public void setPairSearchTime(int pairSearchTime)

Setter for property pairSearchTime.

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getPairMeanDispersalDistance

public double getPairMeanDispersalDistance()

Getter for property pairMeanDispersalDistance.

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setPairMeanDispersalDistance

public void setPairMeanDispersalDistance(double pairMeanDispersalDistance)

Setter for property pairMeanDispersalDistance.

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getModelInitialPairs

public int getModelInitialPairs()

Getter for property modelInitialPairs.

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setModelInitialPairs

public void setModelInitialPairs(int modelInitialPairs)

Setter for property modelInitialPairs.

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getPairSurvivalSeed

public int getPairSurvivalSeed()

Getter for property pairSurvivalSeed.

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setPairSurvivalSeed

public void setPairSurvivalSeed(int pairSurvivalSeed)

Setter for property pairSurvivalSeed.

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getPairReproductionSeed

public int getPairReproductionSeed()

Getter for property pairReproductionSeed.

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setPairReproductionSeed

public void setPairReproductionSeed(int pairReproductionSeed)

Setter for property pairReproductionSeed.

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getPairDispersalSeed

public int getPairDispersalSeed()

Getter for property pairDispersalSeed.

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setPairDispersalSeed

public void setPairDispersalSeed(int pairDispersalSeed)

Setter for property pairDispersalSeed.

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getAgeSurvivalTable

public java.lang.String getAgeSurvivalTable()

Getter for property survivalTable.

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setAgeSurvivalTable

public void setAgeSurvivalTable(java.lang.String table)

Setter for property survivalTable.

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getAgeReproductionTable

public java.lang.String getAgeReproductionTable()

Getter for property survivalTable.

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setAgeReproductionTable

public void setAgeReproductionTable(java.lang.String table)

Setter for property survivalTable.

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getLandReproductionTable

public java.lang.String getLandReproductionTable()

Getter for property landReproductionTable.

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setLandReproductionTable

public void setLandReproductionTable(java.lang.String table)

Setter for property landReproductionTable.

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getLandSurvivalTable

public java.lang.String getLandSurvivalTable()

Getter for property landSurvivalTable.

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setLandSurvivalTable

public void setLandSurvivalTable(java.lang.String table)

Setter for property landSurvivalTable.

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getPairMaxAge

public int getPairMaxAge()

Getter for property maxAge.

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getLandscape

public Landscape getLandscape()

Getter for property landscape.

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getHabitatSpaceFile

public java.lang.String getHabitatSpaceFile()

Getter for property habitatSpace.

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setHabitatSpaceFile

public void setHabitatSpaceFile(java.lang.String habitatSpaceFile)

Setter for property habitatSpace.

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getIterationSurvivalMean

public double getIterationSurvivalMean()

Getter for property iterationSurvivalMean.

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setIterationSurvivalMean

public void setIterationSurvivalMean(double iterationSurvivalMean)

Setter for property iterationSurvivalMean.

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getIterationSurvivalStd

public double getIterationSurvivalStd()

Getter for property iterationSurvivalStd.

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setIterationSurvivalStd

public void setIterationSurvivalStd(double iterationSurvivalStd)

Setter for property iterationSurvivalStd.

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getCurrentIterationSurvival

public double getCurrentIterationSurvival()

Getter for property currentIterationSurvival.

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getMaxIterations

public double getMaxIterations()

Getter for property maxIterations.

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setMaxIterations

public void setMaxIterations(double maxIterations)

Setter for property maxIterations.

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getSchedule

public Schedule getSchedule()

Getter for property schedule.

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setSchedule

public void setSchedule(Schedule schedule)

Setter for property schedule.

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getDispersalStatistics

public org.mrd.analysis.RunningBasicStatistics getDispersalStatistics()

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getIterationDispersalSurvival

public double getIterationDispersalSurvival()

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> mrd >> models >> [ cagn overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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