jebl.evolution.coalescent
Class ConstExponential

java.lang.Object
  extended by jebl.evolution.coalescent.ConstantPopulation
      extended by jebl.evolution.coalescent.ExponentialGrowth
          extended by jebl.evolution.coalescent.ConstExponential
All Implemented Interfaces:
DemographicFunction

public class ConstExponential
extends ExponentialGrowth

This class models exponential growth from an initial population size.

Author:
Alexei Drummond, Andrew Rambaut

Nested Class Summary
 
Nested classes/interfaces inherited from interface jebl.evolution.coalescent.DemographicFunction
DemographicFunction.Utils
 
Constructor Summary
ConstExponential()
          Construct demographic model with default settings
ConstExponential(double N0, double r, double N1)
          Construct demographic model with given settings
 
Method Summary
 double getArgument(int n)
          Returns the value of the nth argument of this function.
 int getArgumentCount()
          Returns the number of arguments for this function.
 String getArgumentName(int n)
          Returns the name of the nth argument of this function.
 double getDemographic(double t)
          Gets the value of the demographic function N(t) at time t.
 double getIntegral(double start, double finish)
          Calculates the integral 1/N(x) dx between start and finish.
 double getIntensity(double t)
          Returns value of demographic intensity function at time t (= integral 1/N(x) dx from 0 to t).
 double getInverseIntensity(double x)
          Returns value of inverse demographic intensity function (returns time, needed for simulation of coalescent intervals).
 double getLowerBound(int n)
          Returns the lower bound of the nth argument of this function.
 double getN1()
           
 double getUpperBound(int n)
          Returns the upper bound of the nth argument of this function.
 boolean hasIntegral()
          returns whether an analytical expression for the integral is implemented
 void setArgument(int n, double value)
          Sets the value of the nth argument of this function.
 void setN1(double N1)
           
 void setProportion(double p)
           
 
Methods inherited from class jebl.evolution.coalescent.ExponentialGrowth
getGrowthRate, setDoublingTime, setGrowthRate
 
Methods inherited from class jebl.evolution.coalescent.ConstantPopulation
getN0, setN0
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ConstExponential

public ConstExponential()
Construct demographic model with default settings


ConstExponential

public ConstExponential(double N0,
                        double r,
                        double N1)
Construct demographic model with given settings

Method Detail

getN1

public double getN1()

setN1

public void setN1(double N1)

setProportion

public void setProportion(double p)

getDemographic

public double getDemographic(double t)
Description copied from interface: DemographicFunction
Gets the value of the demographic function N(t) at time t.

Specified by:
getDemographic in interface DemographicFunction
Overrides:
getDemographic in class ExponentialGrowth

getIntensity

public double getIntensity(double t)
Description copied from interface: DemographicFunction
Returns value of demographic intensity function at time t (= integral 1/N(x) dx from 0 to t).

Specified by:
getIntensity in interface DemographicFunction
Overrides:
getIntensity in class ExponentialGrowth

getInverseIntensity

public double getInverseIntensity(double x)
Description copied from interface: DemographicFunction
Returns value of inverse demographic intensity function (returns time, needed for simulation of coalescent intervals).

Specified by:
getInverseIntensity in interface DemographicFunction
Overrides:
getInverseIntensity in class ExponentialGrowth

hasIntegral

public boolean hasIntegral()
Description copied from interface: DemographicFunction
returns whether an analytical expression for the integral is implemented

Specified by:
hasIntegral in interface DemographicFunction
Overrides:
hasIntegral in class ConstantPopulation
Returns:
a boolean

getIntegral

public double getIntegral(double start,
                          double finish)
Description copied from class: ConstantPopulation
Calculates the integral 1/N(x) dx between start and finish. The inherited function in DemographicFunction.Abstract calls a numerical integrater which is unecessary.

Specified by:
getIntegral in interface DemographicFunction
Overrides:
getIntegral in class ConstantPopulation

getArgumentCount

public int getArgumentCount()
Description copied from interface: DemographicFunction
Returns the number of arguments for this function.

Specified by:
getArgumentCount in interface DemographicFunction
Overrides:
getArgumentCount in class ExponentialGrowth

getArgumentName

public String getArgumentName(int n)
Description copied from interface: DemographicFunction
Returns the name of the nth argument of this function.

Specified by:
getArgumentName in interface DemographicFunction
Overrides:
getArgumentName in class ExponentialGrowth

getArgument

public double getArgument(int n)
Description copied from interface: DemographicFunction
Returns the value of the nth argument of this function.

Specified by:
getArgument in interface DemographicFunction
Overrides:
getArgument in class ExponentialGrowth

setArgument

public void setArgument(int n,
                        double value)
Description copied from interface: DemographicFunction
Sets the value of the nth argument of this function.

Specified by:
setArgument in interface DemographicFunction
Overrides:
setArgument in class ExponentialGrowth

getLowerBound

public double getLowerBound(int n)
Description copied from interface: DemographicFunction
Returns the lower bound of the nth argument of this function.

Specified by:
getLowerBound in interface DemographicFunction
Overrides:
getLowerBound in class ExponentialGrowth

getUpperBound

public double getUpperBound(int n)
Description copied from interface: DemographicFunction
Returns the upper bound of the nth argument of this function.

Specified by:
getUpperBound in interface DemographicFunction
Overrides:
getUpperBound in class ExponentialGrowth