java.lang.Object
- jebl.evolution.coalescent.ConstantPopulation
- - jebl.evolution.coalescent.ExponentialGrowth
  - - jebl.evolution.coalescent.LogisticGrowth
    - - jebl.evolution.coalescent.ExponentialLogistic

All Implemented Interfaces:

DemographicFunction
```
public class ExponentialLogistic
extends LogisticGrowth
```
This class models logistic growth from an initial exponential phase.

Version:

$Id: ExponentialLogistic.java 937 2008-08-08 00:11:32Z rambaut $

Author:

Andrew Rambaut, Alexei Drummond

Nested Class Summary
- Nested classes/interfaces inherited from interface jebl.evolution.coalescent.DemographicFunction
  DemographicFunction.Utils

Constructor Summary

Constructors
Constructor	Description
`ExponentialLogistic()`	Construct demographic model with default settings
`ExponentialLogistic(double N0, double r, double c, double time, double r2)`	Construct demographic model with given settings

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`double`	`getArgument(int n)`	Returns the value of the nth argument of this function.
`int`	`getArgumentCount()`	Returns the number of arguments for this function.
`java.lang.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 demographic intensity function at time t (= integral 1/N(x) dx from 0 to t).
`double`	`getLowerBound(int n)`	Returns the lower bound of the nth argument of this function.
`double`	`getR2()`
`double`	`getTime()`
`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`	`setR2(double r2)`
`void`	`setTime(double time)`

Methods inherited from class jebl.evolution.coalescent.LogisticGrowth
getShape, setShape, setTime50

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

- Constructor Detail
  - ExponentialLogistic
```
public ExponentialLogistic()
```
    Construct demographic model with default settings
  - ExponentialLogistic
```
public ExponentialLogistic(double N0,
                           double r,
                           double c,
                           double time,
                           double r2)
```
    Construct demographic model with given settings
    
    Parameters:
    
    N0 - Current population size
    
    r - Logistic-phase growth rate
    
    c - Logistic shape
    
    time - Exponential-logistic phase transition time
    
    r2 - Exponential-phase growth rate
- Method Detail
  - getR2
```
public double getR2()
```
  - setR2
```
public void setR2(double r2)
```
  - getTime
```
public double getTime()
```
  - setTime
```
public void setTime(double time)
```
  - getDemographic
```
public double getDemographic(double t)
```
    Description copied from class: LogisticGrowth
    
    Gets the value of the demographic function N(t) at time t.
    
    Specified by:
    
    getDemographic in interface DemographicFunction
    
    Overrides:
    
    getDemographic in class LogisticGrowth
    
    Parameters:
    
    t - the time
    
    Returns:
    
    the value of the demographic function N(t) at time t.
  - getIntensity
```
public double getIntensity(double t)
```
    Description copied from class: LogisticGrowth
    
    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 LogisticGrowth
  - getInverseIntensity
```
public double getInverseIntensity(double x)
```
    Description copied from class: LogisticGrowth
    
    Returns value of demographic intensity function at time t (= integral 1/N(x) dx from 0 to t).
    
    Specified by:
    
    getInverseIntensity in interface DemographicFunction
    
    Overrides:
    
    getInverseIntensity in class LogisticGrowth
  - 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 LogisticGrowth
    
    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 LogisticGrowth
  - 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 java.lang.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

Class ExponentialLogistic

Nested Class Summary

Nested classes/interfaces inherited from interface jebl.evolution.coalescent.DemographicFunction

Constructor Summary

Method Summary

Methods inherited from class jebl.evolution.coalescent.LogisticGrowth

Methods inherited from class jebl.evolution.coalescent.ExponentialGrowth

Methods inherited from class jebl.evolution.coalescent.ConstantPopulation

Methods inherited from class java.lang.Object

Constructor Detail

ExponentialLogistic

ExponentialLogistic

Method Detail

getR2

setR2

getTime

setTime

getDemographic

getIntensity

getInverseIntensity

hasIntegral

getIntegral

getArgumentCount

getArgumentName

getArgument

setArgument

getLowerBound

getUpperBound