java.lang.Object
- jebl.evolution.coalescent.ConstantPopulation
- - jebl.evolution.coalescent.ExponentialGrowth
  - - jebl.evolution.coalescent.CataclysmicDemographic

All Implemented Interfaces:

DemographicFunction
```
public class CataclysmicDemographic
extends ExponentialGrowth
```
This class models an exponentially growing (or shrinking) population (Parameters: N0=present-day population size; r=growth rate). This model is nested with the constant-population size model (r=0).

Version:

$Id: CataclysmicDemographic.java 586 2006-12-15 15:49:15Z twobeers $

Author:

Alexei Drummond, Andrew Rambaut

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

Constructor Summary

Constructors
Constructor	Description
`CataclysmicDemographic()`	Construct demographic model with default settings
`CataclysmicDemographic(double N0, double r, double d, double t)`	Construct demographic model with given settings

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`double`	`getCataclysmTime()`
`double`	`getDeclineRate()`	returns the positive-valued decline rate
`double`	`getDemographic(double t)`	Gets the value of the demographic function N(t) at time t.
`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).
`boolean`	`hasIntegral()`	returns whether an analytical expression for the integral is implemented
`void`	`setCataclysmTime(double t)`
`void`	`setDeclineRate(double d)`	sets the decline rate.
`void`	`setSpikeFactor(double f)`	An alternative parameterization of this model.

Methods inherited from class jebl.evolution.coalescent.ExponentialGrowth
getArgument, getArgumentCount, getArgumentName, getGrowthRate, getLowerBound, getUpperBound, setArgument, setDoublingTime, setGrowthRate

Methods inherited from class jebl.evolution.coalescent.ConstantPopulation
getIntegral, getN0, setN0

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - CataclysmicDemographic
```
public CataclysmicDemographic()
```
    Construct demographic model with default settings
  - CataclysmicDemographic
```
public CataclysmicDemographic(double N0,
                              double r,
                              double d,
                              double t)
```
    Construct demographic model with given settings
    
    Parameters:
    
    N0 - present-day population size
    
    r - growth rate
- Method Detail
  - getDeclineRate
```
public final double getDeclineRate()
```
    returns the positive-valued decline rate
  - setDeclineRate
```
public void setDeclineRate(double d)
```
    sets the decline rate.
  - getCataclysmTime
```
public final double getCataclysmTime()
```
  - setCataclysmTime
```
public final void setCataclysmTime(double t)
```
  - setSpikeFactor
```
public final void setSpikeFactor(double f)
```
    An alternative parameterization of this model. This function sets the decline rate using N0 & t which must already have been set.
  - 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

Class CataclysmicDemographic

Nested Class Summary

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

Constructor Summary

Method Summary

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

CataclysmicDemographic

CataclysmicDemographic

Method Detail

getDeclineRate

setDeclineRate

getCataclysmTime

setCataclysmTime

setSpikeFactor

getDemographic

getIntensity

getInverseIntensity

hasIntegral