ExponentialGrowth (Java Evolutionary Biology Library)

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jebl.evolution.coalescent
Class ExponentialGrowth

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

All Implemented Interfaces:: DemographicFunction

Direct Known Subclasses:: CataclysmicDemographic, ConstExponential, Expansion, LogisticGrowth

public class ExponentialGrowth
extends ConstantPopulation
extends ConstantPopulation

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).

Author:: Alexei Drummond, Andrew Rambaut

Nested Class Summary

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

Constructor Summary
`ExponentialGrowth()` Construct demographic model with default settings
`ExponentialGrowth(double N0, double r)` 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`	`getGrowthRate()` returns growth rate.
`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`	`getUpperBound(int n)` Returns the upper bound of the nth argument of this function.
`void`	`setArgument(int n, double value)` Sets the value of the nth argument of this function.
`void`	`setDoublingTime(double doublingTime)` An alternative parameterization of this model.
`void`	`setGrowthRate(double r)` sets growth rate.

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

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

Constructor Detail

ExponentialGrowth

public ExponentialGrowth()

Construct demographic model with default settings

ExponentialGrowth

public ExponentialGrowth(double N0,
                         double r)

Construct demographic model with given settings

Method Detail

getGrowthRate

public final double getGrowthRate()

returns growth rate.

setGrowthRate

public void setGrowthRate(double r)

sets growth rate.

setDoublingTime

public void setDoublingTime(double doublingTime)

An alternative parameterization of this model. This function sets growth rate for a given doubling time.