pal.coalescent
Class ExponentialGrowth

java.lang.Object
  extended by pal.coalescent.DemographicModel
      extended by pal.coalescent.ConstantPopulation
          extended by pal.coalescent.ExponentialGrowth
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, Parameterized, Report, Summarizable, Units
Direct Known Subclasses:
ConstExpGrowth, ExpandingPopulation

public class ExponentialGrowth
extends ConstantPopulation
implements Report, Parameterized, java.io.Serializable, Summarizable

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). Parts of this class were inspired by C++ code generously provided by Oliver Pybus.

Version:
$Id: ExponentialGrowth.java,v 1.10 2001/07/12 12:17:43 korbinian Exp $
Author:
Alexei Drummond, Korbinian Strimmer
See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface pal.misc.Parameterized
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
 
Field Summary
 double r
          growth rate r
 double rSE
          standard error of growth rate r
 
Fields inherited from class pal.coalescent.ConstantPopulation
N0, N0SE
 
Fields inherited from class pal.coalescent.DemographicModel
fo
 
Fields inherited from interface pal.misc.Units
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS
 
Constructor Summary
ExponentialGrowth(double size, double growth, int units)
          Construct demographic model of an exponentially growing population
ExponentialGrowth(int units)
          Construct demographic model with default settings
 
Method Summary
 java.lang.Object clone()
           
 double getDefaultValue(int k)
          get default value of parameter
 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 getLowerLimit(int k)
          get lower parameter limit
 int getNumParameters()
          get number of parameters
 double getParameter(int k)
          get model parameter
 java.lang.String[] getSummaryTypes()
           
 double getSummaryValue(int summaryType)
           
 double getUpperLimit(int k)
          get upper parameter limit
 void report(java.io.PrintWriter out)
          print human readable report (e.g., on parameters and associated model)
 void setParameter(double value, int k)
          set model parameter
 void setParameterSE(double value, int k)
          set standard errors for model parameter
 java.lang.String toString()
           
 
Methods inherited from class pal.coalescent.ConstantPopulation
getN0
 
Methods inherited from class pal.coalescent.DemographicModel
computeLogLikelihood, computeLogLikelihood, getIntegral, getLogL, getSimulatedInterval, getUnits, setLogL, setUnits, testConsistency
 
Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

r

public double r
growth rate r


rSE

public double rSE
standard error of growth rate r

Constructor Detail

ExponentialGrowth

public ExponentialGrowth(int units)
Construct demographic model with default settings


ExponentialGrowth

public ExponentialGrowth(double size,
                         double growth,
                         int units)
Construct demographic model of an exponentially growing population

Method Detail

getSummaryTypes

public java.lang.String[] getSummaryTypes()
Specified by:
getSummaryTypes in interface Summarizable
Overrides:
getSummaryTypes in class ConstantPopulation

getSummaryValue

public double getSummaryValue(int summaryType)
Specified by:
getSummaryValue in interface Summarizable
Overrides:
getSummaryValue in class ConstantPopulation

clone

public java.lang.Object clone()
Overrides:
clone in class ConstantPopulation

getGrowthRate

public double getGrowthRate()
returns growth rate.


getDemographic

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

Overrides:
getDemographic in class ConstantPopulation

getIntensity

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

Overrides:
getIntensity in class ConstantPopulation

getInverseIntensity

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

Overrides:
getInverseIntensity in class ConstantPopulation

getNumParameters

public int getNumParameters()
Description copied from interface: Parameterized
get number of parameters

Specified by:
getNumParameters in interface Parameterized
Overrides:
getNumParameters in class ConstantPopulation
Returns:
number of parameters

getParameter

public double getParameter(int k)
Description copied from interface: Parameterized
get model parameter

Specified by:
getParameter in interface Parameterized
Overrides:
getParameter in class ConstantPopulation
Parameters:
k - parameter number
Returns:
parameter value

getUpperLimit

public double getUpperLimit(int k)
Description copied from interface: Parameterized
get upper parameter limit

Specified by:
getUpperLimit in interface Parameterized
Overrides:
getUpperLimit in class ConstantPopulation
Parameters:
k - parameter number
Returns:
upper bound

getLowerLimit

public double getLowerLimit(int k)
Description copied from interface: Parameterized
get lower parameter limit

Specified by:
getLowerLimit in interface Parameterized
Overrides:
getLowerLimit in class ConstantPopulation
Parameters:
k - parameter number
Returns:
lower bound

getDefaultValue

public double getDefaultValue(int k)
Description copied from interface: Parameterized
get default value of parameter

Specified by:
getDefaultValue in interface Parameterized
Overrides:
getDefaultValue in class ConstantPopulation
Parameters:
k - parameter number
Returns:
default value

setParameter

public void setParameter(double value,
                         int k)
Description copied from interface: Parameterized
set model parameter

Specified by:
setParameter in interface Parameterized
Overrides:
setParameter in class ConstantPopulation
Parameters:
value - parameter value
k - parameter number

setParameterSE

public void setParameterSE(double value,
                           int k)
Description copied from interface: Parameterized
set standard errors for model parameter

Specified by:
setParameterSE in interface Parameterized
Overrides:
setParameterSE in class ConstantPopulation
Parameters:
value - standard error of parameter value
k - parameter number

toString

public java.lang.String toString()
Overrides:
toString in class ConstantPopulation

report

public void report(java.io.PrintWriter out)
Description copied from interface: Report
print human readable report (e.g., on parameters and associated model)

Specified by:
report in interface Report
Overrides:
report in class ConstantPopulation
Parameters:
out - output stream