Package pal.coalescent

Class ConstantPopulation

java.lang.Object
pal.coalescent.DemographicModel
pal.coalescent.ConstantPopulation
All Implemented Interfaces:
Serializable, Cloneable, Parameterized, Report, Summarizable, Units
Direct Known Subclasses:
ExponentialGrowth
public class ConstantPopulation extends DemographicModel implements Report, Summarizable, Parameterized, Serializable
This class models coalescent intervals for a constant population (parameter: N0=present-day population size).
If time units are set to Units.EXPECTED_SUBSTITUTIONS then the N0 parameter will be interpreted as N0 * mu.
Also note that if you are dealing with a diploid population N0 will be out by a factor of 2.
Version:
$Id: ConstantPopulation.java,v 1.14 2003/09/14 05:14:15 matt Exp $
Author:
Alexei Drummond + @author Korbinian Strimmer
See Also:

  • Field Details

    • N0

      public double N0
      population size

    • N0SE

      public double N0SE
      standard error of population size

  • Constructor Details

    • ConstantPopulation

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

    • ConstantPopulation

      public ConstantPopulation(double size, int units)
      Construct demographic model of a constant population size.

  • Method Details

    • clone

      public Object clone()
      Specified by:
      clone in class DemographicModel

    • getSummaryTypes

      public String[] getSummaryTypes()
      Specified by:
      getSummaryTypes in interface Summarizable

    • getSummaryValue

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

    • getN0

      public double getN0()
      returns initial population size.

    • getDemographic

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

    • 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).
      Specified by:
      getIntensity in class DemographicModel

    • 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).
      Specified by:
      getInverseIntensity in class DemographicModel

    • getNumParameters

      public int getNumParameters()
      Description copied from interface: Parameterized
      get number of parameters
      Specified by:
      getNumParameters in interface Parameterized
      Returns:
      number of parameters

    • getParameter

      public double getParameter(int k)
      Description copied from interface: Parameterized
      get model parameter
      Specified by:
      getParameter in interface Parameterized
      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
      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
      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
      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
      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
      Parameters:
      value - standard error of parameter value
      k - parameter number

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • report

      public void report(PrintWriter out)
      Description copied from interface: Report
      print human readable report (e.g., on parameters and associated model)
      Specified by:
      report in interface Report
      Parameters:
      out - output stream