Class ConstantPopulation

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Cloneable, Parameterized, Report, Summarizable, Units
    Direct Known Subclasses:
    ExponentialGrowth

    public class ConstantPopulation
    extends DemographicModel
    implements Report, Summarizable, Parameterized, java.io.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:
    Serialized Form
    • Field Detail

      • N0

        public double N0
        population size
      • N0SE

        public double N0SE
        standard error of population size
    • Constructor Detail

      • 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 Detail

      • getN0

        public double getN0()
        returns initial population size.
      • 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 java.lang.String toString()
        Overrides:
        toString in class java.lang.Object
      • 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
        Parameters:
        out - output stream