Package jebl.evolution.coalescent

Class EmpiricalDemographicFunction

  • All Implemented Interfaces:
    DemographicFunction
    public class EmpiricalDemographicFunction
extends java.lang.Object
implements DemographicFunction
    Version:
    $Id$
    Author:
    Oliver Pybus, Andrew Rambaut

    • Constructor Summary

      Constructors 
      Constructor Description
      EmpiricalDemographicFunction​(double[] populationSizes, double[] times, boolean stepwise)  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      double getArgument​(int n)
      Returns the value of the nth argument of this function.
      int getArgumentCount()
      Returns the number of arguments for this function.
      java.lang.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 getIntegral​(double start, double finish)
      Calculates the integral 1/N(x) dx between start and finish
      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.
      boolean hasIntegral()
      returns whether an analytical expression for the integral is implemented
      void setArgument​(int n, double value)
      Sets the value of the nth argument of this function.

      • Methods inherited from class java.lang.Object

        equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • EmpiricalDemographicFunction

        public EmpiricalDemographicFunction​(double[] populationSizes,
                                    double[] times,
                                    boolean stepwise)

    • Method Detail

      • getDemographic

        public double getDemographic​(double t)
        Gets the value of the demographic function N(t) at time t.
        Specified by:
        getDemographic in interface DemographicFunction

      • getIntensity

        public double getIntensity​(double t)
        Returns value of demographic intensity function at time t (= integral 1/N(x) dx from 0 to t).
        Specified by:
        getIntensity in interface DemographicFunction

      • getInverseIntensity

        public double getInverseIntensity​(double x)
        Returns value of inverse demographic intensity function (returns time, needed for simulation of coalescent intervals).
        Specified by:
        getInverseIntensity in interface DemographicFunction

      • 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
        Returns:
        a boolean

      • getIntegral

        public double getIntegral​(double start,
                          double finish)
        Description copied from interface: DemographicFunction
        Calculates the integral 1/N(x) dx between start and finish
        Specified by:
        getIntegral in interface DemographicFunction

      • getArgumentName

        public java.lang.String getArgumentName​(int n)
        Returns the name of the nth argument of this function.
        Specified by:
        getArgumentName in interface DemographicFunction

      • getArgument

        public double getArgument​(int n)
        Returns the value of the nth argument of this function.
        Specified by:
        getArgument in interface DemographicFunction

      • setArgument

        public void setArgument​(int n,
                        double value)
        Sets the value of the nth argument of this function.
        Specified by:
        setArgument in interface DemographicFunction

      • getLowerBound

        public double getLowerBound​(int n)
        Returns the lower bound of the nth argument of this function.
        Specified by:
        getLowerBound in interface DemographicFunction

      • getUpperBound

        public double getUpperBound​(int n)
        Returns the upper bound of the nth argument of this function.
        Specified by:
        getUpperBound in interface DemographicFunction