Package pal.coalescent

Class DemographicModel

java.lang.Object
pal.coalescent.DemographicModel
All Implemented Interfaces:
Serializable, Cloneable, Parameterized, Report, Summarizable, Units
Direct Known Subclasses:
ConstantPopulation
public abstract class DemographicModel extends Object implements Units, Parameterized, Report, Cloneable, Serializable, Summarizable
This abstract class contains methods that are of general use for modelling coalescent intervals given a demographic model. Parts of this class were derived from C++ code provided by Oliver Pybus.
Version:
$Id: DemographicModel.java,v 1.12 2002/02/02 08:32:52 alexi Exp $
Author:
Alexei Drummond, Korbinian Strimmer
See Also:

  • Field Details

  • Constructor Details

    • DemographicModel

      public DemographicModel()

  • Method Details

    • clone

      public abstract Object clone()
      Overrides:
      clone in class Object

    • getDemographic

      public abstract double getDemographic(double t)
      Gets the value of the demographic function N(t) at time t.

    • getIntensity

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

    • getInverseIntensity

      public abstract double getInverseIntensity(double x)
      Returns value of inverse demographic intensity function (returns time, needed for simulation of coalescent intervals).

    • getSimulatedInterval

      public double getSimulatedInterval(int numLin, double timeOfLastCoal)
      Returns an random interval size selected from the Kingman prior of the demographic model.

    • getIntegral

      public double getIntegral(double start, double finish)
      Calculates the integral 1/N(x) dx between start and finish.

    • computeLogLikelihood

      public double computeLogLikelihood(double width, double timeOfPrevCoal, int numLineages)
      Returns the likelihood of a given *coalescent* interval

    • computeLogLikelihood

      public double computeLogLikelihood(double width, double timeOfPrevCoal, int numLineages, int type)
      Returns the likelihood of a given interval,coalescent or otherwise.

    • setUnits

      public void setUnits(int u)
      sets units of measurement.
      Parameters:
      u - units

    • getUnits

      public int getUnits()
      returns units of measurement.

    • setLogL

      public void setLogL(double l)
      sets log likelihood
      Parameters:
      l - log-likelihood

    • getLogL

      public double getLogL()
      returns log-likelihood.

    • testConsistency

      public void testConsistency(int steps, double maxTime)
      This function tests the consistency of the getIntensity and getInverseIntensity methods of this demographic model. If the model is inconsistent then a RuntimeException will be thrown.
      Parameters:
      model - the demographic model to test.
      steps - the number of steps between 0.0 and maxTime to test.
      maxTime - the maximum time to test.