Package pal.eval

Class DemographicValue

java.lang.Object
pal.eval.DemographicValue
All Implemented Interfaces:
MultivariateFunction
public class DemographicValue extends Object implements MultivariateFunction
estimates demographic parameters by maximising the coalescent prior for a tree with given branch lengths.
Version:
$Id: DemographicValue.java,v 1.6 2002/04/16 05:37:05 matt Exp $
Author:
Alexei Drummond

  • Field Details

  • Constructor Details

    • DemographicValue

      public DemographicValue()

  • Method Details

    • setDemographicModel

      public void setDemographicModel(DemographicModel m)
      define model
      Parameters:
      m - model of demographic

    • getDemographicModel

      public DemographicModel getDemographicModel()
      Returns the demographic model of this likelihood value

    • getCoalescentIntervals

      public CoalescentIntervals getCoalescentIntervals()
      Returns the coalescent tree of this likelihood value.

    • setCoalescentIntervals

      public void setCoalescentIntervals(CoalescentIntervals ci)
      define coalescent tree.
      Parameters:
      t - tree

    • compute

      public double compute()
      compute log-likelihood for current model return negative log-likelihood

    • optimize

      public double optimize()
      optimize log-likelihood using default optimizer return minimum negative log-likelihood

    • optimize

      public double optimize(MultivariateMinimum givenMvm)
      optimize log-likelihood value and compute corresponding SEs given an optimizer
      Returns:
      minimimum negative log-likelihood value

    • evaluate

      public double evaluate(double[] params)
      Description copied from interface: MultivariateFunction
      compute function value
      Specified by:
      evaluate in interface MultivariateFunction
      Parameters:
      params - function argument (vector)
      Returns:
      function value

    • getNumArguments

      public int getNumArguments()
      Description copied from interface: MultivariateFunction
      get number of arguments
      Specified by:
      getNumArguments in interface MultivariateFunction
      Returns:
      number of arguments

    • getLowerBound

      public double getLowerBound(int n)
      Description copied from interface: MultivariateFunction
      get lower bound of argument n
      Specified by:
      getLowerBound in interface MultivariateFunction
      Parameters:
      n - argument number
      Returns:
      lower bound

    • getUpperBound

      public double getUpperBound(int n)
      Description copied from interface: MultivariateFunction
      get upper bound of argument n
      Specified by:
      getUpperBound in interface MultivariateFunction
      Parameters:
      n - argument number
      Returns:
      upper bound

    • computeLogLikelihood

      protected void computeLogLikelihood()

    • getOrthogonalHints

      public OrthogonalHints getOrthogonalHints()
      Specified by:
      getOrthogonalHints in interface MultivariateFunction
      Returns:
      null