Package pal.coalescent

Class SkylinePlot

java.lang.Object
pal.coalescent.SkylinePlot
All Implemented Interfaces:
Serializable, Report, Units
public class SkylinePlot extends Object implements Report, Units, Serializable
Skyline plot derived from a strictly bifurcating tree or a coalescent interval. This class provides the "classic" skyline plot method by Pybus, Rambaut and Harvey .2000. Genetics 155:1429-1437, as well as the "generalized" skyline plot method described in Strimmer and Pybus. 2001. MBE submitted.
Version:
$Id: SkylinePlot.java,v 1.16 2001/07/11 13:51:16 korbinian Exp $
Author:
Korbinian Strimmer
See Also:

  • Constructor Details

    • SkylinePlot

      public SkylinePlot(Tree tree, double epsilon)
      Construct skyline plot from tree
      Parameters:
      epsilon - smoothing parameter (if set < 0 then epsilon will be optimized)

    • SkylinePlot

      public SkylinePlot(CoalescentIntervals ci, double epsilon)
      Construct skyline plot from given coalescent intervals
      Parameters:
      epsilon - smoothing parameter (if set < 0 then epsilon will be optimized)

  • Method Details

    • 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

    • computeClassic

      public void computeClassic()
      Compute classic skyline plot

    • computeGeneralized

      public void computeGeneralized(double epsilon)
      Compute generalized skyline plot

    • optimize

      public void optimize()
      Optimize generalized skyline plot

    • getLogLikelihood

      public double getLogLikelihood()
      Compute log-likelihood

    • getAICC

      public double getAICC()
      Compute AICC-corrected log-likelihood

    • findInterval

      public double findInterval(double time)
      Find interval corresponding to a specific time

    • getMaxTime

      public double getMaxTime()
      Returns the largest value of time defined in this plot (= maximum value for epsilon)

    • getMaxPopulationSize

      public double getMaxPopulationSize()
      Returns the largest estimate of population size.

    • getIntervals

      public CoalescentIntervals getIntervals()
      Returns the coalescent intervals in this skyline plot.

    • getSize

      public int getSize()
      Returns the number of intervals in this skyline plot.

    • getParameterCount

      public int getParameterCount()
      Returns the number of composite intervals (=number of parameters).

    • getEpsilon

      public double getEpsilon()
      Returns epsilon

    • getPopulationSize

      public double getPopulationSize(int i)
      Returns the population size in interval i.

    • getUnits

      public int getUnits()
      Returns unit of time.