Class SkylinePlot

  • All Implemented Interfaces:
    java.io.Serializable, Report, Units

    public class SkylinePlot
    extends java.lang.Object
    implements Report, Units, java.io.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:
    Serialized Form
    • Constructor Detail

      • 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 Detail

      • 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
      • 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.