Uses of Class
pal.coalescent.CoalescentIntervals

Packages that use CoalescentIntervals
pal.coalescent Classes to model population genetic processes using the coalescent. 
pal.eval Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters. 
 

Uses of CoalescentIntervals in pal.coalescent
 

Methods in pal.coalescent that return CoalescentIntervals
static CoalescentIntervals IntervalsExtractor.extractFromClockTree(Tree tree)
          extracts intervals from clock tree.
static CoalescentIntervals IntervalsExtractor.extractFromClockTree(Tree tree, double minSize)
          extracts intervals from clock tree.
static CoalescentIntervals IntervalsExtractor.extractFromTree(Tree tree)
          extracts intervals from serial clock tree.
static CoalescentIntervals IntervalsExtractor.extractFromTree(Tree tree, MutationRateModel muModel)
          extracts intervals in generation times from serial clock tree (in mutation times) after taking into account mutation rate model.
 CoalescentIntervals CoalescentTree.getCoalescentIntervals()
           
 CoalescentIntervals SkylinePlot.getIntervals()
          Returns the coalescent intervals in this skyline plot.
 CoalescentIntervals CoalescentSimulator.simulateIntervals(int numLines, DemographicModel model)
          Simulates a set of CoalescentIntervals from a genealogy assuming contemporaneous tips.
 CoalescentIntervals SerialCoalescentSimulator.simulateIntervals(TimeOrderCharacterData tocd, DemographicModel model, boolean createTree)
          Simulates a set of CoalescentIntervals from a genealogy.
 

Methods in pal.coalescent with parameters of type CoalescentIntervals
 void CoalescentIntervals.groupIntervals(CoalescentIntervals reference)
          Group intervals following a given (compatible) reference.
 

Constructors in pal.coalescent with parameters of type CoalescentIntervals
SkylinePlot(CoalescentIntervals ci, double epsilon)
          Construct skyline plot from given coalescent intervals
 

Uses of CoalescentIntervals in pal.eval
 

Fields in pal.eval declared as CoalescentIntervals
protected  CoalescentIntervals DemographicValue.intervals
           
 

Methods in pal.eval that return CoalescentIntervals
 CoalescentIntervals DemographicValue.getCoalescentIntervals()
          Returns the coalescent tree of this likelihood value.
 

Methods in pal.eval with parameters of type CoalescentIntervals
 void DemographicValue.setCoalescentIntervals(CoalescentIntervals ci)
          define coalescent tree.