Uses of Class
pal.coalescent.DemographicModel

Packages that use DemographicModel
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. 
pal.supgma   
pal.xml Utility classes for converting PAL objects to and from XML documents. 
 

Uses of DemographicModel in pal.coalescent
 

Subclasses of DemographicModel in pal.coalescent
 class ConstantPopulation
          This class models coalescent intervals for a constant population (parameter: N0=present-day population size).
 class ConstExpConst
          This class models a population that grows exponentially from an initial population size alpha N0 at time y to a size N0 at time x until the present-day.
 class ConstExpGrowth
          This class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.
 class ExpandingPopulation
          This class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.
 class ExponentialGrowth
          This class models an exponentially growing (or shrinking) population (Parameters: N0=present-day population size; r=growth rate).
 

Methods in pal.coalescent that return DemographicModel
 DemographicModel DemographicTree.getDemographicModel()
           
 DemographicModel DemographicClockTree.getDemographicModel()
          Return the demographic model being used to optimize the likelihood of this tree.
 

Methods in pal.coalescent with parameters of type DemographicModel
 double CoalescentIntervals.computeLogLikelihood(DemographicModel model)
          Returns the log likelihood of this set of coalescent intervals, given a demographic model.
 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.
 

Constructors in pal.coalescent with parameters of type DemographicModel
DemographicClockTree(Tree t, DemographicModel model)
          take any tree and afford it with an interface suitable for a clock-like genealogy, under a certain demographic assumption.
SerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, int numberOfTreesToGenerate)
          Results will not contain alignments
SerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, int numberOfTreesToGenerate, TreeOperation treeFinisher)
          Results will not contain alignments
SerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, int numberOfTreesToGenerate, TreeOperation treeFinisher, SimulatedAlignment.Factory alignmentFactory)
           
SerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, TreeOperation treeFinisher, SimulatedAlignment.Factory alignmentFactory)
           
 

Uses of DemographicModel in pal.eval
 

Fields in pal.eval declared as DemographicModel
protected  DemographicModel DemographicValue.model
           
 

Methods in pal.eval that return DemographicModel
 DemographicModel DemographicValue.getDemographicModel()
          Returns the demographic model of this likelihood value
 

Methods in pal.eval with parameters of type DemographicModel
 void DemographicValue.setDemographicModel(DemographicModel m)
          define model
 

Uses of DemographicModel in pal.supgma
 

Methods in pal.supgma that return DemographicModel
 DemographicModel ThetaHandler.generateDemographicModel(double[] deltas, double[] thetas, TimeOrderCharacterData tocd)
          May return null if not possible to infer demographic model
 

Uses of DemographicModel in pal.xml
 

Methods in pal.xml that return DemographicModel
static DemographicModel ElementParser.parseDemographicModel(org.w3c.dom.Element e)
          Parses an element from an DOM document into a DemographicModel.
 

Methods in pal.xml with parameters of type DemographicModel
static org.w3c.dom.Element ElementFactory.createDemographicModelElement(DemographicModel demo, org.w3c.dom.Document document)
          Creates an XML element representing a demographic model.