Uses of Class
pal.coalescent.DemographicModel
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Packages that use DemographicModel Package Description 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. -
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Uses of DemographicModel in pal.coalescent
Subclasses of DemographicModel in pal.coalescent Modifier and Type Class Description 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 Modifier and Type Method Description DemographicModel
DemographicClockTree. getDemographicModel()
Return the demographic model being used to optimize the likelihood of this tree.DemographicModel
DemographicTree. getDemographicModel()
Methods in pal.coalescent with parameters of type DemographicModel Modifier and Type Method Description 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 Constructor Description 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 alignmentsSerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, int numberOfTreesToGenerate, TreeOperation treeFinisher)
Results will not contain alignmentsSerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, int numberOfTreesToGenerate, TreeOperation treeFinisher, SimulatedAlignment.Factory alignmentFactory)
SerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, TreeOperation treeFinisher, SimulatedAlignment.Factory alignmentFactory)
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Uses of DemographicModel in pal.eval
Fields in pal.eval declared as DemographicModel Modifier and Type Field Description protected DemographicModel
DemographicValue. model
Methods in pal.eval that return DemographicModel Modifier and Type Method Description DemographicModel
DemographicValue. getDemographicModel()
Returns the demographic model of this likelihood valueMethods in pal.eval with parameters of type DemographicModel Modifier and Type Method Description void
DemographicValue. setDemographicModel(DemographicModel m)
define model -
Uses of DemographicModel in pal.supgma
Methods in pal.supgma that return DemographicModel Modifier and Type Method Description 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 Modifier and Type Method Description 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 Modifier and Type Method Description static org.w3c.dom.Element
ElementFactory. createDemographicModelElement(DemographicModel demo, org.w3c.dom.Document document)
Creates an XML element representing a demographic model.
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