Uses of Class
pal.coalescent.DemographicModel
Packages that use DemographicModel
Package
Description
Classes to model population genetic processes using the coalescent.
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
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.coalescentModifier and TypeClassDescriptionclass
This class models coalescent intervals for a constant population (parameter: N0=present-day population size).class
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
This class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.class
This class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.class
This class models an exponentially growing (or shrinking) population (Parameters: N0=present-day population size; r=growth rate).Methods in pal.coalescent that return DemographicModelModifier and TypeMethodDescriptionDemographicClockTree.getDemographicModel()
Return the demographic model being used to optimize the likelihood of this tree.DemographicTree.getDemographicModel()
Methods in pal.coalescent with parameters of type DemographicModelModifier and TypeMethodDescriptiondouble
CoalescentIntervals.computeLogLikelihood
(DemographicModel model) Returns the log likelihood of this set of coalescent intervals, given a demographic model.CoalescentSimulator.simulateIntervals
(int numLines, DemographicModel model) Simulates a set of CoalescentIntervals from a genealogy assuming contemporaneous tips.SerialCoalescentSimulator.simulateIntervals
(TimeOrderCharacterData tocd, DemographicModel model, boolean createTree) Simulates a set of CoalescentIntervals from a genealogy.Constructors in pal.coalescent with parameters of type DemographicModelModifierConstructorDescriptionDemographicClockTree
(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) -
Uses of DemographicModel in pal.eval
Fields in pal.eval declared as DemographicModelMethods in pal.eval that return DemographicModelModifier and TypeMethodDescriptionDemographicValue.getDemographicModel()
Returns the demographic model of this likelihood valueMethods in pal.eval with parameters of type DemographicModelModifier and TypeMethodDescriptionvoid
DemographicValue.setDemographicModel
(DemographicModel m) define model -
Uses of DemographicModel in pal.supgma
Methods in pal.supgma that return DemographicModelModifier and TypeMethodDescriptionThetaHandler.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 DemographicModelModifier and TypeMethodDescriptionstatic DemographicModel
ElementParser.parseDemographicModel
(Element e) Parses an element from an DOM document into a DemographicModel.Methods in pal.xml with parameters of type DemographicModelModifier and TypeMethodDescriptionstatic Element
ElementFactory.createDemographicModelElement
(DemographicModel demo, Document document) Creates an XML element representing a demographic model.