Uses of Class pal.coalescent.DemographicModel

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.

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 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
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 value

Methods 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.