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Packages that use DemographicModel | |
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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 |
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Subclasses of DemographicModel in pal.coalescent | |
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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 | |
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DemographicModel |
DemographicTree.getDemographicModel()
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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 | |
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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 | |
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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. |
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SerialCoalescentGenerator(TimeOrderCharacterData tocd,
DemographicModel demographicModel,
int numberOfTreesToGenerate)
Results will not contain alignments |
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SerialCoalescentGenerator(TimeOrderCharacterData tocd,
DemographicModel demographicModel,
int numberOfTreesToGenerate,
TreeOperation treeFinisher)
Results will not contain alignments |
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SerialCoalescentGenerator(TimeOrderCharacterData tocd,
DemographicModel demographicModel,
int numberOfTreesToGenerate,
TreeOperation treeFinisher,
SimulatedAlignment.Factory alignmentFactory)
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SerialCoalescentGenerator(TimeOrderCharacterData tocd,
DemographicModel demographicModel,
TreeOperation treeFinisher,
SimulatedAlignment.Factory alignmentFactory)
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Uses of DemographicModel in pal.eval |
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Fields in pal.eval declared as DemographicModel | |
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protected DemographicModel |
DemographicValue.model
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Methods in pal.eval that return DemographicModel | |
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DemographicModel |
DemographicValue.getDemographicModel()
Returns the demographic model of this likelihood value |
Methods in pal.eval with parameters of type DemographicModel | |
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void |
DemographicValue.setDemographicModel(DemographicModel m)
define model |
Uses of DemographicModel in pal.supgma |
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Methods in pal.supgma that return DemographicModel | |
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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 |
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Methods in pal.xml that return DemographicModel | |
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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 | |
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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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