Package | Description |
---|---|
pal.coalescent |
Classes to model population genetic processes using the coalescent.
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pal.eval |
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
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pal.supgma | |
pal.xml |
Utility classes for converting PAL objects to and from XML documents.
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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.
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class |
ExpandingPopulation |
This class models a population that grows
exponentially from an inital population size alpha N0 to a present-day size N0.
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class |
ExponentialGrowth |
This class models an exponentially growing (or shrinking) population
(Parameters: N0=present-day population size; r=growth rate).
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Modifier and Type | Method | Description |
---|---|---|
DemographicModel |
DemographicClockTree.getDemographicModel() |
Return the demographic model being used to optimize the
likelihood of this tree.
|
DemographicModel |
DemographicTree.getDemographicModel() |
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.
|
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.
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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
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SerialCoalescentGenerator(TimeOrderCharacterData tocd,
DemographicModel demographicModel,
int numberOfTreesToGenerate,
TreeOperation treeFinisher,
SimulatedAlignment.Factory alignmentFactory) |
|
SerialCoalescentGenerator(TimeOrderCharacterData tocd,
DemographicModel demographicModel,
TreeOperation treeFinisher,
SimulatedAlignment.Factory alignmentFactory) |
Modifier and Type | Field | Description |
---|---|---|
protected DemographicModel |
DemographicValue.model |
Modifier and Type | Method | Description |
---|---|---|
DemographicModel |
DemographicValue.getDemographicModel() |
Returns the demographic model of this likelihood value
|
Modifier and Type | Method | Description |
---|---|---|
void |
DemographicValue.setDemographicModel(DemographicModel m) |
define model
|
Modifier and Type | Method | Description |
---|---|---|
DemographicModel |
ThetaHandler.generateDemographicModel(double[] deltas,
double[] thetas,
TimeOrderCharacterData tocd) |
May return null if not possible to infer demographic model
|
Modifier and Type | Method | Description |
---|---|---|
static DemographicModel |
ElementParser.parseDemographicModel(org.w3c.dom.Element e) |
Parses an element from an DOM document into a DemographicModel.
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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.
|