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.
|
Modifier and Type | Method | Description |
---|---|---|
static CoalescentIntervals |
IntervalsExtractor.extractFromClockTree(Tree tree) |
extracts intervals from clock tree.
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static CoalescentIntervals |
IntervalsExtractor.extractFromClockTree(Tree tree,
double minSize) |
extracts intervals from clock tree.
|
static CoalescentIntervals |
IntervalsExtractor.extractFromTree(Tree tree) |
extracts intervals from serial clock tree.
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static CoalescentIntervals |
IntervalsExtractor.extractFromTree(Tree tree,
MutationRateModel muModel) |
extracts intervals in generation times from serial clock tree (in mutation times)
after taking into account mutation rate model.
|
CoalescentIntervals |
CoalescentTree.getCoalescentIntervals() |
|
CoalescentIntervals |
SkylinePlot.getIntervals() |
Returns the coalescent intervals in this skyline plot.
|
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.
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Modifier and Type | Method | Description |
---|---|---|
void |
CoalescentIntervals.groupIntervals(CoalescentIntervals reference) |
Group intervals following a given (compatible) reference.
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Constructor | Description |
---|---|
SkylinePlot(CoalescentIntervals ci,
double epsilon) |
Construct skyline plot from given coalescent intervals
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Modifier and Type | Field | Description |
---|---|---|
protected CoalescentIntervals |
DemographicValue.intervals |
Modifier and Type | Method | Description |
---|---|---|
CoalescentIntervals |
DemographicValue.getCoalescentIntervals() |
Returns the coalescent tree of this likelihood value.
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Modifier and Type | Method | Description |
---|---|---|
void |
DemographicValue.setCoalescentIntervals(CoalescentIntervals ci) |
define coalescent tree.
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