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Packages that use CoalescentIntervals | |
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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. |
Uses of CoalescentIntervals in pal.coalescent |
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Methods in pal.coalescent that return CoalescentIntervals | |
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static CoalescentIntervals |
IntervalsExtractor.extractFromClockTree(Tree tree)
extracts intervals from clock tree. |
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. |
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()
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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. |
Methods in pal.coalescent with parameters of type CoalescentIntervals | |
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void |
CoalescentIntervals.groupIntervals(CoalescentIntervals reference)
Group intervals following a given (compatible) reference. |
Constructors in pal.coalescent with parameters of type CoalescentIntervals | |
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SkylinePlot(CoalescentIntervals ci,
double epsilon)
Construct skyline plot from given coalescent intervals |
Uses of CoalescentIntervals in pal.eval |
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Fields in pal.eval declared as CoalescentIntervals | |
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protected CoalescentIntervals |
DemographicValue.intervals
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Methods in pal.eval that return CoalescentIntervals | |
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CoalescentIntervals |
DemographicValue.getCoalescentIntervals()
Returns the coalescent tree of this likelihood value. |
Methods in pal.eval with parameters of type CoalescentIntervals | |
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void |
DemographicValue.setCoalescentIntervals(CoalescentIntervals ci)
define coalescent tree. |
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