Uses of Class
pal.coalescent.CoalescentIntervals
Packages that use CoalescentIntervals
Package
Description
Classes to model population genetic processes using the coalescent.
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
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Uses of CoalescentIntervals in pal.coalescent
Methods in pal.coalescent that return CoalescentIntervalsModifier and TypeMethodDescriptionstatic 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.CoalescentTree.getCoalescentIntervals()
SkylinePlot.getIntervals()
Returns the coalescent intervals in this skyline plot.CoalescentSimulator.simulateIntervals
(int numLines, DemographicModel model) Simulates a set of CoalescentIntervals from a genealogy assuming contemporaneous tips.SerialCoalescentSimulator.simulateIntervals
(TimeOrderCharacterData tocd, DemographicModel model, boolean createTree) Simulates a set of CoalescentIntervals from a genealogy.Methods in pal.coalescent with parameters of type CoalescentIntervalsModifier and TypeMethodDescriptionvoid
CoalescentIntervals.groupIntervals
(CoalescentIntervals reference) Group intervals following a given (compatible) reference.Constructors in pal.coalescent with parameters of type CoalescentIntervalsModifierConstructorDescriptionSkylinePlot
(CoalescentIntervals ci, double epsilon) Construct skyline plot from given coalescent intervals -
Uses of CoalescentIntervals in pal.eval
Fields in pal.eval declared as CoalescentIntervalsMethods in pal.eval that return CoalescentIntervalsModifier and TypeMethodDescriptionDemographicValue.getCoalescentIntervals()
Returns the coalescent tree of this likelihood value.Methods in pal.eval with parameters of type CoalescentIntervalsModifier and TypeMethodDescriptionvoid
DemographicValue.setCoalescentIntervals
(CoalescentIntervals ci) define coalescent tree.