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 CoalescentIntervalsIntervalsExtractor.extractFromClockTree(Tree tree) extracts intervals from clock tree.static CoalescentIntervalsIntervalsExtractor.extractFromClockTree(Tree tree, double minSize) extracts intervals from clock tree.static CoalescentIntervalsIntervalsExtractor.extractFromTree(Tree tree) extracts intervals from serial clock tree.static CoalescentIntervalsIntervalsExtractor.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 TypeMethodDescriptionvoidCoalescentIntervals.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 TypeMethodDescriptionvoidDemographicValue.setCoalescentIntervals(CoalescentIntervals ci) define coalescent tree.