Uses of Class
pal.coalescent.CoalescentIntervals
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Packages that use CoalescentIntervals 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. -
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Uses of CoalescentIntervals in pal.coalescent
Methods in pal.coalescent that return CoalescentIntervals Modifier and Type Method Description static 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.CoalescentIntervalsCoalescentTree. getCoalescentIntervals()CoalescentIntervalsSkylinePlot. getIntervals()Returns the coalescent intervals in this skyline plot.CoalescentIntervalsCoalescentSimulator. simulateIntervals(int numLines, DemographicModel model)Simulates a set of CoalescentIntervals from a genealogy assuming contemporaneous tips.CoalescentIntervalsSerialCoalescentSimulator. simulateIntervals(TimeOrderCharacterData tocd, DemographicModel model, boolean createTree)Simulates a set of CoalescentIntervals from a genealogy.Methods in pal.coalescent with parameters of type CoalescentIntervals Modifier and Type Method Description voidCoalescentIntervals. groupIntervals(CoalescentIntervals reference)Group intervals following a given (compatible) reference.Constructors in pal.coalescent with parameters of type CoalescentIntervals Constructor Description SkylinePlot(CoalescentIntervals ci, double epsilon)Construct skyline plot from given coalescent intervals -
Uses of CoalescentIntervals in pal.eval
Fields in pal.eval declared as CoalescentIntervals Modifier and Type Field Description protected CoalescentIntervalsDemographicValue. intervalsMethods in pal.eval that return CoalescentIntervals Modifier and Type Method Description CoalescentIntervalsDemographicValue. getCoalescentIntervals()Returns the coalescent tree of this likelihood value.Methods in pal.eval with parameters of type CoalescentIntervals Modifier and Type Method Description voidDemographicValue. setCoalescentIntervals(CoalescentIntervals ci)define coalescent tree.
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