Uses of Class
pal.coalescent.CoalescentIntervals

Packages that use CoalescentIntervals

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

Methods in pal.coalescent that return CoalescentIntervals

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()
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

void	CoalescentIntervals.groupIntervals(CoalescentIntervals reference) Group intervals following a given (compatible) reference.

Constructors in pal.coalescent with parameters of type CoalescentIntervals

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

protected CoalescentIntervals

DemographicValue.intervals

Methods in pal.eval that return CoalescentIntervals

CoalescentIntervals

DemographicValue.getCoalescentIntervals() Returns the coalescent tree of this likelihood value.

Methods in pal.eval with parameters of type CoalescentIntervals

void	DemographicValue.setCoalescentIntervals(CoalescentIntervals ci) define coalescent tree.