Package jebl.evolution.coalescent
Class Coalescent
java.lang.Object
jebl.evolution.coalescent.Coalescent
- All Implemented Interfaces:
MultivariateFunction
A likelihood function for the coalescent. Takes a tree and a demographic model.
Parts of this class were derived from C++ code provided by Oliver Pybus.
- Version:
- $Id: Coalescent.java 390 2006-07-20 14:33:51Z rambaut $
- Author:
- Andrew Rambaut, Alexei Drummond
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Constructor Summary
ConstructorsConstructorDescriptionCoalescent
(IntervalList intervals, DemographicFunction demographicFunction) Coalescent
(RootedTree tree, DemographicFunction demographicFunction) -
Method Summary
Modifier and TypeMethodDescriptionstatic final double
calculateAnalyticalLogLikelihood
(IntervalList intervals) Calculates the log likelihood of this set of coalescent intervals, using an analytical integration over theta.double
Calculates the log likelihood of this set of coalescent intervals, given a demographic model.static final double
calculateLogLikelihood
(IntervalList intervals, DemographicFunction demographicFunction) Calculates the log likelihood of this set of coalescent intervals, given a demographic model.double
evaluate
(double[] argument) compute function valuedouble
getLowerBound
(int n) get lower bound of argument nint
get number of argumentsdouble
getUpperBound
(int n) get upper bound of argument n
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Constructor Details
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Coalescent
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Coalescent
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Method Details
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calculateLogLikelihood
public double calculateLogLikelihood()Calculates the log likelihood of this set of coalescent intervals, given a demographic model. -
calculateLogLikelihood
public static final double calculateLogLikelihood(IntervalList intervals, DemographicFunction demographicFunction) Calculates the log likelihood of this set of coalescent intervals, given a demographic model. -
calculateAnalyticalLogLikelihood
Calculates the log likelihood of this set of coalescent intervals, using an analytical integration over theta. -
evaluate
public double evaluate(double[] argument) Description copied from interface:MultivariateFunction
compute function value- Specified by:
evaluate
in interfaceMultivariateFunction
- Parameters:
argument
- function argument (vector)- Returns:
- function value
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getNumArguments
public int getNumArguments()Description copied from interface:MultivariateFunction
get number of arguments- Specified by:
getNumArguments
in interfaceMultivariateFunction
- Returns:
- number of arguments
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getLowerBound
public double getLowerBound(int n) Description copied from interface:MultivariateFunction
get lower bound of argument n- Specified by:
getLowerBound
in interfaceMultivariateFunction
- Parameters:
n
- argument number- Returns:
- lower bound
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getUpperBound
public double getUpperBound(int n) Description copied from interface:MultivariateFunction
get upper bound of argument n- Specified by:
getUpperBound
in interfaceMultivariateFunction
- Parameters:
n
- argument number- Returns:
- upper bound
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getOrthogonalHints
- Specified by:
getOrthogonalHints
in interfaceMultivariateFunction
- Returns:
- an Orthogonal Hints object that can be used by Orthogonal based optimisers to get information about the function
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