Package jebl.evolution.coalescent
Class Coalescent
- java.lang.Object
-
- jebl.evolution.coalescent.Coalescent
-
- All Implemented Interfaces:
MultivariateFunction
public class Coalescent extends java.lang.Object implements 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
-
-
Constructor Summary
Constructors Constructor Description Coalescent(IntervalList intervals, DemographicFunction demographicFunction)
Coalescent(RootedTree tree, DemographicFunction demographicFunction)
-
Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static double
calculateAnalyticalLogLikelihood(IntervalList intervals)
Calculates the log likelihood of this set of coalescent intervals, using an analytical integration over theta.double
calculateLogLikelihood()
Calculates the log likelihood of this set of coalescent intervals, given a demographic model.static 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
getNumArguments()
get number of argumentsOrthogonalHints
getOrthogonalHints()
double
getUpperBound(int n)
get upper bound of argument n
-
-
-
Constructor Detail
-
Coalescent
public Coalescent(RootedTree tree, DemographicFunction demographicFunction)
-
Coalescent
public Coalescent(IntervalList intervals, DemographicFunction demographicFunction)
-
-
Method Detail
-
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
public static final double calculateAnalyticalLogLikelihood(IntervalList intervals)
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
-
getNumArguments
public int getNumArguments()
Description copied from interface:MultivariateFunction
get number of arguments- Specified by:
getNumArguments
in interfaceMultivariateFunction
- Returns:
- number of arguments
-
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
-
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
-
getOrthogonalHints
public OrthogonalHints 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
-
-