public class Coalescent extends java.lang.Object implements MultivariateFunction
Constructor and Description |
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Coalescent(IntervalList intervals,
DemographicFunction demographicFunction) |
Coalescent(RootedTree tree,
DemographicFunction demographicFunction) |
Modifier and Type | Method and Description |
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static double |
calculateAnalyticalLogLikelihood(IntervalList intervals)
Calculates the log likelihood of this set of coalescent intervals,
using an analytical integration over theta.
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double |
calculateLogLikelihood()
Calculates the log likelihood of this set of coalescent intervals,
given a demographic model.
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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 value
|
double |
getLowerBound(int n)
get lower bound of argument n
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int |
getNumArguments()
get number of arguments
|
OrthogonalHints |
getOrthogonalHints() |
double |
getUpperBound(int n)
get upper bound of argument n
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public Coalescent(RootedTree tree, DemographicFunction demographicFunction)
public Coalescent(IntervalList intervals, DemographicFunction demographicFunction)
public double calculateLogLikelihood()
public static final double calculateLogLikelihood(IntervalList intervals, DemographicFunction demographicFunction)
public static final double calculateAnalyticalLogLikelihood(IntervalList intervals)
public double evaluate(double[] argument)
MultivariateFunction
evaluate
in interface MultivariateFunction
argument
- function argument (vector)public int getNumArguments()
MultivariateFunction
getNumArguments
in interface MultivariateFunction
public double getLowerBound(int n)
MultivariateFunction
getLowerBound
in interface MultivariateFunction
n
- argument numberpublic double getUpperBound(int n)
MultivariateFunction
getUpperBound
in interface MultivariateFunction
n
- argument numberpublic OrthogonalHints getOrthogonalHints()
getOrthogonalHints
in interface MultivariateFunction
http://code.google.com/p/jebl2/