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java.lang.Object jebl.evolution.coalescent.Coalescent
public class Coalescent
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.
Constructor Summary | |
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Coalescent(IntervalList intervals,
DemographicFunction demographicFunction)
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Coalescent(RootedTree tree,
DemographicFunction demographicFunction)
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Method Summary | |
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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. |
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 value |
double |
getLowerBound(int n)
get lower bound of argument n |
int |
getNumArguments()
get number of arguments |
OrthogonalHints |
getOrthogonalHints()
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double |
getUpperBound(int n)
get upper bound of argument n |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public Coalescent(RootedTree tree, DemographicFunction demographicFunction)
public Coalescent(IntervalList intervals, DemographicFunction demographicFunction)
Method Detail |
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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 number
public double getUpperBound(int n)
MultivariateFunction
getUpperBound
in interface MultivariateFunction
n
- argument number
public OrthogonalHints getOrthogonalHints()
getOrthogonalHints
in interface MultivariateFunction
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