pal.eval
public class ChiSquareValue extends java.lang.Object implements MultivariateFunction
Constructor and Description |
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ChiSquareValue(DistanceMatrix m,
boolean w)
initialization
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Modifier and Type | Method and Description |
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double |
compute()
compute (weighted) least-square value
for current tree (fixed branch lengths)
return chi-square value
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double |
evaluate(double[] params)
compute (weighted) least-squares value
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double |
getLowerBound(int n)
get lower bound of argument n
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int |
getNumArguments()
get number of parameters in tree
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OrthogonalHints |
getOrthogonalHints() |
Tree |
getTree()
Returns the (parameterized) tree of this likelihood value.
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double |
getUpperBound(int n)
get upper bound of argument n
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double |
optimiseParameters()
optimise parameters of a tree by minimising its chi-square value
(tree must be a ParameterizedTree)
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double |
optimiseParameters(MultivariateMinimum mm)
optimise parameters of a tree by minimising its chi-square value
(tree must be a ParameterizedTree)
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void |
setTree(Tree t)
define (parameterized) tree
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public ChiSquareValue(DistanceMatrix m, boolean w)
m
- distance matrixw
- determines whether weighted or
unweighted chi-squares are computedpublic void setTree(Tree t)
t
- treepublic Tree getTree()
public double compute()
public double optimiseParameters()
public double optimiseParameters(MultivariateMinimum mm)
mm
- optimiser for ParameterizedTreepublic double evaluate(double[] params)
evaluate
in interface MultivariateFunction
params
- parameters (branch lengths) of the treepublic int getNumArguments()
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