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