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java.lang.Objectpal.eval.ModelParameters
public class ModelParameters
estimates substitution model parameters from the data
Field Summary | |
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static int |
FRACDIGITS
fractional digits desired for parameters |
Constructor Summary | |
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ModelParameters(SitePattern sp,
SubstitutionModel m)
Constructor |
Method Summary | |
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double[] |
estimate()
estimate (approximate) values for the model parameters from the data using a neighbor-joining tree |
double[] |
estimateFromTree(ParameterizedTree t)
estimate (approximate) values for the model parameters from the data using a given (parameterized) tree |
double |
evaluate(double[] params)
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 |
Field Detail |
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public static final int FRACDIGITS
Constructor Detail |
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public ModelParameters(SitePattern sp, SubstitutionModel m)
sp
- site patternm
- substitution modelMethod Detail |
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public double[] estimate()
public double[] estimateFromTree(ParameterizedTree t)
public double evaluate(double[] params)
MultivariateFunction
evaluate
in interface MultivariateFunction
params
- 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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