Package pal.eval
Class ModelParameters
- java.lang.Object
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- pal.eval.ModelParameters
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- All Implemented Interfaces:
MultivariateFunction
public class ModelParameters extends java.lang.Object implements MultivariateFunction
estimates substitution model parameters from the data- Version:
- $Id: ModelParameters.java,v 1.9 2002/12/05 04:27:28 matt Exp $
- Author:
- Korbinian Strimmer
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Field Summary
Fields Modifier and Type Field Description static int
FRACDIGITS
fractional digits desired for parameters
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Constructor Summary
Constructors Constructor Description ModelParameters(SitePattern sp, SubstitutionModel m)
Constructor
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description double[]
estimate()
estimate (approximate) values for the model parameters from the data using a neighbor-joining treedouble[]
estimateFromTree(ParameterizedTree t)
estimate (approximate) values for the model parameters from the data using a given (parameterized) treedouble
evaluate(double[] params)
compute function valuedouble
getLowerBound(int n)
get lower bound of argument nint
getNumArguments()
get number of argumentsOrthogonalHints
getOrthogonalHints()
double
getUpperBound(int n)
get upper bound of argument n
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Field Detail
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FRACDIGITS
public static final int FRACDIGITS
fractional digits desired for parameters- See Also:
- Constant Field Values
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Constructor Detail
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ModelParameters
public ModelParameters(SitePattern sp, SubstitutionModel m)
Constructor- Parameters:
sp
- site patternm
- substitution model
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Method Detail
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estimate
public double[] estimate()
estimate (approximate) values for the model parameters from the data using a neighbor-joining tree- Returns:
- parameter estimates
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estimateFromTree
public double[] estimateFromTree(ParameterizedTree t)
estimate (approximate) values for the model parameters from the data using a given (parameterized) tree- Returns:
- parameter estimates
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evaluate
public double evaluate(double[] params)
Description copied from interface:MultivariateFunction
compute function value- Specified by:
evaluate
in interfaceMultivariateFunction
- Parameters:
params
- function argument (vector)- Returns:
- function value
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getNumArguments
public int getNumArguments()
Description copied from interface:MultivariateFunction
get number of arguments- Specified by:
getNumArguments
in interfaceMultivariateFunction
- Returns:
- number of arguments
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getLowerBound
public double getLowerBound(int n)
Description copied from interface:MultivariateFunction
get lower bound of argument n- Specified by:
getLowerBound
in interfaceMultivariateFunction
- Parameters:
n
- argument number- Returns:
- lower bound
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getUpperBound
public double getUpperBound(int n)
Description copied from interface:MultivariateFunction
get upper bound of argument n- Specified by:
getUpperBound
in interfaceMultivariateFunction
- Parameters:
n
- argument number- Returns:
- upper bound
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getOrthogonalHints
public OrthogonalHints getOrthogonalHints()
- Specified by:
getOrthogonalHints
in interfaceMultivariateFunction
- Returns:
- null
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