Package pal.eval
Class ModelParameters
java.lang.Object
pal.eval.ModelParameters
- All Implemented Interfaces:
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
FieldsModifier and TypeFieldDescriptionstatic final int
fractional digits desired for parameters -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptiondouble[]
estimate()
estimate (approximate) values for the model parameters from the data using a neighbor-joining treedouble[]
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
get number of argumentsdouble
getUpperBound
(int n) get upper bound of argument n
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Field Details
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FRACDIGITS
public static final int FRACDIGITSfractional digits desired for parameters- See Also:
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Constructor Details
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ModelParameters
Constructor- Parameters:
sp
- site patternm
- substitution model
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Method Details
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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
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
- Specified by:
getOrthogonalHints
in interfaceMultivariateFunction
- Returns:
- null
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