pal.eval
public class ModelParameters extends java.lang.Object implements MultivariateFunction
Modifier and Type | Field and Description |
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static int |
FRACDIGITS
fractional digits desired for parameters
|
Constructor and Description |
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ModelParameters(SitePattern sp,
SubstitutionModel m)
Constructor
|
Modifier and Type | Method and Description |
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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() |
double |
getUpperBound(int n)
get upper bound of argument n
|
public static final int FRACDIGITS
public ModelParameters(SitePattern sp, SubstitutionModel m)
sp
- site patternm
- substitution modelpublic 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 numberpublic double getUpperBound(int n)
MultivariateFunction
getUpperBound
in interface MultivariateFunction
n
- argument numberpublic OrthogonalHints getOrthogonalHints()
getOrthogonalHints
in interface MultivariateFunction