pal.eval
Class ModelParameters
java.lang.Object
|
+--pal.eval.ModelParameters
- All Implemented Interfaces:
- MultivariateFunction
- public class ModelParameters
- extends java.lang.Object
- implements MultivariateFunction
estimates substitution model parameters from the data
Field Summary |
static int |
FRACDIGITS
fractional digits desired for parameters |
Method Summary |
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 |
double |
getUpperBound(int n)
get upper bound of argument n |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
FRACDIGITS
public static final int FRACDIGITS
- fractional digits desired for parameters
ModelParameters
public ModelParameters(SitePattern sp,
SubstitutionModel m)
- Constructor
- Parameters:
sp
- site patternm
- substitution model
estimate
public double[] estimate()
- estimate (approximate) values for the model parameters
from the data using a neighbor-joining tree
- Returns:
- parameter estimates
estimateFromTree
public double[] estimateFromTree(ParameterizedTree t)
- estimate (approximate) values for the model parameters
from the data using a given (parameterized) tree
- Returns:
- parameter estimates
evaluate
public double evaluate(double[] params)
- Description copied from interface:
MultivariateFunction
- compute function value
- Specified by:
evaluate
in interface MultivariateFunction
- Following copied from interface:
pal.math.MultivariateFunction
- Parameters:
argument
- function argument (vector)- Returns:
- function value
getNumArguments
public int getNumArguments()
- Description copied from interface:
MultivariateFunction
- get number of arguments
- Specified by:
getNumArguments
in interface MultivariateFunction
- Following copied from interface:
pal.math.MultivariateFunction
- Returns:
- number of arguments
getLowerBound
public double getLowerBound(int n)
- Description copied from interface:
MultivariateFunction
- get lower bound of argument n
- Specified by:
getLowerBound
in interface MultivariateFunction
- Following copied from interface:
pal.math.MultivariateFunction
- Parameters:
n
- argument number- Returns:
- lower bound
getUpperBound
public double getUpperBound(int n)
- Description copied from interface:
MultivariateFunction
- get upper bound of argument n
- Specified by:
getUpperBound
in interface MultivariateFunction
- Following copied from interface:
pal.math.MultivariateFunction
- Parameters:
n
- argument number- Returns:
- upper bound