pal.tree
Class LogParameterizedTree

java.lang.Object
  pal.tree.ParameterizedTree.ParameterizedTreeBase
      pal.tree.LogParameterizedTree

All Implemented Interfaces:

java.io.Serializable, IdGroup, Parameterized, Units, UnitsProvider, ParameterizedTree, Tree

public class LogParameterizedTree
extends ParameterizedTree.ParameterizedTreeBase
implements ParameterizedTree

This class logarithmically transforms tree parameters. Hopefully this makes the function look more like a quadratic for the optimizer!

Version:

$Id: LogParameterizedTree.java,v 1.9 2003/06/04 03:17:52 matt Exp $

Author:

Alexei Drummond

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface pal.tree.ParameterizedTree

ParameterizedTree.Factory, ParameterizedTree.ParameterizedTreeBase

Nested classes/interfaces inherited from interface pal.misc.Parameterized

Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils

Nested classes/interfaces inherited from interface pal.tree.Tree

Tree.TreeBase

Field Summary

Fields inherited from interface pal.misc.Units

DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS

Constructor Summary

LogParameterizedTree(ParameterizedTree params)
Takes a parameterized object and transforms the parameters logarithmically.

Method Summary

double	getDefaultValue(int n) get default value of parameter
double	getLowerLimit(int n) get lower parameter limit
int	getNumParameters() get number of parameters
double	getParameter(int n) get model parameter
java.lang.String	getParameterizationInfo()
double	getUpperLimit(int n) get upper parameter limit
void	setParameter(double logParam, int n) set model parameter
void	setParameterSE(double paramSE, int n) set standard errors for model parameter

Methods inherited from class pal.tree.ParameterizedTree.ParameterizedTreeBase

createNodeList, getAttribute, getBaseTree, getCopy, getExternalNode, getExternalNodeCount, getIdCount, getIdentifier, getInternalNode, getInternalNodeCount, getNodeCount, getOrthogonalHints, getRoot, getUnits, setAttribute, setBaseTree, setIdentifier, setRoot, toString, whichIdNumber

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface pal.tree.ParameterizedTree

getOrthogonalHints

Methods inherited from interface pal.tree.Tree

createNodeList, getAttribute, getCopy, getExternalNode, getExternalNodeCount, getInternalNode, getInternalNodeCount, getRoot, getUnits, setAttribute, setRoot

Methods inherited from interface pal.misc.IdGroup

getIdCount, getIdentifier, setIdentifier, whichIdNumber

Constructor Detail

LogParameterizedTree

public LogParameterizedTree(ParameterizedTree params)

Takes a parameterized object and transforms the parameters logarithmically.

Method Detail

getNumParameters

public int getNumParameters()

Description copied from interface: Parameterized

get number of parameters

Specified by:

getNumParameters in interface Parameterized

Returns:

number of parameters

setParameter

public void setParameter(double logParam,
                         int n)

Description copied from interface: Parameterized

set model parameter

Specified by:

setParameter in interface Parameterized

Parameters:

logParam - parameter value

n - parameter number

getParameter

public double getParameter(int n)

Description copied from interface: Parameterized

get model parameter

Specified by:

getParameter in interface Parameterized

Parameters:

n - parameter number

Returns:

parameter value

setParameterSE

public void setParameterSE(double paramSE,
                           int n)

Description copied from interface: Parameterized

set standard errors for model parameter

Specified by:

setParameterSE in interface Parameterized

Parameters:

paramSE - standard error of parameter value

n - parameter number

getLowerLimit

public double getLowerLimit(int n)

Description copied from interface: Parameterized

get lower parameter limit

Specified by:

getLowerLimit in interface Parameterized

Parameters:

n - parameter number

Returns:

lower bound

getUpperLimit

public double getUpperLimit(int n)

Description copied from interface: Parameterized

get upper parameter limit

Specified by:

getUpperLimit in interface Parameterized

Parameters:

n - parameter number

Returns:

upper bound

getDefaultValue

public double getDefaultValue(int n)

Description copied from interface: Parameterized

get default value of parameter

Specified by:

getDefaultValue in interface Parameterized

Parameters:

n - parameter number

Returns:

default value

getParameterizationInfo

public java.lang.String getParameterizationInfo()

Specified by:

getParameterizationInfo in interface ParameterizedTree