Package pal.tree
Class LogParameterizedTree
- java.lang.Object
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- pal.tree.ParameterizedTree.ParameterizedTreeBase
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- pal.tree.LogParameterizedTree
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- 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
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Nested Class Summary
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Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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Nested classes/interfaces inherited from interface pal.misc.Parameterized
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
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Nested classes/interfaces inherited from interface pal.tree.ParameterizedTree
ParameterizedTree.Factory, ParameterizedTree.ParameterizedTreeBase
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Nested classes/interfaces inherited from interface pal.tree.Tree
Tree.TreeBase
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Field Summary
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Fields inherited from interface pal.misc.Units
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS
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Constructor Summary
Constructors Constructor Description LogParameterizedTree(ParameterizedTree params)
Takes a parameterized object and transforms the parameters logarithmically.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description double
getDefaultValue(int n)
get default value of parameterdouble
getLowerLimit(int n)
get lower parameter limitint
getNumParameters()
get number of parametersdouble
getParameter(int n)
get model parameterjava.lang.String
getParameterizationInfo()
double
getUpperLimit(int n)
get upper parameter limitvoid
setParameter(double logParam, int n)
set model parametervoid
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
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
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Methods inherited from interface pal.misc.IdGroup
getIdCount, getIdentifier, setIdentifier, whichIdNumber
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Methods inherited from interface pal.tree.ParameterizedTree
getOrthogonalHints
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Methods inherited from interface pal.tree.Tree
createNodeList, getAttribute, getCopy, getExternalNode, getExternalNodeCount, getInternalNode, getInternalNodeCount, getRoot, getUnits, setAttribute, setRoot
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Constructor Detail
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LogParameterizedTree
public LogParameterizedTree(ParameterizedTree params)
Takes a parameterized object and transforms the parameters logarithmically.
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Method Detail
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getNumParameters
public int getNumParameters()
Description copied from interface:Parameterized
get number of parameters- Specified by:
getNumParameters
in interfaceParameterized
- Returns:
- number of parameters
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setParameter
public void setParameter(double logParam, int n)
Description copied from interface:Parameterized
set model parameter- Specified by:
setParameter
in interfaceParameterized
- Parameters:
logParam
- parameter valuen
- parameter number
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getParameter
public double getParameter(int n)
Description copied from interface:Parameterized
get model parameter- Specified by:
getParameter
in interfaceParameterized
- Parameters:
n
- parameter number- Returns:
- parameter value
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setParameterSE
public void setParameterSE(double paramSE, int n)
Description copied from interface:Parameterized
set standard errors for model parameter- Specified by:
setParameterSE
in interfaceParameterized
- Parameters:
paramSE
- standard error of parameter valuen
- parameter number
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getLowerLimit
public double getLowerLimit(int n)
Description copied from interface:Parameterized
get lower parameter limit- Specified by:
getLowerLimit
in interfaceParameterized
- Parameters:
n
- parameter number- Returns:
- lower bound
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getUpperLimit
public double getUpperLimit(int n)
Description copied from interface:Parameterized
get upper parameter limit- Specified by:
getUpperLimit
in interfaceParameterized
- Parameters:
n
- parameter number- Returns:
- upper bound
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getDefaultValue
public double getDefaultValue(int n)
Description copied from interface:Parameterized
get default value of parameter- Specified by:
getDefaultValue
in interfaceParameterized
- Parameters:
n
- parameter number- Returns:
- default value
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getParameterizationInfo
public java.lang.String getParameterizationInfo()
- Specified by:
getParameterizationInfo
in interfaceParameterizedTree
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