Package pal.tree
Class LogParameterizedTree
java.lang.Object
pal.tree.ParameterizedTree.ParameterizedTreeBase
pal.tree.LogParameterizedTree
- All Implemented Interfaces:
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:
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Nested Class Summary
Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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.ParameterizedTree
ParameterizedTree.Factory, ParameterizedTree.ParameterizedTreeBase
Nested classes/interfaces inherited from interface pal.tree.Tree
Tree.TreeBase
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Field Summary
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
ConstructorsConstructorDescriptionTakes a parameterized object and transforms the parameters logarithmically. -
Method Summary
Modifier and TypeMethodDescriptiondouble
getDefaultValue
(int n) get default value of parameterdouble
getLowerLimit
(int n) get lower parameter limitint
get number of parametersdouble
getParameter
(int n) get model parameterdouble
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 parameterMethods 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.misc.IdGroup
getIdCount, getIdentifier, setIdentifier, whichIdNumber
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
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Constructor Details
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LogParameterizedTree
Takes a parameterized object and transforms the parameters logarithmically.
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Method Details
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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
- Specified by:
getParameterizationInfo
in interfaceParameterizedTree
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