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java.lang.Objectpal.tree.ParameterizedTree.ParameterizedTreeBase
pal.tree.LogParameterizedTree
public class LogParameterizedTree
This class logarithmically transforms tree parameters. Hopefully this makes the function look more like a quadratic for the optimizer!
Nested Class Summary |
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Nested classes/interfaces inherited from interface pal.tree.ParameterizedTree |
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ParameterizedTree.Factory, ParameterizedTree.ParameterizedTreeBase |
Nested classes/interfaces inherited from interface pal.misc.Parameterized |
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Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils |
Nested classes/interfaces inherited from interface pal.tree.Tree |
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Tree.TreeBase |
Field Summary |
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Fields inherited from interface pal.misc.Units |
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DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS |
Constructor Summary | |
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LogParameterizedTree(ParameterizedTree params)
Takes a parameterized object and transforms the parameters logarithmically. |
Method Summary | |
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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()
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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 |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface pal.tree.ParameterizedTree |
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getOrthogonalHints |
Methods inherited from interface pal.tree.Tree |
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createNodeList, getAttribute, getCopy, getExternalNode, getExternalNodeCount, getInternalNode, getInternalNodeCount, getRoot, getUnits, setAttribute, setRoot |
Methods inherited from interface pal.misc.IdGroup |
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getIdCount, getIdentifier, setIdentifier, whichIdNumber |
Constructor Detail |
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public LogParameterizedTree(ParameterizedTree params)
Method Detail |
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public int getNumParameters()
Parameterized
getNumParameters
in interface Parameterized
public void setParameter(double logParam, int n)
Parameterized
setParameter
in interface Parameterized
logParam
- parameter valuen
- parameter numberpublic double getParameter(int n)
Parameterized
getParameter
in interface Parameterized
n
- parameter number
public void setParameterSE(double paramSE, int n)
Parameterized
setParameterSE
in interface Parameterized
paramSE
- standard error of parameter valuen
- parameter numberpublic double getLowerLimit(int n)
Parameterized
getLowerLimit
in interface Parameterized
n
- parameter number
public double getUpperLimit(int n)
Parameterized
getUpperLimit
in interface Parameterized
n
- parameter number
public double getDefaultValue(int n)
Parameterized
getDefaultValue
in interface Parameterized
n
- parameter number
public java.lang.String getParameterizationInfo()
getParameterizationInfo
in interface ParameterizedTree
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