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java.lang.Objectpal.tree.ParameterizedTree.ParameterizedTreeBase
pal.tree.ClockTree
public class ClockTree
provides parameter interface to a clock tree (parameters are the minimal node height differences at each internal node)
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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protected double[] |
parameter
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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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ClockTree()
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ClockTree(Tree t)
take any tree and afford it with an interface suitable for a clock-like tree (parameters are the minimal node height differences at each internal node). |
Method Summary | |
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Tree |
getCopy()
The cheapy copy that just creates a SimpleTree |
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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static ParameterizedTree.Factory |
getParameterizedTreeFactory()
Obtain a ParameterizedTree.Factory for generating Clock trees |
double |
getUpperLimit(int n)
get upper parameter limit |
protected void |
heights2parameters()
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protected void |
parameters2Heights()
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void |
setParameter(double param,
int n)
set model parameter |
void |
setParameterSE(double paramSE,
int n)
set standard errors for model parameter |
void |
update()
make clocktree consistent with branch lengths |
Methods inherited from class pal.tree.ParameterizedTree.ParameterizedTreeBase |
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createNodeList, getAttribute, getBaseTree, 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, getExternalNode, getExternalNodeCount, getInternalNode, getInternalNodeCount, getRoot, getUnits, setAttribute, setRoot |
Methods inherited from interface pal.misc.IdGroup |
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getIdCount, getIdentifier, setIdentifier, whichIdNumber |
Field Detail |
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protected double[] parameter
Constructor Detail |
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public ClockTree()
public ClockTree(Tree t)
This parameterisation of a clock-tree, ensuring that all parameters are independent of each other is due to Andrew Rambaut (personal communication).
Method Detail |
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public void update()
public int getNumParameters()
Parameterized
getNumParameters
in interface Parameterized
public void setParameter(double param, int n)
Parameterized
setParameter
in interface Parameterized
param
- 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
protected void parameters2Heights()
protected void heights2parameters()
public Tree getCopy()
ParameterizedTree.ParameterizedTreeBase
getCopy
in interface Tree
getCopy
in class ParameterizedTree.ParameterizedTreeBase
public java.lang.String getParameterizationInfo()
getParameterizationInfo
in interface ParameterizedTree
public static final ParameterizedTree.Factory getParameterizedTreeFactory()
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