pal.tree
public class ClockTree extends ParameterizedTree.ParameterizedTreeBase implements ParameterizedTree
ParameterizedTree.Factory, ParameterizedTree.ParameterizedTreeBase
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
Tree.TreeBase
Modifier and Type | Field and Description |
---|---|
protected double[] |
parameter |
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS
Constructor and Description |
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ClockTree() |
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).
|
Modifier and Type | Method and Description |
---|---|
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() |
static ParameterizedTree.Factory |
getParameterizedTreeFactory()
Obtain a ParameterizedTree.Factory for generating Clock trees
|
double |
getUpperLimit(int n)
get upper parameter limit
|
protected void |
heights2parameters() |
protected void |
parameters2Heights() |
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
|
createNodeList, getAttribute, getBaseTree, getExternalNode, getExternalNodeCount, getIdCount, getIdentifier, getInternalNode, getInternalNodeCount, getNodeCount, getOrthogonalHints, getRoot, getUnits, setAttribute, setBaseTree, setIdentifier, setRoot, toString, whichIdNumber
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
getOrthogonalHints
createNodeList, getAttribute, getExternalNode, getExternalNodeCount, getInternalNode, getInternalNodeCount, getRoot, getUnits, setAttribute, setRoot
getIdCount, getIdentifier, setIdentifier, whichIdNumber
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).
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 numberpublic 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 numberpublic double getUpperLimit(int n)
Parameterized
getUpperLimit
in interface Parameterized
n
- parameter numberpublic double getDefaultValue(int n)
Parameterized
getDefaultValue
in interface Parameterized
n
- parameter numberprotected 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()