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java.lang.Objectpal.tree.ParameterizedTree.ParameterizedTreeBase
pal.tree.MutationRateModelTree
public class MutationRateModelTree
Provides parameter interface to any clock-like tree with serially sampled tips (parameters are the minimal node height differences at each internal node). Any mutation rate model can be used.
MutationRateModel
,
Serialized FormNested Class Summary |
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Nested classes/interfaces inherited from interface pal.math.OrthogonalHints |
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OrthogonalHints.Utils |
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 |
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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protected |
MutationRateModelTree(MutationRateModelTree toCopy)
Cloning constructor |
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MutationRateModelTree(Tree t,
TimeOrderCharacterData tocd,
MutationRateModel model)
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). |
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MutationRateModelTree(Tree t,
TimeOrderCharacterData tocd,
MutationRateModel model,
boolean includeModelParameters)
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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java.lang.Object |
clone()
|
Tree |
getCopy()
The cheapy copy that just creates a SimpleTree |
double |
getDefaultValue(int n)
get default value of parameter |
int |
getInternalParameterBoundaries(int parameter,
double[] storage)
A boundary is a value of a parameter for which values lower than the boundary and values higher than the boundary are better treated as two separate functions (IE, they are only piecewise connected), and minimisation should be performed over both ranges individually (and then the true minimum taken as the minimuma of the ranges) |
double |
getLnL()
|
double |
getLowerLimit(int n)
Returns lower limit of parameter estimate. |
MutationRateModel |
getMutationRateModel()
returns mu |
int |
getNumParameters()
get number of parameters |
OrthogonalHints |
getOrthogonalHints()
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double |
getParameter(int n)
get model parameter |
java.lang.String |
getParameterizationInfo()
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static ParameterizedTree.Factory |
getParameterizedTreeFactory(MutationRateModel.Factory rateModel,
TimeOrderCharacterData tocd)
Obtain a ParameterizedTree.Factory for generating Unconstrained trees |
OrderEnumerator |
getSuggestedOrdering(OrderEnumerator defaultOrdering)
If there is a "best" ordering to use it can be specified here, if not should return null |
double |
getUpperLimit(int n)
get upper parameter limit |
protected void |
heights2parameters()
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protected void |
parameters2Heights()
|
void |
setLnL(double lnL)
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void |
setMaxRelativeHeight(double value)
Sets the maximum distance between ancestor and latest descendant. |
void |
setParameter(double param,
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, getExternalNode, getExternalNodeCount, getIdCount, getIdentifier, getInternalNode, getInternalNodeCount, getNodeCount, getRoot, getUnits, setAttribute, setBaseTree, setIdentifier, setRoot, toString, whichIdNumber |
Methods inherited from class java.lang.Object |
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equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
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 |
Constructor Detail |
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public MutationRateModelTree(Tree t, TimeOrderCharacterData tocd, MutationRateModel model)
This parameterisation of a clock-tree, ensuring that all parameters are independent of each other is due to Andrew Rambaut (personal communication).
public MutationRateModelTree(Tree t, TimeOrderCharacterData tocd, MutationRateModel model, boolean includeModelParameters)
This parameterisation of a clock-tree, ensuring that all parameters are independent of each other is due to Andrew Rambaut (personal communication).
protected MutationRateModelTree(MutationRateModelTree toCopy)
Method Detail |
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public void setMaxRelativeHeight(double value)
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 double getLowerLimit(int n)
getLowerLimit
in interface Parameterized
n
- parameter number
public double getDefaultValue(int n)
Parameterized
getDefaultValue
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 getUpperLimit(int n)
Parameterized
getUpperLimit
in interface Parameterized
n
- parameter number
public java.lang.String getParameterizationInfo()
getParameterizationInfo
in interface ParameterizedTree
public MutationRateModel getMutationRateModel()
protected void parameters2Heights()
protected void heights2parameters()
public void setLnL(double lnL)
public double getLnL()
public OrthogonalHints getOrthogonalHints()
getOrthogonalHints
in interface ParameterizedTree
getOrthogonalHints
in class ParameterizedTree.ParameterizedTreeBase
public OrderEnumerator getSuggestedOrdering(OrderEnumerator defaultOrdering)
OrthogonalHints
getSuggestedOrdering
in interface OrthogonalHints
defaultOrdering
- The ordering suggested by the optimiser, may be null!
public int getInternalParameterBoundaries(int parameter, double[] storage)
OrthogonalHints
getInternalParameterBoundaries
in interface OrthogonalHints
public Tree getCopy()
ParameterizedTree.ParameterizedTreeBase
getCopy
in interface Tree
getCopy
in class ParameterizedTree.ParameterizedTreeBase
public java.lang.Object clone()
clone
in class java.lang.Object
public static final ParameterizedTree.Factory getParameterizedTreeFactory(MutationRateModel.Factory rateModel, TimeOrderCharacterData tocd)
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