public class MutationRateModelTree extends ParameterizedTree.ParameterizedTreeBase implements OrthogonalHints, ParameterizedTree
MutationRateModel,
Serialized FormOrthogonalHints.UtilsParameterizedTree.Factory, ParameterizedTree.ParameterizedTreeBaseParameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUserTree.TreeBaseDAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS| Modifier | Constructor and Description |
|---|---|
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).
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| Modifier and Type | Method and Description |
|---|---|
java.lang.Object |
clone() |
Tree |
getCopy()
The cheapy copy that just creates a SimpleTree
|
double |
getDefaultValue(int n)
get default value of parameter
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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
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int |
getNumParameters()
get number of parameters
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OrthogonalHints |
getOrthogonalHints() |
double |
getParameter(int n)
get model parameter
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java.lang.String |
getParameterizationInfo() |
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
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double |
getUpperLimit(int n)
get upper parameter limit
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protected void |
heights2parameters() |
protected void |
parameters2Heights() |
void |
setLnL(double lnL) |
void |
setMaxRelativeHeight(double value)
Sets the maximum distance between ancestor and latest descendant.
|
void |
setParameter(double param,
int n)
set model parameter
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void |
setParameterSE(double paramSE,
int n)
set standard errors for model parameter
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createNodeList, getAttribute, getBaseTree, getExternalNode, getExternalNodeCount, getIdCount, getIdentifier, getInternalNode, getInternalNodeCount, getNodeCount, getRoot, getUnits, setAttribute, setBaseTree, setIdentifier, setRoot, toString, whichIdNumberequals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, waitcreateNodeList, getAttribute, getExternalNode, getExternalNodeCount, getInternalNode, getInternalNodeCount, getRoot, getUnits, setAttribute, setRootgetIdCount, getIdentifier, setIdentifier, whichIdNumberpublic 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)
public void setMaxRelativeHeight(double value)
public int getNumParameters()
ParameterizedgetNumParameters in interface Parameterizedpublic void setParameter(double param,
int n)
ParameterizedsetParameter in interface Parameterizedparam - parameter valuen - parameter numberpublic double getParameter(int n)
ParameterizedgetParameter in interface Parameterizedn - parameter numberpublic double getLowerLimit(int n)
getLowerLimit in interface Parameterizedn - parameter numberpublic double getDefaultValue(int n)
ParameterizedgetDefaultValue in interface Parameterizedn - parameter numberpublic void setParameterSE(double paramSE,
int n)
ParameterizedsetParameterSE in interface ParameterizedparamSE - standard error of parameter valuen - parameter numberpublic double getUpperLimit(int n)
ParameterizedgetUpperLimit in interface Parameterizedn - parameter numberpublic java.lang.String getParameterizationInfo()
getParameterizationInfo in interface ParameterizedTreepublic MutationRateModel getMutationRateModel()
protected void parameters2Heights()
protected void heights2parameters()
public void setLnL(double lnL)
public double getLnL()
public OrthogonalHints getOrthogonalHints()
getOrthogonalHints in interface ParameterizedTreegetOrthogonalHints in class ParameterizedTree.ParameterizedTreeBasepublic OrderEnumerator getSuggestedOrdering(OrderEnumerator defaultOrdering)
OrthogonalHintsgetSuggestedOrdering in interface OrthogonalHintsdefaultOrdering - The ordering suggested by the optimiser, may be null!public int getInternalParameterBoundaries(int parameter,
double[] storage)
OrthogonalHintsgetInternalParameterBoundaries in interface OrthogonalHintspublic Tree getCopy()
ParameterizedTree.ParameterizedTreeBasegetCopy in interface TreegetCopy in class ParameterizedTree.ParameterizedTreeBasepublic java.lang.Object clone()
clone in class java.lang.Objectpublic static final ParameterizedTree.Factory getParameterizedTreeFactory(MutationRateModel.Factory rateModel, TimeOrderCharacterData tocd)