Package pal.coalescent
Class DemographicClockTree
- java.lang.Object
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- pal.tree.ParameterizedTree.ParameterizedTreeBase
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- pal.tree.ClockTree
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- pal.coalescent.DemographicClockTree
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- All Implemented Interfaces:
java.io.Serializable
,DemographicTree
,IdGroup
,Parameterized
,Units
,UnitsProvider
,ParameterizedTree
,Tree
public class DemographicClockTree extends ClockTree implements DemographicTree
Provides parameter interface to a clock-like genealogy which is assumed to have some demographic pattern of theta (diversity) as well as branch parameters (the minimal node height differences at each internal node). Must be used in conjunction with DemographicLikelihoodFunction!- Author:
- Alexei Drummond
- See Also:
- Serialized Form
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Nested Class Summary
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Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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Nested classes/interfaces inherited from interface pal.misc.Parameterized
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
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Nested classes/interfaces inherited from interface pal.tree.ParameterizedTree
ParameterizedTree.Factory, ParameterizedTree.ParameterizedTreeBase
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Nested classes/interfaces inherited from interface pal.tree.Tree
Tree.TreeBase
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Field Summary
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Fields inherited from interface pal.misc.Units
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS
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Constructor Summary
Constructors Constructor Description DemographicClockTree(Tree t, DemographicModel model)
take any tree and afford it with an interface suitable for a clock-like genealogy, under a certain demographic assumption.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description double
computeDemoLogLikelihood()
Returns the likelihood of the current demographic model, given the current branch lengths.DemographicModel
getDemographicModel()
Return the demographic model being used to optimize the likelihood of this tree.int
getNumParameters()
get number of parametersprotected void
heights2parameters()
protected void
parameters2Heights()
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Methods inherited from class pal.tree.ClockTree
getCopy, getDefaultValue, getLowerLimit, getParameter, getParameterizationInfo, getParameterizedTreeFactory, getUpperLimit, setParameter, setParameterSE, update
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Methods inherited from class pal.tree.ParameterizedTree.ParameterizedTreeBase
createNodeList, getAttribute, getBaseTree, getExternalNode, getExternalNodeCount, getIdCount, getIdentifier, getInternalNode, getInternalNodeCount, getNodeCount, getOrthogonalHints, getRoot, getUnits, setAttribute, setBaseTree, setIdentifier, setRoot, toString, whichIdNumber
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
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Methods inherited from interface pal.misc.IdGroup
getIdCount, getIdentifier, setIdentifier, whichIdNumber
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Methods inherited from interface pal.tree.ParameterizedTree
getOrthogonalHints
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Methods inherited from interface pal.tree.Tree
createNodeList, getAttribute, getExternalNode, getExternalNodeCount, getInternalNode, getInternalNodeCount, getRoot, getUnits, setAttribute, setRoot
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Constructor Detail
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DemographicClockTree
public DemographicClockTree(Tree t, DemographicModel model)
take any tree and afford it with an interface suitable for a clock-like genealogy, under a certain demographic assumption.This parameterisation of branches, ensuring that all parameters are independent of each other is due to Andrew Rambaut (personal communication).
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Method Detail
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computeDemoLogLikelihood
public double computeDemoLogLikelihood()
Returns the likelihood of the current demographic model, given the current branch lengths.- Specified by:
computeDemoLogLikelihood
in interfaceDemographicTree
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getNumParameters
public int getNumParameters()
Description copied from interface:Parameterized
get number of parameters- Specified by:
getNumParameters
in interfaceParameterized
- Overrides:
getNumParameters
in classClockTree
- Returns:
- number of parameters
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parameters2Heights
protected void parameters2Heights()
- Overrides:
parameters2Heights
in classClockTree
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heights2parameters
protected void heights2parameters()
- Overrides:
heights2parameters
in classClockTree
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getDemographicModel
public DemographicModel getDemographicModel()
Return the demographic model being used to optimize the likelihood of this tree.- Specified by:
getDemographicModel
in interfaceDemographicTree
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