Package pal.coalescent
Class DemographicClockTree
java.lang.Object
pal.tree.ParameterizedTree.ParameterizedTreeBase
pal.tree.ClockTree
pal.coalescent.DemographicClockTree
- All Implemented Interfaces:
Serializable,DemographicTree,IdGroup,Parameterized,Units,UnitsProvider,ParameterizedTree,Tree
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:
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Nested Class Summary
Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.UtilsNested classes/interfaces inherited from interface pal.misc.Parameterized
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.UtilsNested classes/interfaces inherited from interface pal.tree.ParameterizedTree
ParameterizedTree.Factory, ParameterizedTree.ParameterizedTreeBaseNested classes/interfaces inherited from interface pal.tree.Tree
Tree.TreeBase -
Field Summary
Fields inherited from interface pal.misc.Units
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS -
Constructor Summary
ConstructorsConstructorDescriptionDemographicClockTree(Tree t, DemographicModel model) take any tree and afford it with an interface suitable for a clock-like genealogy, under a certain demographic assumption. -
Method Summary
Modifier and TypeMethodDescriptiondoubleReturns the likelihood of the current demographic model, given the current branch lengths.Return the demographic model being used to optimize the likelihood of this tree.intget number of parametersprotected voidprotected voidMethods inherited from class pal.tree.ClockTree
getCopy, getDefaultValue, getLowerLimit, getParameter, getParameterizationInfo, getParameterizedTreeFactory, getUpperLimit, setParameter, setParameterSE, updateMethods 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, whichIdNumberMethods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, waitMethods inherited from interface pal.misc.IdGroup
getIdCount, getIdentifier, setIdentifier, whichIdNumberMethods inherited from interface pal.tree.ParameterizedTree
getOrthogonalHintsMethods inherited from interface pal.tree.Tree
createNodeList, getAttribute, getExternalNode, getExternalNodeCount, getInternalNode, getInternalNodeCount, getRoot, getUnits, setAttribute, setRoot
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Constructor Details
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DemographicClockTree
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 Details
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computeDemoLogLikelihood
public double computeDemoLogLikelihood()Returns the likelihood of the current demographic model, given the current branch lengths.- Specified by:
computeDemoLogLikelihoodin interfaceDemographicTree
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getNumParameters
public int getNumParameters()Description copied from interface:Parameterizedget number of parameters- Specified by:
getNumParametersin interfaceParameterized- Overrides:
getNumParametersin classClockTree- Returns:
- number of parameters
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parameters2Heights
protected void parameters2Heights()- Overrides:
parameters2Heightsin classClockTree
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heights2parameters
protected void heights2parameters()- Overrides:
heights2parametersin classClockTree
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getDemographicModel
Return the demographic model being used to optimize the likelihood of this tree.- Specified by:
getDemographicModelin interfaceDemographicTree
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