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.Utils
Nested classes/interfaces inherited from interface pal.misc.Parameterized
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
Nested classes/interfaces inherited from interface pal.tree.ParameterizedTree
ParameterizedTree.Factory, ParameterizedTree.ParameterizedTreeBase
Nested classes/interfaces inherited from interface pal.tree.Tree
Tree.TreeBase
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Field Summary
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
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 TypeMethodDescriptiondouble
Returns 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.int
get number of parametersprotected void
protected void
Methods inherited from class pal.tree.ClockTree
getCopy, getDefaultValue, getLowerLimit, getParameter, getParameterizationInfo, getParameterizedTreeFactory, getUpperLimit, setParameter, setParameterSE, update
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
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
Methods inherited from interface pal.misc.IdGroup
getIdCount, getIdentifier, setIdentifier, whichIdNumber
Methods inherited from interface pal.tree.ParameterizedTree
getOrthogonalHints
Methods 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:
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
Return the demographic model being used to optimize the likelihood of this tree.- Specified by:
getDemographicModel
in interfaceDemographicTree
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