public class DemographicClockTree extends ClockTree implements DemographicTree
ParameterizedTree.Factory, ParameterizedTree.ParameterizedTreeBase
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
Tree.TreeBase
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS
Constructor and Description |
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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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Modifier and Type | Method and Description |
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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 parameters
|
protected void |
heights2parameters() |
protected void |
parameters2Heights() |
getCopy, getDefaultValue, getLowerLimit, getParameter, getParameterizationInfo, getParameterizedTreeFactory, getUpperLimit, setParameter, setParameterSE, update
createNodeList, getAttribute, getBaseTree, getExternalNode, getExternalNodeCount, getIdCount, getIdentifier, getInternalNode, getInternalNodeCount, getNodeCount, getOrthogonalHints, getRoot, getUnits, setAttribute, setBaseTree, setIdentifier, setRoot, toString, whichIdNumber
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
getOrthogonalHints
createNodeList, getAttribute, getExternalNode, getExternalNodeCount, getInternalNode, getInternalNodeCount, getRoot, getUnits, setAttribute, setRoot
getIdCount, getIdentifier, setIdentifier, whichIdNumber
public DemographicClockTree(Tree t, DemographicModel model)
This parameterisation of branches, ensuring that all parameters are independent of each other is due to Andrew Rambaut (personal communication).
public double computeDemoLogLikelihood()
computeDemoLogLikelihood
in interface DemographicTree
public int getNumParameters()
Parameterized
getNumParameters
in interface Parameterized
getNumParameters
in class ClockTree
protected void parameters2Heights()
parameters2Heights
in class ClockTree
protected void heights2parameters()
heights2parameters
in class ClockTree
public DemographicModel getDemographicModel()
getDemographicModel
in interface DemographicTree