pal.coalescent
Class DemographicClockTree
java.lang.Object
pal.tree.ParameterizedTree.ParameterizedTreeBase
pal.tree.ClockTree
pal.coalescent.DemographicClockTree
- 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
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 |
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).
computeDemoLogLikelihood
public double computeDemoLogLikelihood()
- Returns the likelihood of the current demographic model, given
the current branch lengths.
- Specified by:
computeDemoLogLikelihood
in interface DemographicTree
getNumParameters
public int getNumParameters()
- Description copied from interface:
Parameterized
- get number of parameters
- Specified by:
getNumParameters
in interface Parameterized
- Overrides:
getNumParameters
in class ClockTree
- Returns:
- number of parameters
parameters2Heights
protected void parameters2Heights()
- Overrides:
parameters2Heights
in class ClockTree
heights2parameters
protected void heights2parameters()
- Overrides:
heights2parameters
in class ClockTree
getDemographicModel
public DemographicModel getDemographicModel()
- Return the demographic model being used to optimize the
likelihood of this tree.
- Specified by:
getDemographicModel
in interface DemographicTree