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

Nested Class Summary

Nested classes/interfaces inherited from interface pal.tree.ParameterizedTree

ParameterizedTree.Factory, ParameterizedTree.ParameterizedTreeBase

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.Tree

Tree.TreeBase

Field Summary

Fields inherited from class pal.tree.ClockTree

parameter

Fields inherited from interface pal.misc.Units

DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS

Constructor Summary

Constructors

Constructor and 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.

Method Summary

Methods

Modifier and Type	Method and 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 parameters
protected void	heights2parameters()
protected void	parameters2Heights()

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.tree.ParameterizedTree

getOrthogonalHints

Methods inherited from interface pal.tree.Tree

createNodeList, getAttribute, getExternalNode, getExternalNodeCount, getInternalNode, getInternalNodeCount, getRoot, getUnits, setAttribute, setRoot

Methods inherited from interface pal.misc.IdGroup

getIdCount, getIdentifier, setIdentifier, whichIdNumber

Constructor Detail

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).

Method Detail

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