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.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

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	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

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	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.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

- 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

Class DemographicClockTree

Nested Class Summary

Nested classes/interfaces inherited from interface pal.misc.IdGroup

Nested classes/interfaces inherited from interface pal.misc.Parameterized

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

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

Field Summary

Fields inherited from class pal.tree.ClockTree

Fields inherited from interface pal.misc.Units

Constructor Summary

Method Summary

Methods inherited from class pal.tree.ClockTree

Methods inherited from class pal.tree.ParameterizedTree.ParameterizedTreeBase

Methods inherited from class java.lang.Object

Methods inherited from interface pal.misc.IdGroup

Methods inherited from interface pal.tree.ParameterizedTree

Methods inherited from interface pal.tree.Tree

Constructor Detail

DemographicClockTree

Method Detail

computeDemoLogLikelihood

getNumParameters

parameters2Heights

heights2parameters

getDemographicModel