pal.tree
Class MutationRateModelTree

java.lang.Object
  pal.tree.ParameterizedTree.ParameterizedTreeBase
      pal.tree.MutationRateModelTree

All Implemented Interfaces:

java.io.Serializable, OrthogonalHints, IdGroup, Parameterized, Units, UnitsProvider, ParameterizedTree, Tree

public class MutationRateModelTree
extends ParameterizedTree.ParameterizedTreeBase
implements OrthogonalHints, ParameterizedTree

Provides parameter interface to any clock-like tree with serially sampled tips (parameters are the minimal node height differences at each internal node). Any mutation rate model can be used.

Version:

$Id: MutationRateModelTree.java,v 1.19 2003/06/04 03:17:52 matt Exp $

Author:

Alexei Drummond

See Also:

MutationRateModel, Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface pal.math.OrthogonalHints

OrthogonalHints.Utils

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

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

Tree.TreeBase

Field Summary

Fields inherited from interface pal.misc.Units

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

Constructor Summary

protected	MutationRateModelTree(MutationRateModelTree toCopy) Cloning constructor
	MutationRateModelTree(Tree t, TimeOrderCharacterData tocd, MutationRateModel model) take any tree and afford it with an interface suitable for a clock-like tree (parameters are the minimal node height differences at each internal node).
	MutationRateModelTree(Tree t, TimeOrderCharacterData tocd, MutationRateModel model, boolean includeModelParameters) take any tree and afford it with an interface suitable for a clock-like tree (parameters are the minimal node height differences at each internal node).

Method Summary

java.lang.Object	clone()
Tree	getCopy() The cheapy copy that just creates a SimpleTree
double	getDefaultValue(int n) get default value of parameter
int	getInternalParameterBoundaries(int parameter, double[] storage) A boundary is a value of a parameter for which values lower than the boundary and values higher than the boundary are better treated as two separate functions (IE, they are only piecewise connected), and minimisation should be performed over both ranges individually (and then the true minimum taken as the minimuma of the ranges)
double	getLnL()
double	getLowerLimit(int n) Returns lower limit of parameter estimate.
MutationRateModel	getMutationRateModel() returns mu
int	getNumParameters() get number of parameters
OrthogonalHints	getOrthogonalHints()
double	getParameter(int n) get model parameter
java.lang.String	getParameterizationInfo()
static ParameterizedTree.Factory	getParameterizedTreeFactory(MutationRateModel.Factory rateModel, TimeOrderCharacterData tocd) Obtain a ParameterizedTree.Factory for generating Unconstrained trees
OrderEnumerator	getSuggestedOrdering(OrderEnumerator defaultOrdering) If there is a "best" ordering to use it can be specified here, if not should return null
double	getUpperLimit(int n) get upper parameter limit
protected void	heights2parameters()
protected void	parameters2Heights()
void	setLnL(double lnL)
void	setMaxRelativeHeight(double value) Sets the maximum distance between ancestor and latest descendant.
void	setParameter(double param, int n) set model parameter
void	setParameterSE(double paramSE, int n) set standard errors for model parameter

Methods inherited from class pal.tree.ParameterizedTree.ParameterizedTreeBase

createNodeList, getAttribute, getBaseTree, getExternalNode, getExternalNodeCount, getIdCount, getIdentifier, getInternalNode, getInternalNodeCount, getNodeCount, getRoot, getUnits, setAttribute, setBaseTree, setIdentifier, setRoot, toString, whichIdNumber

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

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

MutationRateModelTree

public MutationRateModelTree(Tree t,
                             TimeOrderCharacterData tocd,
                             MutationRateModel model)

take any tree and afford it with an interface suitable for a clock-like tree (parameters are the minimal node height differences at each internal node). Includes model parameters as parameters of tree

This parameterisation of a clock-tree, ensuring that all parameters are independent of each other is due to Andrew Rambaut (personal communication).

MutationRateModelTree

public MutationRateModelTree(Tree t,
                             TimeOrderCharacterData tocd,
                             MutationRateModel model,
                             boolean includeModelParameters)

take any tree and afford it with an interface suitable for a clock-like tree (parameters are the minimal node height differences at each internal node).

This parameterisation of a clock-tree, ensuring that all parameters are independent of each other is due to Andrew Rambaut (personal communication).

MutationRateModelTree

protected MutationRateModelTree(MutationRateModelTree toCopy)

Cloning constructor

Method Detail

setMaxRelativeHeight

public void setMaxRelativeHeight(double value)

Sets the maximum distance between ancestor and latest descendant.

getNumParameters

public int getNumParameters()

Description copied from interface: Parameterized

get number of parameters

Specified by:

getNumParameters in interface Parameterized

Returns:

number of parameters

setParameter

public void setParameter(double param,
                         int n)

Description copied from interface: Parameterized

set model parameter

Specified by:

setParameter in interface Parameterized

Parameters:

param - parameter value

n - parameter number

getParameter

public double getParameter(int n)

Description copied from interface: Parameterized

get model parameter

Specified by:

getParameter in interface Parameterized

Parameters:

n - parameter number

Returns:

parameter value

getLowerLimit

public double getLowerLimit(int n)

Returns lower limit of parameter estimate.

Specified by:

getLowerLimit in interface Parameterized

Parameters:

n - parameter number

Returns:

lower bound

getDefaultValue

public double getDefaultValue(int n)

Description copied from interface: Parameterized

get default value of parameter

Specified by:

getDefaultValue in interface Parameterized

Parameters:

n - parameter number

Returns:

default value

setParameterSE

public void setParameterSE(double paramSE,
                           int n)

Description copied from interface: Parameterized

set standard errors for model parameter

Specified by:

setParameterSE in interface Parameterized

Parameters:

paramSE - standard error of parameter value

n - parameter number

getUpperLimit

public double getUpperLimit(int n)

Description copied from interface: Parameterized

get upper parameter limit

Specified by:

getUpperLimit in interface Parameterized

Parameters:

n - parameter number

Returns:

upper bound

getParameterizationInfo

public java.lang.String getParameterizationInfo()

Specified by:

getParameterizationInfo in interface ParameterizedTree

getMutationRateModel

public MutationRateModel getMutationRateModel()

returns mu

parameters2Heights

protected void parameters2Heights()

heights2parameters

protected void heights2parameters()

setLnL

public void setLnL(double lnL)

getLnL

public double getLnL()

getOrthogonalHints

public OrthogonalHints getOrthogonalHints()

Specified by:

getOrthogonalHints in interface ParameterizedTree

Overrides:

getOrthogonalHints in class ParameterizedTree.ParameterizedTreeBase

Returns:

null by default (implying not hint information)

getSuggestedOrdering

public OrderEnumerator getSuggestedOrdering(OrderEnumerator defaultOrdering)

Description copied from interface: OrthogonalHints

If there is a "best" ordering to use it can be specified here, if not should return null

Specified by:

getSuggestedOrdering in interface OrthogonalHints

Parameters:

defaultOrdering - The ordering suggested by the optimiser, may be null!

Returns:

null, or default ordering if no known best ordering

getInternalParameterBoundaries

public int getInternalParameterBoundaries(int parameter,
                                          double[] storage)

Description copied from interface: OrthogonalHints

A boundary is a value of a parameter for which values lower than the boundary and values higher than the boundary are better treated as two separate functions (IE, they are only piecewise connected), and minimisation should be performed over both ranges individually (and then the true minimum taken as the minimuma of the ranges)

Specified by:

getInternalParameterBoundaries in interface OrthogonalHints

Returns:

the number of boundary locations stored in storage, or -1 if not enough room, or 0 if there are no boundaries (other than the normal parameter range)

getCopy

public Tree getCopy()

Description copied from class: ParameterizedTree.ParameterizedTreeBase

The cheapy copy that just creates a SimpleTree

Specified by:

getCopy in interface Tree

Overrides:

getCopy in class ParameterizedTree.ParameterizedTreeBase

Returns:

a clone of this tree

clone

public java.lang.Object clone()

Overrides:

clone in class java.lang.Object

getParameterizedTreeFactory

public static final ParameterizedTree.Factory getParameterizedTreeFactory(MutationRateModel.Factory rateModel,
                                                                          TimeOrderCharacterData tocd)

Obtain a ParameterizedTree.Factory for generating Unconstrained trees