pal.mep

Class ConstantMutationRate

java.lang.Object

pal.mep.MutationRateModel

pal.mep.ConstantMutationRate

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, Parameterized, Report, Summarizable, Units

public class ConstantMutationRate
extends MutationRateModel
implements Report, Summarizable, Parameterized, java.io.Serializable

This class models a constant mutation rate (parameter: mu = mutation rate).

Version:

$Id: ConstantMutationRate.java,v 1.13 2004/08/02 05:22:04 matt Exp $

Author:

Alexei Drummond

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class pal.mep.MutationRateModel

MutationRateModel.Factory

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

Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils

Field Summary

Fields inherited from class pal.mep.MutationRateModel

fo

Fields inherited from interface pal.misc.Units

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

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	ConstantMutationRate(ConstantMutationRate toCopy)
	ConstantMutationRate(double rate, int units, double maximumMutationRate) Construct mutation rate model of a give rate in given units
	ConstantMutationRate(double rate, int units, double minimumMu, double maximumMu) Construct mutation rate model of a give rate in given units, with a given range of possible values
	ConstantMutationRate(int units, double maximumMutationRate) Construct demographic model with default settings

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.Object	clone()
static ConstantMutationRate	createFixed(double rate, int units)
MutationRateModel.Factory	generateFactory()
MutationRateModel	getCopy()
double	getDefaultValue(int k) get default value of parameter
double	getEndTime(double expectedSubs, double startTime) Return the end time at which expected substitutions has occurred, given we start at start time
double	getExpectedSubstitutions(double t) Returns integral of mutation rate function (= integral mu(x) dx from 0 to t).
static MutationRateModel.Factory	getFixedFactory(double rate, int units) Generate a MutationRateModel.Factory class for a ConstantMutationRate
static MutationRateModel.Factory	getFreeFactory(double initialRate, int units, double maximumMutationRate) Generate a MutationRateModel.Factory class for a ConstantMutationRate
static MutationRateModel.Factory	getFreeFactory(double initialRate, int units, double minimumRate, double maximumRate) Generate a MutationRateModel.Factory class for a ConstantMutationRate
static MutationRateModel.Factory	getFreeFactory(int units, double maximumMutationRate) Generate a MutationRateModel.Factory class for a ConstantMutationRate
double	getLowerLimit(int k) get lower parameter limit
double	getMu() returns initial population size.
double	getMutationRate(double t) Gets the mutation rate, value of mu(t) at time t.
int	getNumParameters() get number of parameters
double	getParameter(int k) get model parameter
java.lang.String[]	getSummaryTypes()
double	getSummaryValue(int summaryType)
double	getUpperLimit(int k) get upper parameter limit
void	report(java.io.PrintWriter out) print human readable report (e.g., on parameters and associated model)
void	scale(double scale) Linearly scales this mutation rate model.
void	setMu(double m)
void	setParameter(double value, int k) set model parameter
void	setParameterSE(double value, int k) set standard errors for model parameter
java.lang.String	toSingleLine()
java.lang.String	toString()

Methods inherited from class pal.mep.MutationRateModel

getExpectedSubstitutions, getMaximumMutationRate, getOrthogonalHints, getTime, getUnits, scale, setUnits

Methods inherited from class java.lang.Object

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

Constructor Detail

ConstantMutationRate

public ConstantMutationRate(int units,
                    double maximumMutationRate)

Construct demographic model with default settings

Parameters:

maximumMutationRate - The maximum Mutation rate should be selected wisely - too small and it might not include the "true" rate, too high and the optimisers may have trouble optimising

ConstantMutationRate

public ConstantMutationRate(double rate,
                    int units,
                    double maximumMutationRate)

Construct mutation rate model of a give rate in given units

Parameters:

maximumMutationRate - The maximum Mutation rate should be selected wisely - too small and it might not include the "true" rate, too high and the optimisers may have trouble optimising

ConstantMutationRate

public ConstantMutationRate(double rate,
                    int units,
                    double minimumMu,
                    double maximumMu)

Construct mutation rate model of a give rate in given units, with a given range of possible values

ConstantMutationRate

protected ConstantMutationRate(ConstantMutationRate toCopy)

Method Detail

clone

public java.lang.Object clone()

Specified by:

clone in class MutationRateModel

getCopy

public MutationRateModel getCopy()

Specified by:

getCopy in class MutationRateModel

getSummaryTypes

public java.lang.String[] getSummaryTypes()

Specified by:

getSummaryTypes in interface Summarizable

getSummaryValue

public double getSummaryValue(int summaryType)

Specified by:

getSummaryValue in interface Summarizable

getMu

public double getMu()

returns initial population size.

setMu

public void setMu(double m)

getMutationRate

public final double getMutationRate(double t)

Description copied from class: MutationRateModel

Gets the mutation rate, value of mu(t) at time t.

Specified by:

getMutationRate in class MutationRateModel

getExpectedSubstitutions

public final double getExpectedSubstitutions(double t)

Description copied from class: MutationRateModel

Returns integral of mutation rate function (= integral mu(x) dx from 0 to t).

Specified by:

getExpectedSubstitutions in class MutationRateModel

getEndTime

public final double getEndTime(double expectedSubs,
                double startTime)

Description copied from class: MutationRateModel

Return the end time at which expected substitutions has occurred, given we start at start time

Specified by:

getEndTime in class MutationRateModel

scale

public final void scale(double scale)

Linearly scales this mutation rate model.

Specified by:

scale in class MutationRateModel

Parameters:

scale - getExpectedSubstitutions should return scale instead of 1.0 at time t.

getNumParameters

public int getNumParameters()

Description copied from interface: Parameterized

get number of parameters

Specified by:

getNumParameters in interface Parameterized

Returns:

number of parameters

getParameter

public double getParameter(int k)

Description copied from interface: Parameterized

get model parameter

Specified by:

getParameter in interface Parameterized

Parameters:

k - parameter number

Returns:

parameter value

getUpperLimit

public double getUpperLimit(int k)

Description copied from interface: Parameterized

get upper parameter limit

Specified by:

getUpperLimit in interface Parameterized

Parameters:

k - parameter number

Returns:

upper bound

getLowerLimit

public double getLowerLimit(int k)

Description copied from interface: Parameterized

get lower parameter limit

Specified by:

getLowerLimit in interface Parameterized

Parameters:

k - parameter number

Returns:

lower bound

getDefaultValue

public double getDefaultValue(int k)

Description copied from interface: Parameterized

get default value of parameter

Specified by:

getDefaultValue in interface Parameterized

Parameters:

k - parameter number

Returns:

default value

setParameter

public void setParameter(double value,
                int k)

Description copied from interface: Parameterized

set model parameter

Specified by:

setParameter in interface Parameterized

Parameters:

value - parameter value

k - parameter number

setParameterSE

public void setParameterSE(double value,
                  int k)

Description copied from interface: Parameterized

set standard errors for model parameter

Specified by:

setParameterSE in interface Parameterized

Parameters:

value - standard error of parameter value

k - parameter number

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

report

public void report(java.io.PrintWriter out)

Description copied from interface: Report

print human readable report (e.g., on parameters and associated model)

Specified by:

report in interface Report

Parameters:

out - output stream

toSingleLine

public java.lang.String toSingleLine()

Specified by:

toSingleLine in class MutationRateModel

getFixedFactory

public static final MutationRateModel.Factory getFixedFactory(double rate,
                                        int units)

Generate a MutationRateModel.Factory class for a ConstantMutationRate

getFreeFactory

public static final MutationRateModel.Factory getFreeFactory(int units,
                                       double maximumMutationRate)

Generate a MutationRateModel.Factory class for a ConstantMutationRate

getFreeFactory

public static final MutationRateModel.Factory getFreeFactory(double initialRate,
                                       int units,
                                       double maximumMutationRate)

Generate a MutationRateModel.Factory class for a ConstantMutationRate

getFreeFactory

public static final MutationRateModel.Factory getFreeFactory(double initialRate,
                                       int units,
                                       double minimumRate,
                                       double maximumRate)

Generate a MutationRateModel.Factory class for a ConstantMutationRate

generateFactory

public MutationRateModel.Factory generateFactory()

Specified by:

generateFactory in class MutationRateModel

createFixed

public static final ConstantMutationRate createFixed(double rate,
                               int units)

Returns:

A ConstantMutationRate with a fixed rate (no parameters)