pal.mep

Class SteppedMutationRate

java.lang.Object

pal.mep.MutationRateModel

pal.mep.SteppedMutationRate

All Implemented Interfaces:

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

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

This class models a step-wise mutation rate.
parameters:
mus[] = vector of mutation rates
muChanges[] = vector of change times

Drummond, Forsberg and Rodrigo (2001). The inference of step-wise changes in substitution rates using serial sequence samples. accepted in MBE.

Version:

$Id: SteppedMutationRate.java,v 1.13 2004/10/18 03:45:17 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

Modifier and Type	Field and Description
static java.lang.String	INVALID_INTERVALS_TEXT
static java.lang.String	MAX_TIME_IS_TEXT
static java.lang.String	NEGATIVE_VALUES_TEXT
static java.lang.String	REPEATED_TIMES_TEXT
static java.lang.String	ZERO_TIME_TEXT

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

Constructor and Description
SteppedMutationRate(double[] rates, double[] muChanges, int units, boolean fixed, double maximumMutationRate) Construct mutation rate model of a give rate in given units.
SteppedMutationRate(double[] rates, double[] muChanges, int units, double maximumMutationRate) Construct mutation rate model of a give rate in given units.
SteppedMutationRate(double[] muChanges, int units, double maximumMutationRate) Construct demographic model with default settings
SteppedMutationRate(double[] rates, TimeOrderCharacterData timeInfo) Construct mutation rate model of a give rate in given units.
SteppedMutationRate(double[] rates, TimeOrderCharacterData timeInfo, boolean fixed) Construct mutation rate model of a give rate in given units.

Method Summary

Methods

Modifier and Type	Method and Description
static java.lang.String	checkMuChanges(boolean allowEstimationOutsideSamplingTimes, double[] muChanges, boolean sortMuChanges, double[] sampleTimes, boolean sortSampleTimes) Checks if mu changes are valid for a particular set of sample times.
java.lang.Object	clone()
MutationRateModel.Factory	generateFactory()
MutationRateModel	getCopy()
double	getDefaultValue(int k) get default value of parameter
double[]	getDeltas(double[] times)
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 time) Returns integral of mutation rate function (= integral mu(x) dx from 0 to t).
static MutationRateModel.Factory	getFactory(double[] rates, double[] muChanges, int units, double maximumMutationRate) Generate a MutationRateModel.Factory class for a SteppedMutationRate
static MutationRateModel.Factory	getFactory(double[] muChanges, int units, double maximumMutationRate) Generate a MutationRateModel.Factory class for a SteppedMutationRate
static MutationRateModel.Factory	getFactory(double[] muChanges, TimeOrderCharacterData tocd) Generate a MutationRateModel.Factory class for a SteppedMutationRate
double	getLowerLimit(int k) get lower parameter limit
double	getMu() returns current day mutation rate.
double[]	getMuChanges()
double[]	getMus()
void	getMus(double[] muStore)
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)
static double[]	getTimeIntervals(double[] muChanges, double smallTime, double bigTime)
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

Field Detail

REPEATED_TIMES_TEXT

public static final java.lang.String REPEATED_TIMES_TEXT

See Also:

Constant Field Values

NEGATIVE_VALUES_TEXT

public static final java.lang.String NEGATIVE_VALUES_TEXT

See Also:

Constant Field Values

MAX_TIME_IS_TEXT

public static final java.lang.String MAX_TIME_IS_TEXT

See Also:

Constant Field Values

ZERO_TIME_TEXT

public static final java.lang.String ZERO_TIME_TEXT

See Also:

Constant Field Values

INVALID_INTERVALS_TEXT

public static final java.lang.String INVALID_INTERVALS_TEXT

See Also:

Constant Field Values

Constructor Detail

SteppedMutationRate

public SteppedMutationRate(double[] muChanges,
                   int units,
                   double maximumMutationRate)

Construct demographic model with default settings

SteppedMutationRate

public SteppedMutationRate(double[] rates,
                   double[] muChanges,
                   int units,
                   double maximumMutationRate)

Construct mutation rate model of a give rate in given units.

Parameters:

rates - The initial values of the rates (this array is used for storing the rates)

muChanges - The times for when the mutation rate can change

maximumMutationRate - The maximum mutation rate (1 is a good value...)

SteppedMutationRate

public SteppedMutationRate(double[] rates,
                   double[] muChanges,
                   int units,
                   boolean fixed,
                   double maximumMutationRate)

Construct mutation rate model of a give rate in given units.

Parameters:

fixed - if true the mutation rates are set and are not parameters

rates - The initial values of the rates (this array is used for storing the rates)

muChanges - The times for when the mutation rate can change

maximumMutationRate - The maximum mutation rate (related to how much difference there is between samples, max mu*time diff ~= 1 is a good estimate...)

SteppedMutationRate

public SteppedMutationRate(double[] rates,
                   TimeOrderCharacterData timeInfo)

Construct mutation rate model of a give rate in given units.

Parameters:

rates - The initial values of the rates (this array is used for storing the rates)

timeInfo - the sample information object that relates times to sequences. Will extract the mu change information from this input, such that the mutation rate changes at each sample point

SteppedMutationRate

public SteppedMutationRate(double[] rates,
                   TimeOrderCharacterData timeInfo,
                   boolean fixed)

Construct mutation rate model of a give rate in given units.

Parameters:

fixed - if true the mutation rates are set and are not parameters

rates - The initial values of the rates (this array is used for storing the rates)

timeInfo - the sample information object that relates times to sequences. Will extract the mu change information from this input, such that the mutation rate changes at each sample point

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 current day mutation rate.

setMu

public void setMu(double m)

getMus

public void getMus(double[] muStore)

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 time)

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.

getTimeIntervals

public static double[] getTimeIntervals(double[] muChanges,
                        double smallTime,
                        double bigTime)

getDeltas

public double[] getDeltas(double[] times)

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

getMus

public double[] getMus()

getMuChanges

public final double[] getMuChanges()

toSingleLine

public java.lang.String toSingleLine()

Specified by:

toSingleLine in class MutationRateModel

generateFactory

public MutationRateModel.Factory generateFactory()

Specified by:

generateFactory in class MutationRateModel

getFactory

public static final MutationRateModel.Factory getFactory(double[] muChanges,
                                   int units,
                                   double maximumMutationRate)

Generate a MutationRateModel.Factory class for a SteppedMutationRate

getFactory

public static final MutationRateModel.Factory getFactory(double[] rates,
                                   double[] muChanges,
                                   int units,
                                   double maximumMutationRate)

Generate a MutationRateModel.Factory class for a SteppedMutationRate

getFactory

public static final MutationRateModel.Factory getFactory(double[] muChanges,
                                   TimeOrderCharacterData tocd)

Generate a MutationRateModel.Factory class for a SteppedMutationRate

checkMuChanges

public static final java.lang.String checkMuChanges(boolean allowEstimationOutsideSamplingTimes,
                              double[] muChanges,
                              boolean sortMuChanges,
                              double[] sampleTimes,
                              boolean sortSampleTimes)

Checks if mu changes are valid for a particular set of sample times.

Returns:

null if muChanges okay, or a message describing what is wrong. The things that may be a problem are

• There is a negative muChange time
• There is a repeated muChange time
• There are two or more muChange intervals with in a sample interval that do not overlap with another sample interval (this makes it impossible to infer anything between the separate intervals)