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	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	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

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	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)

Class SteppedMutationRate

Nested Class Summary

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

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

Field Summary

Fields inherited from class pal.mep.MutationRateModel

Fields inherited from interface pal.misc.Units

Constructor Summary

Method Summary

Methods inherited from class pal.mep.MutationRateModel

Methods inherited from class java.lang.Object

Field Detail

REPEATED_TIMES_TEXT

NEGATIVE_VALUES_TEXT

MAX_TIME_IS_TEXT

ZERO_TIME_TEXT

INVALID_INTERVALS_TEXT

Constructor Detail

SteppedMutationRate

SteppedMutationRate

SteppedMutationRate

SteppedMutationRate

SteppedMutationRate

Method Detail

clone

getCopy

getSummaryTypes

getSummaryValue

getMu

setMu

getMus

getMutationRate

getExpectedSubstitutions

getEndTime

scale

getTimeIntervals

getDeltas

getNumParameters

getParameter

getUpperLimit

getLowerLimit

getDefaultValue

setParameter

setParameterSE

toString

report

getMus

getMuChanges

toSingleLine

generateFactory

getFactory

getFactory

getFactory

checkMuChanges