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	Description
	`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
`protected`	`ConstantMutationRate(ConstantMutationRate toCopy)`

Method Summary

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

Class ConstantMutationRate

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

Constructor Detail

ConstantMutationRate

ConstantMutationRate

ConstantMutationRate

ConstantMutationRate

Method Detail

clone

getCopy

getSummaryTypes

getSummaryValue

getMu

setMu

getMutationRate

getExpectedSubstitutions

getEndTime

scale

getNumParameters

getParameter

getUpperLimit

getLowerLimit

getDefaultValue

setParameter

setParameterSE

toString

report

toSingleLine

getFixedFactory

getFreeFactory

getFreeFactory

getFreeFactory

generateFactory

createFixed