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java.lang.Objectpal.mep.MutationRateModel
pal.mep.ConstantMutationRate
public class ConstantMutationRate
This class models a constant mutation rate
(parameter: mu = mutation rate).
Nested Class Summary |
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Nested classes/interfaces inherited from class pal.mep.MutationRateModel |
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MutationRateModel.Factory |
Nested classes/interfaces inherited from interface pal.misc.Parameterized |
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Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils |
Field Summary |
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Fields inherited from class pal.mep.MutationRateModel |
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fo |
Fields inherited from interface pal.misc.Units |
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DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS |
Constructor Summary | |
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protected |
ConstantMutationRate(ConstantMutationRate toCopy)
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ConstantMutationRate(double rate,
int units,
double maximumMutationRate)
Construct mutation rate model of a give rate in given units |
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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 |
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ConstantMutationRate(int units,
double maximumMutationRate)
Construct demographic model with default settings |
Method Summary | |
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java.lang.Object |
clone()
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static ConstantMutationRate |
createFixed(double rate,
int units)
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MutationRateModel.Factory |
generateFactory()
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MutationRateModel |
getCopy()
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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()
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double |
getSummaryValue(int summaryType)
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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)
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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()
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java.lang.String |
toString()
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Methods inherited from class pal.mep.MutationRateModel |
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getExpectedSubstitutions, getMaximumMutationRate, getOrthogonalHints, getTime, getUnits, scale, setUnits |
Methods inherited from class java.lang.Object |
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equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public ConstantMutationRate(int units, double maximumMutationRate)
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 optimisingpublic ConstantMutationRate(double rate, int units, double maximumMutationRate)
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 optimisingpublic ConstantMutationRate(double rate, int units, double minimumMu, double maximumMu)
protected ConstantMutationRate(ConstantMutationRate toCopy)
Method Detail |
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public java.lang.Object clone()
clone
in class MutationRateModel
public MutationRateModel getCopy()
getCopy
in class MutationRateModel
public java.lang.String[] getSummaryTypes()
getSummaryTypes
in interface Summarizable
public double getSummaryValue(int summaryType)
getSummaryValue
in interface Summarizable
public double getMu()
public void setMu(double m)
public final double getMutationRate(double t)
MutationRateModel
getMutationRate
in class MutationRateModel
public final double getExpectedSubstitutions(double t)
MutationRateModel
getExpectedSubstitutions
in class MutationRateModel
public final double getEndTime(double expectedSubs, double startTime)
MutationRateModel
getEndTime
in class MutationRateModel
public final void scale(double scale)
scale
in class MutationRateModel
scale
- getExpectedSubstitutions should return scale instead of 1.0 at time t.public int getNumParameters()
Parameterized
getNumParameters
in interface Parameterized
public double getParameter(int k)
Parameterized
getParameter
in interface Parameterized
k
- parameter number
public double getUpperLimit(int k)
Parameterized
getUpperLimit
in interface Parameterized
k
- parameter number
public double getLowerLimit(int k)
Parameterized
getLowerLimit
in interface Parameterized
k
- parameter number
public double getDefaultValue(int k)
Parameterized
getDefaultValue
in interface Parameterized
k
- parameter number
public void setParameter(double value, int k)
Parameterized
setParameter
in interface Parameterized
value
- parameter valuek
- parameter numberpublic void setParameterSE(double value, int k)
Parameterized
setParameterSE
in interface Parameterized
value
- standard error of parameter valuek
- parameter numberpublic java.lang.String toString()
toString
in class java.lang.Object
public void report(java.io.PrintWriter out)
Report
report
in interface Report
out
- output streampublic java.lang.String toSingleLine()
toSingleLine
in class MutationRateModel
public static final MutationRateModel.Factory getFixedFactory(double rate, int units)
public static final MutationRateModel.Factory getFreeFactory(int units, double maximumMutationRate)
public static final MutationRateModel.Factory getFreeFactory(double initialRate, int units, double maximumMutationRate)
public static final MutationRateModel.Factory getFreeFactory(double initialRate, int units, double minimumRate, double maximumRate)
public MutationRateModel.Factory generateFactory()
generateFactory
in class MutationRateModel
public static final ConstantMutationRate createFixed(double rate, int units)
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