|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object | +--pal.mep.MutationRateModel | +--pal.mep.SteppedMutationRate
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.
Field Summary | |
boolean |
fixedMus
whether or not the mu values are optimizable |
double[] |
muChanges
mutation rate change times |
double[] |
mus
mutation rates |
double[] |
muSEs
mutation rate SEs |
Fields inherited from class pal.mep.MutationRateModel |
fo |
Fields inherited from interface pal.misc.Units |
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, YEARS |
Constructor Summary | |
SteppedMutationRate(double[] rates,
double[] muChanges,
int units)
Construct mutation rate model of a give rate in given units. |
|
SteppedMutationRate(double[] rates,
double[] muChanges,
int units,
boolean fixed)
Construct mutation rate model of a give rate in given units. |
|
SteppedMutationRate(double[] muChanges,
int units)
Construct demographic model with default settings |
Method Summary | |
java.lang.Object |
clone()
|
double |
getDefaultValue(int k)
get default value of parameter |
double[] |
getDeltas(double[] times)
|
double |
getExpectedSubstitutions(double time)
Returns integral of mutation rate function (= integral mu(x) dx from 0 to t). |
double |
getLowerLimit(int k)
get lower parameter limit |
double |
getMu()
returns current day mutation rate. |
double[] |
getMus()
|
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 |
getTime(double expectedSubs)
Return the time at which expected substitutions has occurred. |
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, getUnits, setUnits |
Methods inherited from class java.lang.Object |
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
public double[] mus
public double[] muSEs
public double[] muChanges
public boolean fixedMus
Constructor Detail |
public SteppedMutationRate(double[] muChanges, int units)
public SteppedMutationRate(double[] rates, double[] muChanges, int units)
public SteppedMutationRate(double[] rates, double[] muChanges, int units, boolean fixed)
Method Detail |
public java.lang.Object clone()
clone
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 time)
MutationRateModel
getExpectedSubstitutions
in class MutationRateModel
public final double getTime(double expectedSubs)
MutationRateModel
getTime
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 static double[] getTimeIntervals(double[] muChanges, double smallTime, double bigTime)
public double[] getDeltas(double[] times)
public int getNumParameters()
Parameterized
getNumParameters
in interface Parameterized
pal.misc.Parameterized
public double getParameter(int k)
Parameterized
getParameter
in interface Parameterized
pal.misc.Parameterized
n
- parameter numberpublic double getUpperLimit(int k)
Parameterized
getUpperLimit
in interface Parameterized
pal.misc.Parameterized
n
- parameter numberpublic double getLowerLimit(int k)
Parameterized
getLowerLimit
in interface Parameterized
pal.misc.Parameterized
n
- parameter numberpublic double getDefaultValue(int k)
Parameterized
getDefaultValue
in interface Parameterized
pal.misc.Parameterized
n
- parameter numberpublic void setParameter(double value, int k)
Parameterized
setParameter
in interface Parameterized
pal.misc.Parameterized
param
- parameter valuen
- parameter numberpublic void setParameterSE(double value, int k)
Parameterized
setParameterSE
in interface Parameterized
pal.misc.Parameterized
paramSE
- standard error of parameter valuen
- parameter numberpublic java.lang.String toString()
toString
in class java.lang.Object
public void report(java.io.PrintWriter out)
Report
report
in interface Report
pal.misc.Report
out
- output streampublic double[] getMus()
public java.lang.String toSingleLine()
toSingleLine
in class MutationRateModel
|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |