|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object | +--pal.mep.MutationRateModel | +--pal.mep.WindowedMutationRate
This class models a windowed mutation rate
(parameter: mu = mutation rate).
Field Summary | |
boolean |
backgroundFixed
|
double |
muBackground
mutation rates |
double |
muBackgroundSE
mutation rate SEs |
double |
muWindow
|
double |
muWindowSE
|
double |
windowCenter
mutation rate change times |
double |
windowWidth
|
Fields inherited from class pal.mep.MutationRateModel |
fo |
Fields inherited from interface pal.misc.Units |
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, YEARS |
Constructor Summary | |
WindowedMutationRate(double muWindow,
double muBackground,
double windowCenter,
double windowWidth,
int units)
Construct mutation rate model of a give rate in given units. |
|
WindowedMutationRate(double muWindow,
double muBackground,
double windowCenter,
double windowWidth,
int units,
boolean fixedb)
Construct mutation rate model of a give rate in given units. |
|
WindowedMutationRate(double muBackground,
double windowCenter,
double windowWidth,
int units)
Construct mutation rate model of a give rate in given units. |
|
WindowedMutationRate(double windowCenter,
double windowWidth,
int units)
Construct demographic model with default settings |
Method Summary | |
java.lang.Object |
clone()
|
double |
getDefaultValue(int k)
get default value of parameter |
double |
getExpectedSubstitutions(double time)
Window must not span zero! |
double |
getLowerLimit(int k)
get lower parameter limit |
double |
getMu()
returns current day mutation rate. |
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 expected)
Window must not span zero! |
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 |
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 muBackground
public double muWindow
public double muBackgroundSE
public double muWindowSE
public double windowCenter
public double windowWidth
public boolean backgroundFixed
Constructor Detail |
public WindowedMutationRate(double windowCenter, double windowWidth, int units)
public WindowedMutationRate(double muBackground, double windowCenter, double windowWidth, int units)
public WindowedMutationRate(double muWindow, double muBackground, double windowCenter, double windowWidth, int units, boolean fixedb)
public WindowedMutationRate(double muWindow, double muBackground, double windowCenter, double windowWidth, int units)
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 final double getMutationRate(double t)
MutationRateModel
getMutationRate
in class MutationRateModel
public final double getExpectedSubstitutions(double time)
getExpectedSubstitutions
in class MutationRateModel
public final double getTime(double expected)
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 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 java.lang.String toSingleLine()
toSingleLine
in class MutationRateModel
|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |