java.io.Serializable
, Parameterized
, Report
, Summarizable
, Units
public class ConstExpConst extends ConstExpGrowth implements Report, Parameterized, java.io.Serializable
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
Modifier and Type | Field | Description |
---|---|---|
double |
tx |
time of end of exponential growth
|
double |
txSE |
standard error of time of growth
|
N0, N0SE
alpha, ALPHA_PARAMETERIZATION, alphaSE, LX_PARAMETERIZATION, N1, N1_PARAMETERIZATION, N1SE, parameterization
fo
r, rSE
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS
Constructor | Description |
---|---|
ConstExpConst(double size,
double growth,
double ancestral,
double timeX,
int units,
int parameterization) |
Construct demographic model of constexpconst population.
|
ConstExpConst(int units,
int parameterization) |
Construct demographic model with default settings.
|
Modifier and Type | Method | Description |
---|---|---|
java.lang.Object |
clone() |
Makes a copy of this demographic model.
|
double |
getDefaultValue(int k) |
get default value of parameter
|
double |
getDemographic(double t) |
Gets the value of the demographic function N(t) at time t.
|
double |
getGrowthPhaseDuration() |
|
double |
getIntensity(double t) |
Returns value of demographic intensity function at time t
(= integral 1/N(x) dx from 0 to t).
|
double |
getInverseIntensity(double x) |
Returns value of inverse demographic intensity function
(returns time, needed for simulation of coalescent intervals).
|
double |
getLowerLimit(int k) |
get lower parameter limit
|
int |
getNumParameters() |
get number of parameters
|
double |
getParameter(int k) |
get model parameter
|
double |
getTimeX() |
|
double |
getTransitionTime() |
Gets the time of transition from initial constant phase to exponential phase.
|
double |
getUpperLimit(int k) |
get upper parameter limit
|
static void |
main(java.lang.String[] args) |
|
void |
report(java.io.PrintWriter out) |
print human readable report (e.g., on parameters and associated model)
|
void |
setParameter(double value,
int k) |
set model parameter
|
void |
setParameterSE(double value,
int k) |
set standard errors for model parameter
|
void |
setTimeX(double timeX) |
|
java.lang.String |
toString() |
getN0
calculateRFromLx, getAncestral, getAncestralN0, getGrowthParam, getGrowthRate, getParameterization, isLxParameterized, isN1Parameterized, setAncestral, setGrowthParam, setGrowthPhaseDuration, setParameterization
computeLogLikelihood, computeLogLikelihood, getIntegral, getLogL, getSimulatedInterval, getUnits, setLogL, setUnits, testConsistency
getSummaryTypes, getSummaryValue
public double tx
public double txSE
public ConstExpConst(int units, int parameterization)
public ConstExpConst(double size, double growth, double ancestral, double timeX, int units, int parameterization)
public java.lang.Object clone()
clone
in class ConstExpGrowth
public double getTransitionTime()
getTransitionTime
in class ConstExpGrowth
public double getGrowthPhaseDuration()
getGrowthPhaseDuration
in class ConstExpGrowth
public double getTimeX()
public void setTimeX(double timeX)
public double getDemographic(double t)
DemographicModel
getDemographic
in class ConstExpGrowth
public double getIntensity(double t)
DemographicModel
getIntensity
in class ConstExpGrowth
public double getInverseIntensity(double x)
DemographicModel
getInverseIntensity
in class ConstExpGrowth
public int getNumParameters()
Parameterized
getNumParameters
in interface Parameterized
getNumParameters
in class ConstExpGrowth
public double getParameter(int k)
Parameterized
getParameter
in interface Parameterized
getParameter
in class ConstExpGrowth
k
- parameter numberpublic double getUpperLimit(int k)
Parameterized
getUpperLimit
in interface Parameterized
getUpperLimit
in class ConstExpGrowth
k
- parameter numberpublic double getLowerLimit(int k)
Parameterized
getLowerLimit
in interface Parameterized
getLowerLimit
in class ConstExpGrowth
k
- parameter numberpublic double getDefaultValue(int k)
Parameterized
getDefaultValue
in interface Parameterized
getDefaultValue
in class ConstExpGrowth
k
- parameter numberpublic void setParameter(double value, int k)
Parameterized
setParameter
in interface Parameterized
setParameter
in class ConstExpGrowth
value
- parameter valuek
- parameter numberpublic void setParameterSE(double value, int k)
Parameterized
setParameterSE
in interface Parameterized
setParameterSE
in class ConstExpGrowth
value
- standard error of parameter valuek
- parameter numberpublic java.lang.String toString()
toString
in class ConstExpGrowth
public void report(java.io.PrintWriter out)
Report
report
in interface Report
report
in class ConstExpGrowth
out
- output streampublic static void main(java.lang.String[] args)