public class ConstantPopulation extends DemographicModel implements Report, Summarizable, Parameterized, java.io.Serializable
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
Modifier and Type | Field and Description |
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double |
N0
population size
|
double |
N0SE
standard error of population size
|
fo
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS
Constructor and Description |
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ConstantPopulation(double size,
int units)
Construct demographic model of a constant population size.
|
ConstantPopulation(int units)
Construct demographic model with default settings
|
Modifier and Type | Method and Description |
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java.lang.Object |
clone() |
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 |
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
|
double |
getN0()
returns initial population size.
|
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 |
setParameter(double value,
int k)
set model parameter
|
void |
setParameterSE(double value,
int k)
set standard errors for model parameter
|
java.lang.String |
toString() |
computeLogLikelihood, computeLogLikelihood, getIntegral, getLogL, getSimulatedInterval, getUnits, setLogL, setUnits, testConsistency
public double N0
public double N0SE
public ConstantPopulation(int units)
public ConstantPopulation(double size, int units)
public java.lang.Object clone()
clone
in class DemographicModel
public java.lang.String[] getSummaryTypes()
getSummaryTypes
in interface Summarizable
public double getSummaryValue(int summaryType)
getSummaryValue
in interface Summarizable
public double getN0()
public double getDemographic(double t)
DemographicModel
getDemographic
in class DemographicModel
public double getIntensity(double t)
DemographicModel
getIntensity
in class DemographicModel
public double getInverseIntensity(double x)
DemographicModel
getInverseIntensity
in class DemographicModel
public int getNumParameters()
Parameterized
getNumParameters
in interface Parameterized
public double getParameter(int k)
Parameterized
getParameter
in interface Parameterized
k
- parameter numberpublic double getUpperLimit(int k)
Parameterized
getUpperLimit
in interface Parameterized
k
- parameter numberpublic double getLowerLimit(int k)
Parameterized
getLowerLimit
in interface Parameterized
k
- parameter numberpublic double getDefaultValue(int k)
Parameterized
getDefaultValue
in interface Parameterized
k
- parameter numberpublic 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