pal.coalescent
public class ExpandingPopulation extends ExponentialGrowth implements Report, Parameterized, java.io.Serializable
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
Modifier and Type | Field and Description |
---|---|
double |
alpha
ratio of pop.
|
double |
alphaSE
standard error of time alpha
|
r, rSE
N0, N0SE
fo
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS
Constructor and Description |
---|
ExpandingPopulation(double size,
double growth,
double ratio,
int units)
Construct demographic model of an expanding population
|
ExpandingPopulation(int units)
Construct demographic model with default settings
|
Modifier and Type | Method and Description |
---|---|
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
|
int |
getNumParameters()
get number of parameters
|
double |
getParameter(int k)
get model parameter
|
double |
getRatio()
returns ratio of population sizes
|
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() |
getGrowthRate, getSummaryTypes, getSummaryValue
getN0
computeLogLikelihood, computeLogLikelihood, getIntegral, getLogL, getSimulatedInterval, getUnits, setLogL, setUnits, testConsistency
public double alpha
public double alphaSE
public ExpandingPopulation(int units)
public ExpandingPopulation(double size, double growth, double ratio, int units)
public java.lang.Object clone()
clone
in class ExponentialGrowth
public double getRatio()
public double getDemographic(double t)
DemographicModel
getDemographic
in class ExponentialGrowth
public double getIntensity(double t)
DemographicModel
getIntensity
in class ExponentialGrowth
public double getInverseIntensity(double x)
DemographicModel
getInverseIntensity
in class ExponentialGrowth
public int getNumParameters()
Parameterized
getNumParameters
in interface Parameterized
getNumParameters
in class ExponentialGrowth
public double getParameter(int k)
Parameterized
getParameter
in interface Parameterized
getParameter
in class ExponentialGrowth
k
- parameter numberpublic double getUpperLimit(int k)
Parameterized
getUpperLimit
in interface Parameterized
getUpperLimit
in class ExponentialGrowth
k
- parameter numberpublic double getLowerLimit(int k)
Parameterized
getLowerLimit
in interface Parameterized
getLowerLimit
in class ExponentialGrowth
k
- parameter numberpublic double getDefaultValue(int k)
Parameterized
getDefaultValue
in interface Parameterized
getDefaultValue
in class ExponentialGrowth
k
- parameter numberpublic void setParameter(double value, int k)
Parameterized
setParameter
in interface Parameterized
setParameter
in class ExponentialGrowth
value
- parameter valuek
- parameter numberpublic void setParameterSE(double value, int k)
Parameterized
setParameterSE
in interface Parameterized
setParameterSE
in class ExponentialGrowth
value
- standard error of parameter valuek
- parameter numberpublic java.lang.String toString()
toString
in class ExponentialGrowth
public void report(java.io.PrintWriter out)
Report
report
in interface Report
report
in class ExponentialGrowth
out
- output stream