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java.lang.Objectpal.coalescent.DemographicModel
pal.coalescent.ConstantPopulation
pal.coalescent.ExponentialGrowth
public class ExponentialGrowth
This class models an exponentially growing (or shrinking) population (Parameters: N0=present-day population size; r=growth rate). This model is nested with the constant-population size model (r=0). Parts of this class were inspired by C++ code generously provided by Oliver Pybus.
Nested Class Summary |
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Nested classes/interfaces inherited from interface pal.misc.Parameterized |
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Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils |
Field Summary | |
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double |
r
growth rate r |
double |
rSE
standard error of growth rate r |
Fields inherited from class pal.coalescent.ConstantPopulation |
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N0, N0SE |
Fields inherited from class pal.coalescent.DemographicModel |
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fo |
Fields inherited from interface pal.misc.Units |
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DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS |
Constructor Summary | |
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ExponentialGrowth(double size,
double growth,
int units)
Construct demographic model of an exponentially growing population |
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ExponentialGrowth(int units)
Construct demographic model with default settings |
Method Summary | |
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java.lang.Object |
clone()
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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 |
getGrowthRate()
returns growth rate. |
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 |
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()
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Methods inherited from class pal.coalescent.ConstantPopulation |
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getN0 |
Methods inherited from class pal.coalescent.DemographicModel |
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computeLogLikelihood, computeLogLikelihood, getIntegral, getLogL, getSimulatedInterval, getUnits, setLogL, setUnits, testConsistency |
Methods inherited from class java.lang.Object |
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equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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public double r
public double rSE
Constructor Detail |
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public ExponentialGrowth(int units)
public ExponentialGrowth(double size, double growth, int units)
Method Detail |
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public java.lang.String[] getSummaryTypes()
getSummaryTypes
in interface Summarizable
getSummaryTypes
in class ConstantPopulation
public double getSummaryValue(int summaryType)
getSummaryValue
in interface Summarizable
getSummaryValue
in class ConstantPopulation
public java.lang.Object clone()
clone
in class ConstantPopulation
public double getGrowthRate()
public double getDemographic(double t)
DemographicModel
getDemographic
in class ConstantPopulation
public double getIntensity(double t)
DemographicModel
getIntensity
in class ConstantPopulation
public double getInverseIntensity(double x)
DemographicModel
getInverseIntensity
in class ConstantPopulation
public int getNumParameters()
Parameterized
getNumParameters
in interface Parameterized
getNumParameters
in class ConstantPopulation
public double getParameter(int k)
Parameterized
getParameter
in interface Parameterized
getParameter
in class ConstantPopulation
k
- parameter number
public double getUpperLimit(int k)
Parameterized
getUpperLimit
in interface Parameterized
getUpperLimit
in class ConstantPopulation
k
- parameter number
public double getLowerLimit(int k)
Parameterized
getLowerLimit
in interface Parameterized
getLowerLimit
in class ConstantPopulation
k
- parameter number
public double getDefaultValue(int k)
Parameterized
getDefaultValue
in interface Parameterized
getDefaultValue
in class ConstantPopulation
k
- parameter number
public void setParameter(double value, int k)
Parameterized
setParameter
in interface Parameterized
setParameter
in class ConstantPopulation
value
- parameter valuek
- parameter numberpublic void setParameterSE(double value, int k)
Parameterized
setParameterSE
in interface Parameterized
setParameterSE
in class ConstantPopulation
value
- standard error of parameter valuek
- parameter numberpublic java.lang.String toString()
toString
in class ConstantPopulation
public void report(java.io.PrintWriter out)
Report
report
in interface Report
report
in class ConstantPopulation
out
- output stream
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