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java.lang.Objectpal.coalescent.DemographicModel
pal.coalescent.ConstantPopulation
pal.coalescent.ExponentialGrowth
pal.coalescent.ExpandingPopulation
public class ExpandingPopulation
This class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0. (Parameters: N0=present-day population size; r=growth rate; alpha: ratio of population sizes). This model is nested with the exponential-growth model (alpha -> 0).
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 |
alpha
ratio of pop. |
double |
alphaSE
standard error of time alpha |
Fields inherited from class pal.coalescent.ExponentialGrowth |
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r, rSE |
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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ExpandingPopulation(double size,
double growth,
double ratio,
int units)
Construct demographic model of an expanding population |
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ExpandingPopulation(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 |
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()
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Methods inherited from class pal.coalescent.ExponentialGrowth |
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getGrowthRate, getSummaryTypes, getSummaryValue |
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 alpha
public double alphaSE
Constructor Detail |
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public ExpandingPopulation(int units)
public ExpandingPopulation(double size, double growth, double ratio, int units)
Method Detail |
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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 number
public double getUpperLimit(int k)
Parameterized
getUpperLimit
in interface Parameterized
getUpperLimit
in class ExponentialGrowth
k
- parameter number
public double getLowerLimit(int k)
Parameterized
getLowerLimit
in interface Parameterized
getLowerLimit
in class ExponentialGrowth
k
- parameter number
public double getDefaultValue(int k)
Parameterized
getDefaultValue
in interface Parameterized
getDefaultValue
in class ExponentialGrowth
k
- parameter number
public 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
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