Package pal.coalescent
Class ConstantPopulation
java.lang.Object
pal.coalescent.DemographicModel
pal.coalescent.ConstantPopulation
- All Implemented Interfaces:
Serializable
,Cloneable
,Parameterized
,Report
,Summarizable
,Units
- Direct Known Subclasses:
ExponentialGrowth
public class ConstantPopulation
extends DemographicModel
implements Report, Summarizable, Parameterized, Serializable
This class models coalescent intervals for a constant population
(parameter: N0=present-day population size).
If time units are set to Units.EXPECTED_SUBSTITUTIONS then the N0 parameter will be interpreted as N0 * mu.
Also note that if you are dealing with a diploid population N0 will be out by a factor of 2.
If time units are set to Units.EXPECTED_SUBSTITUTIONS then the N0 parameter will be interpreted as N0 * mu.
Also note that if you are dealing with a diploid population N0 will be out by a factor of 2.
- Version:
- $Id: ConstantPopulation.java,v 1.14 2003/09/14 05:14:15 matt Exp $
- Author:
- Alexei Drummond + @author Korbinian Strimmer
- See Also:
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Nested Class Summary
Nested classes/interfaces inherited from interface pal.misc.Parameterized
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
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Field Summary
FieldsModifier and TypeFieldDescriptiondouble
population sizedouble
standard error of population sizeFields inherited from class pal.coalescent.DemographicModel
fo
Fields inherited from interface pal.misc.Units
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS
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Constructor Summary
ConstructorsConstructorDescriptionConstantPopulation
(double size, int units) Construct demographic model of a constant population size.ConstantPopulation
(int units) Construct demographic model with default settings -
Method Summary
Modifier and TypeMethodDescriptionclone()
double
getDefaultValue
(int k) get default value of parameterdouble
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 limitdouble
getN0()
returns initial population size.int
get number of parametersdouble
getParameter
(int k) get model parameterString[]
double
getSummaryValue
(int summaryType) double
getUpperLimit
(int k) get upper parameter limitvoid
report
(PrintWriter out) print human readable report (e.g., on parameters and associated model)void
setParameter
(double value, int k) set model parametervoid
setParameterSE
(double value, int k) set standard errors for model parametertoString()
Methods inherited from class pal.coalescent.DemographicModel
computeLogLikelihood, computeLogLikelihood, getIntegral, getLogL, getSimulatedInterval, getUnits, setLogL, setUnits, testConsistency
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Field Details
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N0
public double N0population size -
N0SE
public double N0SEstandard error of population size
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Constructor Details
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ConstantPopulation
public ConstantPopulation(int units) Construct demographic model with default settings -
ConstantPopulation
public ConstantPopulation(double size, int units) Construct demographic model of a constant population size.
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Method Details
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clone
- Specified by:
clone
in classDemographicModel
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getSummaryTypes
- Specified by:
getSummaryTypes
in interfaceSummarizable
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getSummaryValue
public double getSummaryValue(int summaryType) - Specified by:
getSummaryValue
in interfaceSummarizable
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getN0
public double getN0()returns initial population size. -
getDemographic
public double getDemographic(double t) Description copied from class:DemographicModel
Gets the value of the demographic function N(t) at time t.- Specified by:
getDemographic
in classDemographicModel
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getIntensity
public double getIntensity(double t) Description copied from class:DemographicModel
Returns value of demographic intensity function at time t (= integral 1/N(x) dx from 0 to t).- Specified by:
getIntensity
in classDemographicModel
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getInverseIntensity
public double getInverseIntensity(double x) Description copied from class:DemographicModel
Returns value of inverse demographic intensity function (returns time, needed for simulation of coalescent intervals).- Specified by:
getInverseIntensity
in classDemographicModel
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getNumParameters
public int getNumParameters()Description copied from interface:Parameterized
get number of parameters- Specified by:
getNumParameters
in interfaceParameterized
- Returns:
- number of parameters
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getParameter
public double getParameter(int k) Description copied from interface:Parameterized
get model parameter- Specified by:
getParameter
in interfaceParameterized
- Parameters:
k
- parameter number- Returns:
- parameter value
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getUpperLimit
public double getUpperLimit(int k) Description copied from interface:Parameterized
get upper parameter limit- Specified by:
getUpperLimit
in interfaceParameterized
- Parameters:
k
- parameter number- Returns:
- upper bound
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getLowerLimit
public double getLowerLimit(int k) Description copied from interface:Parameterized
get lower parameter limit- Specified by:
getLowerLimit
in interfaceParameterized
- Parameters:
k
- parameter number- Returns:
- lower bound
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getDefaultValue
public double getDefaultValue(int k) Description copied from interface:Parameterized
get default value of parameter- Specified by:
getDefaultValue
in interfaceParameterized
- Parameters:
k
- parameter number- Returns:
- default value
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setParameter
public void setParameter(double value, int k) Description copied from interface:Parameterized
set model parameter- Specified by:
setParameter
in interfaceParameterized
- Parameters:
value
- parameter valuek
- parameter number
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setParameterSE
public void setParameterSE(double value, int k) Description copied from interface:Parameterized
set standard errors for model parameter- Specified by:
setParameterSE
in interfaceParameterized
- Parameters:
value
- standard error of parameter valuek
- parameter number
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toString
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report
Description copied from interface:Report
print human readable report (e.g., on parameters and associated model)
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