Package pal.coalescent
Class ConstExpConst
java.lang.Object
pal.coalescent.DemographicModel
pal.coalescent.ConstantPopulation
pal.coalescent.ExponentialGrowth
pal.coalescent.ConstExpGrowth
pal.coalescent.ConstExpConst
- All Implemented Interfaces:
Serializable
,Cloneable
,Parameterized
,Report
,Summarizable
,Units
This class models a population that grows exponentially from an
initial population size alpha N0 at time y to a size N0
at time x until the present-day.
(Parameters: N0=present-day population size; r=growth rate; alpha: ratio of
population sizes).
or
(Parameters: N0=present-day population size; r=growth rate; N1: pre-growth
ancestral population size).
This model is nested with the exponential-growth model (alpha -> 0 and tx -> 0).
- Version:
- $Id: ConstExpConst.java,v 1.2 2002/02/16 00:51:43 alexi Exp $
- Author:
- Alexei Drummond, Andrew Rambaut
- 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
time of end of exponential growthdouble
standard error of time of growthFields inherited from class pal.coalescent.ConstExpGrowth
alpha, ALPHA_PARAMETERIZATION, alphaSE, LX_PARAMETERIZATION, N1, N1_PARAMETERIZATION, N1SE, parameterization
Fields inherited from class pal.coalescent.ExponentialGrowth
r, rSE
Fields inherited from class pal.coalescent.ConstantPopulation
N0, N0SE
Fields 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
ConstructorsConstructorDescriptionConstExpConst
(double size, double growth, double ancestral, double timeX, int units, int parameterization) Construct demographic model of constexpconst population.ConstExpConst
(int units, int parameterization) Construct demographic model with default settings. -
Method Summary
Modifier and TypeMethodDescriptionclone()
Makes a copy of this demographic model.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
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 limitint
get number of parametersdouble
getParameter
(int k) get model parameterdouble
getTimeX()
double
Gets the time of transition from initial constant phase to exponential phase.double
getUpperLimit
(int k) get upper parameter limitstatic void
void
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 parametervoid
setTimeX
(double timeX) toString()
Methods inherited from class pal.coalescent.ConstExpGrowth
calculateRFromLx, getAncestral, getAncestralN0, getGrowthParam, getGrowthRate, getParameterization, isLxParameterized, isN1Parameterized, setAncestral, setGrowthParam, setGrowthPhaseDuration, setParameterization
Methods inherited from class pal.coalescent.ExponentialGrowth
getSummaryTypes, getSummaryValue
Methods inherited from class pal.coalescent.ConstantPopulation
getN0
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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tx
public double txtime of end of exponential growth -
txSE
public double txSEstandard error of time of growth
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Constructor Details
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ConstExpConst
public ConstExpConst(int units, int parameterization) Construct demographic model with default settings. -
ConstExpConst
public ConstExpConst(double size, double growth, double ancestral, double timeX, int units, int parameterization) Construct demographic model of constexpconst population.
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Method Details
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clone
Makes a copy of this demographic model.- Overrides:
clone
in classConstExpGrowth
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getTransitionTime
public double getTransitionTime()Gets the time of transition from initial constant phase to exponential phase.- Overrides:
getTransitionTime
in classConstExpGrowth
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getGrowthPhaseDuration
public double getGrowthPhaseDuration()- Overrides:
getGrowthPhaseDuration
in classConstExpGrowth
- Returns:
- the duration of the growth phase
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getTimeX
public double getTimeX()- Returns:
- the time at which the modern constant pop size gives way to exponential phase.
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setTimeX
public void setTimeX(double timeX) -
getDemographic
public double getDemographic(double t) Description copied from class:DemographicModel
Gets the value of the demographic function N(t) at time t.- Overrides:
getDemographic
in classConstExpGrowth
- Returns:
- the population size at time t.
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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).- Overrides:
getIntensity
in classConstExpGrowth
- Returns:
- the integral of 1 / N(t) from 0 to t.
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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).- Overrides:
getInverseIntensity
in classConstExpGrowth
- Returns:
- the time for the given intensity.
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getNumParameters
public int getNumParameters()Description copied from interface:Parameterized
get number of parameters- Specified by:
getNumParameters
in interfaceParameterized
- Overrides:
getNumParameters
in classConstExpGrowth
- 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
- Overrides:
getParameter
in classConstExpGrowth
- 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
- Overrides:
getUpperLimit
in classConstExpGrowth
- 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
- Overrides:
getLowerLimit
in classConstExpGrowth
- 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
- Overrides:
getDefaultValue
in classConstExpGrowth
- 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
- Overrides:
setParameter
in classConstExpGrowth
- 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
- Overrides:
setParameterSE
in classConstExpGrowth
- Parameters:
value
- standard error of parameter valuek
- parameter number
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toString
- Overrides:
toString
in classConstExpGrowth
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report
Description copied from interface:Report
print human readable report (e.g., on parameters and associated model)- Specified by:
report
in interfaceReport
- Overrides:
report
in classConstExpGrowth
- Parameters:
out
- output stream
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main
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