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java.lang.Objectpal.coalescent.DemographicModel
pal.coalescent.ConstantPopulation
pal.coalescent.ExponentialGrowth
pal.coalescent.ConstExpGrowth
pal.coalescent.ConstExpConst
public class ConstExpConst
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).
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 |
tx
time of end of exponential growth |
double |
txSE
standard error of time of growth |
Fields inherited from class pal.coalescent.ConstExpGrowth |
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alpha, ALPHA_PARAMETERIZATION, alphaSE, LX_PARAMETERIZATION, N1, N1_PARAMETERIZATION, N1SE, parameterization |
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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ConstExpConst(double size,
double growth,
double ancestral,
double timeX,
int units,
int parameterization)
Construct demographic model of constexpconst population. |
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ConstExpConst(int units,
int parameterization)
Construct demographic model with default settings. |
Method Summary | |
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java.lang.Object |
clone()
Makes a copy of this demographic model. |
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 |
getGrowthPhaseDuration()
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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 |
getTimeX()
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double |
getTransitionTime()
Gets the time of transition from initial constant phase to exponential phase. |
double |
getUpperLimit(int k)
get upper parameter limit |
static void |
main(java.lang.String[] args)
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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 |
void |
setTimeX(double timeX)
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java.lang.String |
toString()
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Methods inherited from class pal.coalescent.ConstExpGrowth |
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calculateRFromLx, getAncestral, getAncestralN0, getGrowthParam, getGrowthRate, getParameterization, isLxParameterized, isN1Parameterized, setAncestral, setGrowthParam, setGrowthPhaseDuration, setParameterization |
Methods inherited from class pal.coalescent.ExponentialGrowth |
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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 tx
public double txSE
Constructor Detail |
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public ConstExpConst(int units, int parameterization)
public ConstExpConst(double size, double growth, double ancestral, double timeX, int units, int parameterization)
Method Detail |
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public java.lang.Object clone()
clone
in class ConstExpGrowth
public double getTransitionTime()
getTransitionTime
in class ConstExpGrowth
public double getGrowthPhaseDuration()
getGrowthPhaseDuration
in class ConstExpGrowth
public double getTimeX()
public void setTimeX(double timeX)
public double getDemographic(double t)
DemographicModel
getDemographic
in class ConstExpGrowth
public double getIntensity(double t)
DemographicModel
getIntensity
in class ConstExpGrowth
public double getInverseIntensity(double x)
DemographicModel
getInverseIntensity
in class ConstExpGrowth
public int getNumParameters()
Parameterized
getNumParameters
in interface Parameterized
getNumParameters
in class ConstExpGrowth
public double getParameter(int k)
Parameterized
getParameter
in interface Parameterized
getParameter
in class ConstExpGrowth
k
- parameter number
public double getUpperLimit(int k)
Parameterized
getUpperLimit
in interface Parameterized
getUpperLimit
in class ConstExpGrowth
k
- parameter number
public double getLowerLimit(int k)
Parameterized
getLowerLimit
in interface Parameterized
getLowerLimit
in class ConstExpGrowth
k
- parameter number
public double getDefaultValue(int k)
Parameterized
getDefaultValue
in interface Parameterized
getDefaultValue
in class ConstExpGrowth
k
- parameter number
public void setParameter(double value, int k)
Parameterized
setParameter
in interface Parameterized
setParameter
in class ConstExpGrowth
value
- parameter valuek
- parameter numberpublic void setParameterSE(double value, int k)
Parameterized
setParameterSE
in interface Parameterized
setParameterSE
in class ConstExpGrowth
value
- standard error of parameter valuek
- parameter numberpublic java.lang.String toString()
toString
in class ConstExpGrowth
public void report(java.io.PrintWriter out)
Report
report
in interface Report
report
in class ConstExpGrowth
out
- output streampublic static void main(java.lang.String[] args)
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