ConstExpGrowth

java.lang.Object
- pal.coalescent.DemographicModel
- - pal.coalescent.ConstantPopulation
  - - pal.coalescent.ExponentialGrowth
    - - pal.coalescent.ConstExpGrowth

All Implemented Interfaces:

java.io.Serializable, Parameterized, Report, Summarizable, Units

Direct Known Subclasses:

ConstExpConst
```
public class ConstExpGrowth
extends ExponentialGrowth
implements Report, Parameterized, java.io.Serializable
```
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). 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 or N1 = N0). It is similar but not identical to the model used in ExpandingPopulation.

Version:

$Id: ConstExpGrowth.java,v 1.10 2002/02/16 00:51:43 alexi Exp $

Author:

Alexei Drummond, Andrew Rambaut, Korbinian Strimmer

See Also:

Serialized Form

Nested Class Summary
- Nested classes/interfaces inherited from interface pal.misc.Parameterized
  Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils

Field Summary

Fields
Modifier and Type	Field	Description
`double`	`alpha`	ratio of pop.
`static int`	`ALPHA_PARAMETERIZATION`	use alpha instead of N1 parameterization
`double`	`alphaSE`	standard error of time alpha
`static int`	`LX_PARAMETERIZATION`	use lx instead of growth parameterization
`double`	`N1`	ancestral pop.
`static int`	`N1_PARAMETERIZATION`	use N1 instead of alpha parameterization
`double`	`N1SE`	standard error of ancestral pop.
`int`	`parameterization`	parameterization bit string: first bit: 0 = ALPHA, 1 = N1 second bit: 0 = GROWTH RATE, 1 = LX

Fields inherited from class pal.coalescent.ConstantPopulation
N0, N0SE

Fields inherited from class pal.coalescent.DemographicModel
fo

Fields inherited from class pal.coalescent.ExponentialGrowth
r, rSE

Fields inherited from interface pal.misc.Units
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS

Constructor Summary

Constructors
Constructor	Description
`ConstExpGrowth(double size, double growthParam, double ancestral, int units, int parameterization)`	Construct demographic model of an expanding population.
`ConstExpGrowth(int units, int parameterization)`	Construct demographic model with default settings.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`calculateRFromLx()`
`java.lang.Object`	`clone()`
`double`	`getAncestral()`	returns ancestral parameter.
`double`	`getAncestralN0()`	returns ancestral population size
`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`	`getGrowthParam()`
`double`	`getGrowthPhaseDuration()`
`double`	`getGrowthRate()`	This method overrides superclass to check parameterization.
`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
`int`	`getParameterization()`
`double`	`getTransitionTime()`	Gets the time of transition from ancestral constant phase to exponential phase.
`double`	`getUpperLimit(int k)`	get upper parameter limit
`boolean`	`isLxParameterized()`
`boolean`	`isN1Parameterized()`
`void`	`report(java.io.PrintWriter out)`	print human readable report (e.g., on parameters and associated model)
`void`	`setAncestral(double ancestral)`	Sets the ancestral parameter.
`void`	`setGrowthParam(double g)`	Sets the growth parameter.
`void`	`setGrowthPhaseDuration(double lx)`	Sets the length of the growth phase.
`void`	`setParameter(double value, int k)`	set model parameter
`void`	`setParameterization(int p)`	Sets the parameterization.
`void`	`setParameterSE(double value, int k)`	set standard errors for model parameter
`java.lang.String`	`toString()`

Methods inherited from class pal.coalescent.ConstantPopulation
getN0

Methods inherited from class pal.coalescent.DemographicModel
computeLogLikelihood, computeLogLikelihood, getIntegral, getLogL, getSimulatedInterval, getUnits, setLogL, setUnits, testConsistency

Methods inherited from class pal.coalescent.ExponentialGrowth
getSummaryTypes, getSummaryValue

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - ALPHA_PARAMETERIZATION
```
public static final int ALPHA_PARAMETERIZATION
```
    use alpha instead of N1 parameterization
    
    See Also:
    
    Constant Field Values
  - N1_PARAMETERIZATION
```
public static final int N1_PARAMETERIZATION
```
    use N1 instead of alpha parameterization
    
    See Also:
    
    Constant Field Values
  - LX_PARAMETERIZATION
```
public static final int LX_PARAMETERIZATION
```
    use lx instead of growth parameterization
    
    See Also:
    
    Constant Field Values
  - parameterization
```
public int parameterization
```
    parameterization bit string:
    first bit: 0 = ALPHA, 1 = N1
    second bit: 0 = GROWTH RATE, 1 = LX
  - alpha
```
public double alpha
```
    ratio of pop. sizes
  - alphaSE
```
public double alphaSE
```
    standard error of time alpha
  - N1
```
public double N1
```
    ancestral pop. size
  - N1SE
```
public double N1SE
```
    standard error of ancestral pop. size
- Constructor Detail
  - ConstExpGrowth
```
public ConstExpGrowth(int units,
                      int parameterization)
```
    Construct demographic model with default settings.
    
    Parameters:
    
    parameterization - is a combination of bits representing the parameterization. Valid values are:
    ALPHA_PARAMETERIZATION
    N1_PARAMETERIZATION
    ALPHA_PARAMETERIZATION | LX_PARAMETERIZATION
    N1_PARAMETERIZATION | LX_PARAMETERIZATION
  - ConstExpGrowth
```
public ConstExpGrowth(double size,
                      double growthParam,
                      double ancestral,
                      int units,
                      int parameterization)
```
    Construct demographic model of an expanding population.
- Method Detail
  - clone
```
public java.lang.Object clone()
```
    Overrides:
    
    clone in class ExponentialGrowth
  - getTransitionTime
```
public double getTransitionTime()
```
    Gets the time of transition from ancestral constant phase to exponential phase.
  - getAncestral
```
public double getAncestral()
```
    returns ancestral parameter. This may be either N1 or alpha depending on the parameterization.
  - getGrowthParam
```
public double getGrowthParam()
```
    Returns:
    
    the growth parameter. This may be either growth rate or growth phase duration depending on the parameterization.
  - getGrowthRate
```
public double getGrowthRate()
```
    This method overrides superclass to check parameterization.
    
    Overrides:
    
    getGrowthRate in class ExponentialGrowth
  - setAncestral
```
public void setAncestral(double ancestral)
```
    Sets the ancestral parameter. This may be either N1 or alpha depending on the parameterization.
  - setGrowthParam
```
public void setGrowthParam(double g)
```
    Sets the growth parameter. This may be either growth rate (r) or growth pahse duration (lx) depending on the parameterization.
  - getAncestralN0
```
public double getAncestralN0()
```
    returns ancestral population size
  - getGrowthPhaseDuration
```
public double getGrowthPhaseDuration()
```
    Returns:
    
    the duration of the growth phase
  - setGrowthPhaseDuration
```
public void setGrowthPhaseDuration(double lx)
```
    Sets the length of the growth phase. This method is only valid if ALPHA_LX_PARAMETERIZATION is used.
  - getParameterization
```
public int getParameterization()
```
    Returns:
    
    parameterization
  - isLxParameterized
```
public boolean isLxParameterized()
```
    Returns:
    
    true if using lx instead of growth rate.
  - isN1Parameterized
```
public boolean isN1Parameterized()
```
    Returns:
    
    true if using N1 instead of alpha.
  - setParameterization
```
public void setParameterization(int p)
```
    Sets the parameterization.
    
    Parameters:
    
    parameterization - is a combination of bits representing the parameterization. Valid values are:
    ALPHA_PARAMETERIZATION
    N1_PARAMETERIZATION
    ALPHA_PARAMETERIZATION | LX_PARAMETERIZATION
    N1_PARAMETERIZATION | LX_PARAMETERIZATION
  - calculateRFromLx
```
protected void calculateRFromLx()
```
  - 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 class ExponentialGrowth
  - 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 class ExponentialGrowth
  - 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 class ExponentialGrowth
  - getNumParameters
```
public int getNumParameters()
```
    Description copied from interface: Parameterized
    
    get number of parameters
    
    Specified by:
    
    getNumParameters in interface Parameterized
    
    Overrides:
    
    getNumParameters in class ExponentialGrowth
    
    Returns:
    
    number of parameters
  - getParameter
```
public double getParameter(int k)
```
    Description copied from interface: Parameterized
    
    get model parameter
    
    Specified by:
    
    getParameter in interface Parameterized
    
    Overrides:
    
    getParameter in class ExponentialGrowth
    
    Parameters:
    
    k - parameter number
    
    Returns:
    
    parameter value
  - getUpperLimit
```
public double getUpperLimit(int k)
```
    Description copied from interface: Parameterized
    
    get upper parameter limit
    
    Specified by:
    
    getUpperLimit in interface Parameterized
    
    Overrides:
    
    getUpperLimit in class ExponentialGrowth
    
    Parameters:
    
    k - parameter number
    
    Returns:
    
    upper bound
  - getLowerLimit
```
public double getLowerLimit(int k)
```
    Description copied from interface: Parameterized
    
    get lower parameter limit
    
    Specified by:
    
    getLowerLimit in interface Parameterized
    
    Overrides:
    
    getLowerLimit in class ExponentialGrowth
    
    Parameters:
    
    k - parameter number
    
    Returns:
    
    lower bound
  - getDefaultValue
```
public double getDefaultValue(int k)
```
    Description copied from interface: Parameterized
    
    get default value of parameter
    
    Specified by:
    
    getDefaultValue in interface Parameterized
    
    Overrides:
    
    getDefaultValue in class ExponentialGrowth
    
    Parameters:
    
    k - parameter number
    
    Returns:
    
    default value
  - setParameter
```
public void setParameter(double value,
                         int k)
```
    Description copied from interface: Parameterized
    
    set model parameter
    
    Specified by:
    
    setParameter in interface Parameterized
    
    Overrides:
    
    setParameter in class ExponentialGrowth
    
    Parameters:
    
    value - parameter value
    
    k - parameter number
  - setParameterSE
```
public void setParameterSE(double value,
                           int k)
```
    Description copied from interface: Parameterized
    
    set standard errors for model parameter
    
    Specified by:
    
    setParameterSE in interface Parameterized
    
    Overrides:
    
    setParameterSE in class ExponentialGrowth
    
    Parameters:
    
    value - standard error of parameter value
    
    k - parameter number
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class ExponentialGrowth
  - report
```
public void report(java.io.PrintWriter out)
```
    Description copied from interface: Report
    
    print human readable report (e.g., on parameters and associated model)
    
    Specified by:
    
    report in interface Report
    
    Overrides:
    
    report in class ExponentialGrowth
    
    Parameters:
    
    out - output stream

Class ConstExpGrowth

Nested Class Summary

Nested classes/interfaces inherited from interface pal.misc.Parameterized

Field Summary

Fields inherited from class pal.coalescent.ConstantPopulation

Fields inherited from class pal.coalescent.DemographicModel

Fields inherited from class pal.coalescent.ExponentialGrowth

Fields inherited from interface pal.misc.Units

Constructor Summary

Method Summary

Methods inherited from class pal.coalescent.ConstantPopulation

Methods inherited from class pal.coalescent.DemographicModel

Methods inherited from class pal.coalescent.ExponentialGrowth

Methods inherited from class java.lang.Object

Field Detail

ALPHA_PARAMETERIZATION

N1_PARAMETERIZATION

LX_PARAMETERIZATION

parameterization

alpha

alphaSE

N1

N1SE

Constructor Detail

ConstExpGrowth

ConstExpGrowth

Method Detail

clone

getTransitionTime

getAncestral

getGrowthParam

getGrowthRate

setAncestral

setGrowthParam

getAncestralN0

getGrowthPhaseDuration

setGrowthPhaseDuration

getParameterization

isLxParameterized

isN1Parameterized

setParameterization

calculateRFromLx

getDemographic

getIntensity

getInverseIntensity

getNumParameters

getParameter

getUpperLimit

getLowerLimit

getDefaultValue

setParameter

setParameterSE

toString

report