ConstExpConst

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

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, Parameterized, Report, Summarizable, Units
```
public class ConstExpConst
extends ConstExpGrowth
implements Report, Parameterized, java.io.Serializable
```
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:

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 and Description

double tx
time of end of exponential growth

double txSE
standard error of time of growth
- Fields 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

Fields
Modifier and Type	Field and Description
`double`	`tx` time of end of exponential growth
`double`	`txSE` standard error of time of growth

Constructor Summary

Constructors
Constructor and Description
`ConstExpConst(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

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`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()`
`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()`
`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)`
`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)`
`java.lang.String`	`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

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

- Field Detail
  - tx
```
public double tx
```
    time of end of exponential growth
  - txSE
```
public double txSE
```
    standard error of time of growth
- Constructor Detail
  - 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.
- Method Detail
  - clone
```
public java.lang.Object clone()
```
    Makes a copy of this demographic model.
    
    Overrides:
    
    clone in class ConstExpGrowth
  - getTransitionTime
```
public double getTransitionTime()
```
    Gets the time of transition from initial constant phase to exponential phase.
    
    Overrides:
    
    getTransitionTime in class ConstExpGrowth
  - getGrowthPhaseDuration
```
public double getGrowthPhaseDuration()
```
    Overrides:
    
    getGrowthPhaseDuration in class ConstExpGrowth
    
    Returns:
    
    the duration of the growth phase
  - getTimeX
```
public double getTimeX()
```
    Returns:
    
    the time at which the modern constant pop size gives way to exponential phase.
  - 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 class ConstExpGrowth
    
    Returns:
    
    the population size at time t.
  - 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 ConstExpGrowth
    
    Returns:
    
    the integral of 1 / N(t) from 0 to t.
  - 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 ConstExpGrowth
    
    Returns:
    
    the time for the given intensity.
  - getNumParameters
```
public int getNumParameters()
```
    Description copied from interface: Parameterized
    
    get number of parameters
    
    Specified by:
    
    getNumParameters in interface Parameterized
    
    Overrides:
    
    getNumParameters in class ConstExpGrowth
    
    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 ConstExpGrowth
    
    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 ConstExpGrowth
    
    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 ConstExpGrowth
    
    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 ConstExpGrowth
    
    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 ConstExpGrowth
    
    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 ConstExpGrowth
    
    Parameters:
    
    value - standard error of parameter value
    
    k - parameter number
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class ConstExpGrowth
  - 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 ConstExpGrowth
    
    Parameters:
    
    out - output stream
  - main
```
public static void main(java.lang.String[] args)
```

Class ConstExpConst

Nested Class Summary

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

Field Summary

Fields inherited from class pal.coalescent.ConstExpGrowth

Fields inherited from class pal.coalescent.ExponentialGrowth

Fields inherited from class pal.coalescent.ConstantPopulation

Fields inherited from class pal.coalescent.DemographicModel

Fields inherited from interface pal.misc.Units

Constructor Summary

Method Summary

Methods inherited from class pal.coalescent.ConstExpGrowth

Methods inherited from class pal.coalescent.ExponentialGrowth

Methods inherited from class pal.coalescent.ConstantPopulation

Methods inherited from class pal.coalescent.DemographicModel

Methods inherited from class java.lang.Object

Field Detail

tx

txSE

Constructor Detail

ConstExpConst

ConstExpConst

Method Detail

clone

getTransitionTime

getGrowthPhaseDuration

getTimeX

setTimeX

getDemographic

getIntensity

getInverseIntensity

getNumParameters

getParameter

getUpperLimit

getLowerLimit

getDefaultValue

setParameter

setParameterSE

toString

report

main