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
public class ConstExpConst extends ConstExpGrowth implements Report, Parameterized, 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:

  • Field Details

    • tx

      public double tx
      time of end of exponential growth

    • txSE

      public double txSE
      standard error of time of growth

  • Constructor Details

    • 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 Details

    • clone

      public 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 String toString()
      Overrides:
      toString in class ConstExpGrowth

    • report

      public void report(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(String[] args)