Package pal.coalescent

Class 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

    • 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

      • 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.

      • 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

      • 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)