Package pal.mep

Class ConstantMutationRate

java.lang.Object
pal.mep.MutationRateModel
pal.mep.ConstantMutationRate
All Implemented Interfaces:
Serializable, Cloneable, Parameterized, Report, Summarizable, Units
public class ConstantMutationRate extends MutationRateModel implements Report, Summarizable, Parameterized, Serializable
This class models a constant mutation rate (parameter: mu = mutation rate).
Version:
$Id: ConstantMutationRate.java,v 1.13 2004/08/02 05:22:04 matt Exp $
Author:
Alexei Drummond
See Also:

  • Constructor Details

    • ConstantMutationRate

      public ConstantMutationRate(int units, double maximumMutationRate)
      Construct demographic model with default settings
      Parameters:
      maximumMutationRate - The maximum Mutation rate should be selected wisely - too small and it might not include the "true" rate, too high and the optimisers may have trouble optimising

    • ConstantMutationRate

      public ConstantMutationRate(double rate, int units, double maximumMutationRate)
      Construct mutation rate model of a give rate in given units
      Parameters:
      maximumMutationRate - The maximum Mutation rate should be selected wisely - too small and it might not include the "true" rate, too high and the optimisers may have trouble optimising

    • ConstantMutationRate

      public ConstantMutationRate(double rate, int units, double minimumMu, double maximumMu)
      Construct mutation rate model of a give rate in given units, with a given range of possible values

    • ConstantMutationRate

      protected ConstantMutationRate(ConstantMutationRate toCopy)

  • Method Details

    • clone

      public Object clone()
      Specified by:
      clone in class MutationRateModel

    • getCopy

      public MutationRateModel getCopy()
      Specified by:
      getCopy in class MutationRateModel

    • getSummaryTypes

      public String[] getSummaryTypes()
      Specified by:
      getSummaryTypes in interface Summarizable

    • getSummaryValue

      public double getSummaryValue(int summaryType)
      Specified by:
      getSummaryValue in interface Summarizable

    • getMu

      public double getMu()
      returns initial population size.

    • setMu

      public void setMu(double m)

    • getMutationRate

      public final double getMutationRate(double t)
      Description copied from class: MutationRateModel
      Gets the mutation rate, value of mu(t) at time t.
      Specified by:
      getMutationRate in class MutationRateModel

    • getExpectedSubstitutions

      public final double getExpectedSubstitutions(double t)
      Description copied from class: MutationRateModel
      Returns integral of mutation rate function (= integral mu(x) dx from 0 to t).
      Specified by:
      getExpectedSubstitutions in class MutationRateModel

    • getEndTime

      public final double getEndTime(double expectedSubs, double startTime)
      Description copied from class: MutationRateModel
      Return the end time at which expected substitutions has occurred, given we start at start time
      Specified by:
      getEndTime in class MutationRateModel

    • scale

      public final void scale(double scale)
      Linearly scales this mutation rate model.
      Specified by:
      scale in class MutationRateModel
      Parameters:
      scale - getExpectedSubstitutions should return scale instead of 1.0 at time t.

    • getNumParameters

      public int getNumParameters()
      Description copied from interface: Parameterized
      get number of parameters
      Specified by:
      getNumParameters in interface Parameterized
      Returns:
      number of parameters

    • getParameter

      public double getParameter(int k)
      Description copied from interface: Parameterized
      get model parameter
      Specified by:
      getParameter in interface Parameterized
      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
      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
      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
      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
      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
      Parameters:
      value - standard error of parameter value
      k - parameter number

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • 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
      Parameters:
      out - output stream

    • toSingleLine

      public String toSingleLine()
      Specified by:
      toSingleLine in class MutationRateModel

    • getFixedFactory

      public static final MutationRateModel.Factory getFixedFactory(double rate, int units)
      Generate a MutationRateModel.Factory class for a ConstantMutationRate

    • getFreeFactory

      public static final MutationRateModel.Factory getFreeFactory(int units, double maximumMutationRate)
      Generate a MutationRateModel.Factory class for a ConstantMutationRate

    • getFreeFactory

      public static final MutationRateModel.Factory getFreeFactory(double initialRate, int units, double maximumMutationRate)
      Generate a MutationRateModel.Factory class for a ConstantMutationRate

    • getFreeFactory

      public static final MutationRateModel.Factory getFreeFactory(double initialRate, int units, double minimumRate, double maximumRate)
      Generate a MutationRateModel.Factory class for a ConstantMutationRate

    • generateFactory

      public MutationRateModel.Factory generateFactory()
      Specified by:
      generateFactory in class MutationRateModel

    • createFixed

      public static final ConstantMutationRate createFixed(double rate, int units)
      Returns:
      A ConstantMutationRate with a fixed rate (no parameters)