Package pal.substmodel

Class VariableIndependentSingleSplitDistribution

java.lang.Object
pal.substmodel.VariableIndependentSingleSplitDistribution
All Implemented Interfaces:
NeoParameterized, SingleSplitDistribution
public class VariableIndependentSingleSplitDistribution extends Object implements SingleSplitDistribution

Title: VariableIndependentSingleSplitDistribution

Description: Allows for a split in substitution model parameters where the class distribution before the split maybe different after the split (and the probabilities of being in a before class and an after class are independent)

Author:
Matthew Goode

  • Constructor Details

    • VariableIndependentSingleSplitDistribution

      public VariableIndependentSingleSplitDistribution(int numberOfBaseTransitionCategories)

    • VariableIndependentSingleSplitDistribution

      public VariableIndependentSingleSplitDistribution(int numberOfBaseTransitionCategories, double[] initialParameters)

  • Method Details

    • getDistribution

      public double[] getDistribution()

    • getNumberOfBaseTransitionCategories

      public int getNumberOfBaseTransitionCategories()
      Specified by:
      getNumberOfBaseTransitionCategories in interface SingleSplitDistribution

    • getDistributionInfo

      public double[][] getDistributionInfo()
      Description copied from interface: SingleSplitDistribution
      Obtain the distribution information stored in the following format: [beforeclass][afterclass] For example, the probability of evolving in class 0 before the split, and class 1 after the split - [0][1]
      Specified by:
      getDistributionInfo in interface SingleSplitDistribution
      Returns:
      an appropriate matrix representing the probability of evolving in the different combinations of before and after classes

    • getNumberOfParameters

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

    • setParameters

      public void setParameters(double[] store, int startIndex)
      Description copied from interface: NeoParameterized
      set model parameter
      Specified by:
      setParameters in interface NeoParameterized
      Parameters:
      store - the array holding the parameters
      startIndex - the index into the array that the related parameters start at

    • getParameters

      public void getParameters(double[] store, int startIndex)
      Description copied from interface: NeoParameterized
      get model parameter
      Specified by:
      getParameters in interface NeoParameterized
      startIndex - the index into the array that the related parameters start at

    • getLowerLimit

      public double getLowerLimit(int n)
      Description copied from interface: NeoParameterized
      get lower parameter limit
      Specified by:
      getLowerLimit in interface NeoParameterized
      Parameters:
      n - parameter number
      Returns:
      lower bound

    • getUpperLimit

      public double getUpperLimit(int n)
      Description copied from interface: NeoParameterized
      get upper parameter limit
      Specified by:
      getUpperLimit in interface NeoParameterized
      Parameters:
      n - parameter number
      Returns:
      upper bound

    • getDefaultValues

      public void getDefaultValues(double[] store, int startIndex)
      Description copied from interface: NeoParameterized
      get default value parameter values
      Specified by:
      getDefaultValues in interface NeoParameterized

    • toString

      public String toString()
      Overrides:
      toString in class Object