Package pal.tree

Class ClockTree

    • Field Detail

      • parameter

        protected double[] parameter
    • Constructor Detail

      • ClockTree

        public ClockTree()
      • ClockTree

        public ClockTree​(Tree t)
        take any tree and afford it with an interface suitable for a clock-like tree (parameters are the minimal node height differences at each internal node).

        This parameterisation of a clock-tree, ensuring that all parameters are independent of each other is due to Andrew Rambaut (personal communication).

    • Method Detail

      • update

        public void update()
        make clocktree consistent with branch lengths
      • getNumParameters

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

        public void setParameter​(double param,
                                 int n)
        Description copied from interface: Parameterized
        set model parameter
        Specified by:
        setParameter in interface Parameterized
        Parameters:
        param - parameter value
        n - parameter number
      • getParameter

        public double getParameter​(int n)
        Description copied from interface: Parameterized
        get model parameter
        Specified by:
        getParameter in interface Parameterized
        Parameters:
        n - parameter number
        Returns:
        parameter value
      • setParameterSE

        public void setParameterSE​(double paramSE,
                                   int n)
        Description copied from interface: Parameterized
        set standard errors for model parameter
        Specified by:
        setParameterSE in interface Parameterized
        Parameters:
        paramSE - standard error of parameter value
        n - parameter number
      • getLowerLimit

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

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

        public double getDefaultValue​(int n)
        Description copied from interface: Parameterized
        get default value of parameter
        Specified by:
        getDefaultValue in interface Parameterized
        Parameters:
        n - parameter number
        Returns:
        default value
      • parameters2Heights

        protected void parameters2Heights()
      • heights2parameters

        protected void heights2parameters()
      • getParameterizedTreeFactory

        public static final ParameterizedTree.Factory getParameterizedTreeFactory()
        Obtain a ParameterizedTree.Factory for generating Clock trees