Package pal.tree

Class MutationRateModelTree

    • Constructor Detail

      • MutationRateModelTree

        public MutationRateModelTree​(Tree t,
                                     TimeOrderCharacterData tocd,
                                     MutationRateModel model)
        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). Includes model parameters as parameters of tree

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

      • MutationRateModelTree

        public MutationRateModelTree​(Tree t,
                                     TimeOrderCharacterData tocd,
                                     MutationRateModel model,
                                     boolean includeModelParameters)
        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).

      • MutationRateModelTree

        protected MutationRateModelTree​(MutationRateModelTree toCopy)
        Cloning constructor
    • Method Detail

      • setMaxRelativeHeight

        public void setMaxRelativeHeight​(double value)
        Sets the maximum distance between ancestor and latest descendant.
      • 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
      • getLowerLimit

        public double getLowerLimit​(int n)
        Returns lower limit of parameter estimate.
        Specified by:
        getLowerLimit in interface Parameterized
        Parameters:
        n - parameter number
        Returns:
        lower 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
      • 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
      • 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
      • parameters2Heights

        protected void parameters2Heights()
      • heights2parameters

        protected void heights2parameters()
      • setLnL

        public void setLnL​(double lnL)
      • getLnL

        public double getLnL()
      • getSuggestedOrdering

        public OrderEnumerator getSuggestedOrdering​(OrderEnumerator defaultOrdering)
        Description copied from interface: OrthogonalHints
        If there is a "best" ordering to use it can be specified here, if not should return null
        Specified by:
        getSuggestedOrdering in interface OrthogonalHints
        Parameters:
        defaultOrdering - The ordering suggested by the optimiser, may be null!
        Returns:
        null, or default ordering if no known best ordering
      • getInternalParameterBoundaries

        public int getInternalParameterBoundaries​(int parameter,
                                                  double[] storage)
        Description copied from interface: OrthogonalHints
        A boundary is a value of a parameter for which values lower than the boundary and values higher than the boundary are better treated as two separate functions (IE, they are only piecewise connected), and minimisation should be performed over both ranges individually (and then the true minimum taken as the minimuma of the ranges)
        Specified by:
        getInternalParameterBoundaries in interface OrthogonalHints
        Returns:
        the number of boundary locations stored in storage, or -1 if not enough room, or 0 if there are no boundaries (other than the normal parameter range)
      • clone

        public java.lang.Object clone()
        Overrides:
        clone in class java.lang.Object