Package pal.eval

Class LikelihoodOptimiser


  • public class LikelihoodOptimiser
    extends java.lang.Object
    • Method Detail

      • optimiseLogLikelihood

        public double optimiseLogLikelihood​(Parameterized parameters,
                                            MultivariateMinimum minimiser,
                                            int fxFracDigits,
                                            int xFracDigits)
      • optimiseCombined

        public static final double optimiseCombined​(ParameterizedTree tree,
                                                    Alignment alignment,
                                                    SubstitutionModel model,
                                                    MultivariateMinimum minimiser,
                                                    int fxFracDigits,
                                                    int xFracDigits,
                                                    MinimiserMonitor monitor)
        Optimise parameters to acheive maximum likelihood using a combined stategy. That is, model and tree are optimised concurrently.
        Parameters:
        tree - The tree to be optimised (will be altered by optimisation)
        alignment - The alignment related to tree
        model - The substitution model to be optimised (will be altered by optimisation)
        fxFracDigits - The number of decimal placess to stabilise to in the log likelihood
        xFracDigits - The number of decimal placess to stabilise to in the model/tree parameters
        minimiser - The MultivariateMinimum object that is used for minimising
        monitor - A minimiser monitor to monitor progress
        Returns:
        The maximal log likelihood found
      • optimiseCombined

        public static final double optimiseCombined​(ParameterizedTree tree,
                                                    Alignment alignment,
                                                    SubstitutionModel model,
                                                    MultivariateMinimum minimiser,
                                                    int fxFracDigits,
                                                    int xFracDigits)
        Optimise parameters to acheive maximum likelihood using a combined stategy. That is, model and tree are optimised concurrently.
        Parameters:
        tree - The tree to be optimised (will be altered by optimisation)
        alignment - The alignment related to tree
        model - The substitution model to be optimised (will be altered by optimisation)
        fxFracDigits - The number of decimal placess to stabilise to in the log likelihood
        xFracDigits - The number of decimal placess to stabilise to in the model/tree parameters
        minimiser - The MultivariateMinimum object that is used for minimising
        Returns:
        The maximal log likelihood found
      • optimiseAlternate

        public static final double optimiseAlternate​(ParameterizedTree tree,
                                                     Alignment alignment,
                                                     SubstitutionModel model,
                                                     MultivariateMinimum minimiser,
                                                     int fxFracDigits,
                                                     int xFracDigits)
        Optimise parameters to acheive maximum likelihood using an alternating stategy. That is first the model is optimised, than the tree branch lengths, then the model, then the tree, and so on until convergence.
        Parameters:
        tree - The tree to be optimised (will be altered by optimisation)
        alignment - The alignment related to tree
        model - The substitution model to be optimised (will be altered by optimisation)
        fxFracDigits - The number of decimal placess to stabilise to in the log likelihood
        xFracDigits - The number of decimal placess to stabilise to in the model/tree parameters
        minimiser - The MultivariateMinimum object that is used for minimising
        Returns:
        The maximal log likelihood found
      • optimiseAlternate

        public static final double optimiseAlternate​(ParameterizedTree tree,
                                                     Alignment alignment,
                                                     SubstitutionModel model,
                                                     MultivariateMinimum minimiser,
                                                     int fxFracDigits,
                                                     int xFracDigits,
                                                     MinimiserMonitor monitor)
        Optimise parameters to acheive maximum likelihood using an alternating stategy. That is first the model is optimised, than the tree branch lengths, then the model, then the tree, and so on until convergence.
        Parameters:
        tree - The tree to be optimised (will be altered by optimisation)
        alignment - The alignment related to tree
        model - The substitution model to be optimised (will be altered by optimisation)
        fxFracDigits - The number of decimal placess to stabilise to in the log likelihood
        xFracDigits - The number of decimal placess to stabilise to in the model/tree parameters
        minimiser - The MultivariateMinimum object that is used for minimising
        monitor - A minimiser monitor to monitor progress
        Returns:
        The maximal log likelihood found
      • optimiseTree

        public static final double optimiseTree​(ParameterizedTree tree,
                                                Alignment alignment,
                                                SubstitutionModel model,
                                                MultivariateMinimum minimiser,
                                                int fxFracDigits,
                                                int xFracDigits)
        Optimise tree branchlengths only to acheive maximum likelihood using a combined stategy.
        Parameters:
        tree - The tree to be optimised (will be altered by optimisation)
        alignment - The alignment related to tree
        model - The substitution model to be optimised (will *not * be altered by optimisation)
        fxFracDigits - The number of decimal placess to stabilise to in the log likelihood
        xFracDigits - The number of decimal placess to stabilise to in the model/tree parameters
        minimiser - The MultivariateMinimum object that is used for minimising
        Returns:
        The maximal log likelihood found
      • optimiseTree

        public static final double optimiseTree​(ParameterizedTree tree,
                                                Alignment alignment,
                                                SubstitutionModel model,
                                                MultivariateMinimum minimiser,
                                                int fxFracDigits,
                                                int xFracDigits,
                                                MinimiserMonitor monitor)
        Optimise tree branchlengths only to acheive maximum likelihood using a combined stategy.
        Parameters:
        tree - The tree to be optimised (will be altered by optimisation)
        alignment - The alignment related to tree
        model - The substitution model to be optimised (will *not * be altered by optimisation)
        fxFracDigits - The number of decimal placess to stabilise to in the log likelihood
        xFracDigits - The number of decimal placess to stabilise to in the model/tree parameters
        minimiser - The MultivariateMinimum object that is used for minimising
        monitor - A minimiser monitor to monitor progress
        Returns:
        The maximal log likelihood found
      • optimiseModel

        public static final double optimiseModel​(Tree tree,
                                                 Alignment alignment,
                                                 SubstitutionModel model,
                                                 MultivariateMinimum minimiser,
                                                 int fxFracDigits,
                                                 int xFracDigits,
                                                 MinimiserMonitor monitor)
        Optimise model parameters only to acheive maximum likelihood using a combined stategy.
        Parameters:
        tree - The tree to be optimised (will *not* be altered by optimisation)
        alignment - The alignment related to tree
        model - The substitution model to be optimised (will be altered by optimisation)
        fxFracDigits - The number of decimal placess to stabilise to in the log likelihood
        xFracDigits - The number of decimal placess to stabilise to in the model/tree parameters
        minimiser - The MultivariateMinimum object that is used for minimising
        monitor - A minimiser monitor to monitor progress
        Returns:
        The maximal log likelihood found