Uses of Interface
pal.tree.ParameterizedTree
Packages that use ParameterizedTree
Package
Description
Classes to model population genetic processes using the coalescent.
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
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Uses of ParameterizedTree in pal.coalescent
Classes in pal.coalescent that implement ParameterizedTreeModifier and TypeClassDescriptionclass
Provides parameter interface to a clock-like genealogy which is assumed to have some demographic pattern of theta (diversity) as well as branch parameters (the minimal node height differences at each internal node). -
Uses of ParameterizedTree in pal.eval
Methods in pal.eval with parameters of type ParameterizedTreeModifier and TypeMethodDescriptiondouble[]
ModelParameters.estimateFromTree
(ParameterizedTree t) estimate (approximate) values for the model parameters from the data using a given (parameterized) treestatic final double
LikelihoodOptimiser.optimiseAlternate
(ParameterizedTree tree, Alignment alignment, SubstitutionModel model, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits) Optimise parameters to acheive maximum likelihood using an alternating stategy.static final double
LikelihoodOptimiser.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.static final double
LikelihoodOptimiser.optimiseCombined
(ParameterizedTree tree, Alignment alignment, SubstitutionModel model, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits) Optimise parameters to acheive maximum likelihood using a combined stategy.static final double
LikelihoodOptimiser.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.static final double
LikelihoodOptimiser.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.static final double
LikelihoodOptimiser.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. -
Uses of ParameterizedTree in pal.tree
Classes in pal.tree that implement ParameterizedTreeModifier and TypeClassDescriptionclass
provides parameter interface to a clock tree (parameters are the minimal node height differences at each internal node)class
This class logarithmically transforms tree parameters.class
Provides parameter interface to any clock-like tree with serially sampled tips (parameters are the minimal node height differences at each internal node).class
provides parameter interface to an unconstrained tree (parameters are all available branch lengths)Methods in pal.tree that return ParameterizedTreeModifier and TypeMethodDescriptionParameterizedTree.Factory.generateNewTree
(Tree base) Generate a new parameterized tree wrapped around baseConstructors in pal.tree with parameters of type ParameterizedTreeModifierConstructorDescriptionTakes a parameterized object and transforms the parameters logarithmically.