Uses of Interface
pal.tree.ParameterizedTree
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Packages that use ParameterizedTree Package Description pal.coalescent Classes to model population genetic processes using the coalescent.pal.eval Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters.pal.tree 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 ParameterizedTree Modifier and Type Class Description class
DemographicClockTree
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 ParameterizedTree Modifier and Type Method Description double[]
ModelParameters. estimateFromTree(ParameterizedTree t)
estimate (approximate) values for the model parameters from the data using a given (parameterized) treestatic 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 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 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 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 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 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 ParameterizedTree Modifier and Type Class Description class
ClockTree
provides parameter interface to a clock tree (parameters are the minimal node height differences at each internal node)class
LogParameterizedTree
This class logarithmically transforms tree parameters.class
MutationRateModelTree
Provides parameter interface to any clock-like tree with serially sampled tips (parameters are the minimal node height differences at each internal node).class
UnconstrainedTree
provides parameter interface to an unconstrained tree (parameters are all available branch lengths)Methods in pal.tree that return ParameterizedTree Modifier and Type Method Description ParameterizedTree
ParameterizedTree.Factory. generateNewTree(Tree base)
Generate a new parameterized tree wrapped around baseConstructors in pal.tree with parameters of type ParameterizedTree Constructor Description LogParameterizedTree(ParameterizedTree params)
Takes a parameterized object and transforms the parameters logarithmically.
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