Uses of Class
pal.tree.ParameterizedTree.ParameterizedTreeBase
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Packages that use ParameterizedTree.ParameterizedTreeBase Package Description pal.coalescent Classes to model population genetic processes using the coalescent.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.ParameterizedTreeBase in pal.coalescent
Subclasses of ParameterizedTree.ParameterizedTreeBase in pal.coalescent 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.ParameterizedTreeBase in pal.tree
Subclasses of ParameterizedTree.ParameterizedTreeBase in pal.tree 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)Constructors in pal.tree with parameters of type ParameterizedTree.ParameterizedTreeBase Constructor Description ParameterizedTreeBase(ParameterizedTree.ParameterizedTreeBase toCopy)
Cloning constructor
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