Uses of Class
pal.tree.ParameterizedTree.ParameterizedTreeBase

Packages that use ParameterizedTree.ParameterizedTreeBase
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). 
 

Uses of ParameterizedTree.ParameterizedTreeBase in pal.coalescent
 

Subclasses of ParameterizedTree.ParameterizedTreeBase in pal.coalescent
 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
 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
ParameterizedTree.ParameterizedTreeBase(ParameterizedTree.ParameterizedTreeBase toCopy)
          Cloning constructor