Uses of Interface
pal.misc.Units

Packages that use Units
Package
Description
pal.coalescent
Classes to model population genetic processes using the coalescent.
pal.mep
Classes for the analysis of "measurably evolving populations" (mep).
pal.misc
Classes that don't fit elsewhere ;^)
pal.supgma
 
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 Units in pal.coalescent

    Classes in pal.coalescent that implement Units
    Modifier and Type
    Class
    Description
    class 
    CoalescentIntervals
    A series of coalescent intervals representing the time order information contained in a (serial) clock-constrained tree.
    class 
    ConstantPopulation
    This class models coalescent intervals for a constant population (parameter: N0=present-day population size).
    class 
    ConstExpConst
    This class models a population that grows exponentially from an initial population size alpha N0 at time y to a size N0 at time x until the present-day.
    class 
    ConstExpGrowth
    This class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.
    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).
    class 
    DemographicModel
    This abstract class contains methods that are of general use for modelling coalescent intervals given a demographic model.
    class 
    ExpandingPopulation
    This class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.
    class 
    ExponentialGrowth
    This class models an exponentially growing (or shrinking) population (Parameters: N0=present-day population size; r=growth rate).
    class 
    IntervalsExtractor
    A series of coalescent intervals representing the time order information contained in a (serial) clock-constrained tree.
    class 
    SkylinePlot
    Skyline plot derived from a strictly bifurcating tree or a coalescent interval.

  • Uses of Units in pal.mep

    Classes in pal.mep that implement Units
    Modifier and Type
    Class
    Description
    class 
    ConstantMutationRate
    This class models a constant mutation rate (parameter: mu = mutation rate).
    class 
    MutationRateModel
    This abstract class contains methods that are of general use for modelling mutation rate changes over time.
    class 
    SteppedMutationRate
    This class models a step-wise mutation rate.
    class 
    WindowedMutationRate
    This class models a windowed mutation rate (parameter: mu = mutation rate).

  • Uses of Units in pal.misc

    Subinterfaces of Units in pal.misc
    Modifier and Type
    Interface
    Description
    interface 
    UnitsProvider
    interface for classes that can provide the related Units used, (as
    Classes in pal.misc that implement Units
    Modifier and Type
    Class
    Description
    class 
    TimeOrderCharacterData
    Character data that expresses an order through time.

  • Uses of Units in pal.supgma

    Classes in pal.supgma that implement Units
    Modifier and Type
    Class
    Description
    class 
    SUPGMATree
    constructs an SUPGMA tree from pairwise distances.

  • Uses of Units in pal.tree

    Subinterfaces of Units in pal.tree
    Modifier and Type
    Interface
    Description
    interface 
    ParameterizedTree
    abstract base class for a tree with an Parameterized interface
    interface 
    Tree
    Interface for a phylogenetic or genealogical tree.
    Classes in pal.tree that implement Units
    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 
    ClusterTree
     
    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 
    NeighborJoiningTree
    constructs a neighbor-joining tree from pairwise distances

    Saitou, N., and Nei, M., (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees.
    static class 
    ParameterizedTree.ParameterizedTreeBase
    For parameterisations that work by adjusting a base tree (that is, they aren't really tree's themselves...)
    class 
    ReadTree
    constructs a tree reading in a New Hampshire treefile, taking care for internal labels and branch lengths and binary/nonbinary and rooted/unrooted trees
    class 
    SimpleTree
    data structure for a binary/non-binary rooted/unrooted trees
    static class 
    Tree.TreeBase
     
    class 
    UnconstrainedTree
    provides parameter interface to an unconstrained tree (parameters are all available branch lengths)
    class 
    UPGMATree
    Deprecated.
    Use ClusterTree