Class SpeciesUpdate

Object
SpeciesUpdate
public class SpeciesUpdate extends Object
The implementation of population updates. Population updates are used to update the population size and composition of individuals.

The population update type can be set to one of the following:

synchronous
Synchronized population updates.
Wright-Fisher
Wright-Fisher process (synchronous)
asynchronous
Asynchronous population updates (default).
Bd
Moran process (birth-death, asynchronous).
dB
Moran process (death-birth, asynchronous).
imitate
Moran process (imitate, asynchronous).
ecology
Asynchronous updates (non-constant population size).

The population update type can be set via the command line option --popupdate <u> [&gt;p&lt;] where <u> is the population update type, and &gt;p&lt; the fraction of individuals that reassess their trait.

Author:
Christoph Hauert

  • Nested Class Summary

    Nested Classes
    Modifier and Type
    Class
    Description
    static enum 
    SpeciesUpdate.Type
    Types of species updates (only relevant for multi-species models): size focal species selected proportional to their size fitness focal species selected proportional to their total fitness turns one species is selected after another. sync simultaneous updates of all species (not yet implemented). For size and fitness selection is also proportional to the update rate of each species.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    final CLOption
    clo
    Command line option to set the method for updating the population(s).
    (package private) Module<?>
    module
    The module that is using this species update.
    (package private) SpeciesUpdate.Type
    type
    The species update type.

  • Constructor Summary

    Constructors
    Constructor
    Description
    SpeciesUpdate(Module<?> module)
    Instantiate new population update for use in IBS models.

  • Method Summary

    Modifier and Type
    Method
    Description
    SpeciesUpdate.Type
    getType()
    Gets the population update type.
    boolean
    setType(SpeciesUpdate.Type type)
    Sets the population update type.
    String
    toString()
     

    Methods inherited from class Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

  • Field Details

  • Constructor Details

    • SpeciesUpdate

      public SpeciesUpdate(Module<?> module)
      Instantiate new population update for use in IBS models.
      Parameters:
      module - the module using this species update

  • Method Details

    • setType

      public boolean setType(SpeciesUpdate.Type type)
      Sets the population update type.
      Parameters:
      type - the updating type for the population
      Returns:
      true if population update type changed

    • getType

      public SpeciesUpdate.Type getType()
      Gets the population update type.
      Returns:
      the population update type

    • toString

      public String toString()
      Overrides:
      toString in class Object