.. _glossary:

Glossary
========

.. currentmodule:: epydemic
		   
.. glossary::

   compartments
      The possible dynamical states in a :term:`compartmented model of disease`.
   
   compartmented model of disease
      A disease model that represents the progression of a disease as
      a set of discrete compartments with transitions possible
      between them. Transitions typically occur with some base
      probability, which might be fixed or might vary across the
      course of the simulation. See :ref:`Hethcote <Het00>` for a survey,
   
   continuous time
      A simulation mode in which events occur at unique times
      represented by real numbers. No two events ever happen
      simultaneously, but they can be separated by an arbitrarily
      small interval. Continuous-time simulations can be made
      statistically exact and run faster for situations in which there
      are long periods where no events occur.

   discrete time
      A simulation mode in which time progresses in single integer
      timesteps. During each timestep a collection of events can
      occur. Discrete-time simulations can be easier to code and
      understand.

   dynamical state
      The state of a node or edge at some point in the
      simulation. These typically reflect the :term:`compartments`
      of the simulation, but may be more complex and
      comprise a vector of information.

   event
      A simulation event that changes the state of the underlying
      network or simulation. Events can occur in :term:`continuous
      time` or :term:`discrete time`.

   event function
      A function called when an :term:`event` fires to perform the
      action required. Event functions take four arguments: the
      :term:`Dynamics` object running the simulation, the
      current simulation time, the network, and the element at which
      the event occurs (which will be selected by the chosen
      :term:`process dynamics`). Elements are typically either nodes
      or edges, depending in the :term:`locus` at which the event
      occurs.
      
   locus
      A "place" at which dynamics can occur, that is to say, where
      nodes can change compartments and any other tasks can happen.
      Each :term:`event` is associated with a particular locus: the 
      locus contains the set of nodes or edges to which the event may
      be applied, while the event defines chat happens.

   posted event
      An :term:`event` posted for a definite future time. The
      :term:`process dynamics` will execute the posted events at the
      appropriate time
      
   process dynamics
      The simulation approach used, which selects how and when each
      :term:`event` fires. Process dynamics execute events in time
      order from two possible sources: a random distribution that
      chooses an event based on their relative probability or rate; and
      any :term:`posted event` that has been scheduled.
	    
   stochastic process
      A process whose exact progression is determined by random
      variables drawn from particular probability distributions.

   stochastic dynamics
      Also known as Gillespie dynamics, this :term:`process dynamics` operates
      in :term:`continuous time` with one event occurring at each time
      point.

   synchronous dynamics
      A :term:`process dynamics` using :term:`discrete time`, where a
      simulation passes through a sequence of discrete timesteps which
      may include several (or no) events happening.