.. _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 ` 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.