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:class:`CompartmentedModel`: Compartmented models of disease

.. currentmodule:: epydemic


.. autoclass:: CompartmentedModel
   :show-inheritance:

Compartmented models are designed so that their specification is independent of the :term:`process dynamics` used to simulate them: they can be run in :term:`discrete time` using :term:`synchronous dynamics`, or in :term:`continuous time` using :term:`stochastic dynamics`.

:class:`CompartmentedModel` is an abstract class that must be sub-classed to define actual disease models. epydemic provides implementations of the three "reference" compartmented models, :class:`SIR`, :class:`SIS`, and :class:`SEIR`, as well as several variants of them: Hethcote :cite:`Hethcote-CompartmentedModels` provides a survey of a huge range of others.

Model state variables

These are used as tags for attributes on nodes and edges that store the model state.

.. autoattribute:: CompartmentedModel.COMPARTMENT


.. autoattribute:: CompartmentedModel.OCCUPIED


.. autoattribute:: CompartmentedModel.T_OCCUPIED


.. autoattribute:: CompartmentedModel.T_HITTING

Model setup

Immediately before being run, the model is set up by placing all the nodes into compartments. All edges are also marked as unoccupied.

.. automethod:: CompartmentedModel.reset


.. automethod:: CompartmentedModel.build


.. automethod:: CompartmentedModel.setUp


.. automethod:: CompartmentedModel.initialCompartmentDistribution


.. automethod:: CompartmentedModel.initialCompartments


.. automethod:: CompartmentedModel.changeInitialCompartment

Building and querying the model

Building a model (within :meth:`CompartmentedModel.build`) means specifying the various compartments, loci, and events, and their associated probabilities. The initial occupancy of compartments can be set to allow for random initialisation, and the occupancy of existing components changed to allow better sub-classing.

.. automethod:: CompartmentedModel.addCompartment

. automethod:: CompartmentedModel.changeCompartmentInitialOccupancy

.. automethod:: CompartmentedModel.trackNodesInCompartment


.. automethod:: CompartmentedModel.trackEdgesBetweenCompartments

We can also query the model, which is especially useful within event functions and when generating results in :meth:`CompartmentedModel.results`

.. automethod:: CompartmentedModel.compartments


.. automethod:: CompartmentedModel.compartment

Evolving the network

Events in compartmented models need an interface to change the compartment of nodes, to mark edges used in transmitting the epidemic, and to record the hitting time of nodes.

.. automethod:: CompartmentedModel.setCompartment


.. automethod:: CompartmentedModel.getCompartment


.. automethod:: CompartmentedModel.changeCompartment


.. automethod:: CompartmentedModel.markOccupied


.. automethod:: CompartmentedModel.markHit

The network access interface of :class:`Process` is extended with methods that understand the mappings between nodes, edges, and compartments.

.. automethod:: CompartmentedModel.addNode


.. automethod:: CompartmentedModel.removeNode


.. automethod:: CompartmentedModel.addEdge


.. automethod:: CompartmentedModel.removeEdge

Generating results

The experiment needs to define a results dict to return when it completes.

.. automethod:: CompartmentedModel.results


.. automethod:: CompartmentedModel.skeletonise