Documentation

The core implementation of the SIR model is maintained in the simpar.sim module (details of this model can be found in the Model section). It contains the simpar.sim.Sim class which is initialized with simulation parameters. The simpar.sim.Sim.step() method steps the simulation forward in time.

The simpar.micro module defines a single function called simpar.micro.days_infectious which returns the given number of days someone is expected to be free and infectious given the number of days between surveillance tests, the delay in receiving test results (isolation delay), the sensitivity of the test, and the maximum number of days someone is infectious. Details of this computation can be found in the documentation of this module.

The simpar.groups module defines the simpar.groups.MetaGroup class which represents a meta-group as defined in the Population Model section. It can be initialized from a dictionary. The simpar.groups.Population class is comprised of a set of meta-groups along with a meta-group contact matrix describing how these meta-groups interact with one another. This can also be initialized from a dictionary. It is responsible for managing the indices of the groups associated with each meta-group. Given S, R, D, and H counts at the meta-group level, The simpar.groups.Population.get_init_SIR_and_DH returns the initial counts at the group level. Furthermore, the class offers methods to return the infection matrix, outside rate, and both the infection and discovered recovery fractions.

The simpar.strategy module defines a pandemic response strategy. This is comprised of an isolation regime, arrival testing regime, and testing regime (used once the population has arrived). Each has its own respective class. Both testing regimes maintain lists of the simpar.strategy.Test class which maintains the properties of a test. This can be initialized from a dictionary allowing for representation in a parameter file such as JSON or YAML.

The simpar.scenario module defines the simpar.scenario.Scenario class which maintains all of the parameters pertaining to a scenario under which a disease is spreading. This consists of a simpar.groups.Population alongside environment parameters (e.g. outside rate of infection) and disease parameters (e.g. symptomatic rate). This can be initialized from a dictionary allowing for representation in a parameter file such as JSON or YAML. Furthermore, it offers the simpar.scenario.Scenario.simulate_strategy method which returns a completed simulation run under a given strategy.

Lastly, the simpar.trajectory module defines the simpar.trajectory.Trajectory class which is comprised of a simulation and scenario and strategy on which it was run. This class offers multiple methods for returning key metrics of the simulation.