Infection

class Infection(pars=None, *args, **kwargs)

Bases: Disease

Base class for infectious diseases used in Starsim

This class contains specializations for infectious transmission (i.e., implements network-based transmission with directional beta values) and defines attributes that connectors operate on to capture co-infection

Attributes

infectious	Generally defined as an alias for infected, although these may differ in some diseases.
now	Shortcut to self.t.now()
states	Return a flat list of all states
statesdict	Return a flat dictionary (objdict) of all states
ti	Get the current module timestep
timevec	Shortcut to self.t.timevec

Methods

property infectious

Generally defined as an alias for infected, although these may differ in some diseases. Transmission comes from infectious people; prevalence estimates may include infected people who don’t transmit

init_post()

Set initial values for states. This could involve passing in a full set of initial conditions, or using init_prev, or other. Note that this is different to initialization of the Arr objects i.e., creating their dynamic array, linking them to a People instance. That should have already taken place by the time this method is called.

init_results()

Initialize results

validate_beta(run_checks=False)

Validate beta and return as a map to match the networks

step()

Perform key infection updates, including infection and setting prognoses

static compute_transmission(src, trg, rel_trans, rel_sus, beta_per_dt, randvals)

Compute the probability of a->b transmission

infect()

Determine who gets infected on this timestep via transmission on the network