contact_tracing#

class contact_tracing(trace_probs=None, trace_time=None, start_day=0, end_day=None, presumptive=False, quar_period=None, capacity=None, **kwargs)[source]#

Bases: Intervention

Contact tracing of people who are diagnosed. When a person is diagnosed positive (by either test_num() or test_prob(); this intervention has no effect if there is not also a testing intervention active), a certain proportion of the index case’s contacts (defined by trace_prob) are contacted after a certain number of days (defined by trace_time). After they are contacted, they are placed into quarantine (with effectiveness quar_factor, a simulation parameter) for a certain period (defined by quar_period, another simulation parameter). They may also change their testing probability, if test_prob() is defined.

Parameters:

trace_probs (float/dict) – probability of tracing, per layer (default: 100%, i.e. everyone is traced)
trace_time (float/dict) – days required to trace, per layer (default: 0, i.e. no delay)
start_day (int) – intervention start day (default: 0, i.e. the start of the simulation)
end_day (int) – intervention end day (default: no end)
presumptive (bool) – whether or not to begin isolation and contact tracing on the presumption of a positive diagnosis (default: no)
capacity (int) – optionally specify a maximum number of newly diagnosed people to trace each day
quar_period (int) – number of days to quarantine when notified as a known contact. Default value is pars['quar_period']
kwargs (dict) – passed to Intervention()

Example:

tp = cv.test_prob(symp_prob=0.1, asymp_prob=0.01)
ct = cv.contact_tracing(trace_probs=0.5, trace_time=2)
sim = cv.Sim(interventions=[tp, ct]) # Note that without testing, contact tracing has no effect

Methods

initialize(sim)[source]#: Process the dates and dictionaries

apply(sim)[source]#

Trace and notify contacts

Tracing involves three steps that can independently be overloaded or extended by derived classes

Select which confirmed cases get interviewed by contact tracers
Identify the contacts of the confirmed case
Notify those contacts that they have been exposed and need to take some action

select_cases(sim)[source]#: Return people to be traced at this time step

identify_contacts(sim, trace_inds)[source]#

Return contacts to notify by trace time

In the base class, the trace time is the same per-layer, but derived classes might provide different functionality e.g. sampling the trace time from a distribution. The return value of this method is a dict keyed by trace time so that the Person object can be easily updated in contact_tracing.notify_contacts

Parameters:

sim – Simulation object
trace_inds – Indices of people to trace

Returns: {trace_time: np.array(inds)} dictionary storing which people to notify

notify_contacts(sim, contacts)[source]#

Notify contacts

This method represents notifying people that they have had contact with a confirmed case. In this base class, that involves

Setting the ‘known_contact’ flag and recording the ‘date_known_contact’
Scheduling quarantine

Parameters:

sim – Simulation object
contacts – {trace_time: np.array(inds)} dictionary storing which people to notify