stisim.diseases.sti module#

Template class for SEIS-type STIs Used for chlamydia, gonorrhea, and trich

class stisim.diseases.sti.BaseSTI(name=None, pars=None, init_prev_data=None, **kwargs)[source]#

Bases: Infection

Base class for sexually transmitted infections. Modifies make_new_cases to account for barrier protection.

static make_init_prev_fn(module, sim, uids)[source]#

validate_beta(run_checks=False)[source]#: Validate beta and return as a map to match the networks

infect()[source]#: Determine who gets infected on this timestep via transmission on the network

class stisim.diseases.sti.SEIS(pars=None, name=None, init_prev_data=None, **kwargs)[source]#

Bases: BaseSTI

property treatable#: Active bacterial presence – includes exposed and infected, and responds to treatment

init_results()[source]#: Initialize results

clear_infection(uids)[source]#

step_state()[source]#: Updates for this timestep

update_results()[source]#

Update results

This function is executed after transmission in all modules has been resolved. This allows result updates at this point to capture outcomes dependent on multiple modules, where relevant.

set_exposure(uids)[source]#

set_pars(par, uids)[source]#

set_symptoms(p, uids)[source]#

set_care_seeking(p, symp)[source]#

set_pid(p, f_uids)[source]#

set_pid_care_seeking(p, pid)[source]#

set_duration(p, symp, asymp, pid)[source]#

wipe_dates(uids)[source]#: Clear all previous dates

set_prognoses(uids, source_uids=None)[source]#: Set initial prognoses for adults newly infected