stisim.diseases.syphilis module#

Define syphilis disease module

class stisim.diseases.syphilis.Syphilis(pars=None, init_prev_data=None, init_prev_latent_data=None, **kwargs)[source]#

Bases: BaseSTI

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

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

property naive#: Never exposed

property sus_not_naive#: Susceptible but with syphilis antibodies, which persist after treatment

property active#: Active infection includes primary and secondary stages

property infectious#: Infectious

init_post()[source]#: Make initial cases

init_results()[source]#: Initialize results

step_state()[source]#: Updates to states

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.

finalize_results()[source]#: Finalize results

set_latent_trans(ti=None)[source]#

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

set_secondary_prognoses(uids)[source]#: Set prognoses for people who have just progressed to secondary infection

set_latent_prognoses(uids)[source]#

set_congenital(target_uids, source_uids=None)[source]#: Natural history of syphilis for congenital infection

class stisim.diseases.syphilis.SyphilisPlaceholder(pars=None, **kwargs)[source]#

Bases: Disease

init_pre(sim)[source]#: Link the disease to the sim, create objects, and initialize results; see Module.init_pre() for details

set_prognoses(target_uids, source_uids=None)[source]#

Set prognoses upon infection/acquisition

This function assigns state values upon infection or acquisition of the disease. It would normally be called somewhere towards the end of Disease.make_new_cases(). Infections will optionally be added to the log as part of this operation if logging is enabled (in the Disease parameters)

The sources are relevant for infectious diseases, but would be left as None for NCDs.

Args:: sim (Sim): the STarsim simulation object uids (array): UIDs for agents to assign disease progoses to from_uids (array): Optionally specify the infecting agent

step_state()[source]#: When using a connector to the syphilis module, this is not needed. The connector should update the syphilis-positive state.