stisim.interventions.syphilis_interventions module#

Define syphilis interventions for STIsim

class stisim.interventions.syphilis_interventions.SyphDx(df, *args, **kwargs)[source]#: Bases: STIDx

class stisim.interventions.syphilis_interventions.SyphTx(pars=None, max_capacity=None, years=None, eligibility=None, name=None, **kwargs)[source]#

Bases: STITreatment

Treat a fixed number of people each timestep.

administer(sim, uids, disease='syphilis', return_format='dict')[source]#: Administer treatment, keeping track of unnecessarily treated individuals

change_states(disease, treat_succ)[source]#: Change the states of people who are treated

treat_fetus(sim, mother_uids)[source]#: Treat fetuses of successfully treated mothers. Birth outcomes of successfully treated fetuses will be updated. If fetus is not yet infected, the treatment doesn’t do anything. Treatment success depends on when in the pregnancy the mother gets treated with reduced treatment efficacy above the cut off age

step()[source]#: Apply treatment

class stisim.interventions.syphilis_interventions.NewbornTreatment(pars=None, max_capacity=None, years=None, eligibility=None, name=None, **kwargs)[source]#

Bases: SyphTx

change_states(disease, treat_succ)[source]#: Change states of congenital cases

administer(sim, uids, disease, return_format='dict')[source]#: Administer treatment to newborns

class stisim.interventions.syphilis_interventions.SyphTest(test_prob_data=None, years=None, start=None, stop=None, pars=None, product=None, eligibility=None, name=None, label=None, newborn_test=None, **kwargs)[source]#

Bases: STITest

Base class for syphilis tests

init_pre(sim)[source]#

Perform initialization steps

This method is called once, as part of initializing a Sim. Note: after initialization, initialized=False until init_vals() is called (which is after distributions are initialized).

process_data(sim)[source]#: Turn dataframe into a dictionary

static make_test_prob_fn(self, sim, uids)[source]#: Process symptomatic testing probabilites over time by sex and risk group

step(uids=None)[source]#: Apply the testing intervention

update_results()[source]#: Perform any results updates on each timestep

update_positives()[source]#

update_negatives()[source]#

class stisim.interventions.syphilis_interventions.ANCSyphTest(test_prob_data=None, years=None, start=None, stop=None, pars=None, product=None, eligibility=None, name=None, label=None, newborn_test=None, **kwargs)[source]#

Bases: SyphTest

Test given to pregnant women Need to adjust timing using Trivedi (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7138526/)

get_testers(sim)[source]#: Find who tests by applying eligibility and coverage/uptake

schedule_tests()[source]#: Schedule a test for newly pregnant women

step()[source]#: Apply the testing intervention

class stisim.interventions.syphilis_interventions.NewbornSyphTest(test_prob_data=None, years=None, start=None, stop=None, pars=None, product=None, eligibility=None, name=None, label=None, newborn_test=None, **kwargs)[source]#

Bases: SyphTest

Test given to newborns if the mother was confirmed to have syphilis at any stage of the pregnancy

get_testers(sim)[source]#: Find who tests by applying eligibility and coverage/uptake