interventions.syphilis_interventions

interventions.syphilis_interventions

Define syphilis interventions for STIsim

Classes

Name	Description
ANCSyphTest	Antenatal care syphilis screening for pregnant women.
NewbornSyphTest	Syphilis test for newborns of mothers diagnosed during pregnancy.
NewbornTreatment	Treatment for congenital syphilis in newborns.
SyphDx	Syphilis diagnostic product.
SyphTest	Base class for syphilis screening and testing interventions.
SyphTx	Syphilis treatment intervention.

ANCSyphTest

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,
)

Antenatal care syphilis screening for pregnant women.

Schedules a syphilis test at a random gestational timepoint for each newly pregnant woman. Unlike the base :class:SyphTest, testing probability is not dt-scaled since tests are scheduled once per pregnancy rather than applied each timestep.

Parameters

Name	Type	Description	Default
test_prob_data		Testing probability (see :class:SyphTest).	None
years	list	Calendar years for test_prob_data.	None
start	float	Calendar year when ANC testing begins.	None
stop	float	Calendar year when ANC testing ends.	None
pars	dict	Parameter overrides.	None
product		Diagnostic product.	None
eligibility	func	Override default (pregnant women).	None
name	str	Intervention name.	None
label	str	Label for plotting.	None
newborn_test		Optional :class:NewbornSyphTest for positive mothers.	None
**kwargs		Additional parameter overrides.	{}

Methods

Name	Description
schedule_tests	Schedule a test for newly pregnant women

schedule_tests

interventions.syphilis_interventions.ANCSyphTest.schedule_tests()

Schedule a test for newly pregnant women

NewbornSyphTest

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,
)

Syphilis test for newborns of mothers diagnosed during pregnancy.

Administers scheduled tests to newborns whose mothers tested positive for syphilis at any point during pregnancy. Tests are only given at the scheduled timestep, filtered by acceptance probability.

NewbornTreatment

interventions.syphilis_interventions.NewbornTreatment(
    pars=None,
    eligibility=None,
    max_capacity=None,
    years=None,
    name=None,
    *args,
    **kwargs,
)

Treatment for congenital syphilis in newborns.

Extends :class:SyphTx to treat newborns diagnosed with congenital syphilis. Successful treatment clears the congenital state and resets the birth outcome to normal.

Parameters

Name	Type	Description	Default
pars	dict	Parameter overrides.	None
eligibility	func	Function returning eligible newborn UIDs.	None
max_capacity	int	Maximum treatments per timestep.	None
years	list	Calendar years during which the intervention is active.	None
name	str	Intervention name.	None
**kwargs		Additional parameter overrides.	{}

Methods

Name	Description
administer	Administer treatment to newborns
change_states	Change states of congenital cases

administer

interventions.syphilis_interventions.NewbornTreatment.administer(
    sim,
    uids,
    disease,
    return_format='dict',
)

Administer treatment to newborns

change_states

interventions.syphilis_interventions.NewbornTreatment.change_states(
    disease,
    treat_succ,
)

Change states of congenital cases

SyphDx

interventions.syphilis_interventions.SyphDx(df, *args, **kwargs)

Syphilis diagnostic product.

Wraps :class:STIDx with the disease key set to 'syph'. Used as the default product for syphilis testing interventions.

Parameters

Name	Type	Description	Default
df		Diagnostic performance data (sensitivity/specificity by stage).	required
*args		Positional arguments forwarded to :class:STIDx.	()
**kwargs		Keyword arguments forwarded to :class:STIDx.	{}

SyphTest

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,
)

Base class for syphilis screening and testing interventions.

Provides shared logic for processing test probability data (which can be stratified by risk group, sex, and sex-work status) and scheduling tests. Subclasses like :class:ANCSyphTest and :class:NewbornSyphTest customize eligibility and scheduling.

Parameters

Name	Type	Description	Default
test_prob_data		Testing probability; scalar, array, TimeSeries, or DataFrame stratified by risk group/sex/sex-work status.	None
years	list	Calendar years corresponding to test_prob_data values.	None
start	float	Calendar year when testing begins.	None
stop	float	Calendar year when testing ends.	None
pars	dict	Parameter overrides.	None
product		Diagnostic product (default: SyphDx).	None
eligibility	func	Function returning eligible UIDs.	None
name	str	Intervention name.	None
label	str	Label for plotting.	None
newborn_test		Optional :class:NewbornSyphTest to schedule for positive mothers.	None
**kwargs		Additional parameter overrides.	{}

Methods

Name	Description
make_test_prob_fn	Process symptomatic testing probabilites over time by sex and risk group
process_data	Turn dataframe into a dictionary

make_test_prob_fn

interventions.syphilis_interventions.SyphTest.make_test_prob_fn(sim, uids)

Process symptomatic testing probabilites over time by sex and risk group

process_data

interventions.syphilis_interventions.SyphTest.process_data(sim)

Turn dataframe into a dictionary

SyphTx

interventions.syphilis_interventions.SyphTx(
    pars=None,
    max_capacity=None,
    years=None,
    eligibility=None,
    name=None,
    **kwargs,
)

Syphilis treatment intervention.

Treats diagnosed syphilis cases each timestep, clearing all disease stages (primary, secondary, latent, tertiary) on successful treatment. Also treats fetuses of pregnant mothers, with reduced efficacy in the last trimester.

Parameters

Name	Type	Description	Default
pars	dict	Parameter overrides (e.g. treat_eff, fetus_treat_eff).	None
max_capacity	int	Maximum number of treatments per timestep.	None
years	list	Calendar years during which the intervention is active.	None
eligibility	func	Function returning eligible UIDs.	None
name	str	Intervention name.	None
**kwargs		Additional parameter overrides.	{}

Methods

Name	Description
change_states	Change the states of people who are treated
step	Apply treatment
treat_fetus	Treat fetuses of successfully treated mothers.

change_states

interventions.syphilis_interventions.SyphTx.change_states(disease, treat_succ)

Change the states of people who are treated

step

interventions.syphilis_interventions.SyphTx.step()

Apply treatment

treat_fetus

interventions.syphilis_interventions.SyphTx.treat_fetus(sim, mother_uids)

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