diseases.sti
diseases.sti
Template class for SEIS-type STIs Used for chlamydia, gonorrhea, and trich
Classes
| Name | Description |
|---|---|
| BaseSTI | Base class for sexually transmitted infections. |
| BaseSTIPars | Base parameters shared by all STI disease modules. |
| SEIS | SEIS (Susceptible-Exposed-Infectious-Susceptible) disease template. |
| STIPars | Parameters for SEIS-type STI models. |
BaseSTI
diseases.sti.BaseSTI(
name=None,
pars=None,
init_prev_data=None,
age_range=None,
age_bins=default_age_bins,
sex_keys=default_sex_keys,
**kwargs,
)Base class for sexually transmitted infections.
Extends ss.Infection with STI-specific transmission logic, including network-specific beta values, condom efficacy, and initial prevalence by sex and risk group. All STIsim disease modules inherit from this class.
Parameters
| Name | Type | Description | Default |
|---|---|---|---|
| name | str | Module name used for results and parameter routing. | None |
| pars | dict | Override default parameters from BaseSTIPars. |
None |
| init_prev_data | Initial prevalence data (float or DataFrame by age/sex/risk group). | None |
|
| age_range | list | Age range used for the main (adult) prevalence results. Default: [15, 50]. | None |
| age_bins | list | Bin edges for age-stratified results; None skips them entirely. |
default_age_bins |
| sex_keys | dict | Sex strata for results, mapping result suffix to a people attribute; None skips sex-stratified results, keeping only the whole-population ones. |
default_sex_keys |
| **kwargs | Additional parameters passed to update_pars. |
{} |
Attributes
| Name | Description |
|---|---|
| treatable | Assume infected people are treatable, can be overwritten in subclasses |
Methods
| Name | Description |
|---|---|
| agehist | Return an age histogram |
| init_results | Initialize results |
| make_init_prev | Initialize prevalence by sex and risk group |
| set_outcomes | Set prognoses for newly infected agents and track transmission routes. |
| step | Override to pass network indices to set_outcomes for MTCT tracking |
| validate_beta | Map disease-specific transmission parameters onto the betamap. |
agehist
diseases.sti.BaseSTI.agehist(a)Return an age histogram
init_results
diseases.sti.BaseSTI.init_results()Initialize results
make_init_prev
diseases.sti.BaseSTI.make_init_prev(uids=None, data=None, active=True)Initialize prevalence by sex and risk group
set_outcomes
diseases.sti.BaseSTI.set_outcomes(uids, sources, net_ids=None)Set prognoses for newly infected agents and track transmission routes.
Parameters
| Name | Type | Description | Default |
|---|---|---|---|
| uids | UIDs of agents newly infected this timestep (not all agents) | required | |
| sources | UIDs of the agents who transmitted to each new case | required | |
| net_ids | array of network indices indicating which network each infection came from (used to distinguish prenatal vs postnatal MTCT). Passed from step() via infect(). | None |
step
diseases.sti.BaseSTI.step()Override to pass network indices to set_outcomes for MTCT tracking
validate_beta
diseases.sti.BaseSTI.validate_beta()Map disease-specific transmission parameters onto the betamap.
The parent class (ss.Infection) builds a betamap keyed by standardized network name, with [beta_p1→p2, beta_p2→p1] per network. Here we override entries for STI-specific networks using disease parameters:
- structuredsexual: beta_m2f (and rel_beta_f2m for female→male)
- maternal: beta_m2c (prenatal MTCT)
- breastfeeding: beta_breastfeed (postnatal MTCT, HIV only)
- msm: beta_m2m (bidirectional)BaseSTIPars
diseases.sti.BaseSTIPars(**kwargs)Base parameters shared by all STI disease modules.
Holds transmission parameters (beta values, condom efficacy), timestep settings, and initial prevalence configuration.
SEIS
diseases.sti.SEIS(
pars=None,
name=None,
init_prev_data=None,
age_range=None,
age_bins=default_age_bins,
sex_keys=default_sex_keys,
**kwargs,
)SEIS (Susceptible-Exposed-Infectious-Susceptible) disease template.
Provides the standard natural history framework for bacterial STIs: latent exposure period, sex-stratified symptom onset, symptomatic care-seeking, PID complications in females, and natural clearance. Used as the base class for chlamydia, gonorrhea, and trichomoniasis.
Naming follows starsim’s ss.SEIR: exposed and infectious are the literal E and I compartments, and infected is derived as E plus I, so n_infected and prevalence count everyone carrying the infection while transmission depends on infectious alone. Correspondingly, ti_exposed is the time of acquisition and ti_infectious the time of becoming infectious; ti_infected is not defined, since it is too easily confused with ti_infectious. Only ti_exposed is written exactly once per infection, so incidence is counted off that (see BaseSTI.update_results). Unlike ss.SEIR, step_state() below snaps ti_infectious forward to the timestep the transition actually happens, so it stays a truthful record of onset even when dur_exp is a fraction of a timestep.
Parameters
| Name | Type | Description | Default |
|---|---|---|---|
| pars | dict | Override default parameters from STIPars. |
None |
| name | str | Module name used for results and parameter routing. | None |
| init_prev_data | Optional initial prevalence data by age/sex. | None |
|
| age_range | list | Age range used for the main (adult) prevalence results. Default: [15, 65]. | None |
| age_bins | list | Bin edges for age-stratified results; None skips them entirely. |
default_age_bins |
| sex_keys | dict | Sex strata for results; None skips sex-stratified results. |
default_sex_keys |
| **kwargs | Additional parameters passed to update_pars. |
{} |
Methods
| Name | Description |
|---|---|
| init_results | Initialize results |
| set_prognoses | Set initial prognoses for adults newly infected |
| step_state | Updates for this timestep |
| wipe_dates | Clear all previous dates |
init_results
diseases.sti.SEIS.init_results()Initialize results
set_prognoses
diseases.sti.SEIS.set_prognoses(uids, sources=None)Set initial prognoses for adults newly infected
step_state
diseases.sti.SEIS.step_state()Updates for this timestep
wipe_dates
diseases.sti.SEIS.wipe_dates(uids)Clear all previous dates
STIPars
diseases.sti.STIPars(**kwargs)Parameters for SEIS-type STI models.
Extends BaseSTIPars with natural history parameters including symptom probabilities, care-seeking behavior, PID progression, and clearance durations. Used as the default parameter set for chlamydia, gonorrhea, and trichomoniasis.