Diseases
STIsim includes the following disease modules:
| Disease | Class | Alias | Model type |
|---|---|---|---|
| HIV | sti.HIV |
'hiv' |
CD4-based progression |
| Syphilis | sti.Syphilis |
'syphilis' / 'syph' |
Staged (primary/secondary/latent/tertiary) |
| Chlamydia | sti.Chlamydia |
'ct' |
SEIS |
| Gonorrhea | sti.Gonorrhea |
'ng' |
SEIS |
| Trichomoniasis | sti.Trichomoniasis |
'tv' |
SEIS with persistence |
| Bacterial vaginosis | sti.BV |
'bv' |
CST-based microbiome |
| Genital ulcer disease | sti.GUD |
'gud' |
Simple SIS |
All diseases can be passed to sti.Sim by name (string alias) or as module instances. When passed as a string, default parameters are used. To customize, either pass parameters via sti_pars or create the module directly:
# By name with defaults
sim = sti.Sim(diseases='hiv')
# By name with custom parameters
sim = sti.Sim(diseases=['hiv', 'ng'], sti_pars=dict(hiv=dict(init_prev=0.1)))
# As module instances
sim = sti.Sim(diseases=[sti.HIV(init_prev=0.1), sti.Gonorrhea()])