starsimhub/sti_notification

Analysis of the health impact of STI partner notification in Zimbabwe # sti_notification Zimbabwe-calibrated STIsim modelling study of co-transmitting HIV, syphilis, gonorrhea, chlamydia, trichomoniasis, and bacterial vaginosis. We ran a 4 × 4 × 4 factorial of three demand-side and prevention levers (symptomatic care-seeking, partner-notification intensity, and bundled prevention via condoms and counseling for the diagnosed) layered on top of a point-of-care (POC) NG/CT/TV diagnostic vs syndromic standard-of-care, over 2027–2040. Combined at high intensity these levers approximately halve cumulative new curable-STI infections in Zimbabwe; POC diagnostics also reduce unnecessary treatments by 75–85% and unnecessary partner notification by ~30%, the latter a floor determined by diagnostic specificity rather than PN reach. Companion to `syph_dx_zim` (overtreatment) and `stisim_vddx_zim` (POC vs syndromic diagnostic accuracy for VDS). Built on STIsim. Full findings in `docs/sti_manuscript.md`; scenario design and calibration state in `SYNOPSIS.md`. ## Status Active calibration baseline: **exp 06** (500-draw LHS × K=5 sim-averaging, continuous weighted GoF, top-30 ensemble). Active scenario baseline: **65 cells × 10 draws × K=5 seeds = 3250 sims** (full factorial rerun 2026-07-22). ## Install ```bash pip install -r requirements.txt ``` Tested against `stisim==1.5.7`, `starsim==3.3.2` on Python 3.11 (conda env `starsim`). ## Quick start ```bash # Smoke-test the model (1985–1990, all 7 diseases) python model.py # Smoke-test the scenario factorial (5 cells × 5 draws × K=5 seeds = 125 sims) conda run -n starsim env SMOKE=1 N_WORKERS=30 python run_scenarios.py ``` For the full pipeline (factorial + aggregation + figures), see Regenerating results and figures below. ## Project structure | File / folder | Purpose | |---|---| | `model.py` | `make_sim()` — assembles the Zimbabwe sim (HIV + STIs + networks + interventions) | | `hiv_model.py` | HIV module factory + HIV testing/ART/VMMC/PrEP interventions | | `interventions.py` | Syndromi …