hpvsim/hpvsim_nigeria

HPVsim analyses of Nigeria # hpvsim_nigeria An HPVsim model of cervical cancer for Nigeria. Built on **hpvsim v2.3.0**. Ported from the `hpvsim_pxv_younger` analysis repo. ## Install ```bash pip install -r requirements.txt ``` Requires `hpvsim==2.3.0`. ## What's here | File | Purpose | |------|---------| | `run_sim.py` | Defines the Nigeria simulation (`make_sim`, `run_sim`). Nigeria-specific parameters (sexual behaviour, layer probabilities) are inlined here; mixing and initial conditions use hpvsim defaults. | | `run_calibration.py` | Calibrates the model to Nigeria data (`hpv.Calibration`). | | `run_scenarios.py` | Baseline vs WHO scale-up scenarios. | | `utils.py` | Fonts and calibration datafiles. | | `data/` | Calibration targets (cancer cases, CIN/cancer genotype distributions, ASR, HPV prevalence). | | `results/nigeria_pars.obj` | Calibrated parameter set (validated under v2.3.0). | | `tests/` | Smoke + validation tests. | ## Data provenance - `nigeria_cancer_cases.csv`, `nigeria_asr_cancer_incidence.csv` — cervical cancer incidence (IARC/Globocan). - `nigeria_cancer_types.csv`, `nigeria_cin_types.csv` — HPV genotype distribution in cancers / CIN (ICO/IARC HPV Information Centre). - `nigeria_hpv_prevalence.csv` — HPV/precancer prevalence (validation check). Data and the calibration framework were ported from `hpvsim_pxv_younger`. ## How to run ```bash python run_sim.py # single baseline run + plot (local) # Calibration — RUN only on a multi-core VM (edit `to_run` in the file): python run_calibration.py # 'plot_calibration' extracts/plots locally; # 'run_calibration' fits (VM only) python run_scenarios.py # Baseline vs WHO comparison (2100 horizon) ``` > **Calibration compute:** the calibration is only fast on multi-core machines. Run the > `run_calibration` step on a VM; use `plot_calibration` locally to extract the best > parameters into `results/nigeria_pars.obj`. ## Calibration status The parameter set in `results/nigeria_pars.obj` …