starsimhub/hivsim_eswatini

HIV modeling in Eswatini # HIVSim Eswatini Model Agent-based HIV model for Eswatini, built on STIsim and Starsim. The model includes a structured sexual network with risk groups, HIV transmission, testing (FSW-targeted, general population, low-CD4), ART, and PrEP. It is calibrated to UNAIDS estimates and PHIA household survey data. ## Project Docs ## Prerequisites 1. **Python 3.9+** (we recommend Miniforge) 2. **Install Starsim and STIsim** by cloning and installing locally: ```bash git clone github.com cd starsim pip install -e . cd .. git clone github.com cd stisim pip install -e . cd .. ``` Installing with `-e` (editable mode) means changes to the source code take effect immediately without reinstalling. 3. **Clone this repo**: ```bash git clone github.com cd hivsim_eswatini ``` 4. **Raw data** (not tracked in git): place the `raw_data/` folder in the repo root. This contains UNAIDS Excel files, PHIA survey CSVs, and population data. Ask the project lead for access. 5. **IDE setup**: We recommend VS Code with the Python and Claude Code extensions. Open the `hivsim_eswatini` folder as your workspace. You can run any script by opening it and pressing the play button, or by using the integrated terminal. ## Workflow The scripts are designed to be run in order. Each step produces outputs used by the next. ### Step 1: Format the input data for HIVsim (only needed once, or when raw data changes) Run `utils.py`. This reads raw UNAIDS and PHIA data from `raw_data/` and produces `data/eswatini_hiv_calib.csv` — a single CSV with one row per year and columns matching the sim's result names. The calibrator uses this file to compute goodness-of-fit. ### Step 2: Run a single simulation (for quick testing) Run `run_sims.py`. Runs one sim with default parameters and saves results to `results/eswatini_sim.df`. Also opens a plot window showing HIV dynamics. Use this to check that the mo …