starsimhub/stisim_vddx_zim

Analyses of diagnostics for discharging STIs in Zimbabwe # stisim_vddx_zim Analyses of diagnostics for discharging STIs in Zimbabwe Requires Starsim v2 and STIsim v1. ## Installation 1. Create a new virtual environment: `conda create -n stisim python=3.11 -y; conda activate stisim` 2. Install requirements: `pip install -r requirements.txt` 3. To check that it works, you can run `python model.py` ## Analysis overview Zimbabwe’s national guidelines for STI management recommend that high-risk women presenting with vaginal discharge syndrome (VDS) are prescribed antibiotics for gonorrhea (NG), chlamydia (CT), trichomoniasis (TV), and bacterial vaginosis (BV). The performance of this approach depends on rates of care-seeking and implementation of treatment guidelines. This repository contains scripts to analyze the efficiency and impact of syndromic management on STI transmission, and the potential impact of an NG/CT/TV point-of-care (POC) test for women with VDS. ## Repository structure - `data` contains all the input data used for the model, as well as the `zimbabwe_sti_data.csv` file that contains the data we calibrate to. - `results` contains result files - these are generated by running the four `run_*.py` scripts outlined below, and the are consumed by running the `plot_*.py` scripts. ### Model files - `hiv_model.py` and `model.py` contain an HIV model and a co-transmitting STI-HIV model, respectively. These can be run directly, but more often they will be called by a `run_*.py` script in the process of some analysis. - `analyzers.py` contain some analyzers used within the analyses - `interventions.py` contains interventions, specifically syndromic management and a hypothetical point-of-care (POC) diagnostic - `utils.py` contains utilities - `process_ihme_data.py` is needed to process a large result file (not in the repo) and output the data file `data/zimbabwe_sti_data.csv` used for calibration ### Files to run to produce results 1. Run `run_hiv_calibration.py` to calibrate the HIV model. 2. Run `run_calibration.p …