Repo for scripts and data for HPVsim-GHL training session, February 2023

Organization

The repository is organized as follows:

Running scripts

There are three separate scripts for running and plotting simulations, calibrations, and scenarios. Specifically:

run_sims.py

• This script can be used to run or plot a single simulation.

run_calibration.py

This script is used for calibrating.

• run_calibration section runs a small demonstration calibration, taking less than a minute to run
• run_calibrated_sim runs a simulation using pre-generated parameters found from a more computationally intensive calibration run
• plot_calibration creates plots of the calibration outputs.

run_analyses.py

• run_scenarios compares 4 different scenarios, each with different screening algorithms in place from 2020-2060: HPV as a primary screen, AVE as a primary screen, HPV followed by VIA triage, and HPV followed by AVE triage.
• plot_scenarios produces plots of the scenarios described above.

Input data

• The data folder contains a series of .csv files tagged by country name, which contain the data that we use for calibrating the models.

Installation

If HPVsim is already installed (pip install hpvsim), no other dependencies are required.

Usage

Run the desired analyses by running one of the scripts described above.

Further information

Further information on HPVsim is available here. If you have further questions or would like technical assistance, please reach out to us at [email protected].