HPVsim model for India

This repository includes the code for creating and calibrating a model of HPV transmission and progression in India. The repository is organized to support reproducing the figures and analyses of the HPVsim methods manuscript.

Installation

If HPVsim v2.0.0 is already installed (pip install hpvsim==2.0.0), the only other required dependency is seaborn. Please ensure that you are using Python 3.9 or 3.10 (3.11 is not supported).

Organization

The repository is organized as follows:

Inputs

• data includes all the input datafiles used for making and validating the model.
• behavior_inputs.py contains additional behavioral input parameters.

Running scripts

• run_sim.py contains separate methods for running the sim, extracting sexual behavior, running and plotting a calibration, and running multiple parsets. In order to use the plotting scripts described below, these functions must be run first.

Plotting scripts

There are separate scripts for plotting each figure in the HPVsim methods manuscript. Specifically:

plot_fig2.py

• This script can be used to reproduce Figure 2.

plot_figS1.py

• This script can be used to reproduce Figure S1.

plot_figS2.py

• This script can be used to reproduce Figure S2.

plot_figS3.py

• This script can be used to reproduce Figure S3.

Additional utility scripts

• utils.py contains utilities for numerical calculations, processing data, and creating plots.
• plot_degree.py plots the network degree distribution for casual partnerships.