amath-idm / hpvsim_multical

Inferring the natural history of HPV from global cancer registries: insights from a multi-country calibration

Summary

This repository includes the code for generating the figures and results in the manuscript "Inferring the natural history of HPV from global cancer registries: insights from a multi-country calibration". The citation for the manuscript is:

Inferring the natural history of HPV from global cancer registries: insights from a multi-country calibration (preprint). Stuart RM, Cohen JA, Abeysuriya RG, Sanz-Leon P, Kerr CC, Rao D, Klein DJ.

Structure

• The scripts prefixed run_ are used for running simulations and calibrations.
• The scripts prefixed plot_ are used for plotting figures. The numbering of the figures corresponds to the numbering in the manuscript.
• The data folder contains all the input data used in the analyses
• The results folder contains the finalized parameter sets from the immunovarying calibration.
• The script calibration.py contains the methods and classes for running MultiCals, as used in the constrained calibrations within the manuscript.
• The scripts locations.py and utils.py contain the list of country locations and various utilities, respectively.

Installing and running

• Ensure you have Python installed (if you haven't installed Python already, the easiest is to use Anaconda).
• Install HPVsim
• Clone this repository and run the scripts as desired.