Accumulation of immunity in heavy-tailed sexual contact networks shapes mpox outbreak sizes

Source code accompanying Murayama et al. "Accumulation of immunity in heavy-tailed sexual contact networks shapes mpox outbreak sizes".
Published in The Journal of Infectious Diseases doi: 10.1093/infdis/jiad254

Main file

• countries_analysis.ipynb: Jupyter Notebook to identify where the local growth rate for each country reaches zero.
• US_states_analysis.ipynb: Jupyter Notebook to identify where the growth rate for each US-state reaches zero.
• SAR_estim.ipynb: Jupyter Notebook to reproduce the simulation outputs based on our network model.
• growth_estim.stan: Stan code for fitting observed cumulative incidence data to Gompertz curve with its local growth rate jointly computed.
• inference.R: R code to reproduce the transmission trajectories over time and the relationship between secondary attack risk and herd immunity threshold without accounting for the effect of any interventions or behavioural changes.
• finalsize.R: R code to compute the final sizes.

Licence

MIT

Authors

Hiroaki Murayama, Carl A. B. Pearson, Sam Abbott, Fuminari Miura, Sung-mok Jung, Elizabeth Fearon, Sebastian Funk, Akira Endo