File manuscript.R calls a series of inbuilt OpenCOVID plotting functions that create all figures for the paper of Le Rutte, Shattock et al. (2022): Modelling the impact of Omicron and emerging variants on SARS-CoV-2 transmission and public health burden. Both for Figures 1 and 2 of the main manuscript as well as the Figures from the Supplementary Information. File plotting.R defines these inbuilt plotting functions. Detailed model descriptions and model equations of individual-based transmission model OpenCOVID are described in Shattock et al. (2022) and Le Rutte, Shattock et al. (2022). Open access source-codes for the OpenCOVID model of all analyses as presented in Le Rutte, Shattock et al. (2022) are publicly available at https://github.com/SwissTPH/OpenCOVID/tree/manuscript_december_2021/src.

{"references": ["Le Rutte, E. A., Shattock, A. J., Chitnis, N., Kelly, S. L. & Penny, M. A. The potential impact of Omicron and future variants of concern on SARS-CoV-2 transmission dynamics and public health burden: a modelling study. medRxiv 2021.12.12.21267673 (2022). doi:10.1101/2021.12.12.21267673"]}

Funding for the study was provided by the Botnar Research Centre for Child Health (to MAP) and the Swiss National Science Foundation Professorship of MAP (PP00P3_170702).