R code in RMarkdown documents associated with the m.s. "Immunological characteristics govern the changing severity of COVID-19 during the transition to endemicity"
There are two RMarkdown files, each in a folder with all the necessary files to run the code.
MainSimulations.Rmd (in the folder MainSimulations) provides all the code necessary to generate figures in the main text of the article,
and Supplement.Rmd (in folder Supplement) to generate the figures in the supplement.
The basic age-structured model is present in boht documents.
The extensions to the model (including gamma-distributed duration of immunity and vaccination) are only in the supplementary code.
Any questions regarding the code should be addressed to Jennie Lavine (jslavin at emory dot edu).