This repository performs the Caballo et. al 2023 JAMA analyses in R (except for the heatmap figures).
The data folder contains the data as downloaded from the CDC and the life expectancy data as a .dta file
The code folder has all the scripts that do the data preprocessing, statistical analyses and computations, and plotting
The results folder is created when running the scripts and stores the final dataframes that we use for plotting
The plots folder is created when running the scripts and stores the plots for each of the scripts in each of its subfolders
Navigate to code and then do Rscript excess-mortality-by-age.R, Rscript excess-mortality-by-year.R, Rscript life-years-lost-by-age.R, Rscript life-years-lost-by-year.R.
Swap out the files in data. The header portions of the above R scripts contain a lot of the things that need to be modified like input and output file paths and different age buckets. Note that it is overwhemlingly likely that some alteration of the internal code and plotting will be necessary for each individual project.
For reference, the file preprocess-function.R contains functions that are used by all four scripts.