This is the repository of the script implementing the Objective 2 of the SAFETY-VAC project. The study is registered in the EMA-HMA Catalogues here.
The detailed documentation of the script can be browsed starting from this link. From the tree at this link, you can browse the codebooks of the intermediate dataset (represented by rectangles) and the steps of the R procedure (represented by circles).
To reproduce the script
- clone the repository in your R Studio
- open the folder i_input_subpop: this contains synthetic data where the script can be executed
- open the to_run.R file
- run the header (rows 1-150): this will load packages and set up parameters
- run the steps (rows 155 onwards): they correspond to the circles in the documentation above and each of them generates intermediate datasets; after each step is ru, the intermediate dataset can be opened in the folder g_intermediate
- at the end of the run open the folder g_export and find the produced tables and figures
Some steps also come with test mode, for example 03_T2_11_create_cohort_flowcharts.R. Such steps can be executed in test mode by setting TEST <- T and running them. In this case, the script points to a folder of dummy data that are easy to inspect