Covid Readiness Monitoring final scripts repository

Readiness v3.3.1 Instructions: To run the script this is the checklist of what to do: 1) Download the release and extract the folder. 2) Open the file 01_parameters_program.R inside the folder p_parameters 3) Open the to_run.R file and run just the parameters. 4) Check if everything is working correctly. Especially: Missing packages should be installed automatically by the script but sometimes updating an existing one may cause an error. If the script does not find the output of the pregnancy it produces an error (if the folder has been specified. 5) If everything is ok, run the script. *In case of problems, please open an issue in this same repository. Features to be aware of: 1) A computational graph is provided on this page which shows the interdependence between steps and outputs. This is useful if you need to understand what each step produces and to rerun only a part of the script. 2) Data models for each intermediate dataset (D3, D4, D5) are stored in the codebook on the ROC20 Sharepoint (here) 3) Every step is independent of the others. If a bug occurs in a step, the previous ones can be skipped when the need to rerun comes. 4) Most final tables are exported in csv, RData, html and rtf 5) After each step the environment cleans itself automatically. This consequence is, if there is a RAM shortage issue then it is useless to try and rerun only a single step at a time. Instead, quickly open an issue and we will try to find a solution.

COVID, Covid readiness monitoring