Principal Investigator

• Elisa Martin Merino

Core Scientific Group

• Elisa Martin Merino
• Fabio Riefolo
• Tiago Andres Vaz
• Rosa Gini
• Lamiae Grimaldi
• Olaf Klungel

List of authors of the programming code:

• Tiago Andres Vaz
• Davide Messina
• Roel Elbers
• Albert Cid Royo
• Vjola Hoxhaj
• Belén Castillo Cano
• Dorieke Brink-Kwakkel
• Rosa Gini

based on ConcePTION common data model

using VAC4EU definitions and tools: https://vac4eu.org

How it works

this pipeline implements the "BRIDGE" concept. It works reading a list of codes provided by VAC4EU: ../date/meta/20220930.csv ../date/meta/ALL_drugs_full_codelist.csv ../date/meta/vaccines_codelist.csv

codes later are selected and combined using algorithms. The selection and combination of codes into study variables are defined by metadata:

../date/meta/study_variables.csv ../date/meta/algorithms.csv ../date/meta/specific_additional_concepts.csv

Example: For the study variable CANCER (algorithms.csv) is assigned by the combination of Onc_ANYMALIGNANCY_COV or Onc_MALIGNANTTUMOR_CH and then these two are linked by study_variables.csv looking for STUDY_VARIABLE and ORIGIN joined with the codelist in 20220930.csv by SYSTEM, EVENT_ABBREVIATION and TYPE.

Instructions

1. Connected to GitHub, clone repository or download the .ZIP code

2. Save your files to your Project Folder (ex: /home/cove)

3. Unzip DemonstrationData.zip. Copy and paste data files inside ../CDMInstances/

4. Inside RStudio:

   • clean your environment

   • then, run "main.R"

Results

statistical results and aggregated tables will be generated inside folders "outcome" results to be exported are in "outcome/exports"