From 4fabcb659509f115b09b507de185ee00f0d077f2 Mon Sep 17 00:00:00 2001
From: Thomas  OBADIA <thomas.obadia@pasteur.fr>
Date: Thu, 17 Oct 2024 14:39:49 +0200
Subject: [PATCH] Add README sections about the 02_OBSERVATIONAL sub-project.

---
 README.md | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/README.md b/README.md
index 2347ca6..ff3c5f4 100644
--- a/README.md
+++ b/README.md
@@ -121,6 +121,21 @@ All PvSTATEM partner are welcome to propose new contributions to this repository
   6. Preserve overall code structure by favoring `tidyverse` syntax and `ggplot` plots over base R calls. Base R is acceptable but should be refactored into `tidyverse` syntax as soon as possible,
   7. Document all scripts and methods both inline (comments) and in this README.md (respecting the template just below)
 
+## 02_OBSERVATIONAL
+
+Set of methods used to explore and analyze the content of the **Observational Study** databases hosted by partner institutions.
+
+### R environment setup and database extraction
+
+#### Scripts involed
+
+* [OBSERVATIONAL_00_R_environment.R](<02_OBSERVATIONAL/OBSERVATIONAL_00_R_environment.R>): load all required packages (or complain they are missing) and sets global variables for the 02_OBSERVATIONAL project.
+* [OBSERVATIONAL_01_dump_REDCap_database.R](<02_OBSERVATIONAL/OBSERVATIONAL_01_dump_REDCap_database.R>): extract database from the REDCap server that is passed into the `RCON_OBSERVATIONAL` variable. 
+
+#### Outputs
+
+* `dat_observational_raw`: the raw database from REDCap.
+
 ## README.md template
 
 The README.md should respect the following conventions:
-- 
GitLab