From 588454b07e1162ed1c088f7b606c908e12912c19 Mon Sep 17 00:00:00 2001 From: Soumya Banerjee Date: Wed, 8 Dec 2021 09:28:38 +0000 Subject: [PATCH] Create opal_instructions.txt --- opal_instructions.txt | 42 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 opal_instructions.txt diff --git a/opal_instructions.txt b/opal_instructions.txt new file mode 100644 index 0000000..8e48329 --- /dev/null +++ b/opal_instructions.txt @@ -0,0 +1,42 @@ +Instructions for setting up a new study in the Opal server + +Opal javascript code + +https://opaldoc.obiba.org/en/latest/magma-user-guide/value/value.html + +1. Have a data dictionary ready + + see projects/meat_project/meat_data_dictionary2.xlsx + +2. Find a way of splitting the data by country using R - can either use the CSV or Stata file. +The advantage of the Stata file might be that it preserves some metadata for uploading into Opal. + +Use R script meat_study.R + +3. Upload the data dictionary, data (in Stata format) and create the table. Instructions are here: + +https://gitlab.inesctec.pt/wp4-recap/wp4_workshop/-/wikis/opal + + a. Upload the data + b. Upload the data dictionary as an xls file (this should have harmonization Java code) + c. Click on import data to import data and create a table + d. Click on create view to link this table to a view. This will also ask for data dictionary + which has hamronization script. This will ultimately create a harmonized view. + +4. Create a view by + + a. selecting the table + b. selecting the data dictionary xls file. The file is called meat-harm-dictionary.xlsx + This will also have java script code for data harmonization. + + This will create a harmonized view. + +5. If the categories in the harmonised data are lost then + a. Go to each view, + b. make sure you are looking at Dictionary, + c. Click + Add Variables, + d. Choose Add/update variables from dictionary, + e. Choose the file meat_harm-dictionary2.xlsx + +6. Connect to Opal server from R Studio and write analyst code. See survival_testing_code.R +