OHDSI Studies

Important: This repo was an attempt at organizing OHDSI study packages that wasn't very succesful. Please use the ohdsi-studies organization for sharing OHDSI study packages.

Running a study

Click on one of the folders and read the instructions there to execute one of these studies

Adding and updating studies

Adding a study to this repository

1. Create a study package repository in your own GitHub space. We do not store any packages directly in this repository. Instead, we rely on Git submodules. To create a study package, please create a repository in your own GitHub space. For example, a study package called 'MethodLibraryPleEvaluation' has been created here in @schuemie's personal space.

2. Add the package repository as a submodule. Here are example Git commands:

   First clone the OhdsiStudies repository if you haven't done so:

   git clone https://github.com/OHDSI/OhdsiStudies.git
   cd OhdsiStudies
   

   Then, add your repository as a submodule. Note that the URL is the 'clone' URL. The name after the URL is the name of the folder that will be created in the OhdsiStudies repository. Please keep that the same as the study package name:

   git submodule add https://github.com/schuemie/MethodsLibraryPleEvaluation.git MethodsLibraryPleEvaluation
   git commit -a -m "Adding submodule"
   git push
   

Updating study packages

Note that submodules create a snapshot of the study repository. OhdsiStudies will point to the commit at the time the submodule was added, future changes in the source repository are not automatically visible in OhdsiStudies. Whenever the source study package is updated, we may want to update the submodule in OhdsiStudies. Here's how:

First initialize your submodule. Before initialization, the submodules will just be pointers to the source repositories:

git submodule update --init -- MethodsLibraryPleEvaluation

Change into the submodule directory:

cd MethodsLibraryPleEvaluation

Switch to the source repository master branch if needed:

git checkout master

And pull the latest changes:

git pull

Go to the root folder, add the new changes, and push to OhdsiStudies:

cd ..
git add MethodsLibraryPleEvaluation
git commit -a -m "Updating MethodsLibraryPleEvaluation submodule"
git push