Alzheimer disease patient timeline ShinyApp

Explore timeline of Alzheimer patients doctoral visits and medicine reimbursement. Timeline is at maximum 15 years before and after the diagnose (day when patient got medicine special reimbursement right, erko307). Demo dataset is synthetic and has total number of 13 431 patients. Datasets are not available in GitHub repository.

Application available at http://bioinformatics.uef.fi/alzdemo/

How to clone and develop application in databricks Rstudio cluster

This project is developed in KUH datalake environment by running RStudio in a cluster.

1. Launch RStudio Cluster in databricks and login. Check guide how to install RStudio in databricks cluster here.

2. Copy ssh key to Github. In RStudio terminal run commands

ssh-keygen
cat ~/.ssh/id_rsa.pub

to generate ssh-keyfile and copy ssh-key file to Github keys https://github.com/settings/keys.

3. Clone project to databricks Rstudio cluster

git clone [email protected]:pohjois-savon-tietoallas/demo-alzheimer-shiny.git
$git clone [email protected]:pohjois-savon-tietoallas/demo-alzheimer-shiny.git # without ssh

4. Setup git user credentials

git config --global user.email "[email protected]"
git config --global user.name "User Name"

5. Open project, use script development_init.R for initilizing R environment.

6. Run shinyapp.Rmd (alt + shift + K)

Acknowledgements

We are grateful for all contributors including Juho Kopra and Pohjois-Savo Ai-Hub Team, and comments from clinical advisors from KUH. Also we are grateful for funders and Neurocenter Finland which made this project possible to develop. We would also give big thanks for the Bioinformatics Center for hosting this Shiny App.

Datasets are synthetic, but represent real world data. Original datasets are not freely available. If you are interested of the datasets, please contact Reijo Sund.

Kindly cite this work as follows: Jani Miettinen and Reijo Sund. Alzheimer disease patient timeline Shiny Application. URL: https://github.com/pohjois-savon-tietoallas/demo-alzheimer-shiny

This work is licensed under a Creative Commons Attribution 4.0 International License. This license allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.