2021-04-30 APR

Onboarding with RStudio

Onboarding and researchers using RStudio into Confluence Data Platform:

1. Copy the File ID. This will be used in the R boxr packageIn Rstudio, run the following commands:

2. install.packages("boxr")

3. library(boxr)

4. box_auth()

5. The console will then ask for credentials as shown below

6. enter the following information:

   • Client ID: 627lww8un9twnoa8f9rjvldf7kb56q1m

   • Client Secret: gSKdYKLd65aQpZGrq9x4QVUNnn5C8qqm

7. Discuss why these credentials don't give you access to anything ! <-- important !

8. It's all set, try x = box_read(<fileId>)

9. Run analysis on the file loaded with box_read.

10. Write back with modifications and see how Box tracks versions and authentications

11. Ask for access to this folder to experiment with non-sensitive but realistic data: https://nih.app.box.com/folder/133596945131

12. Configure Github in your RStudio and ask for write permissions to https://github.com/episphere/Rtest

13. Let's now connect your machine's RStudio with your Github account - chose Global Options and generate a public key for git. Commit that public key to your Github ssh.

14. Let's connect Rtest by creating a new project: in Githbub click on the green Code button and copy the ssh link, git@github.com:episphere/Rtest.git , and use it to create a new project.

15. Let's take time at this point to go over the creation and management of code branches in github directly from RStudio. For an overall view of who is doing what check the network in insights (shortcut: https://github.com/episphere/Rtest/network). Use the code you right to read and write back to the shared Box folder.

16. As you take time with #15 analysing data with others, make friends and co-conspirators at https://gitter.im/episphere/Fair. As these interactions unfold, we'll be generating persistent support material at https://github.com/episphere/fair/wiki and https://github.com/episphere/fair/discussions.