Analysis Version Control Using Github in
RStudio
What’s Github, and how is it useful?
Nate Thomas, NH Occupational Health Surveillance Program | Institute on
Disability, University of New Hampshire
12 October 2023
Purpose
Demonstrate:
the benefits of utilizing github as a file retention,
collaboration, and version control toolset.
a quick How-To, to set up github and utilize it within
RStudio.
Disclaimer: This is only intended for familiarization purposes -
github’s functionality and use far exceeds what I’ll be able to go over
here. I’m not affilidated with Github in any way.
Why Use Github?
Have you ever updated a file, and regretted it - wishing you
could revert back to a previous version? - I mash Ctrl+S
continuously during file/document updates as a matter of course… but
sometimes I wish I hadn’t.
Are your analysis files stored in a less than easy to use
and unintuitive C:/users/[username]/Documents folder, like a filing
cabinet without folders? Sometimes if one is just “doing this
one thing quickly” and lax about keeping files rigorously organized you
can really put yourself in a bind - if you have to then update it.
Do you have to pick up analysis from projects months, even
years later - and have a hard time remembering where you were at in the
process? Long term memory should be reserved for your important
moments in life… project status shouldn’t have to be something you need
to keep track of…
What does Github actually do? [www.github.com]
Github provides a free (with limitations) version
control and collaboration system.
Repository (Repo) - a github project container.
Fetch - retrieve new work by others using the repo.
Merge - combine fetched work with your local work.
Pull - Fetch and Merge combined (run at the same time).
Push - Send local work to the repo.
Clone - clones a repo to your local computer.
Every github repo has a unique URL - this exact project is here: https://github.com/unh-iod/CSTE_github_demonstration
A quick aside - SAS can be run in RStudio
My personal preference is to use Github within the RStudio integrated
development environment (IDE). This isn’t just for people using R as
their prefered scripting language.
Example dataset (class) from SAS from the sashelp library
proc means data=sashelp.class;
output out=temp;
run;
proc export data=temp
outfile="sas_data.csv"
dbms=csv
replace;
run;
The MEANS Procedure
Variable N Mean Std Dev Minimum Maximum
-------------------------------------------------------------------------
Age 19 13.3157895 1.4926722 11.0000000 16.0000000
Height 19 62.3368421 5.1270752 51.3000000 72.0000000
Weight 19 100.0263158 22.7739335 50.5000000 150.0000000
-------------------------------------------------------------------------
Passing data from SAS into R:
read.csv("sas_data.csv") %>% data.frame() %>% flextable()
X_TYPE_ | X_FREQ_ | X_STAT_ | Age | Height | Weight |
|---|
0 | 19 | N | 19.000000 | 19.000000 | 19.00000 |
0 | 19 | MIN | 11.000000 | 51.300000 | 50.50000 |
0 | 19 | MAX | 16.000000 | 72.000000 | 150.00000 |
0 | 19 | MEAN | 13.315789 | 62.336842 | 100.02632 |
0 | 19 | STD | 1.492672 | 5.127075 | 22.77393 |
Where to start…?
Source: https://resources.github.com/github-and-rstudio/
Download and install Git
Download and install RStudio.
(1.1.383 or higher).
Create a remote repository on Github:
- Copy the unique URL from github Code tab:
- Open RStudio and create a new project New Project > Version
Control > Git`:
> 
> 
- Paste the unique github repo URL and select a directory in which to
create the R project:
- This will create the folder and copy all contents of the github repo
into the new local directory. This is a new repo and so only contains a
.gitignore file (more on this later):
Adding files to the repo:
- Select Git > Commit:
- Stage the new file for Commit - a “Commit message” is required:
- The new repo branch “Main” is created:
Updating the file
This how you update files already in the repo:
Save the file locally.
Commit the changes:
- Push the changes to the remote github repo:
Reviewing changes to the project on github:
- Navigate to the github repo url: Example
- Select a file to review and select
:
- Select a Commit to review exactly what changed:
Inviting others to collaborate:
- Setting tab in the github repo select Collaborators:
Adding github users is as easy as adding them here.
An email invitation will be sent to the prospective collaborator
- and they will be able to then accept the invitation and work on the
repo.
Ignoring files in the local directory
Select Git > Commit and click 
Enter file names for files that should only be stored locally
(ignored by the repo)
- Select Save - this updates the .gitignore file
Questions?
