Pre-mat workshop quick start

This guide will help you get started with RStudio Server and set up your first R project in GitHub.

Getting started with rstudio server

In order to avoid every student having to install R themselves and deal with operating-system-specific issues, we have set up RStudio Server and given each student access. If you are unfamiliar with R or RStudio, take some time to familiarize yourself with each.

Once you are ready, navigate to the URL you were provided with. This screen should appear:

Enter the username and password you were given at the start of the workshop. This will start an RStudio session in your browser. If it worked, you should see your home screen:

The only difference between using RStudio Server and RStudio (besides the fact that one is in a browser...) is that your scripts, packages, and data are stored on the cloud computer instead of your personal computer.

To get files onto the cloud computer you can:

1. Upload the files from your personal computer using the 'Upload' button in the right-hand 'files' panel.
2. Use RStudio's built-in 'Terminal' to download files via linux shell commands:

wget https://raw.githubusercontent.com/millerh1/premat-workshop/master/README.md

3. Use R commands to download files:

download.file(url="https://raw.githubusercontent.com/millerh1/premat-workshop/master/README.md",
              destfile="README.md")

4. For advanced users, consider using ssh to access the linux server directly. Your username and password are the same which you used to login to RStudio Server.

Setting up a project and adding it to GitHub

As part of this workshop students will complete a short project. You can choose any project you would like as long as it involves analyzing a dataset and reporting the results using R. An example project has been provided here under SARS-CoV-2 project/.

To set up a project in RStudio, click the Project button and follow the prompts to create the project directory. While it is not required to make an RStudio project, there are many benefits to doing so. Chief among these is that you can move the project folder to any location or to any computer and the scripts inside it will still work correctly.

The next step is to initialize your project with git. git is a versioning system for coding projects. When you make changes to your code, you will 'commit' the changes to the git repository and then push these changes to GitHub.

1. Open the 'Terminal' in RStudio:

2. At this point you should be inside your project directory if you followed the RStudio project directions. Now we initialize this project as a git repository. Type this command into the terminal and hit 'Enter':

git init

This is the output if successful:

Initialized empty Git repository in /home/username/my-project/.git/

3. Now we create some content by entering this in the terminal:

echo "# Hello World!" > README.md

4. Add the new project files to the git repo:

git add .

5. Tell git which kinds of files to ignore:

echo ".Rproj.user" > .gitignore

5. Configure your author information with this repository:

git config user.email "[email protected]"
git config user.name "Henry Miller"

6. Commit your changes to the repository:

git commit -m "My first commit!"

The next step is to add the project to GitHub. GitHub is a central repository for computer code and serves as both a convenient storage space for data, a nexus for collaborations, and a resume of your past projects and coding sklls. For this workshop you will create a GitHub account and push your git repository there.

1. Create a GitHub account using your school email.
2. Create a new repository in GitHub (don't bother adding a README)
3. Link this remote GitHub repository with your local git repository by typing the following into the terminal:

git remote add origin https://github.com/millerh1/my-project.git

4. Push the changes your commited earlier to GitHub:

git push -u origin master

5. Refresh your GitHub page -- if this worked it should now say "Hello World!" in the README.

Now that you have successfully set up your GitHub repository you are free to start coding. Anytime you make some significant changes it is good practice to commit these changes to GitHub:

git add .
git commit -m "a description of the changes I made"
git push 

When you finish your analysis return to the README.md file and start documenting what you did. .md files are written in markdown. For a guide on how to write in this language, check out this tutorial.

To see an example of a completed project, check out the SARS-CoV-2 project/ folder.