• Tour of R and RStudio
    • R basics
  • Tour of GitHub
    • Getting Started
      • Configuring SSH and GitHub
      • Configure git
    • Clone the Repo & Start New RStudio Project
  • Bechdel
  • Additional Resources

Tour of R and RStudio

R basics

We can use R as a calculator by typing the following in “Console”:

3 * 5 + 10
x <- 3
x + x^2

For more complex analyses, we need to know definitions of common terms:

  • A variable is a container for storing data. <- and = are known as “assignment operators” and they save a value (or collection of values) as a variable.
y <- 2
x = 1:10

When you type the name of an object into the console, it prints to the screen. The variables can also be found in “Environment”.

x
##  [1]  1  2  3  4  5  6  7  8  9 10
  • A function is literally just a bunch of instructions. Most often, we will work with functions that take input (also called arguments) and return an output.
mean(x)
## [1] 5.5

mean() is a function that takes a numeric input and returns the mean of that input. All functions in R have () and inside those parentheses is where inputs (aka “arguments”) go.

  • A package (also called a library) is a collection of functions and/or data.
library(fivethirtyeight)
  • Data frames are lists of variables. Typically the columns are called “variables”, while the rows are thought of as “observations”. bechdel is a data frame in fivethirtyeight package.
bechdel
  • Let’s check the help documentation of bechdel.
?bechdel

Tour of GitHub

Getting Started

Configuring SSH and GitHub

Until recently, you could use a user name and password to log into GitHub. GitHub has deprecated using a password in that way. Instead, we will be authenticating GitHub using public/private based keys. This is a short overview for how to authenticate in this way.

  1. First, type credentials::ssh_setup_github() into your console.
  2. R will ask “No SSH key found. Generate one now?” You should click 1 for yes.
  3. You will generate a key. It will begin with “ssh-rsa….” R will then ask “Would you like to open a browser now?” You should click 1 for yes.
  4. You may be asked to provide your username and password to log into GitHub. This would be the ones associated with your account that you set up. After entering this information, you should paste the key in and give it a name.

Configure git

We need to configure git so that RStudio can communicate with GitHub. This requires two pieces of information: your name and the email address associated with your GitHub account.

To do so, you will use the terminal, which you can find right next to the console.

git config --global user.name 'username'
git config --global user.email 'useremail'

For example, mine would be

git config --global user.name 'jinbora0720'
git config --global user.email 'bora.jin@duke.edu'

Note: you should not have to do this every time.

Clone the Repo & Start New RStudio Project

  1. Visit course GitHub organization page and accept the invite to join the course.
  2. Select the repository entitled “ae02-GitHubUsername”
  3. Click on the green Code button, select SSH (this might already be selected by default, and if it is, you’ll see the text Clone with SSH). Click on the clipboard icon to copy the repo URL.

  1. In your RStudio, go to File → New Project → Version Control → Git.
  2. Copy and paste the URL of your assignment repo into the dialog box Repository URL. Again, please make sure to have SSH highlighted under Clone when you copy the address.

  1. Click Create Project, and the files from your GitHub repo will be displayed in the Files pane in RStudio.
  2. Click ae02_Bechdel.Rmd to open the template R Markdown file.

Bechdel

  • Put your name for the author, the knit the document.
  • Select all of the updated files in the Git pane, click to commit and write the commit message “Update author name”.
  • Click to push your changes.
  • Refresh your repo on GitHub and see if the files are correctly updated with your commit message.
  • Follow along with the instructions in ae02_Bechdel.Rmd.