The Basics of R and RStudio

Learning Objectives

  • Create an R project.
  • Describe the purpose of RStudio’s script, console, environment, and file/plot/help windows.
  • Assign names to objects in R with <- and =.
  • Solve mathematical operations in R.
  • Organize files and directories for a set of analyses as an R Project.

Introducing R and RStudio

R and RStudio are distinct programs and need separate downloads and installations.

R is:

  • An open-source programming language under GPL
  • Aimed as a statistics and data analysis environment
  • Adapted to build websites, run simulations, and more
  • Good general language as it is both object-orientated and functional language

R is the underlying statistical computing environment, but using R alone is not as intuitive

RStudio is:

  • An graphical Integrated Development Environment (IDE) makes using R much easier and more interactive
  • Makes developing code in R easier

Installation

You need to install R before you install RStudio. Please choose the operating system (OS) that you use from the key information tab.

Open up a new Project

  • Under the File menu, click on New project, choose New directory, then Empty project
  • Enter a name for this new folder, and choose a convenient location for it. This will be your working directory for the rest of the day (e.g., ~/data-carpentry)
  • Confirm that the folder named in the Create project as a sub-directory of the box is where you want the working directory created. Use the Browse button to navigate folders if changes are needed.
  • Click on “Create project”
  • Under the Files tab on the right of the screen, click on New Folder and create a folder named data within your newly created working directory. (e.g., ~/data-carpentry/data)
  • Create a new R script (File > New File > R script) and save it in your working directory (e.g. data-carpentry-script.R)s
  • We can open it by clicking the New File button or using the Ctrl-Shift-N keyboard shortcut (Cmd-Shift-N) on Mac

Layout of RStudio and Interacting with R

layout Parts of the RStudio

  1. Folder setup, Plots, Packages, Help, and more Blue
    • Let’s save the Rscript we have been writing into. Please select File --> Save and enter in a suitable name for your Rscript.
    • You should see this is now available in the folder.
    • The following sections will explore the other tabs in this corner.
  2. Interpreter/Console is where R is actually running Dark purple
    • Work in here interactively.
    • Let’s first try and run our first line of code into our console. I will explain more about this in a bit. 
      "Hello"
    • Type commands directly into the console, but they will be forgotten when you close the session.
  3. Text editor Green
    • Where we write code we want to keep and potentially reuse later
    • Creates a plain text file that stores the code we’ve written
    • Let’s write the same line of code, Hello, as before but this time in the text editor.
    • You can copy-paste into the R console, but the Rstudio script editor allows you to ‘send’ the current line or the currently selected text to the R console using the Ctrl-Enter shortcut.
    • Better to enter the commands in the script editor and save the script. This way, you have a complete record of what you did, you can easily show others how you did it, and you can do it again later on if needed.
    • > indicates that R is ready to accept commands.
    • Let’s write the code that creates an error. 
      "Hello
    • + indicates that R is waiting for you to finish entering a command. This is usually due to not writing the pair of brackets or quotations.
  4. Environment, History, Git, and more Orange
    • You can even use R like a sophisticated calculator. Run the commands below. 
      3 + 5
12/3
    • But if you want to be able to access a value later, we need to assign values to objects .
    • You can either assign a value using <- or =.
    • However, it is good practice to use <- for assignments and = for values of arguments in a function. 
      name <- "Hello"
name = "Hello"
    • You should now be able to see the name in the environment tab. Some details about your new variable should be beside the name.

Hint - A comment is a line of code with # at the beginning. This signifies to the R interpreter to not use this line as code but, in fact, information about the code.

   #Assign 9 to a
   a <- 9
   #Assign 2 to b
   b <- 2

Exercise

  1. How much are a and b added together?
  2. Change the value of a to 10
  3. Assign the value of a and b together to a new variable, c.

Material adapted from (https://datacarpentry.org/R-genomics/01-intro-to-R.html) and (https://datacarpentry.org/semester-biology/materials/r-intro/)