Installing R and RStudio

For this introduction I recommend to install two software packages on your system:

  • R: The software, which does all the calculations.
  • RStudio: The working environment, where all the code will developed.

Note that the instructions of this section were written for a standard installation on a private computer. If you work on a corporate machine, the installation could be different due to different IT requirements of your company.

Installing R

A proper installation of R is the prerequisite of everything that will follow. Fortunately, installing R is easy and can be done quickly by following these steps:

  • Go to
  • Click on CRAN in the download section on the left.
  • Search the list for a server that is in or at least close to your country and click on it.


  • Click on Download R for Windows.
  • Click on base.
  • Click on Download R for Windows and download the file.
  • Execute the file and follow the installation instructions.

Mac OS X

  • Click on Download R for (Mac) OS X.
  • Click on R-.pkg and download the file.
  • Install the file.


If you use Linux, I trust that you are experienced enough that you can follow the installation instructions on the website. Alternatively, consult the person that put Linux on your system in the first place.

Once the installation is finished open R, enter 1+2 into the so-called command line and press return so that you get

## [1] 3

Congratulations, you just did your first calculation in R! You can close the window now…

The simple addition of numbers was probably not the main reason why you started to learn R. Usually, people want to do much more calculations of a more complex nature, which includes multiple operations and code that goes over many lines. Your current installation of R is perfectly able to do that. The main challenge is just to write your code and bring it into R’s command line. One solution to this problem could be to write several lines of code in a text document, copy and paste them into R for execution. But as you might imagine, this is a rather laborious way to proceed, especially when you are still developing your code. Therefore, I recommend to install further software, which makes it easier to work with R. This would be a so-called (integrated) development environment (IDE).

A development environment: RStudio

An IDE1 facilitates the work with a programming language. It assists in writing code, helps to find mistakes2, structures your workplace and allows for the quick execution of commands. This guide uses RStudio, which is widely accepted as a standard IDE for R projects. The software can be found at Search for the (free) version that matches your operating system, download it and install it by following the installation instructions.3

Once the installation is finished, open RStudio and take some seconds to familiarise yourself with its appearance. A first thing you might notice is that the left side looks somehow familiar to the R window from before. That is because it is that window. This so-called R console is the place, where all the calculations are done and the results and error messages show up. This integration of the R console in RStudio can be interpreted as if RStudio is a program that is built around R and can interact with it.

Next, click FileNew File (or press the button with the plus sign on the top left) and then R Script. A new window will appear above the console, which is called the editor. This is the place, where all the code is written into a script, which can be used by you and your colleagues to develop your analysis.

A very useful function of RStudio is that you can execute single or multiple lines of code directly from the editor. Try it out by typing 1+2 into the script and hit return. Nothing else will happen than the text cursor jumping to the next line. This is straightforward, because the editor is nothing else than a mere text editor. In order to execute the code from the editor window you have multiple choices:

  • Use your mouse cursor and mark the area of the script, which you want to execute. Then click Run on the top right of the editor window.
  • Mark the relevant area in the script again and use the keyboard shortcut Ctrl + Return.
  • Put the text cursor in the same line as the command, which you want to execute and press Ctrl + Return. Note that this method will execute all lines around the cursor, which belong to the command.

All of those three methods should lead to the same output in the console, [1] 3. For the time being, you can neglect the [1] in front of the answer.

Once the installation of R and RStudio is finished, we can proceed by understanding a bit more of R’s architecture in the next step.

  1. See, for example, Wikipedia: Integrated development environment.

  2. Mistakes in the code are also called bugs and the process of cleaning your code from such bugs is referred to as debugging.

  3. Note that there are also other IDEs for R – e.g., Bio7, Eclipse or IntelliJ IDEA – and you are free to use them. But since RStudio comes with a lot of nice additional tools, which facilitate the typical R workflow, I will stay with it until something better shows up.