This lab is part of a series designed to accompany a course using The Analysis of Biological Data. The rest of the labs can be found here.


For these labs, you will need two apps on your computer: R and RStudio. Both of these are free, available to download without charge from the web. This setup requires a laptop or desktop computer. RStudio is not natively supported on Chromebooks or iPads/tablets. Desktop computers are available to use in 2004 Biological Sciences during BIOL 300 tutorial times; please consult your section’s TA.

Advanced users are permitted to use VS Code or Positron, but note that these apps are not fully endorsed by the BIOL 300 instructional team. You may need to adapt instructions on your own. See the sections at the end of this page for more information about using VS Code or Positron in BIOL 300.


Step 1: Install R on your computer

A list of sites where R can be downloaded is maintained at https://cran.r-project.org/mirrors.html. In most cases, the best choice is 0-Cloud. From the top box, click on the link that matches your type of computer in the section entitled “Download and Install R”.

Macs – If you have a Mac, you will likely first need to install XQuartz from https://www.xquartz.org. After it downloads, click on the .dmg file that appears in your downloads folder, and then form the folder that opens, click on the XQuartz.pkg file. Follow the installation instructions in the new window that opens.

To load R, choose the MacOS link from the CRAN website above. From the resulting page (called “R for Mac OS X”) choose the .pkg file that matches your version of the operating system – usually this is the first one. Once the .pkg file has downloaded fully, open it and follow instructions on screen.

Windows – After choosing Windows from the CRAN page, click on the first link for labeled “base”. Then click on the large top link “Download R-X.Y.Z for Windows”. Run the .exe file that downloads.


Step 2: Install RStudio onto your computer

Go to the download page for RStudio. Assuming you already installed R, look at the dropdown for “2: Install RStudio” and choose an option that matches your operating system.

Mac – Open the .dmg file that downloads. In the resulting window, drag & drop the RStudio icon into the Applications icon.

Windows – Run the .exe installer file that downloads.


Step 3: Get set up for BIOL 300 with ABDLabs

A .zip file that contains all the data sets, R scripts, and some other features can be downloaded in a folder called ABDLabs. After you download this file, first ensure that you move it outside of your computer’s Downloads folder. Keeping this within the Downloads problem often causes permission errors and other bugs. Most BIOL 300 students end up moving ABDLabs.zip to the Desktop. After moving the .zip file, unzip it. It should then open a folder called ABDLabs. Windows users: please be sure to fully unzip the entire file and not just open the zip file, as this can cause problems. The best practice is to right-click on it and choose “Extract All” or a similar option.

Inside ABDLabs is one file and two folders. The folder DataForLabs contains all the data sets that you will need to complete these labs; any new data we create during the course should also be saved there. The folder called LearningTheTools has an R script for each week, containing all the commands described in that week’s instructions. You’ll learn how to use these in Lab 1. The file ABDLabs.Rproj will provide a way to open RStudio and ensure your working directory and relative paths are set up on your computer; see further guidance below.


Step 4: Starting a new session in R

There is a file in the ABDLabs folder called ABDLabs.Rproj. You can double click on this file to start R and Rstudio automatically. If you start your session in R from this file, it will automatically load some packages of extra functionality that you will need for some tasks. Opening ABDLabs.Rproj will also automatically tell R to look inside the ABDLabs folder for files like the data sets. Starting from this file will make your life a little easier, and will also enforce a standard environment for all submitted work.


Support for VS Code or Positron

These labs are designed around RStudio, but we permit usage of Visual Studio Code (VS Code) or Positron for those who are already familiar with these apps. If you are not familiar with ether VS Code or Positron, we strongly recommend that you use RStudio for these labs.

The BIOL 300 instructional team only officially supports RStudio for our labs. The tutorials, screenshots, and troubleshooting guidance throughout the course assume that you are using RStudio. If you choose to use VS Code or Positron instead, you may occasionally need to adapt instructions and/or troubleshoot applications-specific issues on your own.

Regardless of the app you choose, all submitted R scripts must be .R file types and must follow BIOL 300 course conventions. Your submitted scripts must be able to reproduce results when run in a standard RStudio environment. Course conventions include formatting expectations, commenting practices, file naming, and script organization.

BIOL 300 does not support the use of Jupyter notebooks. While advanced users may be able to configure Jupyter to work with R, troubleshooting support for these setups will be limited.

Using VS Code with R

To use R in VS Code, you will first need to install the R extension for VS Code.

After installing VS Code, open the Extensions panel and search for “R” by Yuki Ueda (REditorSupport.r). Installing this extension provides features such as syntax highlighting, code execution, plotting support, and connections to the R console.

The ABDLabs folder distributed with these labs contains an .Rproj file. This file is used by RStudio to define the project working directory and session settings. VS Code does not directly use .Rproj files, but you can still work with the labs successfully by opening the entire ABDLabs folder in VS Code’s Explorer or via File → Open Folder.... Doing so helps ensure that relative file paths used throughout the labs work correctly.

Using Positron with R

Positron is a newer data-science environment developed by Posit, the company behind RStudio. It combines features of RStudio and VS Code into a modern interface that supports R, Python, Quarto, and other tools.

Because Positron is still under active development, some features may behave differently than they do in RStudio. However, many people find that it offers a familiar workflow while also providing additional flexibility and modern editing tools.

The .Rproj file included in the ABDLabs folder is primarily intended for use with RStudio. Positron can still work with projects that contain .Rproj files, but it does not rely on them in the same way that RStudio does. As with VS Code, the best approach is to open the ABDLabs folder in the Explorer or via File → Open Folder.... Doing so helps ensure that relative file paths used throughout the labs work correctly.