Setup for R workshops

Last updated on 2024-04-09 | Edit this page

R and RStudio

  • R and RStudio are separate downloads and installations. R is the underlying statistical computing environment, but using R alone is no fun. RStudio is a graphical integrated development environment (IDE) that makes using R much easier and more interactive. You need to install R before you install RStudio. After installing both programs, you will need to install some specific R packages within RStudio. Follow the instructions below for your operating system, and then follow the instructions to install tidyverse and RSQLite.

Windows

  • Open RStudio, and click on “Help” > “Check for updates”. If a new version is available, quit RStudio, and download the latest version for RStudio.

  • To check which version of R you are using, start RStudio and the first thing that appears in the console indicates the version of R you are running. Alternatively, you can type sessionInfo(), which will also display which version of R you are running. Go on the CRAN website and check whether a more recent version is available. If so, please download and install it. You can check here for more information on how to remove old versions from your system if you wish to do so.

  • Follow the steps in the instructions for everyone at the bottom of this page.

  • Download R from the CRAN website.

  • Run the .exe file that was just downloaded

  • Go to the RStudio download page

  • Under Installers select RStudio x.yy.zzz - Windows Vista/7/8/10 (where x, y, and z represent version numbers)

  • Double click the file to install it

  • Once it’s installed, open RStudio to make sure it works and you don’t get any error messages

  • Follow the steps in the instructions for everyone at the bottom of this page.

macOS

  • Open RStudio, and click on “Help” > “Check for updates”. If a new version is available, quit RStudio, and download the latest version for RStudio.

    • To check the version of R you are using, start RStudio and the first thing that appears on the terminal indicates the version of R you are running. Alternatively, you can type sessionInfo(), which will also display which version of R you are running. Go on the CRAN website and check whether a more recent version is available. If so, please download and install it.
  • Follow the steps in the instructions for everyone at the bottom of this page.

  • Download R from the CRAN website.

  • Select the .pkg file for the latest R version

  • Double click on the downloaded file to install R

  • It is also a good idea to install XQuartz (needed by some packages)

  • Go to the RStudio download page

  • Under Installers select RStudio x.yy.zzz - Mac OS X 10.6+ (64-bit) (where x, y, and z represent version numbers)

  • Double click the file to install RStudio

  • Once it’s installed, open RStudio to make sure it works and you don’t get any error messages.

  • Follow the steps in the instructions for everyone at the bottom of this page.

Linux

  • Follow the instructions for your distribution from CRAN, they provide information to get the most recent version of R for common distributions. For most distributions, you could use your package manager (e.g., for Debian/Ubuntu run sudo apt-get install r-base, and for Fedora sudo yum install R), but we don’t recommend this approach as the versions provided by this are usually out of date. In any case, make sure you have at least R 3.5.1.
  • Go to the RStudio download page
  • Under Installers select the version that matches your distribution, and install it with your preferred method (e.g., with Debian/Ubuntu sudo dpkg -i rstudio-x.yy.zzz-amd64.deb at the terminal).
  • Once it’s installed, open RStudio to make sure it works and you don’t get any error messages.
  • Follow the steps in the instructions for everyone

For everyone

  • After installing R and RStudio, you need to install the tidyverse and RSQLite packages. Start RStudio by double-clicking the icon and then type: install.packages(c("tidyverse", "RSQLite")). You can also do this by going to Tools -> Install Packages and typing the names of the packages you want to install, separated by a comma.

Software


Software Install Manual Available for Description
Spreadsheet program Link Link Linux, MacOS, Windows Spreadsheet program for organizing tabular data.
OpenRefine Link Link Linux, MacOS, Windows Program for reproducibly cleaning data.
R See install instructions below. Linux, MacOS, Windows Programming language for data analysis and visualisation.
RStudio Link Cheatsheet Linux, MacOS, Windows Integrated development environment for R.
SQLite Browser Link Link Linux, MacOS, Windows Tool for creating, designing, and editing database files.

SQL


  • SQL is a specialized programming language used with databases. We use a simple database manager called SQLite in our lessons. We will use the DB Browser for SQLite program, which is available for all major platforms.

  • To install the DB Browser, go to their download page and choose the correct installer for your operating system. Once the installer is downloaded, double click on it (you may need to open your Downloads folder), follow any other instructions that appear, and DB Browser should install. After installing, you can delete the installer .dmg file.

Data


You can download all of the data used in this workshop by clicking this download link. The file is 38.4 MB.

Clicking the download link will automatically download all of the files to your default download directory as a single compressed (.zip) file. To expand this file, double click the folder icon in your file navigator application (for Macs, this is the Finder application).

For a full description of the data used in this workshop see the data page.

Spreadsheet program

  • To interact with spreadsheets, we can use LibreOffice, Microsoft Excel, Gnumeric, OpenOffice.org, or other programs. Commands may differ a bit between programs, but the general ideas for thinking about spreadsheets are the same. For this workshop, we recommend using either Microsoft Excel (paid software) or LibreOffice (free and open source). Other spreadsheet programs may not have all of the features we will be exploring in this workshop.

  • To install LibreOffice, go to their download page. The website should automatically select the correct option for your operating system. Click the “Download” button. You will go to a page that asks about a donation, but you don’t need to make one. Your download should begin automatically. Once the installer is downloaded, double click on it (you may need to open your Downloads folder) and LibreOffice should install.

OpenRefine

  • OpenRefine is a Java program that runs on your local machine (not on the cloud). Although it displays in your browser, no web connection is needed and your data remains local. You need to have a ‘Java Runtime Environment’ (JRE) installed on your computer to run OpenRefine. If you don’t already have one installed and are running Windows, then you can download the “Windows kit with embedded Java” version from the downloads page. You can also download and install Java from https://java.com by going to the site and clicking “Free Java Download”.

  • To install OpenRefine, go to their download page. From the download page, select either “Windows kit”, “Mac kit”, or “Linux kit” - depending on your operating system - and follow the instructions next to your download link. This lesson has been tested with the recent versions of OpenRefine, at least 3.4.1. If you are using an older version, it is recommended you upgrade to the latest tested version.

  • You may get an error message: “OpenRefine.app can’t be opened because it is from an unidentified developer.” If you get this message, open your system preferences and click “Security & Privacy”. You will see a message “OpenRefine.app was blocked from opening because it is from an unidentified developer.” Click “Open Anyway” and “Yes”. OpenRefine should open in your default web browser.

  • OpenRefine does not support Internet Explorer or Edge. Please use Firefox, Chrome or Safari instead.

Congratulations! You are now ready for the workshop!