Install and Setup
First things first, you need to install R and Positron and configure your environment in a way that is conducive to our workflow in the lab.
If you do not have R or Positron installed on your computer, then follow the install instructions below.
If you already have R or Positron installed on your computer, then you may want to update your installations.
Install Software
Install R
Download and install R from the R Project website.
- Go to the R Project website.
- Click on the “CRAN” link under “Download, Packages” in the left-hand menu.
- Choose the 0-Cloud mirror option.
- Select the base installation (for Windows) or the Latest Release (for Mac) option.
- Open and run the installer file that you downloaded. Follow the prompts to complete the installation.
Install Positron
Download and install Positron from the Positron website.
- Go to the Positron website.
- Click on the “Download” button.
- Select the appropriate version for your operating system.
- Open and run the installer file that you downloaded. Follow the prompts to complete the installation.
Update Software
Update R
Warning: When updating R (not RStudio), it may remove all packages you have installed.
First check what version of R you have installed by opening Positron and checking the R version number in the console when you start it up. If you have an R version older than 4.6.0, then you should update your R installation.
Use the installr package to update R on Windows. To do this, run the following code in the Positron console:
install.packages("installr")
library(installr)
updateR()Update Positron
To update Positron, go to the Positron website and download the latest version for your operating system. Then, open and run the installer file that you downloaded. Follow the prompts to complete the installation.
Getting to Know Positron
While R is the programming language that we will be using, Positron is the software that we will use to write and run R code. Positron is an Integrated Development Environment (IDE) for R. It provides a user-friendly interface for writing and running R code, as well as tools for debugging and visualizing data.
Open Positron and go through the Welcome Tour and Setup Guides to get familiar with the interface and features.
Configure Positron
Have a lab member or Dr. Tsukahara walk you through the Positron interface, and help you configure the settings to match the lab’s workflow. The following sections provide a summary of the recommended settings.
Install Extensions
To install an extension, click the Extensions icon (left sidebar) and search for the extension name.
Feel free to explore the available extensions, but the following are recommended for our lab workflow:
- Fira Code — a fancy monospaced font with ligatures (e.g.,
!=becomes ≠). - Material Icon Theme — icon themes change the look of folders and files.
- One Dark Pro — a dark theme for your IDE.
- GitHub Theme — a light theme for your IDE.
- vscode-pets — adds a cute pet to your IDE.
Opening Settings
- Press Cmd, or click the gear icon (bottom-left) → Settings.
- In the Settings window, click the Search settings bar at the top and type in the name of the setting you want to change. The list of settings will filter as you type.
Files & whitespace
| Setting | Search for | Action |
|---|---|---|
| Files: Associations | files associations |
Click Add Item → Item: renv.lock, Value: json |
| Files: Trim Trailing Whitespace | trim trailing |
Check |
| Files: Insert Final Newline | insert final newline |
Check |
| Files: Trim Final Newlines | trim final newlines |
Check |
Editor
| Setting | Search for | Action |
|---|---|---|
| Editor: Font Family | font family |
Set to Fira Code (keep existing fallbacks after it) |
| Editor: Font Ligatures | font ligatures |
Check |
| Editor: Font Size | editor font size |
Set to 14 |
| Editor: Format On Type | format on type |
Check |
| Editor: Tab Size | tab size |
Set to 2 |
| Editor: Detect Indentation | detect indentation |
Uncheck |
| Editor: Auto Indent | auto indent |
Dropdown → full |
| Editor: Wrapping Indent | wrapping indent |
Dropdown → indent |
| Editor: Default Formatter | default formatter |
Dropdown → Positron R (positron.positron-r) |
Quarto
| Setting | Search for | Action |
|---|---|---|
| Quarto › Cells › Background: Color | quarto background color |
Dropdown → useTheme |
| Quarto › Visual Editor: Markdown Wrap | quarto markdown wrap |
Dropdown → sentence |
| Quarto › Visual Editor: Default List Spacing | quarto list spacing |
Dropdown → tight |
Positron & keybindings
| Setting | Search for | Action |
|---|---|---|
| Positron › Assistant: Enable | positron assistant enable |
Check |
| Workbench › Keybindings: Rstudio Keybindings | rstudio keybindings |
Check |
Workbench, window & appearance
| Setting | Search for | Action |
|---|---|---|
| Workbench: Startup Editor | startup editor |
Dropdown → readme |
| Symbols: Hides Explorer Arrows | hides explorer arrows |
Uncheck (needs Symbols extension) |
| Window: Restore Windows | restore windows |
Dropdown → none |
| Window: Close When Empty | close when empty |
Check |
Icon theme (vscode-icons): set this via the picker rather than search — open the Command Palette (Cmd/Ctrl+Shift+P) → Preferences: File Icon Theme → choose VSCode Icons.
## Git & GitHub
| Setting | Search for | Action |
|---|---|---|
| Git: Autofetch | git autofetch |
Check |
| Git: Enable Smart Commit | smart commit |
Check |
| Git: Confirm Sync | confirm sync |
Uncheck |
| GitHub › Copilot › Next Edit Suggestions: Enabled | next edit suggestions |
Check (needs Copilot extension) |
Special cases
Markdown-only whitespace override ("[markdown]": { trimTrailingWhitespace: false }): in the Settings search bar type @lang:markdown, find Trim Trailing Whitespace, and uncheck it. The funnel scopes that single change to Markdown only and writes the language block for you.
Editor: Rulers ([80]): this array has no graphical control. Searching for rulers only offers an Edit in settings.json link, so this one entry must stay in JSON — add "editor.rulers": [80].