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Written for version 0.1.14.

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On your computer, data feed into R, which produces results. A blocked red arrow shows that the chat app cannot access restricted data; the LLM runs in the cloud. Code panels align across the computer, GitHub and cloud assistant, with arrows for code changes, reviewed code, project files and pull requests. Cleared results go to GitHub. A person reviews, approves and merges there. GitHub also holds the analysis plan, decision issues and history. The project website displays explanations, code and cleared results.

Code moves between your computer, GitHub and the assistant; a person approves every change. By default, data stay on your computer.

Find the line that fits you. Each says what to have ready and the first thing to type to the assistant once the plugin is installed. You don’t need to name a skill or know the Git words: the assistant explains them as they come up.

New to GitHub? The GitHub glossary explains repository, branch, commit, pull request and issue; Happy Git and GitHub for the useR shows how to use them from RStudio. The plugin’s own terms (analysis plan, decision issue, decider, AGENTS.md) are explained on Home.

I’m starting a new project

  • Have ready: the idea or protocol, and about an hour. You don’t need R, Git or a GitHub account yet; the assistant walks you through what the work needs.
  • Type: “I have no GitHub account and no R. Help me get this project started.”
  • Then: it asks a few questions one at a time, including who decides the scientific questions, and drafts the plan and the repository. Whoever sets up can own the repository; it can move to the PI later. More on Start a project.

I’m joining a project that already exists

  • Have ready: the repository’s link, and access from whoever owns it if you’ll change code.
  • Type: “I’m joining this project: [repository link]. What’s done, what’s open, and what’s waiting on me?”
  • Then: it works from the repository (the plan, open issues and pull requests), not from the last person’s files or chats, and gives one next step at a time. More on Join or leave a project.

I’m taking over, or answering reviewer comments

  • Have ready: the repository’s link, and the reviewers’ requests.
  • Type: “The analysts have left and I need to answer reviewer comments. Where does this project stand, and who decides what?”
  • Then: it finds the deciders in the project’s AGENTS.md. A reviewer’s request to change the methods is a new decision for them, not something to change directly; once the plan is locked, a change is recorded as a dated amendment.

I’m the PI or a decider

  • You’ll be asked to: confirm who decides what; protect the main branch and switch on the website (the assistant gives the steps); settle open questions in their GitHub issues, or by email.
  • By email: your exact words are posted in the issue. If the repository is public, they are public.
  • Optional: a weekly check-in that tells you only what is waiting on you.

I’m a clinician advising the project

  • You don’t need R, GitHub or the plugin. Read the project’s website, starting at Clinical background and Study design and methods. Yellow text is not yet decided, and links to the open question.
  • To give input: reply by email, or comment on the linked issue if you have a GitHub account. A public repository’s issues can be read without an account.
  • If you’re named a decider for part of the study, your reply settles that question, and your exact words are posted in the issue.