Start a project

Written for version 0.1.14.

What it is for

Setting up a new analysis project, or tidying an existing one (a folder of scripts, or one long R Markdown file), so it becomes a GitHub repository in a consistent layout that the next person can pick up.

When to use it

  • You have an idea, a protocol or an old script, and no repository yet.
  • You have a repository that grew without a plan and want it organized.
  • A setup was started in an earlier chat and not finished.

What happens

The assistant asks a short set of questions, one at a time, and reuses anything you have already told it or that is already in the files. It does not ask you to install R or Git unless the work needs them; a clinician can help with the protocol from the browser.

Then it proposes a setup plan and, once you agree, drafts:

  • the analysis plan (analysis-plan.md), from a template that fits the design (observational, economic or descriptive), with a decision issue for every scientific choice still open rather than a guess;
  • AGENTS.md, the project’s rules for any assistant: who the deciders are and for what, every data source and the package that reads it, and what an assistant may never read;
  • the website starter, once you’ve said whether the site will be published from a folder in the repository or by a GitHub workflow;
  • a README, a reference list, and a .gitignore that keeps data and secrets out of the repository;
  • steps for the maintainer to protect the main branch, so every change arrives through a pull request, and to switch on the website.

It also offers, without requiring them: your own ChatGPT or Claude project for this repository with instructions filled in for how you like to work, milestones with dates, and a periodic check-in that tells you what is waiting on you.

What it will not do

  • Choose a scientific option. It drafts the options; a decider settles them.
  • Open data that may be restricted while taking stock of a folder.
  • Install tools, publish anything or change repository settings on its own.
  • Overwrite files an existing project already has. It lists what differs from the starter instead.

Ask it, for example

  • “Set up my R analysis project from my latest RMD and protocol.”
  • “I have no GitHub account and no R. Help me get this project started.”
  • “We started setting this up last week; carry on from where it stopped.”

Where the detail lives