STAT 406 — Course Website / Lectures

This repository generates the course website and holds all lecture materials. It is hosted at https://github.com/ubc-stat/stat-406 and published to https://ubc-stat.github.io/stat-406/.

For course infrastructure setup and management (Canvas, Slack, clickers, R package, homeworks/labs/exams, etc.), see the README in [https://github.com/UBC-STAT/stat-406-instructors/](the STAT 406 instructors repo).

Contents

The entire site and all materials are Quarto (.qmd) files.

• _quarto.yml — top-level site configuration (navbar, footer, render list, theme).
• index.qmd, syllabus.qmd, faq.qmd — landing page and standalone pages.
• schedule/index.qmd — the schedule: module outlines, learning objectives, and the date-by-date table linking to every slide deck and lecture note.
• schedule/slides/ — the intro material, as Quarto reveal.js slides (00-intro.qmd, 00-r-review.qmd, 00-version-control.qmd). Slide-specific config lives in _metadata.yml (reveal.js format), _config.R, _titleslide.qmd, themer.scss, and tachyons-minimal.css.
• schedule/lectures/ — the rest of the lectures, as Quarto notes (lecture_01_*.qmd … lecture_20_*.qmd), rendered to HTML. Format config is in that folder's _metadata.yml.
• schedule/Rcode/ — standalone R code for the lectures.
• schedule/notebooks/ — Jupyter notebooks that generate lecture figures into schedule/figures/. Not rendered as part of the site; run manually to regenerate plots.
• schedule/handouts/ — supplementary handouts (programming, RMarkdown, git lab).
• computing/ — platform-specific setup instructions (mac_arm.qmd, mac_x86.qmd, ubuntu.qmd, windows.qmd).
• assets/ — shared styles (styles.scss, index.css) and images.
• _freeze/ — cached results of executed R chunks (see below). Checked in.

Some notes:

• _quarto.yml contains the configuration for the site.
• schedule/slides/_metadata.yml contains configuration for the slides; schedule/lectures/_metadata.yml for the lecture notes.
• Installing the course package should install all necessary packages to render the site. But some may be missing.

Updating the website

The site is configured following https://quarto.org/docs/publishing/github-pages.html#publish-action. Deployment is automatic:

1. Push to main on GitHub. The Quarto Publish GitHub Action (.github/workflows/publish.yml) renders the site and pushes the compiled output to the gh-pages branch, which is what gets served.
2. All R code must be run before pushing. The site uses execute: freeze: auto, so the Action does not run R — it reuses the cached chunk output in _freeze/. This avoids needing an renv setup in the Action. Commit any changes to the _freeze/ files whenever you edit code in a .qmd, or the published site won't reflect your changes.

Debugging

If the website doesn't update after a push:

• Check whether the build Action failed (repo → Actions tab).
• If it failed, run quarto render locally and look for the errors there.
• If it renders successfully locally, commit any updated _freeze/ files and push again to re-trigger the build.