build: 🔧 add files to auto-build website (#4)

@arborzhang I added several files to automatically build the website.

Whenever you use a new R package, you need to always run
`usethis::use_package("PACKAGENAME")` (where PACKAGENAME is the package
you will use), so that the website builder knows how to install and use
it. Just like how you do with the UKB RAP project.

In general, it's good practice to name files all lower case (it looks
nicer in the URL for the website) and to always start each "chapter"
(session or any file you want as a page on the website) with a single
`#` header. You don't need to use the YAML header.

Slides are a bit trickier. Let me know if or how you want to use them
and I can help out with that.

In the `_quarto.yml` file is a list of files you can add to put into the
website. I'l make direct comments on them in the PR.

.github/workflows/build-website.yml

@@ -0,0 +1,42 @@
+name: Build website to GitHub Pages
+
+on:
+  push:
+    branches:
+      - main
+
+# You need these permissions to publish to GitHub pages
+permissions: 
+  contents: write
+  pages: write
+
+jobs:
+  build-deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tinytex: false
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+
+      - name: Install R package dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache-version: 2
+
+      - name: Publish to GitHub Pages (and render) 
+        uses: quarto-dev/quarto-actions/publish@v2
+        with:
+          target: gh-pages
+        env:
+          # This secret is always available for github actions
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} 

.gitignore

@@ -1,6 +1,25 @@
+# RStudio and R files
+.Rbuildignore
 .Rproj.user
 .Rhistory
-.RData
-.Ruserdata
-.DS_Store
+.Rdata
+
+# Temporary files
+*.tmp
+
+# Authentication files
+.httr-oauth
+
+# MacOS
 .DS_Store
+
+# Quarto
+/.quarto/
+
+# Website generation
+_site
+_book
+_freeze
+*_files
+*.html
+

DESCRIPTION

@@ -0,0 +1,20 @@
+Package: ideg.mediation.course
+Type: Website
+Version: 0.1
+Title: "Mediation course"
+Depends: 
+    R (>= 3.6.0),
+    tidyverse
+Encoding: UTF-8
+LazyData: true
+Imports: 
+    CMAverse,
+    DiagrammeR,
+    DiagrammeRsvg,
+    dplyr,
+    here,
+    knitr,
+    medflex,
+    mediation,
+    readr,
+    rmarkdown

README.md

@@ -4,20 +4,24 @@
 4.0](https://img.shields.io/badge/License-CC%20BY%204.0-lightgrey.svg)](https://creativecommons.org/licenses/by/4.0/)
 
 ## Description
+
 This short workshop on Directed Acyclic Graphs (DAGs) and mediation analysis
-is offered as part of the [International Diabetes Epidemiology Group (IDEG) 
-Trainee Workshop](https://www.ideg-diabetes.org/idegtraineeworkshop) in 
+is offered as part of the [International Diabetes Epidemiology Group (IDEG)
+Trainee Workshop](https://www.ideg-diabetes.org/idegtraineeworkshop) in
 Bangkok, Thailand, on 3 April 2025.
 
 This repository contains the lesson, lecture, and assignment material
 for the course, including the website source files and other associated
 course administration files.
 
+To install the packages needed to build this website, run:
+
+``` r
+pak::pak()
+```
 
-## Contributing
+Build the website either in RStudio with `Ctrl-Shift-B` or:
 
-If you are interested in contributing to the course material, please
-refer to the [contributing guidelines](CONTRIBUTING.md). Please note
-that the project is released with a [Contributor Code of
-Conduct](CODE_OF_CONDUCT.md). By contributing to this project, you agree
-to abide by its terms.
+``` r
+quarto::quarto_render()
+```

_quarto.yml

@@ -0,0 +1,34 @@
+project:
+  type: book
+  # pre-render: quarto render slides/*.qmd
+  # resources:
+  #   - slides/*.html
+
+book:
+  title: "Mediation course"
+  author: 
+    - Jie Zhang
+    - Daniel Witte
+  date: last-modified
+  repo-url: https://github.com/steno-aarhus/IDEG-mediation-course
+  site-url: https://steno-aarhus.github.io/IDEG-mediation-course
+  chapters:
+    - index.qmd
+    - part: "Preamble"
+    - part: "Sessions"
+      chapters:
+      - sessions/welcome.qmd
+      - sessions/motivation.qmd
+      - sessions/traditional-mediation-analysis.qmd
+  appendices:
+    - appendix/welcome.qmd
+  page-footer:
+    center:
+      - text: "License: CC BY 4.0"
+
+format: html
+
+editor:
+  markdown:
+    wrap: 72
+    canonical: true

Appendix/1.Welcome.qmd → appendix/welcome.qmd

@@ -1,20 +1,23 @@
 ---
 title: "Mediation Ananlysis"
-format: html
-editor: visual
 ---
 
 ## Welcome
 
-Welcome to the short workshop on Directed Acyclic Graphs (DAGs) and mediation analysis!
+Welcome to the short workshop on Directed Acyclic Graphs (DAGs) and
+mediation analysis!
 
 Instrctors: Daniel Witte, Jie Zhang
 
 Time duration: 75 mins
 
 # Course Outline
 
-During this 75-minute course, you will learn about traditional mediation approaches before exploring the theory of causal mediation, accompanied by hands-on R coding practice. We hope this will be the beginning of your journey in mediation analysis and open the door to more interesting research studies!
+During this 75-minute course, you will learn about traditional mediation
+approaches before exploring the theory of causal mediation, accompanied
+by hands-on R coding practice. We hope this will be the beginning of
+your journey in mediation analysis and open the door to more interesting
+research studies!
 
 ::: callout-note
 ## Learning outcomes
@@ -46,7 +49,9 @@ During this 75-minute course, you will learn about traditional mediation approac
 
 ## Important things before the course
 
-To make the most of our training course in Bangkok, please complete the pre-course tasks before you arrive. This will ensure we can start our sessions smoothly and dive right into the content!
+To make the most of our training course in Bangkok, please complete the
+pre-course tasks before you arrive. This will ensure we can start our
+sessions smoothly and dive right into the content!
 
 ## Course outline
 
@@ -58,8 +63,14 @@ To make the most of our training course in Bangkok, please complete the pre-cour
 
 ## Acknowledgement
 
-This course is developed based on 'Mediation Analysis Course' developed by Daniel B. Ibsen, Omar Silverman, Jie Zhang from Steno Diabetes Center Aarhus in Denmark, and Nima Hejarzi and Ivan Diaz from the US, which is sponsored by the Danish Diabetes and Endocrine Academy.
+This course is developed based on 'Mediation Analysis Course' developed
+by Daniel B. Ibsen, Omar Silverman, Jie Zhang from Steno Diabetes Center
+Aarhus in Denmark, and Nima Hejarzi and Ivan Diaz from the US, which is
+sponsored by the Danish Diabetes and Endocrine Academy.
 
-The repository contains the lesson, lecture, and assignment material for the course, including the website source files and other associated course administration files. You can always go to check the website to learn more about mediation.
+The repository contains the lesson, lecture, and assignment material for
+the course, including the website source files and other associated
+course administration files. You can always go to check the website to
+learn more about mediation.
 
-[https://analysis-of-mechanisms.netlify.app/https://analysis-of-mechanisms.netlify.app/](https://analysis-of-mechanisms.netlify.app/)
+[https://analysis-of-mechanisms.netlify.app/https://analysis-of-mechanisms.netlify.app/](https://analysis-of-mechanisms.netlify.app/)

index.qmd

@@ -68,7 +68,7 @@ Instructors: Daniel Witte (DW), Jie Zhang (JZ)
 
 ## Building the course
 
-The course material was created using [Quarto](https://quarto.org/) to write the lessons and create the book format, [GitHub](https://github.com/) to host the [Git](https://git-scm.com/) repository of the material, and [GitHub Actions](https://github.com/features/actions) with [Netlify](https://www.netlify.com/) to create and host the website. The original source material for this course is found on the [`steno-aarhus/mediation-analysis-course`](https://github.com/steno-aarhus/IDEG-mediation-course) GitHub repository.
+The course material was created using [Quarto](https://quarto.org/) to write the lessons and create the book format, [GitHub](https://github.com/) to host the [Git](https://git-scm.com/) repository of the material, and [GitHub Actions](https://github.com/features/actions) to create and host the website. The original source material for this course is found on the [`steno-aarhus/mediation-analysis-course`](https://github.com/steno-aarhus/IDEG-mediation-course) GitHub repository.
 
 ## Re-use and licensing {#licensing}