Convert repository into a Quarto website

.github/workflows/preview.yml

@@ -11,7 +11,7 @@ on:
       - 'man/**'
       - 'pkgdown/**'
       - 'vignettes/**'
-      - '_quarto.yml'
+      - '_quarto*.yml'
       - '.github/workflows/preview.yml'
       - '.github/workflows/publish.yml'
       - '*.qmd'
@@ -58,12 +58,12 @@ jobs:
       - name: list files
         shell: bash
         run: |
-          echo "contents of _book:\n"
-          ls _book/
+          echo "contents of _site:\n"
+          ls _site/
           echo "contents of .:\n"
           ls .
       - name: Deploy PR Preview
         uses: rossjrw/pr-preview-action@main
         with:
-          source-dir: _book/
+          source-dir: _site/
 

.gitignore

@@ -21,6 +21,9 @@ test.qmd
 *.tex
 /.quarto/
 /_book/
+/_site/
+/_slides/
+/_handouts/
 _freeze/
 *.pdf
 rsconnect

CONTRIBUTING.md → CONTRIBUTING.qmd

@@ -1,3 +1,9 @@
+---
+title: "Contributing to rme"
+format:
+  html: default
+---
+
 # Contributing to `rme`
 
 Contributions to these notes are very much appreciated; anything from

Intro-to-GLMs.qmd

@@ -1,3 +1,13 @@
+---
+title: "Introduction to GLMs"
+format:
+  html: default
+  revealjs:
+    output-file: Intro-to-GLMs-slides.html
+  pdf:
+    output-file: Intro-to-GLMs-handout.pdf
+---
+
 # Introduction
 
 ---

Linear-models-overview.qmd

@@ -1,3 +1,13 @@
+---
+title: "Linear (Gaussian) Models"
+format:
+  html: default
+  revealjs:
+    output-file: Linear-models-overview-slides.html
+  pdf:
+    output-file: Linear-models-overview-handout.pdf
+---
+
 # Linear (Gaussian) Models
 
 ---

_def-base-cuhaz.qmd

@@ -7,7 +7,7 @@ The **baseline cumulative hazard**,
 **base cumulative hazard**,
 or **reference cumulative hazard**,
 denoted $H_0(t)$ or $\Lambda_0(t)$,
-is the cumulative hazard function (@def-cuhaz)
+is the [cumulative hazard function](intro-to-survival-analysis.html#def-cuhaz)
 for the subpopulation of individuals
 whose covariates are all equal to their reference levels:
 ::::

_quarto-handout.yml

@@ -1,5 +1,56 @@
+project:
+  output-dir: _handouts
+  render:
+    - "index.qmd"
+    - "Intro-to-GLMs.qmd"
+    - "glms.qmd"
+    - "Linear-models-overview.qmd"
+    - "logistic-regression.qmd"
+    - "count-regression.qmd"
+    - "intro-multilevel-models.qmd"
+    - "time-to-event-models.qmd"
+    - "intro-to-survival-analysis.qmd"
+    - "proportional-hazards-models.qmd"
+    - "parametric-survival-models.qmd"
+    - "top-ten-concepts.qmd"
+    - "appendices-are-prereqs.qmd"
+    - "math-prereqs.qmd"
+    - "probability.qmd"
+    - "estimation.qmd"
+    - "inference.qmd"
+    - "intro-MLEs.qmd"
+    - "intro-bayes.qmd"
+    - "common-mistakes.qmd"
+    - "notation.qmd"
+    - "intro-to-R.qmd"
+    - "midterm-formula-sheet.qmd"
+
+bibliography: references.bib
+
 format:
   pdf:
     geometry:
       - top=15mm
       - bottom=20mm
+    keep-md: false
+    keep-tex: false
+    toc: true
+    fig-pos: "H"
+    toc-title: Contents
+    df-print: tibble
+    links-as-notes: true
+    documentclass: article
+    colorlinks: true
+    number-sections: true
+    number-depth: 3
+
+execute:
+  warning: false
+  message: false
+  cache: false
+  freeze: auto
+
+knitr:
+  opts_chunk:
+    collapse: true
+    comment: "#>"

_quarto-revealjs.yml

@@ -1,19 +1,29 @@
 project:
   output-dir: _slides
   render:
-    - intro-to-GLMs.qmd
-    - intro-MLEs.qmd
-    - glms.qmd
-    - Linear-models-overview.qmd
-    - logistic-regression.qmd
-    - count-regression.qmd
-    - time-to-event-models.qmd
-    - intro-to-survival-analysis.qmd
-    - proportional-hazards-models.qmd
-    - parametric-survival-models.qmd
-    - probability.qmd
-    - estimation.qmd
-    - intro-MLEs.qmd
+    - "index.qmd"
+    - "Intro-to-GLMs.qmd"
+    - "glms.qmd"
+    - "Linear-models-overview.qmd"
+    - "logistic-regression.qmd"
+    - "count-regression.qmd"
+    - "intro-multilevel-models.qmd"
+    - "time-to-event-models.qmd"
+    - "intro-to-survival-analysis.qmd"
+    - "proportional-hazards-models.qmd"
+    - "parametric-survival-models.qmd"
+    - "top-ten-concepts.qmd"
+    - "appendices-are-prereqs.qmd"
+    - "math-prereqs.qmd"
+    - "probability.qmd"
+    - "estimation.qmd"
+    - "inference.qmd"
+    - "intro-MLEs.qmd"
+    - "intro-bayes.qmd"
+    - "common-mistakes.qmd"
+    - "notation.qmd"
+    - "intro-to-R.qmd"
+    - "midterm-formula-sheet.qmd"
 
 format:
   revealjs:

_quarto-website.yml

@@ -0,0 +1,169 @@
+project:
+  type: website
+  output-dir: _site
+  render:
+    # Only render the files that were in the original book
+    - index.qmd
+    - Intro-to-GLMs.qmd
+    - glms.qmd
+    - Linear-models-overview.qmd
+    - logistic-regression.qmd
+    - count-regression.qmd
+    - intro-multilevel-models.qmd
+    - time-to-event-models.qmd
+    - intro-to-survival-analysis.qmd
+    - proportional-hazards-models.qmd
+    - parametric-survival-models.qmd
+    - top-ten-concepts.qmd
+    - appendices-are-prereqs.qmd
+    - math-prereqs.qmd
+    - probability.qmd
+    - estimation.qmd
+    - inference.qmd
+    - intro-MLEs.qmd
+    - intro-bayes.qmd
+    - common-mistakes.qmd
+    - notation.qmd
+    - intro-to-R.qmd
+    - CONTRIBUTING.qmd
+    - midterm-formula-sheet.qmd
+
+website:
+  title: "Regression Models for Epidemiology"
+  site-url: https://d-morrison.github.io/rme/
+  description: "Lecture notes for Epidemiology 204: Quantitative Epidemiology III (Statistical Models)"
+  page-footer:
+    left:
+      - text: "Copyright 2024-2026, Douglas Ezra Morrison"
+  back-to-top-navigation: true
+  page-navigation: true
+  reader-mode: true
+  repo-url: https://github.com/d-morrison/rme
+  repo-actions: [edit, issue, source]
+  google-analytics: "G-VS314RJ2KP"
+  navbar:
+    left:
+      - text: "Home"
+        href: index.qmd
+      - text: "Chapters"
+        menu:
+          - text: "Introduction to GLMs"
+            href: Intro-to-GLMs.qmd
+          - text: "---"
+          - text: "Generalized Linear Models"
+            href: glms.qmd
+          - text: "Linear Models Overview"
+            href: Linear-models-overview.qmd
+          - text: "Logistic Regression"
+            href: logistic-regression.qmd
+          - text: "Count Regression"
+            href: count-regression.qmd
+          - text: "Multilevel Models"
+            href: intro-multilevel-models.qmd
+          - text: "---"
+          - text: "Time to Event Models"
+            href: time-to-event-models.qmd
+          - text: "Introduction to Survival Analysis"
+            href: intro-to-survival-analysis.qmd
+          - text: "Proportional Hazards Models"
+            href: proportional-hazards-models.qmd
+          - text: "Parametric Survival Models"
+            href: parametric-survival-models.qmd
+          - text: "---"
+          - text: "Top Ten Concepts"
+            href: top-ten-concepts.qmd
+      - text: "Appendices"
+        menu:
+          - text: "Math Prerequisites"
+            href: math-prereqs.qmd
+          - text: "Probability"
+            href: probability.qmd
+          - text: "Estimation"
+            href: estimation.qmd
+          - text: "Inference"
+            href: inference.qmd
+          - text: "Introduction to MLEs"
+            href: intro-MLEs.qmd
+          - text: "Introduction to Bayesian Statistics"
+            href: intro-bayes.qmd
+          - text: "Common Mistakes"
+            href: common-mistakes.qmd
+          - text: "Notation"
+            href: notation.qmd
+          - text: "Introduction to R"
+            href: intro-to-R.qmd
+          - text: "Midterm Formula Sheet"
+            href: midterm-formula-sheet.qmd
+
+bibliography: references.bib
+
+format:
+  html:
+    theme:
+      light: cosmo
+      dark: darkly
+    toc: true
+    toc-location: right
+    toc-depth: 3
+    code-fold: true
+    code-tools: true
+    code-link: true
+    code-summary: "Show R code"
+    css: custom.scss
+    highlight-style: pygments
+    lightbox: true
+    link-external-icon: true
+    embed-resources: false
+    fig-cap-location: top
+    html-math-method: mathjax
+    number-sections: true
+    number-depth: 3
+    df-print: paged
+    date: last-modified
+    date-format: "[Last modified:] YYYY-MM-DD: H:mm:ss (z)"
+    subject: "Epidemiology 204"
+  revealjs:
+    lightbox: true
+    theme: dark
+    embed-resources: false
+    fig-cap-location: top
+    html-math-method: mathjax
+    smaller: true
+    number-sections: true
+    progress: true
+    incremental: false
+    df-print: paged
+    number-depth: 2
+    slide-number: true
+    shift-heading-level-by: -1
+    slide-level: 2
+    scrollable: true
+    echo: true
+    margin: 0.0
+    code-fold: true
+    code-link: true
+    code-summary: "[R code]"
+    auto-stretch: true
+    fig-height: 5
+    fig-width: 7
+  pdf:
+    geometry:
+      - top=15mm
+      - bottom=20mm
+    keep-md: false
+    keep-tex: false
+    toc: true
+    fig-pos: "H"
+    toc-title: Contents
+    df-print: tibble
+    links-as-notes: true
+    documentclass: article
+    colorlinks: true
+    number-sections: true
+    number-depth: 3
+
+comments:
+  hypothesis:
+    theme: clean
+    openSidebar: false
+    enableExperimentalNewNoteButton: true

_quarto.yml

@@ -1,9 +1,22 @@
 profile:
-  default: book
+  default: website
+
 editor_options:
   chunk_output_type: console
+
 editor:
   markdown:
     wrap: 72
 
-bibliography: references.bib
+execute:
+  warning: false
+  message: false
+  cache: false
+  freeze: auto
+
+knitr:
+  opts_chunk:
+    collapse: true
+    comment: "#>"
+    R.options:
+      knitr.graphics.auto_pdf: true

_sec-pdf.qmd

@@ -1,6 +1,6 @@
 
 For a time-to-event variable $T$ with a continuous distribution, the
-**probability density function** is defined as usual (see @sec-prob-dens).
+**probability density function** is defined as usual (see [probability density function](probability.html#sec-prob-dens)).
 
 ::: notes
 In most time-to-event models, this density is assumed to be 0 for all $t<0$;

_sec-surv-conditional-hazards.qmd

@@ -69,7 +69,7 @@ Now, let's define ***how*** the hazard function depends on covariates.
 We typically use a log link to model the relationship between
 the hazard function, $\haz(t|\vx)$, and
 the linear component, $\eta(t|\vx)$,
-as we did for Poisson models in @sec-count-reg;
+as we did for Poisson models in [models for count outcomes](count-regression.html#sec-count-reg);
 that is:
 
 :::