From b8dbac732825186361e382380f85073c9e31e89f Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 13 Apr 2026 22:15:25 +0000
Subject: [PATCH 1/6] Initial plan


From 086751634e0983783fadc74160c4686a1b2e730a Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 13 Apr 2026 22:20:30 +0000
Subject: [PATCH 2/6] add .qmd vignette with macros table and preview/publish
 workflows

Agent-Logs-Url: https://github.com/d-morrison/macros/sessions/382aa7c9-3613-494f-91a9-416c4f1e4b0f

Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
---
 .github/workflows/preview.yml | 65 ++++++++++++++++++++++++
 .github/workflows/publish.yml | 39 +++++++++++++++
 .gitignore                    |  2 +
 _quarto.yml                   | 21 ++++++++
 index.qmd                     | 76 ++++++++++++++++++++++++++++
 macros-table.qmd              | 94 +++++++++++++++++++++++++++++++++++
 6 files changed, 297 insertions(+)
 create mode 100644 .github/workflows/preview.yml
 create mode 100644 .github/workflows/publish.yml
 create mode 100644 .gitignore
 create mode 100644 _quarto.yml
 create mode 100644 index.qmd
 create mode 100644 macros-table.qmd

diff --git a/.github/workflows/preview.yml b/.github/workflows/preview.yml
new file mode 100644
index 0000000..6311e45
--- /dev/null
+++ b/.github/workflows/preview.yml
@@ -0,0 +1,65 @@
+name: Quarto Preview
+
+on:
+  pull_request:
+    types:
+      - opened
+      - reopened
+      - synchronize
+      - closed
+
+jobs:
+  build-deploy:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: write
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          packages: |
+            any::knitr
+            any::rmarkdown
+            any::DT
+
+      - name: Render
+        uses: quarto-dev/quarto-actions/render@v2
+
+      - name: Deploy PR Preview
+        id: preview-step
+        uses: rossjrw/pr-preview-action@v1
+        with:
+          source-dir: ./_site/
+          action: ${{ github.event.action == 'closed' && 'remove' || 'deploy' }}
+          preview-branch: gh-pages
+          comment: "false"
+
+      - uses: marocchino/sticky-pull-request-comment@v2
+        if: steps.preview-step.outputs.deployment-action == 'deploy'
+        with:
+          header: pr-preview
+          recreate: true
+          message: |
+            [PR Preview Action](https://github.com/rossjrw/pr-preview-action) ${{ steps.preview-step.outputs.action-version }}
+            :---:
+            :rocket: View preview at ${{ steps.preview-step.outputs.preview-url }}
+
+      - uses: marocchino/sticky-pull-request-comment@v2
+        if: steps.preview-step.outputs.deployment-action == 'remove'
+        with:
+          header: pr-preview
+          recreate: true
+          message: |
+            [PR Preview Action](https://github.com/rossjrw/pr-preview-action) ${{ steps.preview-step.outputs.action-version }}
+            :---:
+            Preview removed because the pull request was closed.
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
new file mode 100644
index 0000000..662ed29
--- /dev/null
+++ b/.github/workflows/publish.yml
@@ -0,0 +1,39 @@
+on:
+  workflow_dispatch:
+  push:
+    branches: main
+
+name: Quarto Publish
+
+jobs:
+  build-deploy:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          packages: |
+            any::knitr
+            any::rmarkdown
+            any::DT
+
+      - name: Render
+        uses: quarto-dev/quarto-actions/render@v2
+
+      - name: Deploy 🚀
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          folder: _site/
+          clean-exclude: pr-preview/
+          force: false
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..47c274c
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,2 @@
+/.quarto/
+/_site/
diff --git a/_quarto.yml b/_quarto.yml
new file mode 100644
index 0000000..9fc539e
--- /dev/null
+++ b/_quarto.yml
@@ -0,0 +1,21 @@
+project:
+  type: website
+
+website:
+  title: "macros"
+  navbar:
+    left:
+      - href: index.qmd
+        text: Home
+      - href: macros-table.qmd
+        text: Macro Reference
+
+format:
+  html:
+    theme: cosmo
+    toc: true
+
+execute:
+  warning: false
+  message: false
+  freeze: auto
diff --git a/index.qmd b/index.qmd
new file mode 100644
index 0000000..d12c535
--- /dev/null
+++ b/index.qmd
@@ -0,0 +1,76 @@
+---
+title: "macros"
+---
+
+This repository contains LaTeX macros for mathematical notation used in statistical and regression modeling, originally from the [rme repository](https://github.com/d-morrison/rme).
+
+## Contents
+
+- `macros.qmd`: LaTeX macro definitions for use in Quarto documents
+- [Macro Reference](macros-table.qmd): Searchable table of all macros
+
+These macros provide convenient shorthand for common mathematical expressions used in:
+
+- Probability and statistics
+- Regression models (linear, logistic, Poisson, survival analysis)
+- Maximum likelihood estimation
+- Mathematical notation (vectors, matrices, derivatives, etc.)
+
+## Using as a Git Submodule
+
+### Adding the submodule to your project
+
+From the root of your project repository, run:
+
+```bash
+git submodule add https://github.com/d-morrison/macros.git macros
+git commit -m "Add macros submodule"
+```
+
+This will clone the `macros` repository into a `macros/` subdirectory and record it as a submodule.
+
+### Cloning a project that already uses this submodule
+
+When cloning a repository that includes this submodule, initialize and fetch the submodule content with:
+
+```bash
+git clone --recurse-submodules <your-repo-url>
+```
+
+Or, if you have already cloned the repository without `--recurse-submodules`:
+
+```bash
+git submodule update --init
+```
+
+### Updating the submodule
+
+To pull the latest changes from this repository into your project:
+
+```bash
+git submodule update --remote macros
+git commit -m "Update macros submodule"
+```
+
+### Including the macros in a Quarto document
+
+In your Quarto document's YAML front matter, reference the `macros.qmd` file using the `include-in-header` or via `_quarto.yml`:
+
+```yaml
+---
+include-in-header:
+  - macros/macros.qmd
+---
+```
+
+Or, in a shared `_quarto.yml` configuration file:
+
+```yaml
+format:
+  html:
+    include-in-header:
+      - macros/macros.qmd
+  pdf:
+    include-in-header:
+      - macros/macros.qmd
+```
diff --git a/macros-table.qmd b/macros-table.qmd
new file mode 100644
index 0000000..c462d9c
--- /dev/null
+++ b/macros-table.qmd
@@ -0,0 +1,94 @@
+---
+title: "Macro Reference"
+---
+
+This page provides a searchable table of all macros defined in `macros.qmd`.
+
+```{r}
+#| label: parse-macros
+#| echo: false
+
+parse_macros <- function(file_path = "macros.qmd") {
+  lines <- readLines(file_path, warn = FALSE)
+
+  # Remove HTML comments and blank lines
+  lines <- grep("^\\s*<!--", lines, invert = TRUE, value = TRUE)
+  lines <- grep("^\\s*$", lines, invert = TRUE, value = TRUE)
+
+  # Collect entries, joining multi-line definitions
+  entries <- character(0)
+  current <- ""
+  for (line in lines) {
+    if (grepl("^\\\\(def|providecommand|renewcommand)", line, perl = TRUE)) {
+      if (nzchar(current)) entries <- c(entries, current)
+      current <- line
+    } else {
+      current <- paste(current, trimws(line))
+    }
+  }
+  if (nzchar(current)) entries <- c(entries, current)
+
+  rows <- lapply(entries, function(entry) {
+    # Match \def\name{definition}
+    m <- regmatches(
+      entry,
+      regexec(
+        "^\\\\def\\\\([^{ \t]+)\\{(.*)\\}\\s*$",
+        entry,
+        perl = TRUE
+      )
+    )[[1]]
+    if (length(m) == 3 && nzchar(m[1])) {
+      return(data.frame(
+        name       = paste0("\\", m[2]),
+        args       = 0L,
+        definition = m[3],
+        stringsAsFactors = FALSE
+      ))
+    }
+
+    # Match \providecommand or \renewcommand
+    m <- regmatches(
+      entry,
+      regexec(
+        paste0(
+          "^\\\\(?:providecommand|renewcommand)",
+          "\\{\\\\([^}]+)\\}(?:\\[(\\d+)\\])?\\{(.*)\\}\\s*$"
+        ),
+        entry,
+        perl = TRUE
+      )
+    )[[1]]
+    if (length(m) == 4 && nzchar(m[1])) {
+      return(data.frame(
+        name       = paste0("\\", m[2]),
+        args       = if (nzchar(m[3])) as.integer(m[3]) else 0L,
+        definition = m[4],
+        stringsAsFactors = FALSE
+      ))
+    }
+
+    NULL
+  })
+
+  do.call(rbind, Filter(Negate(is.null), rows))
+}
+
+macros <- parse_macros("macros.qmd")
+```
+
+```{r}
+#| label: macros-table
+#| echo: false
+
+DT::datatable(
+  macros,
+  colnames  = c("Macro", "# Args", "Definition"),
+  rownames  = FALSE,
+  filter    = "top",
+  options   = list(
+    pageLength = 25,
+    dom        = "lftip"
+  )
+)
+```

From 6ef6e13023217eb3337ef9bfaf69fbd2ef942eee Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 13 Apr 2026 23:18:35 +0000
Subject: [PATCH 3/6] add example source and rendered columns to macros table

Agent-Logs-Url: https://github.com/d-morrison/macros/sessions/9eb1876f-db61-41eb-a78a-3484a6ce5abb

Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
---
 macros-table.qmd | 43 ++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 40 insertions(+), 3 deletions(-)

diff --git a/macros-table.qmd b/macros-table.qmd
index c462d9c..fffb334 100644
--- a/macros-table.qmd
+++ b/macros-table.qmd
@@ -2,6 +2,20 @@
 title: "Macro Reference"
 ---
 
+```{r}
+#| label: embed-macros
+#| echo: false
+#| results: asis
+
+# Embed macro definitions in a hidden display-math block so MathJax defines
+# them globally for the rendered example column below.
+lines <- readLines("macros.qmd", warn = FALSE)
+lines <- lines[!grepl("^\\s*<!--", lines) & nzchar(trimws(lines))]
+cat('<div style="display:none">\n$$\n')
+cat(paste(lines, collapse = "\n"), "\n")
+cat('$$\n</div>\n')
+```
+
 This page provides a searchable table of all macros defined in `macros.qmd`.
 
 ```{r}
@@ -75,6 +89,24 @@ parse_macros <- function(file_path = "macros.qmd") {
 }
 
 macros <- parse_macros("macros.qmd")
+
+# Build example usage strings based on argument count.
+# 0-arg macros: \name  |  n-arg macros: \name{x}{y}...
+arg_placeholders <- c("x", "y", "z", "w")
+make_arg_str <- function(n) {
+  if (n == 0L) return("")
+  paste0("{", arg_placeholders[seq_len(min(n, 4L))], "}", collapse = "")
+}
+example_call <- paste0(
+  macros$name,
+  vapply(macros$args, make_arg_str, character(1L))
+)
+
+# Plain-text source column (searchable, not HTML-escaped in output)
+macros$example_source <- example_call
+
+# Rendered column: MathJax inline-math delimiters; DT renders with escape=FALSE
+macros$example_rendered <- paste0("\\(", example_call, "\\)")
 ```
 
 ```{r}
@@ -82,13 +114,18 @@ macros <- parse_macros("macros.qmd")
 #| echo: false
 
 DT::datatable(
-  macros,
-  colnames  = c("Macro", "# Args", "Definition"),
+  macros[, c("name", "args", "definition", "example_source", "example_rendered")],
+  colnames  = c("Macro", "# Args", "Definition", "Example Source", "Example"),
   rownames  = FALSE,
+  escape    = FALSE,
   filter    = "top",
   options   = list(
     pageLength = 25,
-    dom        = "lftip"
+    dom        = "lftip",
+    # Re-typeset MathJax after each DataTables draw (pagination, search, etc.)
+    drawCallback = DT::JS(
+      "function() { if (window.MathJax) { MathJax.typesetPromise(); } }"
+    )
   )
 )
 ```

From c4ea7c4a41c8b740aa670c0e2387821353bd4563 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 14 Apr 2026 00:02:05 +0000
Subject: [PATCH 4/6] fix: use ::: fenced-div so pandoc processes macro
 definitions as MathJax math

Agent-Logs-Url: https://github.com/d-morrison/macros/sessions/fdcf3409-0ae3-48ad-b6c5-02ce9825713a

Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
---
 macros-table.qmd | 22 +++++++++++++++++-----
 1 file changed, 17 insertions(+), 5 deletions(-)

diff --git a/macros-table.qmd b/macros-table.qmd
index fffb334..e7b8ba6 100644
--- a/macros-table.qmd
+++ b/macros-table.qmd
@@ -7,13 +7,14 @@ title: "Macro Reference"
 #| echo: false
 #| results: asis
 
-# Embed macro definitions in a hidden display-math block so MathJax defines
-# them globally for the rendered example column below.
+# Embed macro definitions in a hidden Quarto fenced-div so pandoc processes
+# the $$ block into a real MathJax display-math element (not raw HTML).
+# Raw <div>...</div> blocks are passed through by pandoc without math processing.
 lines <- readLines("macros.qmd", warn = FALSE)
 lines <- lines[!grepl("^\\s*<!--", lines) & nzchar(trimws(lines))]
-cat('<div style="display:none">\n$$\n')
+cat('::: {style="display:none"}\n$$\n')
 cat(paste(lines, collapse = "\n"), "\n")
-cat('$$\n</div>\n')
+cat('$$\n:::\n')
 ```
 
 This page provides a searchable table of all macros defined in `macros.qmd`.
@@ -124,7 +125,18 @@ DT::datatable(
     dom        = "lftip",
     # Re-typeset MathJax after each DataTables draw (pagination, search, etc.)
     drawCallback = DT::JS(
-      "function() { if (window.MathJax) { MathJax.typesetPromise(); } }"
+      "function(settings) {
+        var table = this;
+        if (window.MathJax) {
+          if (MathJax.startup && MathJax.startup.promise) {
+            MathJax.startup.promise.then(function() {
+              MathJax.typesetPromise([table.api().table().node()]);
+            });
+          } else {
+            MathJax.typesetPromise([table.api().table().node()]);
+          }
+        }
+      }"
     )
   )
 )

From feb70aa3e5eba75a81fe3533d24945f92ee546c0 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 15 Apr 2026 22:10:43 +0000
Subject: [PATCH 5/6] fix: convert \providecommand to \def for MathJax v3; fix
 drawCallback; add copilot-instructions

Agent-Logs-Url: https://github.com/d-morrison/macros/sessions/ce9b76e7-b915-4ffe-8e7f-3bbb1bd3c270

Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
---
 .github/copilot-instructions.md | 11 +++++++++++
 .gitignore                      |  2 ++
 macros-table.qmd                | 33 ++++++++++++++++++++++++---------
 3 files changed, 37 insertions(+), 9 deletions(-)
 create mode 100644 .github/copilot-instructions.md

diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md
new file mode 100644
index 0000000..1d14095
--- /dev/null
+++ b/.github/copilot-instructions.md
@@ -0,0 +1,11 @@
+# Copilot Instructions
+
+## Quarto rendering
+
+Before requesting review on any change to a `.qmd` file:
+
+1. **Always render the document locally** (`quarto render <file>` or `quarto preview`) and inspect the HTML output.
+2. **Verify that math renders correctly** — open the rendered HTML and confirm MathJax typesetting is visible and correct.
+3. **Do not push until rendering succeeds** and the output looks as intended.
+
+This step is required because MathJax rendering failures are silent in R/knitr output and only visible in the browser.
diff --git a/.gitignore b/.gitignore
index 47c274c..2f7dfc0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,4 @@
 /.quarto/
 /_site/
+/_freeze/
+/*.deb
diff --git a/macros-table.qmd b/macros-table.qmd
index e7b8ba6..7ac7d43 100644
--- a/macros-table.qmd
+++ b/macros-table.qmd
@@ -12,6 +12,27 @@ title: "Macro Reference"
 # Raw <div>...</div> blocks are passed through by pandoc without math processing.
 lines <- readLines("macros.qmd", warn = FALSE)
 lines <- lines[!grepl("^\\s*<!--", lines) & nzchar(trimws(lines))]
+
+# MathJax v3 does NOT support \providecommand.
+# Convert \providecommand{\name}[n]{body} to TeX primitive \def\name#1...#n{body},
+# which always works in MathJax regardless of whether the command is already defined.
+lines <- vapply(lines, function(line) {
+  m <- regmatches(
+    line,
+    regexec(
+      "^\\\\providecommand\\{\\\\([^}]+)\\}(?:\\[(\\d+)\\])?\\{(.*)\\}\\s*$",
+      line,
+      perl = TRUE
+    )
+  )[[1]]
+  if (length(m) == 4L && nzchar(m[1L])) {
+    nargs    <- if (nzchar(m[3L])) as.integer(m[3L]) else 0L
+    args_str <- if (nargs > 0L) paste0("#", seq_len(nargs), collapse = "") else ""
+    return(paste0("\\def\\", m[2L], args_str, "{", m[4L], "}"))
+  }
+  line
+}, character(1L), USE.NAMES = FALSE)
+
 cat('::: {style="display:none"}\n$$\n')
 cat(paste(lines, collapse = "\n"), "\n")
 cat('$$\n:::\n')
@@ -126,15 +147,9 @@ DT::datatable(
     # Re-typeset MathJax after each DataTables draw (pagination, search, etc.)
     drawCallback = DT::JS(
       "function(settings) {
-        var table = this;
-        if (window.MathJax) {
-          if (MathJax.startup && MathJax.startup.promise) {
-            MathJax.startup.promise.then(function() {
-              MathJax.typesetPromise([table.api().table().node()]);
-            });
-          } else {
-            MathJax.typesetPromise([table.api().table().node()]);
-          }
+        if (window.MathJax && MathJax.typesetPromise) {
+          (MathJax.startup ? MathJax.startup.promise : Promise.resolve())
+            .then(function() { MathJax.typesetPromise(); });
         }
       }"
     )

From 6d99bb1029ba3d2f5b52073d091f70a0c59bb9d8 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 16 Apr 2026 01:25:09 +0000
Subject: [PATCH 6/6] feat: wrap name/definition/example_source columns in code
 tags for monospace font

Agent-Logs-Url: https://github.com/d-morrison/macros/sessions/0bf4724c-af82-40ac-b3a9-15432b2fa9bf

Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
---
 macros-table.qmd | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/macros-table.qmd b/macros-table.qmd
index 7ac7d43..479552e 100644
--- a/macros-table.qmd
+++ b/macros-table.qmd
@@ -124,8 +124,13 @@ example_call <- paste0(
   vapply(macros$args, make_arg_str, character(1L))
 )
 
-# Plain-text source column (searchable, not HTML-escaped in output)
-macros$example_source <- example_call
+# Wrap text columns in <code> tags for monospace font (escape=FALSE lets them render as HTML)
+code <- function(x) paste0("<code>", x, "</code>")
+macros$name        <- code(macros$name)
+macros$definition  <- code(macros$definition)
+
+# Plain-text source column wrapped in <code>; escape=FALSE renders the tags
+macros$example_source <- code(example_call)
 
 # Rendered column: MathJax inline-math delimiters; DT renders with escape=FALSE
 macros$example_rendered <- paste0("\\(", example_call, "\\)")