Merge branch 'main' of https://github.com/rostools/r-cubed-advanced

.github/workflows/assign-pr-to-creator.yml

@@ -0,0 +1,24 @@
+name: Assign PR to creator
+
+on:
+  pull_request: 
+    types:
+      - reopened
+      - opened
+
+permissions:
+  pull-requests: write
+
+jobs:
+  assign-pr-to-creator:
+    name: Assign PR to creator
+    runs-on: ubuntu-latest
+    steps:
+      - name: Assign PR to creator
+        if: ${{ github.event_name == 'pull_request' }}
+        run: |
+          gh pr edit $PR --add-assignee $AUTHOR
+        env:
+          AUTHOR: ${{ github.event.pull_request.user.login }}
+          PR: ${{ github.event.pull_request.html_url }}
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}

_extensions/rostools/r3-theme/_extension.yml

@@ -1,16 +1,18 @@
 title: r3-theme
 author: Luke W. Johnston
-version: 1.0.3
-quarto-required: ">=1.2.0"
+version: 1.0.5
+quarto-required: ">=1.3.0"
 contributes:
   format:
     html:
+      highlight-style: a11y
+      code-line-numbers: true
       df-print: tibble
       code-overflow: scroll
       from: markdown+emoji
       code-link: true
       theme:
-        - litera
+        - zephyr
         - custom-site.scss
 
     revealjs:
@@ -33,22 +35,20 @@ contributes:
       favicon: "favicon.ico"
       repo-branch: main
       repo-actions: [edit, issue, source]
-      search:
-        location: navbar
-        type: overlay
+      search: true
 
     execute:
-      freeze: auto
       warning: false
 
+    csl: vancouver.csl
+
     callout-appearance: minimal
     reference-location: margin
     crossref:
       chapters: true
 
     knitr:
       opts_chunk:
-        class-output: sourceCode
         comment: "#>"
         fig-dpi: 72
         fig-width: 5.5

_extensions/rostools/r3-theme/custom-site.scss

@@ -9,13 +9,12 @@ $font-family-serif: "Nanum Gothic", sans-serif !default;
 $font-family-sans-serif: "Nanum Gothic", sans-serif !default;
 $headings-font-family: "Cabin", sans-serif !default;
 $font-size-root: 18px !default;
-$code-block-border-left: "grey60" !default;
 
 /*-- scss:rules --*/
 
 svg {
   display: block;
-  max-width: 100%;
+  max-width: 100% !important;
   margin: 0 auto;
   height: auto !important;
   width: auto !important;
@@ -26,3 +25,7 @@ svg {
   width: 100%;
   height: 425px;
 }
+
+kbd {
+  padding: .15rem .15rem;
+}

_variables.yml

@@ -1,20 +1,19 @@
-# Automatically created by `r3admin::copy_common_file('_variables.yml')` on 2023-11-04.
 keybind:
-  palette: '{{< kbd linux=Ctrl-Shift-P mac=Cmd-Shift-P win=Ctrl-Shift-P >}}'
-  git: '{{< kbd linux=Ctrl-Alt-M mac=Cmd-Option-M win=Ctrl-Alt-M >}} or with the Palette ({{< var keybind.palette >}}, then type "commit")'
-  chunk: '{{< kbd linux=Ctrl-Alt-I mac=Cmd-Option-I win=Ctrl-Alt-I >}} or with the Palette ({{< var keybind.palette >}}, then type "new chunk")'
-  restart-r: '{{< kbd linux=Ctrl-Shift-F10 mac=Cmd-Shift-F10 win=Ctrl-Shift-F10 >}} or with the Palette ({{< var keybind.palette >}}, then type "restart")'
-  source: '{{< kbd linux=Ctrl-Shift-S mac=Cmd-Shift-S win=Ctrl-Shift-S >}} or with the Palette ({{< var keybind.palette >}}, then type "source")'
-  render: '{{< kbd linux=Ctrl-Shift-K mac=Cmd-Shift-K win=Ctrl-Shift-K >}} or with the Palette ({{< var keybind.palette >}}, then type "render")'
-  roxygen: '{{< kbd linux=Ctrl-Shift-Alt-R mac=Cmd-Shift-Alt-R win=Ctrl-Shift-Alt-R >}} or with the Palette ({{< var keybind.palette >}}, then type "roxygen comment")'
-  outline: '{{< kbd linux=Ctrl-Shift-O mac=Cmd-Shift-O win=Ctrl-Shift-O >}} or with the Palette ({{< var keybind.palette >}}, then type "outline")'
+  palette: '{{< kbd Ctrl-Shift-P >}}'
+  git: '{{< kbd Ctrl-Alt-M >}} or with the Palette ({{< var keybind.palette >}}, then type "commit")'
+  chunk: '{{< kbd Ctrl-Alt-I >}} or with the Palette ({{< var keybind.palette >}}, then type "new chunk")'
+  restart-r: '{{< kbd Ctrl-Shift-F10 >}} or with the Palette ({{< var keybind.palette >}}, then type "restart")'
+  source: '{{< kbd Ctrl-Shift-S >}} or with the Palette ({{< var keybind.palette >}}, then type "source")'
+  render: '{{< kbd Ctrl-Shift-K >}} or with the Palette ({{< var keybind.palette >}}, then type "render")'
+  roxygen: '{{< kbd Ctrl-Shift-Alt-R >}} or with the Palette ({{< var keybind.palette >}}, then type "roxygen comment")'
+  outline: '{{< kbd Ctrl-Shift-O >}} or with the Palette ({{< var keybind.palette >}}, then type "outline")'
   styler: 'the Palette ({{< var keybind.palette >}}, then type "style file")'
-  outline: '{{< kbd linux=Ctrl-Shift-O mac=Cmd-Shift-O win=Ctrl-Shift-O >}} or with the Palette ({{< var keybind.palette >}}, then type "outline")'
-  targets_make: 'the Palette ({{< var keybind.palette >}}, then type "targets run")'
-  targets_vis: 'the Palette ({{< var keybind.palette >}}, then type "targets visual")'
-  targets_outdated: 'the Palette ({{< var keybind.palette >}}, then type "targets outdated")'
-  build_site: '{{< kbd linux=Ctrl-Shift-B mac=Cmd-Shift-B win=Ctrl-Shift-B >}}'
-  find: '{{< kbd linux=Ctrl-Shift-F mac=Cmd-Shift-F win=Ctrl-Shift-F >}} or with the Palette ({{< var keybind.palette >}}, then type "find files")'
-  visual_edit: '{{< kbd linux=Ctrl-Shift-F4 mac=Cmd-Shift-F4 win=Ctrl-Shift-F4 >}}'
-
-
+  targets-make: 'the Palette ({{< var keybind.palette >}}, then type "targets run")'
+  targets-vis: 'the Palette ({{< var keybind.palette >}}, then type "targets visual")'
+  targets-outdated: 'the Palette ({{< var keybind.palette >}}, then type "targets outdated")'
+  build-site: '{{< kbd Ctrl-Shift-B >}}'
+  find: '{{< kbd Ctrl-Shift-F >}} or with the Palette ({{< var keybind.palette >}}, then type "find files")'
+  visual-edit: '{{< kbd Ctrl-Shift-F4 >}}'
+  pipe: '{{< kbd Ctrl-Shift-M >}}'
+  code-section: '{{< kbd Ctrl-Shift-R >}} or with the Palette ({{< var keybind.palette >}}, then type "code section")'
+  run-code: '{{< kbd Ctrl-Enter >}}'

sessions/stats-analyses-multiple.qmd

@@ -327,10 +327,14 @@ to add the original variable names. Then we can add our first
 
 > Time: \~25 minutes.
 
-Convert the code that calculates the model estimates as well as the code
-that adds the original metabolite names into functions. Start with the
-code for the metabolite names, using the scaffold below as a starting
-point.
+::: {.callout-warning appearance="default"}
+There are two parts to this exercise and two solution chunks.
+:::
+
+**Part 1**: Convert the code that calculates the model estimates as well
+as the code that adds the original metabolite names into functions.
+Start with the code for the metabolite names, using the scaffold below
+as a starting point.
 
 1.  Name the new function `add_original_metabolite_names`.
 2.  Within the `function()`, add two arguments, where the first is
@@ -370,8 +374,8 @@ add_original_metabolite_names <- function(model_results, data) {
 }
 ```
 
-Do the same thing with the code that creates the model results, using
-the scaffold below as a starting point.
+**Part 2**: Do the same thing with the code that creates the model
+results, using the scaffold below as a starting point.
 
 ``` r
 calculate_estimates <- function(data) {
@@ -714,4 +718,3 @@ targets::tar_make()
     than fewer, bigger ones.
 -   Use dot-whisker plots like `geom_pointrange()` to visualize the
     estimates and their standard error.
-