Initial commit

.Rprofile

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+source("renv/activate.R")

.github/workflows/quarto-publish.yml

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+on:
+  push:
+    branches: main
+
+name: Render and Publish
+
+jobs:
+  build-deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+        with:
+          # To install LaTeX to build PDF book
+          tinytex: true
+          # uncomment below and fill to pin a version
+          # version: 1.2.335
+
+      - name: Install Quarto Extensions
+        run: |
+          quarto install --no-prompt extension jmbuhr/quarto-qrcode
+          quarto install --no-prompt extension grantmcdermott/quarto-revealjs-clean
+          quarto install --no-prompt extension ArthurData/quarto-confetti
+
+      - name: Install Python and Dependencies
+        uses: actions/[email protected]
+        with:
+          python-version: '3.10'
+          cache: 'pip'
+      - run: pip install -r requirements.txt
+
+      - name: Install R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: '4.2.0'
+
+      - name: Install R Dependencies
+        uses: r-lib/actions/setup-renv@v2
+        with:
+          cache-version: 1
+
+      - name: Publish to GitHub Pages (and render)
+        uses: quarto-dev/quarto-actions/publish@v2
+        with:
+          target: gh-pages
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # this secret is always available for github actions

.gitignore

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+/.quarto/
+_site/*
+\#*
+*~
+.quarto/*
+_extensions/*

.markdownlint-cli2.yaml

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+# Configuration
+config:
+  # MD013 - line-length
+  line_length:
+    line_length: 120
+    code_blocks: false
+    tables: false
+  html:
+    allowed_elements:
+      - div
+
+globs:
+  - "**/*.md"
+  - "**/*.qmd"
+
+ignore:
+  - ".quarto/*"
+  - "_site/*"
+
+# Fix any fixable errors
+fix: true

.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0  # Use the ref you want to point at
+    hooks:
+      - id: trailing-whitespace
+        types: [yaml, markdown]
+      - id: end-of-file-fixer
+      - id: check-yaml
+
+  - repo: https://github.com/DavidAnson/markdownlint-cli2
+    rev: v0.9.2
+    hooks:
+      - id: markdownlint-cli2
+        args: []
+
+ci:
+  autofix_prs: true
+  autofix_commit_msg: '[pre-commit.ci] Fixing issues with pre-commit'
+  autoupdate_schedule: weekly
+  autoupdate_commit_msg: '[pre-commit.ci] pre-commit-autoupdate'

LICENSE

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README.md

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+# Template Quarto Revealjs site
+
+This template can be used to publish a [RevealJS](https://revealjs.com/) website that has been written in
+[Quarto](https://www.quarto.org). It includes a [GitHub Action](https://docs.github.com/en/actions) which will convert
+the Quarto source to HTML and publish them via [GitHub Pages](https://pages.github.com/).
+
+Its a useful way of making slides portable as they are then available via the URL and naturally the slides are version
+controlled.
+
+## Usage
+
+### Use the Template
+
+Start by clicking on the "_Use this Template_" button and selecting "_Create a new repository_". You will have to choose
+a name for the repository and this should reflect the nature of your talk. When ready click on "_Create repository from
+template_" and this will copy all the resources into a new repository under your GitHub account ready for you to start
+using.
+
+### Repository settings
+
+You **MUST** make sure your repository action settings are configured to allow read and write permissions.
+
+![image](https://user-images.githubusercontent.com/20887250/216280796-86028c95-76b7-418a-a3eb-e614a8ab874a.png)
+
+You can find this settings at `https://github.com/[USER]/[repo]/settings/actions`.
+
+### Clone the repository
+
+Typically you will work on files on your local computer, staging and committing changes and periodically pushing to
+GitHub for backup and publishing. How you clone depends on what client you use but at the command line you can use...
+
+``` bash
+git clone https://github.com/<USERNAME>/<REPOSITORY>
+```
+
+Substitute `<USERNAME>` and `<REPOSITORY>` appropriately.
+
+### Edit `_quarto.yaml`
+
+How you should edit `_quarto.yaml` and change the `site-url` to reflect your GitHub user account and the name of the
+repository you have chosen for this project. Its probably wise to modify the `title` and `description` too. The sample
+code below shows in capitals the fields you should modify.
+
+``` yaml
+project:
+  type: website
+
+website:
+  title: "<INSERT_TITLE>"
+  site-url: https://<YOUR_GITHUB_USERNAME>.github.io/<NAME_OF_REPOSITORY>
+  description: "<INSERT_DESCRIPTION>"
+```
+
+### Install Extensions
+
+This template uses some [extensions](https://quarto.org/docs/extensions/)
+([quarto-clean](https://github.com/grantmcdermott/quarto-revealjs-clean), [QR
+extension](https://github.com/jmbuhr/quarto-qrcode) and [confetti](https://github.com/ArthurData/quarto-confetti)) and
+these need to be installed locally _before_ you can proceed.
+
+``` bash
+quarto install --no-prompt extension jmbuhr/quarto-qrcode
+quarto install --no-prompt extension grantmcdermott/quarto-revealjs-clean
+quarto install --no-prompt extension ArthurData/quarto-confetti
+```
+
+### Publish Locally
+
+You will need to run `quarto publish gh-pages` once locally before deploying this template. This creates a new branch
+`gh-pages` which is where the resulting pages are published to and pushes them to GitHub.
+
+``` bash
+quarto publish gh-pages
+```
+
+### Write your slides
+
+You are now ready to create your slides by editing the `index.qmd` in the root of the repository. For more information
+on writing RevealJS slides in Quarto see the [RevealJS](https://quarto.org/docs/presentations/revealjs/) guide and the
+[Revealjs Reference](https://quarto.org/docs/reference/formats/presentations/revealjs.html).
+
+When you stage, commit and push your commits to GitHub the `quarto-publish.yaml` will run.
+
+## pre-commit
+
+A [pre-commit](https://pre-commit.com) configuration is included (see `.pre-commit-config.yaml`) and includes a hook for
+[markdownlint-cli2](https://github.com/DavidAnson/markdownlint-cli2) (see `.markdownlint-cli2.yaml` for
+configuration). To use `pre-commit` you will have to install `pre-commit install` in your cloned repository. This requires
+`pre-commit` to be installed on your system or within a Python Virtual Environment. To find out more about installing
+and configuring `pre-commit` see the article [pre-commit : Protecting your future
+self](https://rse.shef.ac.uk/blog/pre-commit/) or refer to the official documentation.
+
+## Extensions
+
+There are a growing number of useful [Quarto extensions](https://quarto.org/docs/extensions/). Three are included in this
+template and they are also installed during the publishing and deployment of the resulting slides as they are listed in
+the `quarto-publish.yml`. You should have installed these locally as instructed above.
+
+If you use additional extensions then as well as installing them locally on your computer you **MUST** remember to add
+them to the `Install Quarto Extensions` section of `.github/workflows/quarto-publish.yaml` otherwise your pages will not
+build and deploy.
+
+### QR Code generation
+
+The [quarto-qrcode](https://github.com/jmbuhr/quarto-qrcode) extension is particularly useful as it simplifies
+generating and embedding [QR Codes](https://en.wikipedia.org/wiki/QR_code) that link to websites in your slides.
+
+### Clean Theme
+
+The [quarto-revealjs-clean](https://github.com/grantmcdermott/quarto-revealjs-clean/) theme is a nice (clean!)
+theme. For a full example of all the features of this theme see the authors
+[quarto-revealjs-clean-demo](https://github.com/grantmcdermott/quarto-revealjs-clean-demo).
+
+### Confetti
+
+The [confetti](https://github.com/ArthurData/quarto-confetti) extension adds some eye-candy and throws confetti over
+your slides whenever you press the `c` button. They originate from the mouse location and therefore follow it around.
+
+## Embedding Code
+
+The beauty of Quarto is that it is a literate programming system which means you can embed code that is executed and the
+results, whether that is tables, figures, or numbers, can be included in the resulting document. Quarto supports several
+languages including perhaps the two of the most popular languages [R](https://www.r-project.org) and
+[Python](https://www.python.org).
+
+### R
+
+You will likely have [R](https://www.r-project.org) installed locally along with all the packages that are required (and
+perhaps even use reproducible environments using [renv](https://rstudio.github.io/renv/) or
+[pak](https://pak.r-lib.org)).
+
+For slides to build and execute your R code correctly you need to enable installation of R and the required packages in
+the `.github/workflows/quarto-publish.yaml`. A sample section is already present that should just need un-commenting,
+but may need tweaking if you use any packages to manage a reproducible environment.
+
+### Python
+
+Similarly with Python you likely have Virtual Environments configured locally to run your Python code, and these should
+have be detailed in a `requirements.txt` file so they can be installed when the GitHub Workflow is executed to build
+your pages on GitHub.
+
+You will need to enable installation of Python and these packages in the `.github/workflows/quarto-publish.yaml` and
+a sample section is already present that can be un-commented if required.

_quarto.yml

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+project:
+  type: website
+
+website:
+  title: "<TITLE>"
+  site-url: https://<YOUR_GITHUB_USERNAME>.github.io/<NAME_OF_REPOSITORY
+  description: "<DESCRIPTION>"