diff --git a/.filenameignore b/.filenameignore new file mode 100644 index 0000000..a917e18 --- /dev/null +++ b/.filenameignore @@ -0,0 +1,20 @@ +# Paths to ignore for filename/path validation checks. +# Patterns use fnmatch syntax and are relative to repo root. + +_site/** +.quarto/** +.github/** +_extensions/ +assets/bootstrap-grid.min.css + +# Common documentation files to ignore +LICENSE-CODE.md +LICENSE.md +LICENSE +README.md +README +README-template.md +CITATION.cff +CITATION-template.cff +_quarto.yml +404.qmd diff --git a/.github/workflows/README.md b/.github/workflows/README.md new file mode 100644 index 0000000..5f3fdc7 --- /dev/null +++ b/.github/workflows/README.md @@ -0,0 +1,77 @@ +# Workflows (GitHub Actions) + +This document explains the GitHub Actions workflows in `.github/workflows/` in beginner-to-intermediate friendly language: what each workflow does, how it is triggered, and what is essential to keep working. + +## Quick summary + +- Location: `.github/workflows/` +- How to run: workflows run automatically on `push` to `main`, on a schedule, or manually via the **Actions** tab → "Run workflow" (if `workflow_dispatch` is enabled). + +--- + +## Individual workflows + +### citation-check.yml — Validate `CITATION.cff` + +- Purpose: Validate the project's `CITATION.cff` so metadata (authors, ORCID, affiliations) is well-formed and machine-readable. +- Triggers: `push` to `main` when `CITATION.cff` changes, and manual runs (`workflow_dispatch`). +- What it does: checks out the repo and runs `dieghernan/cff-validator@v3`. +- Essentials to keep: the `Checkout` step and the validator step. No extra secrets are required. +- Tips: safe to update the validator action version; don't remove checkout. + +### filename-check.yml — Enforce filename rules + +- Purpose: Ensure file and path names meet limits (length, depth, allowed extensions) to prevent publishing problems. +- Triggers: `push` to `main`, `pull_request`, and manual runs. +- What it does: uses `NeuroShepherd/check-filenames-action@v1` with inputs such as `max-path-length`, `max-depth`, and allowed `file-types`. It may respect a `.filenameignore` file when present. +- Essentials to keep: the check-filenames action and its configuration inputs. +- Tips: adjust `max-path-length`/`max-depth` or add `.filenameignore` entries if legitimate files are flagged. + +### publish.yaml — Render and publish the Quarto site + +- Purpose: Build the Quarto site and publish the rendered site to the `gh-pages` branch. +- Triggers: `push` to `main`, weekly schedule (cron), and manual runs. +- What it does (high-level): checks out code, installs Quarto, installs system and R dependencies as needed, renders the site, and publishes to `gh-pages` using `quarto-actions/publish@v2`. +- Essentials to keep: + - `quarto-dev/quarto-actions/setup@v2` (Quarto install) + - the render and publish step (`quarto-actions/publish@v2`) + - repository permission for `contents: write` to allow publishing +- Notes: + - If you use R, the workflow detects `renv.lock` and restores packages; include `renv.lock` for reproducible builds. + - The workflow installs system libraries via `apt` (image handling, PDF, and some R packages require these). Remove packages only if you understand the consequences. +- Common edits: change schedule timing or branch triggers. Removing the publish step disables automatic deployment. + +### style.yaml — Format R/QMD code using `styler` + +- Purpose: Automatically format R and Quarto/R Markdown code using `styler::style_dir()` and optionally commit formatted code. +- Triggers: currently manual (`workflow_dispatch`) — push triggers are commented out. +- What it does: installs R and `styler`, runs `styler::style_dir()`, and if files were reformatted the workflow commits and pushes changes using `GITHUB_TOKEN`. +- Essentials to keep: the style run and cache steps; the commit step is optional depending on whether you want automatic changes. +- Tips: to avoid unexpected commits, run manually or restrict to PR checks instead of auto-committing. + +--- + +## Quick guidance — what to change vs what to leave alone + +- Safe to change: + - Schedules and branch triggers + - Input limits for checks (e.g., filename length, allowed file types) + - Action versions (bump to newer versions) +- Be careful editing: + - The `publish` workflow's render/publish steps — removing them will stop site builds and deployment. + - System dependency installation (`apt` lines) used by rendering and some R packages. + - The auto-commit logic in `style.yaml` if you don't want automatic pushes. That is this workflow only runs on `workflow_dispatch` meaning it currently can only be manually triggered in Actions. + +## How to run workflows manually + +- In GitHub: Open the repository → **Actions** tab → choose a workflow → click **Run workflow** (if available). +- Locally: To test Quarto rendering locally, use `quarto preview` or `quarto render` in your project directory. + +## Where to look for failures + +- Open the **Actions** tab in GitHub, select the workflow run, and inspect step logs to see errors and stack traces. + +--- + + + diff --git a/.github/workflows/citation-check.yml b/.github/workflows/citation-check.yml new file mode 100644 index 0000000..db7b4eb --- /dev/null +++ b/.github/workflows/citation-check.yml @@ -0,0 +1,21 @@ +on: + workflow_dispatch: + push: + branches: [main] + paths: + - CITATION.cff + +name: Check CITATION.cff is Valid +jobs: + Validate-CITATION-cff: + runs-on: ubuntu-latest + name: Validate CITATION.cff + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + + steps: + - name: Checkout + uses: actions/checkout@v4 + + - name: Validate CITATION.cff + uses: dieghernan/cff-validator@v3 diff --git a/.github/workflows/filename-check.yml b/.github/workflows/filename-check.yml new file mode 100644 index 0000000..7fc2971 --- /dev/null +++ b/.github/workflows/filename-check.yml @@ -0,0 +1,22 @@ +name: Filename Checks + +on: + workflow_dispatch: + pull_request: + push: + branches: + - main + +jobs: + check-names: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - name: Check filenames + uses: NeuroShepherd/check-filenames-action@v1 + with: + max-path-length: "65" + max-depth: "2" + file-types: "html,md,qmd,css,scss,rmd,pdf,png,jpg,svg,yml" + ignore-file: ".filenameignore" + dotfile-mode: "strip-leading-dot" \ No newline at end of file diff --git a/.github/workflows/link-checker.yml b/.github/workflows/link-checker.yml new file mode 100644 index 0000000..7fa9f73 --- /dev/null +++ b/.github/workflows/link-checker.yml @@ -0,0 +1,44 @@ +name: Link Checker + +on: + schedule: + - cron: '0 0 1 * *' + workflow_dispatch: + +jobs: + check-links: + runs-on: ubuntu-latest + permissions: + issues: write + steps: + - name: Check links + id: check + uses: filiph/linkcheck@master + continue-on-error: true + with: + arguments: https://${{ github.repository_owner }}.github.io/${{ github.event.repository.name }}/ + + - name: Create issue on broken links + if: steps.check.outputs.exit_code != '0' + uses: actions/github-script@v7 + with: + script: | + const fs = require('fs'); + const report = fs.readFileSync('log', 'utf8'); + + const { data: issues } = await github.rest.issues.listForRepo({ + owner: context.repo.owner, + repo: context.repo.repo, + state: 'open', + labels: 'link-checker' + }); + + if (issues.length === 0) { + await github.rest.issues.create({ + owner: context.repo.owner, + repo: context.repo.repo, + title: '🔗 Broken Links Found on Site', + body: `The monthly link checker detected broken links.\n\n${report}`, + labels: ['link-checker'] + }); + } \ No newline at end of file diff --git a/.github/workflows/publish.yaml b/.github/workflows/publish.yaml new file mode 100644 index 0000000..a1937d4 --- /dev/null +++ b/.github/workflows/publish.yaml @@ -0,0 +1,106 @@ +on: + workflow_dispatch: + schedule: + - cron: "0 23 * * 0" + push: + branches: [main] + +name: Render Quarto Site + +jobs: + quarto-publish: + 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 + with: + tinytex: true + + - name: Install system dependencies + run: | + sudo apt-get update + sudo apt install -y \ + libcurl4-openssl-dev \ + libfontconfig1-dev \ + libssl-dev \ + libxml2-dev \ + libpng-dev \ + libjpeg-dev \ + libtiff-dev \ + libcairo2-dev \ + libxt-dev \ + libfreetype6-dev \ + libharfbuzz-dev \ + libfribidi-dev \ + zlib1g-dev \ + libv8-dev \ + libglpk-dev \ + librsvg2-bin + + - name: Install R with renv + uses: r-lib/actions/setup-r@v2 + with: + r-version: renv + if: ${{ hashFiles('renv.lock') != '' }} + + - name: Install R Dependencies with renv + uses: r-lib/actions/setup-renv@v2 + with: + cache-version: 1 + if: ${{ hashFiles('renv.lock') != '' }} + + - name: Install R latest + uses: r-lib/actions/setup-r@v2 + if: ${{ hashFiles('renv.lock') == '' }} + + - name: Set R library path (no lockfile) + run: echo "R_LIBS_USER=$HOME/.local/lib/R/site-library" >> "$GITHUB_ENV" + if: ${{ hashFiles('renv.lock') == '' }} + + - name: Cache R library (no lockfile) + uses: actions/cache@v4 + with: + path: ~/.local/lib/R/site-library + key: ${{ runner.os }}-r-nolock-${{ hashFiles('**/*.R', '**/*.Rmd', '**/*.qmd', '_quarto.yml') }} + restore-keys: | + ${{ runner.os }}-r-nolock- + if: ${{ hashFiles('renv.lock') == '' }} + + - name: Install R latest dependencies + run: | + lib <- Sys.getenv("R_LIBS_USER") + if (nzchar(lib)) { + dir.create(lib, recursive = TRUE, showWarnings = FALSE) + .libPaths(c(lib, .libPaths())) + } + install.packages("renv") + install.packages("rmarkdown") + install.packages("yaml") + deps <- unique(stats::na.omit(renv::dependencies()$Package)) + if (length(deps) > 0) install.packages(deps) + shell: Rscript {0} + if: ${{ hashFiles('renv.lock') == '' }} + + - name: Ensure Quarto R runtime packages + run: | + lib <- Sys.getenv("R_LIBS_USER") + if (nzchar(lib)) { + dir.create(lib, recursive = TRUE, showWarnings = FALSE) + .libPaths(c(lib, .libPaths())) + } + pkgs <- c("knitr", "rmarkdown") + missing <- pkgs[!vapply(pkgs, requireNamespace, logical(1), quietly = TRUE)] + if (length(missing) > 0) install.packages(missing) + shell: Rscript {0} + + - name: Render and Publish + uses: quarto-dev/quarto-actions/publish@v2 + with: + target: gh-pages + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml deleted file mode 100644 index ddc3d7d..0000000 --- a/.github/workflows/publish.yml +++ /dev/null @@ -1,58 +0,0 @@ -on: - workflow_dispatch: - schedule: - - cron: "0 23 * * 0" - 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: Install misc. system dependencies - run: | - sudo apt-get update - sudo apt-get install \ - libcurl4-openssl-dev \ - libfontconfig1-dev \ - libssl-dev \ - libxml2-dev \ - libpng-dev \ - libjpeg-dev \ - libtiff-dev \ - libcairo2-dev \ - libxt-dev \ - libfreetype6-dev \ - libharfbuzz-dev \ - libfribidi-dev \ - zlib1g-dev \ - libv8-dev \ - libglpk-dev \ - librsvg2-bin - - - name: Set up Quarto - uses: quarto-dev/quarto-actions/setup@v2 - - - name: Install R - uses: r-lib/actions/setup-r@v2 - with: - r-version: renv - - - name: Install R Dependencies - uses: r-lib/actions/setup-renv@v2 - with: - cache-version: 1 - - - name: Render and Publish - uses: quarto-dev/quarto-actions/publish@v2 - with: - target: gh-pages - env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/style.yaml b/.github/workflows/style.yaml index ed74bb8..a249278 100644 --- a/.github/workflows/style.yaml +++ b/.github/workflows/style.yaml @@ -74,4 +74,4 @@ jobs: git push origin else echo "No changes to commit." - fi \ No newline at end of file + fi diff --git a/.github/workflows/update-extension.yml b/.github/workflows/update-extension.yml new file mode 100644 index 0000000..4e52ef7 --- /dev/null +++ b/.github/workflows/update-extension.yml @@ -0,0 +1,32 @@ +name: Update Tutorial Template Extension + +on: + schedule: + - cron: "0 0 2 * *" + workflow_dispatch: + +permissions: read-all + +jobs: + update-downstream-tutorials: + # prevent action from running in actual extension repo--else, recursive installations + # only users of the extension should have these auto-updates + if: github.repository != 'lmu-osc/tutorial-template' + runs-on: ubuntu-latest + permissions: + contents: write + steps: + - name: Checkout repo + uses: actions/checkout@v5 + with: + fetch-depth: 0 + + - name: Setup Quarto + uses: quarto-dev/quarto-actions/setup@v2 + + - name: Update tutorial-template extension + run: quarto update lmu-osc/tutorial-template --no-prompt + + - uses: stefanzweifel/git-auto-commit-action@v7 + with: + commit_message: "Update tutorial-template extension (GHA)" diff --git a/.gitignore b/.gitignore index 93d9305..fb72d94 100644 --- a/.gitignore +++ b/.gitignore @@ -1,10 +1,66 @@ -.Rproj.user +# History files .Rhistory +.Rapp.history + +# Session Data files .RData +.RDataTmp + +# User-specific files .Ruserdata +# Example code in package build process +*-Ex.R + +# Output files from R CMD build +/*.tar.gz + +# Output files from R CMD check +/*.Rcheck/ + +# RStudio files +.Rproj.user/ + +# produced vignettes +vignettes/*.html +vignettes/*.pdf + +# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3 +.httr-oauth + +# knitr and R markdown default cache directories +*_cache/ +/cache/ + +# Temporary files created by R markdown +*.utf8.md +*.knit.md + +# R Environment Variables +.Renviron + +# pkgdown site +docs/ + +# translation temp files +po/*~ + +# RStudio Connect folder +rsconnect/ + +# Quarto /.quarto/ -/_site/ + +# Future-proofing: ignore commonly included files that should not be tracked +# Inspired by usethis::git_vaccinate() options +.DS_Store +.Rproj.user +.httr-oauth +.quarto +_site/ **_files/ **/*.quarto_ipynb + +# ignore posi assistant settings +.posit/assistant diff --git a/404.qmd b/404.qmd new file mode 100644 index 0000000..515733c --- /dev/null +++ b/404.qmd @@ -0,0 +1,14 @@ +--- +title: Uh-oh, looks like the page is missing! +description: The page you are looking for cannot be found 😟 +--- + +The page you are looking for either does not exist or has been moved. Please check the URL and try again. If you believe this is an error, please contact the website administrator for assistance. + +Note: many pages within our old tutorials have been moved to new locations as part of standardization efforts. It's likely the page you are looking for has been moved to a new location within the site. + + diff --git a/CITATION.cff b/CITATION.cff index 224f27c..fdca02a 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,9 +1,10 @@ cff-version: 1.2.0 message: "If you use this software, please cite it as below." authors: -- family-names: "Volker" - given-names: "Thom Benjamin" - orcid: "https://orcid.org/0000-0002-2408-7820" + - family-names: "Volker" + given-names: "Thom Benjamin" + orcid: "https://orcid.org/0000-0002-2408-7820" + affiliation: "Utrecht University; Statistics Netherlands" title: "Generating and Evaluating Synthetic Data in R" abstract: "A tutorial for generating and evaluating synthetic data in R" version: 1.0.0 diff --git a/_extensions/lmu-osc/tutorial-template/_extension.yml b/_extensions/lmu-osc/tutorial-template/_extension.yml new file mode 100644 index 0000000..a393f3f --- /dev/null +++ b/_extensions/lmu-osc/tutorial-template/_extension.yml @@ -0,0 +1,48 @@ +title: tutorial-template +author: Patrick Callahan +description: A template website for the LMU Open Science Center's tutorials +version: 1.0.3 +license: CC0-1.0 +quarto-required: ">=1.9.0" +contributes: + metadata: + project: + brand: _extensions/lmu-osc/osc-brand/brand.yml + project: + project: + type: website + website: + search: + location: sidebar + repo-actions: [edit, source, issue] + back-to-top-navigation: true + page-navigation: true + # favicon: Quarto detects the "small" image from the brand file automatically + reader-mode: true + navbar: + background: primary + logo: small + format: tutorial-template-html+tutorial + formats: + html+tutorial: + theme: + light: + [flatly, brand, _extensions/lmu-osc/osc-brand/lmu-osc-custom.scss] + dark: [darkly, brand, _extensions/lmu-osc/osc-brand/lmu-osc-custom.scss] + toc: true + toc-title: " " + code-tools: true + code-overflow: wrap + code-copy: true + code-link: true + smooth-scroll: true + link-external-icon: true + link-external-newwindow: true + footnotes-hover: true + citations-hover: true + crossrefs-hover: true + grid: + sidebar-width: 300px + css: + - assets/bootstrap-grid.min.css + html+base: osc-brand-html diff --git a/_extensions/lmu-osc/tutorial-template/_extensions/lmu-osc/osc-brand/_extension.yml b/_extensions/lmu-osc/tutorial-template/_extensions/lmu-osc/osc-brand/_extension.yml new file mode 100644 index 0000000..07ccc65 --- /dev/null +++ b/_extensions/lmu-osc/tutorial-template/_extensions/lmu-osc/osc-brand/_extension.yml @@ -0,0 +1,16 @@ +title: LMU Open Science Center Brand +author: Patrick Callahan +version: 1.0.0 +url: https://github.com/lmu-osc/osc-brand +description: LMU Open Science Center brand assets and default HTML format +license: MIT +quarto-required: ">=1.9.0" +contributes: + metadata: + project: + brand: brand.yml + formats: + html: + theme: + light: [flatly, brand, lmu-osc-custom.scss] + dark: [darkly, brand, lmu-osc-custom.scss] diff --git a/_extensions/lmu-osc/tutorial-template/_extensions/lmu-osc/osc-brand/brand.yml b/_extensions/lmu-osc/tutorial-template/_extensions/lmu-osc/osc-brand/brand.yml new file mode 100644 index 0000000..3dd6c6f --- /dev/null +++ b/_extensions/lmu-osc/tutorial-template/_extensions/lmu-osc/osc-brand/brand.yml @@ -0,0 +1,120 @@ +# minimal brand.yml enabling dark mode + +meta: + name: + full: LMU Open Science Center + short: OSC + link: + home: https://www.osc.lmu.de/ + github: https://github.com/lmu-osc + bluesky: https://bsky.app/profile/lmu-osc.bsky.social + description: | + Home of open science praxis at Ludwig-Maximilian Universität München. + founded: 2019 + author: Pat Callahan + +# replace with your brand colors, logos, and typography! +color: + palette: + lmu-green: "#00883A" + lmu-black: "#232323" + lmu-white: "#FFF" + lmu-darkgrey: "#626468" + lmu-darkgray: "#626468" + lmu-middlegrey: "#C0C1C3" + lmu-middlegray: "#C0C1C3" + lmu-lightgrey: "#E6E6E7" + lmu-lightgray: "#E6E6E7" + lmu-lichtgrau: "#F5F5F5" + lmu-blue: "#0F1987" + lmu-cyan: "#009FE3" + lmu-violet: "#8C4091" + lmu-red: "#D71919" + lmu-orange: "#F18700" + background: + light: lmu-white + dark: lmu-black + foreground: + light: lmu-black + dark: lmu-white + primary: + light: lmu-green + dark: lmu-green + secondary: + light: lmu-black + dark: lmu-middlegray + tertiary: + light: lmu-blue + dark: lmu-violet + success: + light: lmu-cyan + dark: lmu-cyan + info: + light: lmu-violet + dark: lmu-violet + warning: + light: lmu-orange + dark: lmu-orange + danger: + light: lmu-red + dark: lmu-red + +logo: + images: + icon: + path: lmu-osc-favicon.jpg + alt: "LMU Open Science Center open book icon" + default: + path: lmu-osc-logo.svg + alt: "LMU Open Science Center logo" + dark: + path: lmu-osc-logo-dark.svg + alt: "LMU Open Science Center logo" + large: + path: lmu-osc-logo-large.jpg + alt: "LMU Open Science Center logo, large" + small: icon + medium: + light: default + dark: dark + large: + light: large + dark: large + +# https://www.lmu.de/de/die-lmu/struktur/zentrale-universitaetsverwaltung/presse-und-kommunikation-puk/lmu-brand-guide/designgrundsaetze/schrift/ +# Compatil is the official font, but license limited. Online content should use Roboto, and other software e.g. presentations use Arial +typography: + fonts: + - family: Roboto + source: google + - family: Arial + source: google + - family: Fira Code + source: google + base: + family: "Roboto, Arial" + # size: 1.1rem + # line-height: 1.65 + # weight: + # style: + headings: + family: "Roboto, Arial" + color: secondary + monospace: + family: "Fira Code" + # size: + # weight: + monospace-inline: + family: "Fira Code" + # color: + # background-color: + monospace-block: + family: "Fira Code" + # line-height: + # color: + # background-color: + # link: + # weight: + # color: + # background-color: + # decoration: diff --git a/_extensions/lmu-osc/tutorial-template/_extensions/lmu-osc/osc-brand/lmu-osc-custom.scss b/_extensions/lmu-osc/tutorial-template/_extensions/lmu-osc/osc-brand/lmu-osc-custom.scss new file mode 100644 index 0000000..4dc2397 --- /dev/null +++ b/_extensions/lmu-osc/tutorial-template/_extensions/lmu-osc/osc-brand/lmu-osc-custom.scss @@ -0,0 +1,35 @@ +/*-- scss:defaults --*/ + +// Define custom brand SCSS variables +// These can reference Bootstrap theme variables (which are derived from brand.yml) +// but note that Bootstrap vars are only available in the /*-- scss:rules --*/ section. + +/*-- scss:rules --*/ + + +#quarto-content +h1, #quarto-content h1[class], #quarto-content .h1[class], +h2, #quarto-content h2[class], #quarto-content .h2[class], +h3, #quarto-content h3[class], #quarto-content .h3[class] { + margin-top: 1.33rem; + margin-bottom: 0.75rem; +} + +#quarto-content +h4, #quarto-content h4[class], #quarto-content .h4[class], +h5, #quarto-content h5[class], #quarto-content .h5[class], +h6, #quarto-content h6[class], #quarto-content .h6[class] { + margin-top: 0.66rem; + margin-bottom: 0.5rem; +} + +#quarto-content +h2, #quarto-content h2[class], #quarto-content .h2[class] { + border-bottom: $brand-lmu-violet 2px solid; +} + +#quarto-content +h3, #quarto-content h3[class], #quarto-content .h3[class] { + border-bottom: $brand-lmu-violet 1.5px solid; + padding-bottom: 0.25rem; +} \ No newline at end of file diff --git a/assets/LMU_OSC_favicon.jpg b/_extensions/lmu-osc/tutorial-template/_extensions/lmu-osc/osc-brand/lmu-osc-favicon.jpg similarity index 100% rename from assets/LMU_OSC_favicon.jpg rename to _extensions/lmu-osc/tutorial-template/_extensions/lmu-osc/osc-brand/lmu-osc-favicon.jpg diff --git a/_extensions/lmu-osc/tutorial-template/_extensions/lmu-osc/osc-brand/lmu-osc-logo-dark.svg b/_extensions/lmu-osc/tutorial-template/_extensions/lmu-osc/osc-brand/lmu-osc-logo-dark.svg new file mode 100644 index 0000000..338367e --- /dev/null +++ b/_extensions/lmu-osc/tutorial-template/_extensions/lmu-osc/osc-brand/lmu-osc-logo-dark.svg @@ -0,0 +1,281 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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print{.d-print-inline{display:inline!important}.d-print-inline-block{display:inline-block!important}.d-print-block{display:block!important}.d-print-grid{display:grid!important}.d-print-inline-grid{display:inline-grid!important}.d-print-table{display:table!important}.d-print-table-row{display:table-row!important}.d-print-table-cell{display:table-cell!important}.d-print-flex{display:flex!important}.d-print-inline-flex{display:inline-flex!important}.d-print-none{display:none!important}} +/*# sourceMappingURL=bootstrap-grid.min.css.map */ \ No newline at end of file diff --git a/_quarto.yml b/_quarto.yml index d63ef26..321e6e5 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -1,28 +1,19 @@ # Begin Project project: - type: website + type: tutorial-template # End Project - # Begin Website website: title: "Generating and Evaluating Synthetic Data in R" page-footer: - center: "© 2026 Thom Volker. Published by LMU Open Science Center. Licensed under CC BY-SA 4.0." border: false - search: - location: sidebar + center: "© 2026 Thom Volker. Published by LMU Open Science Center. Licensed under CC BY-SA 4.0." repo-url: https://github.com/lmu-osc/synthetic-data-tutorial - repo-actions: [edit, issue] - back-to-top-navigation: true - page-navigation: true - favicon: assets/LMU_OSC_favicon.jpg - margin-header: | - ![](/assets/LMU_OSC_logo.svg){width="175"} + navbar: right: - - href: about.qmd - text: About + - about.qmd left: - href: index.qmd text: Home @@ -30,12 +21,11 @@ website: - icon: github menu: - text: Source Code - url: https://github.com/lmu-osc/synthetic-data-tutorial + href: https://github.com/lmu-osc/synthetic-data-tutorial - text: Report a Bug - url: https://github.com/lmu-osc/synthetic-data-tutorial/issues + href: https://github.com/lmu-osc/synthetic-data-tutorial/issues - icon: house-heart - url: https://www.osc.uni-muenchen.de/index.html - + url: https://www.osc.lmu.de/ sidebar: style: "docked" @@ -54,24 +44,27 @@ website: href: publishing/index.qmd # End Website +# Begin Includes +include-in-header: + - file: matomo-analytics.html +include-after-body: + - file: footer/footer.html +# End Includes # Begin Format format: - html: - theme: - - cosmo - - lmu-osc-custom.scss + tutorial-template-html+tutorial: css: - - https://raw.githubusercontent.com/lmu-osc/branding-resources/refs/heads/main/lmu-osc-styles.css + - footer/footer-style.css + - styles.css toc: true - fontsize: 13pt code-overflow: wrap grid: sidebar-width: 300px - include-in-header: - - file: matomo-analytics.html # End Format # Begin Editor editor: source # End Editor + +bibliography: references.bib diff --git a/about.qmd b/about.qmd index 8311acd..e500538 100644 --- a/about.qmd +++ b/about.qmd @@ -7,11 +7,12 @@ citation: title: "Generating and evaluating synthetic data in R" container-title: "LMU Open Science Center" url: https://lmu-osc.github.io/synthetic-data-tutorial/ - # doi: "TODO: DOI HERE" + doi: "10.5281/zenodo.18318778" author: - name: Thom Benjamin Volker roles: [conceptualization, formal analysis, funding acquisition, investigation, methodology, project administration, software, resources, validation, visualization, writing - original draft, writing - editing & review] - degrees: MSc. + degrees: + - M.Sc. affiliation: - id: uu name: Utrecht University @@ -27,14 +28,13 @@ author: google-scholar: true --- - ## Contributors This site was authored by Thom Volker, and edits and contributions were made by Malika Ihle, Alberto Villagran, Felix Schönbrodt and Patrick Callahan. ## Licenses -The overall project is available under the **[CC BY-SA 4.0](https://creativecommons.org/licenses/by-sa/4.0/)** license found at [LICENSE](LICENSE.md); all code without any narrative text is also (at your option) available under the **[CC0 1.0 Universal](https://creativecommons.org/publicdomain/zero/1.0/)** license found at [LICENSE-CODE](LICENSE-CODE.md). +The overall project is available under the [**CC BY-SA 4.0**](https://creativecommons.org/licenses/by-sa/4.0/) license found at [LICENSE](LICENSE.md); all code without any narrative text is also (at your option) available under the [**CC0 1.0 Universal**](https://creativecommons.org/publicdomain/zero/1.0/) license found at [LICENSE-CODE](LICENSE-CODE.md). Why two licenses? The CC BY-SA 4.0 license is for the content of the website, while the CC0 1.0 Universal license is for the code and other content that may be reused in other projects, particularly because the CC BY-SA 4.0 license is not intended to be used with software. @@ -42,3 +42,6 @@ Why two licenses? The CC BY-SA 4.0 license is for the content of the website, wh This tutorial was primarily written in 2025 using `R` version `4.5.0`. Major changes to `R` can be found at the [R website](https://cran.r-project.org/) for the most up-to-date information, and to confirm that our tutorial is not out-of-date. +## Tutorial Template Quarto Extension + +This tutorial was written using the [`lmu-osc/tutorial-template`](https://github.com/lmu-osc/tutorial-template) Quarto extension [@callahan2026]. diff --git a/assets/lmu-osc-favicon.jpg b/assets/lmu-osc-favicon.jpg new file mode 100644 index 0000000..a06a839 Binary files /dev/null and b/assets/lmu-osc-favicon.jpg differ diff --git a/assets/lmu-osc-logo.svg b/assets/lmu-osc-logo.svg new file mode 100644 index 0000000..e7b48ef --- /dev/null +++ b/assets/lmu-osc-logo.svg @@ -0,0 +1,281 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/footer/accessibilty.qmd b/footer/accessibilty.qmd new file mode 100644 index 0000000..9ed86c5 --- /dev/null +++ b/footer/accessibilty.qmd @@ -0,0 +1,122 @@ +--- +title: "Accessibility" +page-layout: full +--- + + + +:::{.accessibility-container} + +The Ludwig-Maximilians-Universität München strives to make its offers accessible in accordance with § 9 Act on Digitalisation in the Free State of Bavaria (Bayerisches Digitalgesetz – BayDig). + +This Accessibility Statement applies to applications available at [https://www.lmu.de/de/index.html](https://www.lmu.de/de/index.html), [https://www.lmu.de/de/index.html](https://www.lmu.de/de/index.html) and all subdomain pages. + +#### Status of Compliance + +Partially compliant: This application partially corresponds to § 1 BayEGovV. + +##### Legal Name +Ludwig-Maximilians-Universität München + +##### Website(s): +[https://www.lmu.de/de/index.html](https://www.lmu.de/de/index.html), [https://www.lmu.de/de/index.html](https://www.lmu.de/de/index.html) and all subdomain pages. + +#### Known Accessibility Issues +List and explanation of the problems encountered when implementing the accessibility of these websites + +##### Content Not Accessible to People With Disabilities +- Apart from the main pages, alternative text-based content for images and tables may be missing. There may also be errors in content hierarchy and links may be unintelligible. +- PDF documents created before 09/23/2018 have not yet been converted to a fully accessible format. +- Some documents have been provided by institutions of the LMU, which are not yet all available in a fully accessible version. +- Many of our videos also lack subtitles and audio descriptions. +We will be adding written directions for the maps used to give directions. +- Quotes are often not indicated as such using the appropriate HTML tag. +- Responsive design (for viewing on mobile devices) is only partially available for the websites, screen orientation is otherwise limited to landscape format. 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However, we endeavor to check the included links regularly with regard to these named criteria. + +::: \ No newline at end of file diff --git a/footer/privacy.qmd b/footer/privacy.qmd new file mode 100644 index 0000000..3f31fd0 --- /dev/null +++ b/footer/privacy.qmd @@ -0,0 +1,179 @@ +--- +title: "Privacy Policy" +format: + html: + toc: false + page-layout: full +--- + + + +For data collected by the LMU Open Science Center, [LMU's general privacy policy](https://www.lmu.de/en/footer/privacy-policy/index.html){target="_blank"} applies. + +Additionally, this site is hosted on the webhosting service GitHub Pages ([https://docs.github.com/en/pages](https://docs.github.com/en/pages)) with it's own privacy policy available at [https://docs.github.com/de/site-policy/privacy-policies/github-general-privacy-statement](https://docs.github.com/de/site-policy/privacy-policies/github-general-privacy-statement). + + + + +#### Matomo Tracking Opt-Out + +This opt-out is only for the Matomo web analytics tool in use directly the LMU Open Science Center website. It does not affect any other tracking or analytics tools that may be in use on this site, including those used by GitHub Pages. + +```{=html} +
+ +``` \ No newline at end of file diff --git a/index.qmd b/index.qmd index 8a15a50..86e3236 100644 --- a/index.qmd +++ b/index.qmd @@ -15,7 +15,7 @@ All in all, synthetic data makes open science practices easier and might spark c The tutorial focuses on the generation of tabular synthetic data. This precludes the generation of text data or other high-dimensional data sources (fMRI, intensive longitudinal data, etc.). Some extensions to multilevel-data are discussed, but this is not the main goal of the materials. In total, the tutorial is intended to take approximately 2-3 hours to complete, and is split into the following sections: -1. [Statistical Disclosure Control](sdc/) provides a very brief introduction to methods used to protect individuals’ private information, while keeping the released data useful for analysis. +1. [Statistical Disclosure Control](sdc/) provides a very brief introduction to methods used to protect individuals' private information, while keeping the released data useful for analysis. 2. [Synthetic data: The general idea](synthetic/) conceptually introduces the idea of synthetic data and contains an optional section on coding your own simple synthesizer. 3. [Generating synthetic data](generation/) introduces the idea of synthetic data and outlines how it can be generated in `R`. 4. [Evaluating synthetic data quality](evaluation/) addresses the privacy-utility trade-off, and discusses how the quality of synthetic data can be evaluated from both sides of this trade-off. @@ -48,3 +48,29 @@ install.packages("mvtnorm") ``` ::: + + +:::: {.columns} + +::: {.column width="47.5%"} + +::: {.callout-tip title="Support the LMU Open Science Center!"} + +**Like this tutorial? Be sure to give [the repository](https://github.com/lmu-osc/synthetic-data-tutorial) a star and [follow us on GitHub](https://github.com/lmu-osc)!** +::: + +::: + +::: {.column width="5%"} +::: + +::: {.column width="47.5%"} + + +::: {.callout-tip title="Questions about this tutorial?"} +**If you have questions for the author of this tutorial, please take a look at the [About](about.qmd) page.** +::: + +::: + +:::: diff --git a/lmu-osc-custom.scss b/lmu-osc-custom.scss deleted file mode 100644 index d09be92..0000000 --- a/lmu-osc-custom.scss +++ /dev/null @@ -1,10 +0,0 @@ -/*-- scss:defaults --*/ -// Base document colors -$navbar-bg: #00883A; -$link-color: #006426; -$sidebar-hl: #006426; - -.dropdown-menu { - right: 0 !important; - left: auto !important; - } diff --git a/references.bib b/references.bib index 37bd07a..d99a3a0 100644 --- a/references.bib +++ b/references.bib @@ -1,3 +1,14 @@ + +@book{callahan2026, + title = {LMU Open Science Center Tutorial Template: A Quarto Extension}, + author = {Callahan, Patrick}, + year = {2026}, + month = {07}, + date = {2026-07}, + doi = {10.5281/zenodo.21263721}, + url = {https://github.com/lmu-osc/tutorial-template} +} + @article{bowen_dp_synthesis_2020, author = {Claire McKay Bowen and Fang Liu}, journal = {Statistical Science}, @@ -111,15 +122,6 @@ @book{hundepool2024 year = {2024} } -@Book{ggplot2, - author = {Hadley Wickham}, - title = {ggplot2: Elegant Graphics for Data Analysis}, - publisher = {Springer-Verlag New York}, - year = {2016}, - isbn = {978-3-319-24277-4}, - url = {https://ggplot2.tidyverse.org}, -} - @Article{glmmTMB, author = {Mollie E. Brooks and Kasper Kristensen and Koen J. {van Benthem} and Arni Magnusson and Casper W. Berg and Anders Nielsen and Hans J. Skaug and Martin Maechler and Benjamin M. Bolker}, title = {{glmmTMB} Balances Speed and Flexibility Among Packages for Zero-inflated Generalized Linear Mixed Modeling}, @@ -194,7 +196,7 @@ @Book{mvtnorm isbn = {978-3-642-01688-2}, } -@Article{murray_multiple_2018, +@Article{murray_multiple_2018, author={Murray, Jared S.}, title={Multiple Imputation: A Review of Practical and Theoretical Findings}, journal={Statistical Science}, @@ -248,7 +250,7 @@ @misc{raabetal_guidelines_2017 @InProceedings{raab_disclosure_2024, author="Raab, Gillian M.", editor="Domingo-Ferrer, Josep and {\"O}nen, Melek", - title="Privacy Risk from Synthetic Data: Practical Proposals", + title="Privacy Risk from Synthetic Data: Practical Proposals", booktitle="Privacy in Statistical Databases", year="2024", publisher="Springer Nature Switzerland", @@ -373,5 +375,3 @@ @article{yucel_sequential_2017 issn = {2325-0984}, doi = {10.1093/jssam/smx004} } - -