_quarto.yml

project:
  type: website
  pre-render:
    - bash scripts/make-environment-full.sh
  preview:
    browser: true
  render:
    - "*.qmd"
    - "pages/**/*.qmd"
    - "!_*.md"
    - "!examples/"

website:
  title: "DES RAP"
  site-url: "https://pythonhealthdatascience.github.io/des_rap_book/"
  google-analytics: "G-W2FC4GDHFK"
  cookie-consent: true
  page-navigation: true
  search: false
  favicon: images/stars_logo_blue.png
  navbar:
    logo: images/stars_logo_white.png
    collapse-below: "sm"
    left:
      - text: Step-by-step guide
        href: pages/guide/introduction.qmd
      - text: Examples
        href: pages/example_models/example_models.qmd
      - text: Frameworks
        menu:
          - pages/frameworks/levels_of_rap.qmd
          - pages/frameworks/stars_reproducibility.qmd
      - text: Intros
        menu:
          - text: Intro to DES
            href: pages/intros/des.qmd
          - text: Intro to reproducibility and RAPs
            href: pages/intros/rap.qmd
          - text: Intro to FOSS
            href: pages/intros/foss.qmd
      - text: Impact
        href: pages/impact/impact.qmd
    right:
      - icon: github
        text: "GitHub"
        href: https://github.com/pythonhealthdatascience/des_rap_book
  announcement:
    dismissable: false
    content: |
      <div class="language-selector">
        Choose your language:&nbsp;&nbsp;
        <button class="language-button" onclick="setLanguage('python')">Python</button>
        <button class="language-button" onclick="setLanguage('r')">R</button>
      </div>
    position: below-navbar
  sidebar:
    - id: learn
      title: "Learn"
      style: "docked"
      contents:
        - text: Introduction
          href: pages/guide/introduction.qmd
        - section: "Setup"
          contents:
          - pages/guide/setup/version.qmd
          - pages/guide/setup/environment.qmd
          - pages/guide/setup/package.qmd
          - pages/guide/setup/code_structure.qmd
          - pages/guide/setup/conceptual.qmd
        - section: "Model inputs"
          contents:
          - pages/guide/inputs/input_modelling.qmd
          - pages/guide/inputs/input_data.qmd
          - pages/guide/inputs/parameters_script.qmd
          - pages/guide/inputs/parameters_file.qmd
          - pages/guide/inputs/parameters_validation.qmd
        - section: "Model building"
          contents:
          - pages/guide/model/distributions.qmd
          - pages/guide/model/patients.qmd
          - pages/guide/model/process.qmd
          - pages/guide/model/logs.qmd
        - section: "Output analysis"
          contents:
          - pages/guide/output_analysis/warmup.qmd
          - pages/guide/output_analysis/outputs.qmd
          - pages/guide/output_analysis/replications.qmd
          - pages/guide/output_analysis/length_warmup.qmd
          - pages/guide/output_analysis/n_reps.qmd
          - pages/guide/output_analysis/parallel.qmd
        - section: "Experimentation"
          contents:
          - pages/guide/experiments/scenarios.qmd
          - pages/guide/experiments/tables_figures.qmd
          - pages/guide/experiments/full_run.qmd
        - section: "Verification & validation"
          contents:
          - pages/guide/verification_validation/verification_validation.qmd
          - pages/guide/verification_validation/tests.qmd
          - pages/guide/verification_validation/mathematical.qmd
          - pages/guide/verification_validation/quality_assurance.qmd
        - section: "Style & documentation"
          contents:
          - pages/guide/style_docs/linting.qmd
          - pages/guide/style_docs/docstrings.qmd
          - pages/guide/style_docs/github_actions.qmd
          - pages/guide/style_docs/documentation.qmd
        - section: "Collaboration & sharing"
          contents:
          - pages/guide/sharing/peer_review.qmd
          - pages/guide/sharing/licence.qmd
          - pages/guide/sharing/citation.qmd
          - pages/guide/sharing/changelog.qmd
          - pages/guide/sharing/archive.qmd
        - section: "Closing remarks"
          contents:
          - pages/guide/further_info/conclusion.qmd
          - pages/guide/further_info/feedback.qmd

  page-footer:
    left:
      - text: |
           The STARS project is supported by the Medical Research Council [grant number MR/Z503915/1]. It is also supported by the National Institute for Health and Care Research (NIHR) under the NIHR Applied Research Collaboration South West Peninsula (Grant Reference Number NIHR200167). The views expressed are those of the author(s) and not necessarily those of the NIHR or the Department of Health and Social Care.
    center:
      - text: |
          Part of the <a href="https://pythonhealthdatascience.github.io/stars/" target="_blank" rel="noopener">STARS research project</a>.<br>
          Code licence: <a href="https://opensource.org/license/mit" target="_blank" rel="noopener">MIT</a>.  
          Text licence: <a href="https://creativecommons.org/licenses/by-sa/4.0/" target="_blank" rel="noopener">CC-BY-SA 4.0</a>.<br>
          <a href="/pages/changelog.qmd">Changelog</a>
    right:
      - text: |
          Heather A, Monks T, Harper A et al. Reproducible analytical pipelines for healthcare discrete‑event simulation: An open guide and worked examples [version 1; peer review: awaiting peer review]. NIHR Open Res 2026, 6:68 (https://doi.org/10.3310/nihropenres.14296.1)

format:
  html:
    theme:
      - cosmo
    toc: true
    toc-depth: 2
    number-sections: false
    crossrefs-hover: false
    lightbox: true
    title-block-banner: images/banner.png
    title-block-banner-color: "#ffffff"
    css:
      - styles/headings.css
      - styles/general.css
      - styles/buttons.css
      - styles/language-selector.css
      - styles/callout.css
      - styles/tables.css
      - styles/webex.css
    include-after-body:
      - scripts/webex.js
      - scripts/language-selector.js

params:
  language: "python"  # Default language parameter