_quarto.yml

project:
  type: website
  output-dir: docs
  pre-render: init.R
  resources:
    - "apple-touch-icon-precomposed.png"
    - "apple-touch-icon.png"
    - "images/cgem-logo.png"
    - "images/GitHub-Mark-32px.png"
    - "images/MRC_HGU_Edinburgh RGB.png"
  render:
    - "index.qmd"
    - "source/pre/preprocessing.qmd"
    - "source/pre/baseline.qmd"
    - "source/selection/fcal.qmd"
    - "source/selection/crp.qmd"
    - "source/post/associations.qmd"
    - "source/post/FCALvsCRP.qmd"
    - "source/post/Diagnosis.qmd"
    - "not-found.qmd"
  post-render:
    - "scripts/Fig3.R"
    - "scripts/outline-traj.R"
    - "scripts/Diagnostic-biomarker-spread.R"
  execute-dir: project
format:
  html:
    theme:
      light: [default, theme.scss]
      dark: [darkly]
    code-fold: true
    code-link: true
    toc: true
    code-tools:
      source: true
      toggle: true
    html-math-method: katex
    embed-resources: false
    mainfont: "Mulish"
    monofont: "Noto Sans Mono"

website:
  title: "Analysis by Constantine-Cooke et al."
  twitter-card:
    creator: "@IBDNathan"
    site: "@EdinUni_IGC"
  favicon: "favicon.png"
  page-navigation: true
  open-graph: true
  navbar:
    background: "#F02D3A"
    foreground: "white"
    search: true
    right:
      - href: index.qmd
        text: "About"
      - text: "Before model fitting"
        menu:
        - href: "source/pre/preprocessing.qmd"
          text: "Preprocessing"
        - href: "source/pre/baseline.qmd"
          text: "Baseline data"
      - text: "Model fitting"
        menu:
        - href: source/selection/fcal.qmd
          text: "Faecal calprotectin"
        - href: source/selection/crp.qmd
          text: "C-reactive protein"
      - text: "After model fitting"
        menu:
        - href: source/post/associations.qmd
          text: "Associations"
        - href: source/post/FCALvsCRP.qmd
          text: "Comparison between FC and CRP"
      - icon: github
        href: "https://github.com/VallejosGroup/Lothian-IBDR"
  page-footer:
    background: "#F02D3A"
    right:
      - icon: twitter
        href: https://x.com/IBDNathan
  repo-url: https://github.com/VallejosGroup/Lothian-IBDR
  repo-actions: [issue]
  reader-mode: true
bibliography: references.bib
google-scholar: true
date: "last-modified"
title-block-banner: false

execute:
  freeze: auto
  cache: true

affiliations:
  - id: HGU
    name: "MRC Human Genetics Unit"
    city: "Edinburgh"
    region: "Scotland"
    country: "United Kingdom"
    url: "https://www.ed.ac.uk/mrc-human-genetics-unit"
  - id: CGEM
    name: "Centre for Genomic and Experimental Medicine"
    city: "Edinburgh"
    country: "United Kingdom"
    url: "https://www.ed.ac.uk/centre-genomic-medicine"
  - id: IBD
    name: "Edinburgh IBD Unit"
    city: "Edinburgh"
    country: "United Kingdom"
    url: "https://services.nhslothian.scot/EdinburghIBDUnit/Pages/default.aspx"