_quarto.yml

project:
  type: book
  output-dir: docs
  resources:
    - .nojekyll
#  pre-render: assets/_refs.r

execute: 
  cache: true
  freeze: auto

version: 1.0.0
year: 2024

book:
  google-analytics: G-LLHQEESR2L
  doi: 10.5281/zenodo.10891227
  title: "How to fit an animal model"
  subtitle: "An ecologist guide"
  description: |
    Tutorial on how to fit an animal model using multiple R packages.
    Updated and extended tutorials from An ecologist guide to animal model [@wilson2010].
  cover-image: images/cover/cover_en.png
  author: 
    - Julien Martin
    - Mathieu Videlier
  date: today
  date-format: iso 
  reader-mode: true
  search: true
  page-footer:
    left: |
      By J Martin & M Videlier
    right: |
      This book was built with <a href="https://quarto.org/">Quarto</a>.
#  cover-image: images/blue_dragon.jpg
#  favicon: cover.jpg
  favicon: images/cover/book_fav.png
  site-url: https://juliengamartin.github.io/wam_tuto/
  repo-url: https://github.com/juliengamartin/wam_tuto/
  repo-actions: [edit, issue]
  downloads: [pdf, epub]
  navbar:
    background: light
#    logo: quarto.png
#    logo-alt: "Quarto logo."
    collapse-below: lg
    title: "Wam tutorial"
    left:
      - text: Extra resources
        menu:
          - text: WamWiki
            href: https://wildanimalmodels.org/
          - text: Tutorials by P de Vilemereuil
            href: https://devillemereuil.legtux.org/downloads/

  chapters:
    - index.qmd
    - 01_intro.Rmd
    - part: 02_00-univ.Rmd
      chapters:
        - 02_01-univ_asreml.Rmd  
#        - 02_02-univ_gremlin.Rmd 
        - 02_03-univ_mcmcglmm.Rmd
        - 02_04-univ_brms.Rmd    
#        - 02_05-univ_stan.Rmd    
    - part: 03_00-biv.Rmd          
      chapters:
        - 03_01-biv_asreml.Rmd   
#        - 03_02-biv_gremlin.Rmd  
        - 03_03-biv_mcmcglmm.Rmd 
        - 03_04-biv_brms.Rmd     
#        - 03_05-biv_stan.Rmd     
    - part : 04_00-rep.Rmd
      chapters:          
        - 04_01-rep_asreml.Rmd   
#        - 04_02-rep_gremlin.Rmd  
        - 04_03-rep_mcmcglmm.Rmd 
        - 04_04-rep_brms.Rmd     
#        - 04_05-rep_stan.Rmd     
    - 05_code_cheatsheet.Rmd
    - 98_references.qmd
#  appendices:
#    - 99_app_rep-lmer.Rmd


bibliography: [biblio/book.bib, biblio/grateful-refs.bib]
biblio-style: apalike
csl: biblio/ecology.csl

format:
  html:
    theme:
      light: cosmo
      dark: [cosmo, css/theme-dark.scss]
      #- r4ds.scss
    css: css/style.css
    code-link: true

    author-meta: "Julien Martin"
    callout-appearance: simple
    params:
      echo_sol: true
      fit_all: false

#  pdf:
#    documentclass: scrbook
#    include-in-header: latex/preamble.tex
#    include-before-body: latex/before_body.tex
#    include-after-body: latex/after_body.tex
#    toc-depth: 2
#  pdf: 
#    from: markdown+emoji
##    number-depth: 2
##    toc-depth: 2
#    df-print: paged
#    number-sections: true
#    documentclass: scrreprt
#    pdf-engine: lualatex
##    keep-tex: true
#    classoption:
#      - "chapterprefix=true"
#      - "headings=big"
#      - "twoside=semi"
#    papersize: letter
#    fontsize: 11pt
#    geometry:
#    - top=2cm
#    - bottom=2cm
#    - left=2cm
#    - right=2cm
#    - footskip=1cm
#    block-headings: false
#    colorlinks: true
#    linestretch: 1.5
#    template-partials:
#      - latex/before-title.tex
#      - latex/before-body.tex
##        - title.tex
##      - toc.tex
#
#  epub:
#    dev: svglite
#    stylesheet: css/epub.css
#    toc: true
#
#
#