_quarto.yml

project:
  type: book
  output-dir: docs

execute:
  cache: true

book:
  title: Introduction to Data Science
  subtitle: Data Wrangling and Visualization with R
  reader-mode: true
  page-footer:
    left: |
      Introduction to Data Science was written by Rafael A. Irizarry
    right: |
      This book was built with <a href=https://quarto.org/>Quarto</a>.
  cover-image: cover.png
  favicon: cover.png
  site-url: http://rafalab.dfci.harvard.edu/dsbook-part-1
  repo-url: https://github.com/rafalab/dsbook-part-1
  repo-branch: main
  repo-actions: [source, issue]
  sidebar:
    collapse-level: 1
  
  chapters:
    - index.qmd

    - intro.qmd
    
    - part: R/intro-to-R.qmd
      chapters:
        - R/getting-started.qmd
        - R/R-basics.qmd
        - R/programming-basics.qmd
        - R/tidyverse.qmd
        - R/data-table.qmd
        - R/importing-data.qmd
    
    - part:  dataviz/intro-dataviz.qmd
      chapters:
        - dataviz/distributions.qmd
        - dataviz/ggplot2.qmd
        - dataviz/dataviz-principles.qmd
        - dataviz/dataviz-in-practice.qmd

    - part: wrangling/intro-to-wrangling.qmd
      chapters:
        - wrangling/reshaping-data.qmd
        - wrangling/joining-tables.qmd
        - wrangling/dates-and-times.qmd
        - wrangling/locales.qmd
        - wrangling/web-scraping.qmd
        - wrangling/string-processing.qmd
        - wrangling/text-analysis.qmd
  
    - part: productivity/intro-productivity.qmd
      chapters:
        - productivity/unix.qmd
        - productivity/git.qmd
        - productivity/reproducible-projects.qmd

    # - part: productivity/installations.qmd
    #   chapters:
    #     - productivity/installing-r-and-rstudio.qmd
    #     - productivity/installing-git.qmd

format:
  html:
    theme:
      - cosmo
      - r4ds.scss
    code-link: true
    author-meta: Rafael A. Irizarry
    callout-appearance: simple
  pdf: 
    documentclass: krantz
    classoption: [krantz2,10pt,twoside,onecolumn,final,openright]
    include-in-header: preamble.tex
    header-includes: |
     \usepackage{amssymb}
     \usepackage{amsmath}
     \usepackage{graphicx}
     \usepackage{subfigure}
     \usepackage{makeidx}
     \usepackage{multicol}
    keep-tex: true
    

knitr:
  opts_chunk:
    comment: "#>"
    collapse: TRUE
    cache: TRUE
    width: 72
    tidy.opts: list(width.cutoff=72, tidy=TRUE)
    out.width: 70%
    fig.align: 'center'
    fig.width: 6
    fig.height: 3.708  # width * 1 / phi
    fig.show: hold
    R.options:
      digits: 3
      width: 72
      formatR.indent: 2
      dplyr.summarise.inform: FALSE
      dplyr.print_min: 5 
      dplyr.print_max: 5
      ggrepel.max.overlaps: 100

editor: source