├── .github └── FUNDING.yml ├── .gitignore ├── .travis.yml ├── 01-intro.Rmd ├── 02-literature.Rmd ├── 03-method.Rmd ├── 04-application.Rmd ├── 05-summary.Rmd ├── 06-references.Rmd ├── DESCRIPTION ├── Dockerfile ├── LICENSE ├── README.md ├── _bookdown.yml ├── _build.sh ├── _deploy.sh ├── _output.yml ├── _publish.R ├── book.bib ├── bookdown-demo.Rproj ├── index.Rmd ├── now.json ├── preamble.tex ├── style.css └── toc.css /.github/FUNDING.yml: -------------------------------------------------------------------------------- 1 | github: [yihui] 2 | patreon: 3 | custom: 4 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | .Rproj.user 2 | .Rhistory 3 | .RData 4 | _book 5 | _bookdown_files 6 | rsconnect 7 | -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 1 | language: r 2 | cache: packages 3 | pandoc_version: 2.9.2.1 4 | 5 | addons: 6 | apt: 7 | packages: 8 | - ghostscript 9 | 10 | before_script: 11 | - chmod +x ./_build.sh 12 | - chmod +x ./_deploy.sh 13 | 14 | script: 15 | - ./_build.sh 16 | - ./_deploy.sh 17 | -------------------------------------------------------------------------------- /01-intro.Rmd: -------------------------------------------------------------------------------- 1 | # Introduction {#intro} 2 | 3 | You can label chapter and section titles using `{#label}` after them, e.g., we can reference Chapter \@ref(intro). If you do not manually label them, there will be automatic labels anyway, e.g., Chapter \@ref(methods). 4 | 5 | Figures and tables with captions will be placed in `figure` and `table` environments, respectively. 6 | 7 | ```{r nice-fig, fig.cap='Here is a nice figure!', out.width='80%', fig.asp=.75, fig.align='center'} 8 | par(mar = c(4, 4, .1, .1)) 9 | plot(pressure, type = 'b', pch = 19) 10 | ``` 11 | 12 | Reference a figure by its code chunk label with the `fig:` prefix, e.g., see Figure \@ref(fig:nice-fig). Similarly, you can reference tables generated from `knitr::kable()`, e.g., see Table \@ref(tab:nice-tab). 13 | 14 | ```{r nice-tab, tidy=FALSE} 15 | knitr::kable( 16 | head(iris, 20), caption = 'Here is a nice table!', 17 | booktabs = TRUE 18 | ) 19 | ``` 20 | 21 | You can write citations, too. For example, we are using the **bookdown** package [@R-bookdown] in this sample book, which was built on top of R Markdown and **knitr** [@xie2015]. 22 | -------------------------------------------------------------------------------- /02-literature.Rmd: -------------------------------------------------------------------------------- 1 | # Literature 2 | 3 | Here is a review of existing methods. 4 | -------------------------------------------------------------------------------- /03-method.Rmd: -------------------------------------------------------------------------------- 1 | # Methods 2 | 3 | We describe our methods in this chapter. 4 | 5 | Math can be added in body using usual syntax like this 6 | 7 | ## math example 8 | 9 | $p$ is unknown but expected to be around 1/3. Standard error will be approximated 10 | 11 | $$ 12 | SE = \sqrt{\frac{p(1-p)}{n}} \approx \sqrt{\frac{1/3 (1 - 1/3)} {300}} = 0.027 13 | $$ 14 | 15 | You can also use math in footnotes like this^[where we mention $p = \frac{a}{b}$]. 16 | 17 | We will approximate standard error to 0.027[^longnote] 18 | 19 | [^longnote]: $p$ is unknown but expected to be around 1/3. Standard error will be approximated 20 | 21 | $$ 22 | SE = \sqrt{\frac{p(1-p)}{n}} \approx \sqrt{\frac{1/3 (1 - 1/3)} {300}} = 0.027 23 | $$ 24 | -------------------------------------------------------------------------------- /04-application.Rmd: -------------------------------------------------------------------------------- 1 | # Applications 2 | 3 | Some _significant_ applications are demonstrated in this chapter. 4 | 5 | ## Example one 6 | 7 | ## Example two 8 | -------------------------------------------------------------------------------- /05-summary.Rmd: -------------------------------------------------------------------------------- 1 | # Final Words 2 | 3 | We have finished a nice book. 4 | -------------------------------------------------------------------------------- /06-references.Rmd: -------------------------------------------------------------------------------- 1 | `r if (knitr:::is_html_output()) ' 2 | # References {-} 3 | '` 4 | -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: placeholder 2 | Type: Book 3 | Title: Does not matter. 4 | Version: 0.0.1 5 | Imports: bookdown 6 | Remotes: rstudio/bookdown 7 | -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- 1 | FROM conoria/alpine-r-bookdown 2 | 3 | WORKDIR /usr/src 4 | 5 | COPY . . 6 | 7 | RUN R -q -e 'bookdown::render_book("index.Rmd", "bookdown::gitbook")' && mv _book /public 8 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | CC0 1.0 Universal 2 | 3 | Statement of Purpose 4 | 5 | The laws of most jurisdictions throughout the world automatically confer 6 | exclusive Copyright and Related Rights (defined below) upon the creator and 7 | subsequent owner(s) (each and all, an "owner") of an original work of 8 | authorship and/or a database (each, a "Work"). 9 | 10 | Certain owners wish to permanently relinquish those rights to a Work for the 11 | purpose of contributing to a commons of creative, cultural and scientific 12 | works ("Commons") that the public can reliably and without fear of later 13 | claims of infringement build upon, modify, incorporate in other works, reuse 14 | and redistribute as freely as possible in any form whatsoever and for any 15 | purposes, including without limitation commercial purposes. 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Affirmer offers the Work as-is and makes no representations or warranties 99 | of any kind concerning the Work, express, implied, statutory or otherwise, 100 | including without limitation warranties of title, merchantability, fitness 101 | for a particular purpose, non infringement, or the absence of latent or 102 | other defects, accuracy, or the present or absence of errors, whether or not 103 | discoverable, all to the greatest extent permissible under applicable law. 104 | 105 | c. Affirmer disclaims responsibility for clearing rights of other persons 106 | that may apply to the Work or any use thereof, including without limitation 107 | any person's Copyright and Related Rights in the Work. Further, Affirmer 108 | disclaims responsibility for obtaining any necessary consents, permissions 109 | or other rights required for any use of the Work. 110 | 111 | d. Affirmer understands and acknowledges that Creative Commons is not a 112 | party to this document and has no duty or obligation with respect to this 113 | CC0 or use of the Work. 114 | 115 | For more information, please see 116 | 117 | 118 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | [![Build Status](https://travis-ci.com/rstudio/bookdown-demo.svg?branch=master)](https://travis-ci.com/rstudio/bookdown-demo) 2 | 3 | This is a minimal example of a book based on R Markdown and **bookdown** (https://github.com/rstudio/bookdown). Please see the page "[Get Started](https://bookdown.org/yihui/bookdown/get-started.html)" at https://bookdown.org/yihui/bookdown/ for how to compile this example into HTML. You may generate a copy of the book in `bookdown::pdf_book` format by calling `bookdown::render_book('index.Rmd', 'bookdown::pdf_book')`. More detailed instructions are available here https://bookdown.org/yihui/bookdown/build-the-book.html. 4 | 5 | You can find the preview of this example at https://bookdown.org/yihui/bookdown-demo/. 6 | -------------------------------------------------------------------------------- /_bookdown.yml: -------------------------------------------------------------------------------- 1 | book_filename: "bookdown-demo" 2 | language: 3 | ui: 4 | chapter_name: "Chapter " 5 | delete_merged_file: true 6 | -------------------------------------------------------------------------------- /_build.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | 3 | set -ev 4 | 5 | Rscript -e "bookdown::render_book('index.Rmd', 'bookdown::gitbook')" 6 | Rscript -e "bookdown::render_book('index.Rmd', 'bookdown::pdf_book')" 7 | Rscript -e "bookdown::render_book('index.Rmd', 'bookdown::epub_book')" 8 | 9 | -------------------------------------------------------------------------------- /_deploy.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | 3 | set -e 4 | 5 | [ -z "${GITHUB_PAT}" ] && exit 0 6 | [ "${TRAVIS_BRANCH}" != "master" ] && exit 0 7 | 8 | git config --global user.email "xie@yihui.name" 9 | git config --global user.name "Yihui Xie" 10 | 11 | git clone -b gh-pages https://${GITHUB_PAT}@github.com/${TRAVIS_REPO_SLUG}.git book-output 12 | cd book-output 13 | cp -r ../_book/* ./ 14 | git add --all * 15 | git commit -m"Update the book" || true 16 | git push -q origin gh-pages 17 | -------------------------------------------------------------------------------- /_output.yml: -------------------------------------------------------------------------------- 1 | bookdown::gitbook: 2 | css: style.css 3 | config: 4 | toc: 5 | before: | 6 |
  • A Minimal Book Example
    • 7 | after: | 8 |
  • Published with bookdown
    • 9 | edit: https://github.com/rstudio/bookdown-demo/edit/master/%s 10 | download: ["pdf", "epub"] 11 | bookdown::pdf_book: 12 | includes: 13 | in_header: preamble.tex 14 | latex_engine: xelatex 15 | citation_package: natbib 16 | keep_tex: yes 17 | bookdown::epub_book: default 18 | bookdown::bs4_book: default 19 | -------------------------------------------------------------------------------- /_publish.R: -------------------------------------------------------------------------------- 1 | # publish the book with different HTML styles; you should not need this script 2 | 3 | unlink('_book', recursive = TRUE) 4 | 5 | x = readLines('index.Rmd') 6 | i = 1 7 | s = paste0('title: "A Minimal Book Example (', c('Bootstrap', 'Tufte'), ' Style)"') 8 | for (fmt in c('html_book', 'tufte_html_book')) { 9 | unlink('_book', recursive = TRUE) 10 | file.copy('index.Rmd', '_index.Rmd') 11 | file.copy('_output.yml', '_output.yml2') 12 | writeLines( 13 | gsub('^title: ".*"', s[i], gsub('gitbook', fmt, x)), 'index.Rmd' 14 | ) 15 | cat( 16 | 'bookdown::', fmt, ':\n', ' css: [style.css, toc.css]\n', sep = '', file = '_output.yml', 17 | append = TRUE 18 | ) 19 | cmd = sprintf("bookdown::render_book('index.Rmd', 'bookdown::%s', quiet = TRUE)", fmt) 20 | res = xfun::Rscript(c('-e', shQuote(cmd))) 21 | file.rename('_index.Rmd', 'index.Rmd') 22 | file.rename('_output.yml2', '_output.yml') 23 | if (res != 0) stop('Failed to compile the book to ', fmt) 24 | i = i + 1 25 | bookdown::publish_book(paste0('bookdown-demo', i)) 26 | } 27 | unlink('_book', recursive = TRUE) 28 | 29 | # default formats 30 | formats = c( 31 | 'bookdown::pdf_book', 'bookdown::epub_book', 'bookdown::gitbook' 32 | ) 33 | 34 | # render the book to all formats unless they are specified via command-line args 35 | for (fmt in formats) { 36 | cmd = sprintf("bookdown::render_book('index.Rmd', '%s', quiet = TRUE)", fmt) 37 | res = xfun::Rscript(c('-e', shQuote(cmd))) 38 | if (res != 0) stop('Failed to compile the book to ', fmt) 39 | } 40 | 41 | bookdown::publish_book('bookdown-demo') 42 | -------------------------------------------------------------------------------- /book.bib: -------------------------------------------------------------------------------- 1 | @Book{xie2015, 2 | title = {Dynamic Documents with {R} and knitr}, 3 | author = {Yihui Xie}, 4 | publisher = {Chapman and Hall/CRC}, 5 | address = {Boca Raton, Florida}, 6 | year = {2015}, 7 | edition = {2nd}, 8 | note = {ISBN 978-1498716963}, 9 | url = {http://yihui.name/knitr/}, 10 | } 11 | -------------------------------------------------------------------------------- /bookdown-demo.Rproj: -------------------------------------------------------------------------------- 1 | Version: 1.0 2 | 3 | RestoreWorkspace: Default 4 | SaveWorkspace: Default 5 | AlwaysSaveHistory: Default 6 | 7 | EnableCodeIndexing: Yes 8 | UseSpacesForTab: Yes 9 | NumSpacesForTab: 2 10 | Encoding: UTF-8 11 | 12 | RnwWeave: knitr 13 | LaTeX: pdfLaTeX 14 | 15 | AutoAppendNewline: Yes 16 | StripTrailingWhitespace: Yes 17 | 18 | BuildType: Website 19 | -------------------------------------------------------------------------------- /index.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "A Minimal Book Example" 3 | author: "Yihui Xie" 4 | date: "`r Sys.Date()`" 5 | site: bookdown::bookdown_site 6 | output: bookdown::gitbook 7 | documentclass: book 8 | bibliography: [book.bib, packages.bib] 9 | biblio-style: apalike 10 | link-citations: yes 11 | github-repo: rstudio/bookdown-demo 12 | description: "This is a minimal example of using the bookdown package to write a book. The output format for this example is bookdown::gitbook." 13 | --- 14 | 15 | # Prerequisites 16 | 17 | This is a _sample_ book written in **Markdown**. You can use anything that Pandoc's Markdown supports, e.g., a math equation $a^2 + b^2 = c^2$. 18 | 19 | The **bookdown** package can be installed from CRAN or Github: 20 | 21 | ```{r eval=FALSE} 22 | install.packages("bookdown") 23 | # or the development version 24 | # devtools::install_github("rstudio/bookdown") 25 | ``` 26 | 27 | Remember each Rmd file contains one and only one chapter, and a chapter is defined by the first-level heading `#`. 28 | 29 | To compile this example to PDF, you need XeLaTeX. You are recommended to install TinyTeX (which includes XeLaTeX): . 30 | 31 | ```{r include=FALSE} 32 | # automatically create a bib database for R packages 33 | knitr::write_bib(c( 34 | .packages(), 'bookdown', 'knitr', 'rmarkdown' 35 | ), 'packages.bib') 36 | ``` 37 | -------------------------------------------------------------------------------- /now.json: -------------------------------------------------------------------------------- 1 | { 2 | "type": "static", 3 | "public": true 4 | } 5 | -------------------------------------------------------------------------------- /preamble.tex: -------------------------------------------------------------------------------- 1 | \usepackage{booktabs} 2 | \usepackage{amsthm} 3 | \makeatletter 4 | \def\thm@space@setup{% 5 | \thm@preskip=8pt plus 2pt minus 4pt 6 | \thm@postskip=\thm@preskip 7 | } 8 | \makeatother 9 | -------------------------------------------------------------------------------- /style.css: -------------------------------------------------------------------------------- 1 | p.caption { 2 | color: #777; 3 | margin-top: 10px; 4 | } 5 | p code { 6 | white-space: inherit; 7 | } 8 | pre { 9 | word-break: normal; 10 | word-wrap: normal; 11 | } 12 | pre code { 13 | white-space: inherit; 14 | } 15 | -------------------------------------------------------------------------------- /toc.css: -------------------------------------------------------------------------------- 1 | #TOC ul, 2 | #TOC li, 3 | #TOC span, 4 | #TOC a { 5 | margin: 0; 6 | padding: 0; 7 | position: relative; 8 | } 9 | #TOC { 10 | line-height: 1; 11 | border-radius: 5px 5px 0 0; 12 | background: #141414; 13 | background: linear-gradient(to bottom, #333333 0%, #141414 100%); 14 | border-bottom: 2px solid #0fa1e0; 15 | width: auto; 16 | } 17 | #TOC:after, 18 | #TOC ul:after { 19 | content: ''; 20 | display: block; 21 | clear: both; 22 | } 23 | #TOC a { 24 | background: #141414; 25 | background: linear-gradient(to bottom, #333333 0%, #141414 100%); 26 | color: #ffffff; 27 | display: block; 28 | padding: 19px 20px; 29 | text-decoration: none; 30 | text-shadow: none; 31 | } 32 | #TOC ul { 33 | list-style: none; 34 | } 35 | #TOC > ul > li { 36 | display: inline-block; 37 | float: left; 38 | margin: 0; 39 | } 40 | #TOC > ul > li > a { 41 | color: #ffffff; 42 | } 43 | #TOC > ul > li:hover:after { 44 | content: ''; 45 | display: block; 46 | width: 0; 47 | height: 0; 48 | position: absolute; 49 | left: 50%; 50 | bottom: 0; 51 | border-left: 10px solid transparent; 52 | border-right: 10px solid transparent; 53 | border-bottom: 10px solid #0fa1e0; 54 | margin-left: -10px; 55 | } 56 | #TOC > ul > li:first-child > a { 57 | border-radius: 5px 0 0 0; 58 | } 59 | #TOC.align-right > ul > li:first-child > a, 60 | #TOC.align-center > ul > li:first-child > a { 61 | border-radius: 0; 62 | } 63 | #TOC.align-right > ul > li:last-child > a { 64 | border-radius: 0 5px 0 0; 65 | } 66 | #TOC > ul > li.active > a, 67 | #TOC > ul > li:hover > a { 68 | color: #ffffff; 69 | box-shadow: inset 0 0 3px #000000; 70 | background: #070707; 71 | background: linear-gradient(to bottom, #262626 0%, #070707 100%); 72 | } 73 | #TOC .has-sub { 74 | z-index: 1; 75 | } 76 | #TOC .has-sub:hover > ul { 77 | display: block; 78 | } 79 | #TOC .has-sub ul { 80 | display: none; 81 | position: absolute; 82 | width: 200px; 83 | top: 100%; 84 | left: 0; 85 | } 86 | #TOC .has-sub ul li a { 87 | background: #0fa1e0; 88 | border-bottom: 1px dotted #31b7f1; 89 | filter: none; 90 | display: block; 91 | line-height: 120%; 92 | padding: 10px; 93 | color: #ffffff; 94 | } 95 | #TOC .has-sub ul li:hover a { 96 | background: #0c7fb0; 97 | } 98 | #TOC ul ul li:hover > a { 99 | color: #ffffff; 100 | } 101 | #TOC .has-sub .has-sub:hover > ul { 102 | display: block; 103 | } 104 | #TOC .has-sub .has-sub ul { 105 | display: none; 106 | position: absolute; 107 | left: 100%; 108 | top: 0; 109 | } 110 | #TOC .has-sub .has-sub ul li a { 111 | background: #0c7fb0; 112 | border-bottom: 1px dotted #31b7f1; 113 | } 114 | #TOC .has-sub .has-sub ul li a:hover { 115 | background: #0a6d98; 116 | } 117 | #TOC ul ul li.last > a, 118 | #TOC ul ul li:last-child > a, 119 | #TOC ul ul ul li.last > a, 120 | #TOC ul ul ul li:last-child > a, 121 | #TOC .has-sub ul li:last-child > a, 122 | #TOC .has-sub ul li.last > a { 123 | border-bottom: 0; 124 | } 125 | #TOC ul { 126 | font-size: 1.2rem; 127 | } 128 | --------------------------------------------------------------------------------