Bookdown demo from:

rstudio/bookdown-demo@1b6389e

.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+_publish.R
+_book
+_bookdown_files
+rsconnect

.travis.yml

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+language: r
+cache: packages
+pandoc_version: 1.19.2.1
+
+before_script:
+  - chmod +x ./_build.sh
+  - chmod +x ./_deploy.sh
+
+script:
+  - ./_build.sh
+  - ./_deploy.sh

01-intro.Rmd

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+# Introduction {#intro}
+
+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).
+
+Figures and tables with captions will be placed in `figure` and `table` environments, respectively.
+
+```{r nice-fig, fig.cap='Here is a nice figure!', out.width='80%', fig.asp=.75, fig.align='center'}
+par(mar = c(4, 4, .1, .1))
+plot(pressure, type = 'b', pch = 19)
+```
+
+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).
+
+```{r nice-tab, tidy=FALSE}
+knitr::kable(
+  head(iris, 20), caption = 'Here is a nice table!',
+  booktabs = TRUE
+)
+```
+
+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].

02-literature.Rmd

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+# Literature
+
+Here is a review of existing methods.

03-method.Rmd

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+# Methods
+
+We describe our methods in this chapter.

04-application.Rmd

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+# Applications
+
+Some _significant_ applications are demonstrated in this chapter.
+
+## Example one
+
+## Example two

05-summary.Rmd

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+# Final Words
+
+We have finished a nice book.

06-references.Rmd

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+`r if (knitr:::is_html_output()) '# References {-}'`

DESCRIPTION

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+Package: placeholder
+Type: Book
+Title: Does not matter.
+Version: 0.0.1
+Imports: bookdown
+Remotes: rstudio/bookdown

LICENSE

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+CC0 1.0 Universal
+
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+

README.md

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+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" at https://bookdown.org/ for how to compile this example.
+
+You can find the preview of this example at https://bookdown.org/yihui/bookdown-demo/

_bookdown.yml

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+book_filename: "bookdown-demo"
+language:
+  ui:
+    chapter_name: "Chapter "
+delete_merged_file: true

_build.sh

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+#!/bin/sh
+
+Rscript -e "bookdown::render_book('index.Rmd', 'bookdown::gitbook')"

_deploy.sh

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+#!/bin/sh
+
+set -e
+
+[ -z "${GITHUB_PAT}" ] && exit 0
+[ "${TRAVIS_BRANCH}" != "master" ] && exit 0
+
+git config --global user.email "[email protected]"
+git config --global user.name "Yihui Xie"
+
+git clone -b gh-pages https://${GITHUB_PAT}@github.com/${TRAVIS_REPO_SLUG}.git book-output
+cd book-output
+cp -r ../_book/* ./
+git add --all *
+git commit -m"Update the book" || true
+git push -q origin gh-pages

_output.yml

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+bookdown::gitbook:
+  css: style.css
+  config:
+    toc:
+      before: |
+        <li><a href="./">A Minimal Book Example</a></li>
+      after: |
+        <li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>
+    edit: https://github.com/rstudio/bookdown-demo/edit/master/%s
+    download: ["pdf", "epub"]
+bookdown::pdf_book:
+  includes:
+    in_header: preamble.tex
+  latex_engine: xelatex
+  citation_package: natbib
+  keep_tex: yes
+bookdown::epub_book: default

book.bib

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+@Book{xie2015,
+  title = {Dynamic Documents with {R} and knitr},
+  author = {Yihui Xie},
+  publisher = {Chapman and Hall/CRC},
+  address = {Boca Raton, Florida},
+  year = {2015},
+  edition = {2nd},
+  note = {ISBN 978-1498716963},
+  url = {http://yihui.name/knitr/},
+}

bookdown-demo.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: knitr
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Website

index.Rmd

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+--- 
+title: "A Minimal Book Example"
+author: "Yihui Xie"
+date: "`r Sys.Date()`"
+site: bookdown::bookdown_site
+output: bookdown::gitbook
+documentclass: book
+bibliography: [book.bib, packages.bib]
+biblio-style: apalike
+link-citations: yes
+github-repo: rstudio/bookdown-demo
+description: "This is a minimal example of using the bookdown package to write a book. The output format for this example is bookdown::gitbook."
+---
+
+# Prerequisites
+
+This is a _sample_ book written in **Markdown**. You can use anything that Pandoc's Markdown supports, e.g., a math equation $a^2 + b^2 = c^2$.
+
+For now, you have to install the development versions of **bookdown** from Github:
+
+```{r eval=FALSE}
+devtools::install_github("rstudio/bookdown")
+```
+
+Remember each Rmd file contains one and only one chapter, and a chapter is defined by the first-level heading `#`.
+
+To compile this example to PDF, you need to install XeLaTeX.
+
+```{r include=FALSE}
+# automatically create a bib database for R packages
+knitr::write_bib(c(
+  .packages(), 'bookdown', 'knitr', 'rmarkdown'
+), 'packages.bib')
+```

packages.bib

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+@Manual{R-base,
+  title = {R: A Language and Environment for Statistical Computing},
+  author = {{R Core Team}},
+  organization = {R Foundation for Statistical Computing},
+  address = {Vienna, Austria},
+  year = {2017},
+  url = {https://www.R-project.org/},
+}
+@Manual{R-bookdown,
+  title = {bookdown: Authoring Books and Technical Documents with R Markdown},
+  author = {Yihui Xie},
+  year = {2017},
+  note = {R package version 0.5},
+  url = {https://CRAN.R-project.org/package=bookdown},
+}
+@Manual{R-knitr,
+  title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
+  author = {Yihui Xie},
+  year = {2017},
+  note = {R package version 1.18},
+  url = {https://CRAN.R-project.org/package=knitr},
+}
+@Manual{R-rmarkdown,
+  title = {rmarkdown: Dynamic Documents for R},
+  author = {JJ Allaire and Yihui Xie and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang},
+  year = {2017},
+  note = {R package version 1.8},
+  url = {https://CRAN.R-project.org/package=rmarkdown},
+}

preamble.tex

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+\usepackage{booktabs}
+\usepackage{amsthm}
+\makeatletter
+\def\thm@space@setup{%
+  \thm@preskip=8pt plus 2pt minus 4pt
+  \thm@postskip=\thm@preskip
+}
+\makeatother

style.css

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+p.caption {
+  color: #777;
+  margin-top: 10px;
+}
+p code {
+  white-space: inherit;
+}
+pre {
+  word-break: normal;
+  word-wrap: normal;
+}
+pre code {
+  white-space: inherit;
+}