diff --git a/.gitignore b/.gitignore new file mode 100755 index 0000000..08e52d2 --- /dev/null +++ b/.gitignore @@ -0,0 +1,7 @@ +.Rproj.user +.Rhistory +.RData +_publish.R +_book +_bookdown_files +rsconnect diff --git a/.travis.yml b/.travis.yml new file mode 100755 index 0000000..267a6c1 --- /dev/null +++ b/.travis.yml @@ -0,0 +1,11 @@ +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 diff --git a/01-intro.Rmd b/01-intro.Rmd new file mode 100755 index 0000000..6b16e73 --- /dev/null +++ b/01-intro.Rmd @@ -0,0 +1,21 @@ +# 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]. diff --git a/02-literature.Rmd b/02-literature.Rmd new file mode 100755 index 0000000..00745d0 --- /dev/null +++ b/02-literature.Rmd @@ -0,0 +1,3 @@ +# Literature + +Here is a review of existing methods. diff --git a/03-method.Rmd b/03-method.Rmd new file mode 100755 index 0000000..93f03d8 --- /dev/null +++ b/03-method.Rmd @@ -0,0 +1,3 @@ +# Methods + +We describe our methods in this chapter. diff --git a/04-application.Rmd b/04-application.Rmd new file mode 100755 index 0000000..d5b076e --- /dev/null +++ b/04-application.Rmd @@ -0,0 +1,7 @@ +# Applications + +Some _significant_ applications are demonstrated in this chapter. + +## Example one + +## Example two diff --git a/05-summary.Rmd b/05-summary.Rmd new file mode 100755 index 0000000..c1ac36f --- /dev/null +++ b/05-summary.Rmd @@ -0,0 +1,3 @@ +# Final Words + +We have finished a nice book. diff --git a/06-references.Rmd b/06-references.Rmd new file mode 100755 index 0000000..cfcb081 --- /dev/null +++ b/06-references.Rmd @@ -0,0 +1 @@ +`r if (knitr:::is_html_output()) '# References {-}'` diff --git a/DESCRIPTION b/DESCRIPTION new file mode 100755 index 0000000..5c3a64d --- /dev/null +++ b/DESCRIPTION @@ -0,0 +1,6 @@ +Package: placeholder +Type: Book +Title: Does not matter. +Version: 0.0.1 +Imports: bookdown +Remotes: rstudio/bookdown diff --git a/LICENSE b/LICENSE new file mode 100755 index 0000000..2c4afab --- /dev/null +++ b/LICENSE @@ -0,0 +1,117 @@ +CC0 1.0 Universal + +Statement of Purpose + +The laws of most jurisdictions throughout the world automatically confer +exclusive Copyright and Related Rights (defined below) upon the creator and +subsequent owner(s) (each and all, an "owner") of an original work of +authorship and/or a database (each, a "Work"). + +Certain owners wish to permanently relinquish those rights to a Work for the +purpose of contributing to a commons of creative, cultural and scientific +works ("Commons") that the public can reliably and without fear of later +claims of infringement build upon, modify, incorporate in other works, reuse +and redistribute as freely as possible in any form whatsoever and for any +purposes, including without limitation commercial purposes. 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Affirmer offers the Work as-is and makes no representations or warranties + of any kind concerning the Work, express, implied, statutory or otherwise, + including without limitation warranties of title, merchantability, fitness + for a particular purpose, non infringement, or the absence of latent or + other defects, accuracy, or the present or absence of errors, whether or not + discoverable, all to the greatest extent permissible under applicable law. + + c. Affirmer disclaims responsibility for clearing rights of other persons + that may apply to the Work or any use thereof, including without limitation + any person's Copyright and Related Rights in the Work. Further, Affirmer + disclaims responsibility for obtaining any necessary consents, permissions + or other rights required for any use of the Work. + + d. Affirmer understands and acknowledges that Creative Commons is not a + party to this document and has no duty or obligation with respect to this + CC0 or use of the Work. + +For more information, please see + + diff --git a/README.md b/README.md new file mode 100755 index 0000000..816bbc4 --- /dev/null +++ b/README.md @@ -0,0 +1,3 @@ +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" 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/ diff --git a/_bookdown.yml b/_bookdown.yml new file mode 100755 index 0000000..6586f1a --- /dev/null +++ b/_bookdown.yml @@ -0,0 +1,5 @@ +book_filename: "bookdown-demo" +language: + ui: + chapter_name: "Chapter " +delete_merged_file: true diff --git a/_build.sh b/_build.sh new file mode 100755 index 0000000..394e2dc --- /dev/null +++ b/_build.sh @@ -0,0 +1,3 @@ +#!/bin/sh + +Rscript -e "bookdown::render_book('index.Rmd', 'bookdown::gitbook')" diff --git a/_deploy.sh b/_deploy.sh new file mode 100755 index 0000000..ee544e0 --- /dev/null +++ b/_deploy.sh @@ -0,0 +1,16 @@ +#!/bin/sh + +set -e + +[ -z "${GITHUB_PAT}" ] && exit 0 +[ "${TRAVIS_BRANCH}" != "master" ] && exit 0 + +git config --global user.email "xie@yihui.name" +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 diff --git a/_output.yml b/_output.yml new file mode 100755 index 0000000..342a1d6 --- /dev/null +++ b/_output.yml @@ -0,0 +1,17 @@ +bookdown::gitbook: + css: style.css + config: + toc: + before: | +
  • A Minimal Book Example
    • + after: | +
  • Published with bookdown
    • + 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 diff --git a/book.bib b/book.bib new file mode 100755 index 0000000..f52f3d2 --- /dev/null +++ b/book.bib @@ -0,0 +1,10 @@ +@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/}, +} diff --git a/bookdown-demo.Rproj b/bookdown-demo.Rproj new file mode 100755 index 0000000..e4c1c67 --- /dev/null +++ b/bookdown-demo.Rproj @@ -0,0 +1,18 @@ +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 diff --git a/index.Rmd b/index.Rmd new file mode 100755 index 0000000..4e21b9d --- /dev/null +++ b/index.Rmd @@ -0,0 +1,34 @@ +--- +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') +``` diff --git a/packages.bib b/packages.bib new file mode 100644 index 0000000..093e809 --- /dev/null +++ b/packages.bib @@ -0,0 +1,29 @@ +@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}, +} diff --git a/preamble.tex b/preamble.tex new file mode 100755 index 0000000..8a88e02 --- /dev/null +++ b/preamble.tex @@ -0,0 +1,8 @@ +\usepackage{booktabs} +\usepackage{amsthm} +\makeatletter +\def\thm@space@setup{% + \thm@preskip=8pt plus 2pt minus 4pt + \thm@postskip=\thm@preskip +} +\makeatother diff --git a/style.css b/style.css new file mode 100755 index 0000000..f317b43 --- /dev/null +++ b/style.css @@ -0,0 +1,14 @@ +p.caption { + color: #777; + margin-top: 10px; +} +p code { + white-space: inherit; +} +pre { + word-break: normal; + word-wrap: normal; +} +pre code { + white-space: inherit; +} diff --git a/toc.css b/toc.css new file mode 100755 index 0000000..11f5438 --- /dev/null +++ b/toc.css @@ -0,0 +1,127 @@ +#TOC ul, +#TOC li, +#TOC span, +#TOC a { + margin: 0; + padding: 0; + position: relative; +} +#TOC { + line-height: 1; + border-radius: 5px 5px 0 0; + background: #141414; + background: linear-gradient(to bottom, #333333 0%, #141414 100%); + border-bottom: 2px solid #0fa1e0; + width: auto; +} +#TOC:after, +#TOC ul:after { + content: ''; + display: block; + clear: both; +} +#TOC a { + background: #141414; + background: linear-gradient(to bottom, #333333 0%, #141414 100%); + color: #ffffff; + display: block; + padding: 19px 20px; + text-decoration: none; + text-shadow: none; +} +#TOC ul { + list-style: none; +} +#TOC > ul > li { + display: inline-block; + float: left; + margin: 0; +} +#TOC > ul > li > a { + color: #ffffff; +} +#TOC > ul > li:hover:after { + content: ''; + display: block; + width: 0; + height: 0; + position: absolute; + left: 50%; + bottom: 0; + border-left: 10px solid transparent; + border-right: 10px solid transparent; + border-bottom: 10px solid #0fa1e0; + margin-left: -10px; +} +#TOC > ul > li:first-child > a { + border-radius: 5px 0 0 0; +} +#TOC.align-right > ul > li:first-child > a, +#TOC.align-center > ul > li:first-child > a { + border-radius: 0; +} +#TOC.align-right > ul > li:last-child > a { + border-radius: 0 5px 0 0; +} +#TOC > ul > li.active > a, +#TOC > ul > li:hover > a { + color: #ffffff; + box-shadow: inset 0 0 3px #000000; + background: #070707; + background: linear-gradient(to bottom, #262626 0%, #070707 100%); +} +#TOC .has-sub { + z-index: 1; +} +#TOC .has-sub:hover > ul { + display: block; +} +#TOC .has-sub ul { + display: none; + position: absolute; + width: 200px; + top: 100%; + left: 0; +} +#TOC .has-sub ul li a { + background: #0fa1e0; + border-bottom: 1px dotted #31b7f1; + filter: none; + display: block; + line-height: 120%; + padding: 10px; + color: #ffffff; +} +#TOC .has-sub ul li:hover a { + background: #0c7fb0; +} +#TOC ul ul li:hover > a { + color: #ffffff; +} +#TOC .has-sub .has-sub:hover > ul { + display: block; +} +#TOC .has-sub .has-sub ul { + display: none; + position: absolute; + left: 100%; + top: 0; +} +#TOC .has-sub .has-sub ul li a { + background: #0c7fb0; + border-bottom: 1px dotted #31b7f1; +} +#TOC .has-sub .has-sub ul li a:hover { + background: #0a6d98; +} +#TOC ul ul li.last > a, +#TOC ul ul li:last-child > a, +#TOC ul ul ul li.last > a, +#TOC ul ul ul li:last-child > a, +#TOC .has-sub ul li:last-child > a, +#TOC .has-sub ul li.last > a { + border-bottom: 0; +} +#TOC ul { + font-size: 1.2rem; +}