├── .nojekyll ├── docs ├── .nojekyll ├── bookdown-demo_files │ └── figure-html │ │ └── nice-fig-1.png ├── libs │ └── gitbook-2.6.7 │ │ ├── css │ │ ├── fontawesome │ │ │ └── fontawesome-webfont.ttf │ │ ├── plugin-clipboard.css │ │ ├── plugin-table.css │ │ ├── plugin-search.css │ │ ├── plugin-bookdown.css │ │ ├── plugin-fontsettings.css │ │ └── plugin-highlight.css │ │ └── js │ │ ├── plugin-clipboard.js │ │ ├── jquery.highlight.js │ │ ├── plugin-sharing.js │ │ ├── plugin-fontsettings.js │ │ ├── plugin-search.js │ │ ├── plugin-bookdown.js │ │ ├── clipboard.min.js │ │ └── lunr.js ├── style.css ├── search_index.json ├── literature.html ├── methods.html ├── final-words.html ├── references.html ├── applications.html ├── index.html └── intro.html ├── 05-summary.Rmd ├── 03-method.Rmd ├── .gitattributes ├── 02-literature.Rmd ├── 06-references.Rmd ├── .gitignore ├── DESCRIPTION ├── _bookdown.yml ├── 04-application.Rmd ├── preamble.tex ├── style.css ├── book.bib ├── _output.yml ├── 01-intro.Rmd ├── index.Rmd ├── README.md ├── packages.bib ├── toc.css └── LICENSE /.nojekyll: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /docs/.nojekyll: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /05-summary.Rmd: -------------------------------------------------------------------------------- 1 | # Final Words 2 | 3 | We have finished a nice book. 4 | -------------------------------------------------------------------------------- /03-method.Rmd: -------------------------------------------------------------------------------- 1 | # Methods 2 | 3 | We describe our methods in this chapter. 4 | -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- 1 | # Auto detect text files and perform LF normalization 2 | * text=auto -------------------------------------------------------------------------------- /02-literature.Rmd: -------------------------------------------------------------------------------- 1 | # Literature 2 | 3 | Here is a review of existing methods. 4 | -------------------------------------------------------------------------------- /06-references.Rmd: -------------------------------------------------------------------------------- 1 | `r if (knitr:::is_html_output()) ' 2 | # References {-} 3 | '` 4 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | .Rproj.user 2 | .Rhistory 3 | .RData 4 | _publish.R 5 | _book 6 | _bookdown_files 7 | rsconnect 8 | *.Rproj 9 | 10 | -------------------------------------------------------------------------------- /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 | -------------------------------------------------------------------------------- /_bookdown.yml: -------------------------------------------------------------------------------- 1 | book_filename: "bookdown-demo" 2 | language: 3 | ui: 4 | chapter_name: "Chapter " 5 | delete_merged_file: true 6 | output_dir: "docs" 7 | -------------------------------------------------------------------------------- /04-application.Rmd: -------------------------------------------------------------------------------- 1 | # Applications 2 | 3 | Some _significant_ applications are demonstrated in this chapter. 4 | 5 | ## Example one 6 | 7 | ## Example two 8 | -------------------------------------------------------------------------------- /docs/bookdown-demo_files/figure-html/nice-fig-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RVerse-Tutorials/bookdown-demo/master/docs/bookdown-demo_files/figure-html/nice-fig-1.png -------------------------------------------------------------------------------- /docs/libs/gitbook-2.6.7/css/fontawesome/fontawesome-webfont.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RVerse-Tutorials/bookdown-demo/master/docs/libs/gitbook-2.6.7/css/fontawesome/fontawesome-webfont.ttf -------------------------------------------------------------------------------- /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 | -------------------------------------------------------------------------------- /docs/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 | -------------------------------------------------------------------------------- /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 | -------------------------------------------------------------------------------- /docs/libs/gitbook-2.6.7/css/plugin-clipboard.css: -------------------------------------------------------------------------------- 1 | div.sourceCode { 2 | position: relative; 3 | } 4 | 5 | .copy-to-clipboard-button { 6 | position: absolute; 7 | right: 0; 8 | top: 0; 9 | visibility: hidden; 10 | } 11 | 12 | .copy-to-clipboard-button:focus { 13 | outline: 0; 14 | } 15 | 16 | div.sourceCode:hover > .copy-to-clipboard-button { 17 | visibility: visible; 18 | } 19 | -------------------------------------------------------------------------------- /docs/libs/gitbook-2.6.7/css/plugin-table.css: -------------------------------------------------------------------------------- 1 | .book .book-body .page-wrapper .page-inner section.normal table{display:table;width:100%;border-collapse:collapse;border-spacing:0;overflow:auto}.book .book-body .page-wrapper .page-inner section.normal table td,.book .book-body .page-wrapper .page-inner section.normal table th{padding:6px 13px;border:1px solid #ddd}.book .book-body .page-wrapper .page-inner section.normal table tr{background-color:#fff;border-top:1px solid #ccc}.book .book-body .page-wrapper .page-inner section.normal table tr:nth-child(2n){background-color:#f8f8f8}.book .book-body .page-wrapper .page-inner section.normal table th{font-weight:700} 2 | -------------------------------------------------------------------------------- /docs/libs/gitbook-2.6.7/css/plugin-search.css: -------------------------------------------------------------------------------- 1 | .book .book-summary .book-search { 2 | padding: 6px; 3 | background: transparent; 4 | position: absolute; 5 | top: -50px; 6 | left: 0px; 7 | right: 0px; 8 | transition: top 0.5s ease; 9 | } 10 | .book .book-summary .book-search input, 11 | .book .book-summary .book-search input:focus, 12 | .book .book-summary .book-search input:hover { 13 | width: 100%; 14 | background: transparent; 15 | border: 1px solid #ccc; 16 | box-shadow: none; 17 | outline: none; 18 | line-height: 22px; 19 | padding: 7px 4px; 20 | color: inherit; 21 | box-sizing: border-box; 22 | } 23 | .book.with-search .book-summary .book-search { 24 | top: 0px; 25 | } 26 | .book.with-search .book-summary ul.summary { 27 | top: 50px; 28 | } 29 | .with-search .summary li[data-level] a[href*=".html#"] { 30 | display: none; 31 | } 32 | -------------------------------------------------------------------------------- /_output.yml: -------------------------------------------------------------------------------- 1 | bookdown::gitbook: 2 | css: style.css 3 | split_bib: FALSE # change to TRUE to have refs at end of chapter 4 | config: 5 | toc: 6 | before: | 7 |
  • A Minimal Book Example
    • 8 | after: | 9 |
  • Published with bookdown
    • 10 | download: null 11 | # change to download: ["pdf"] or ["pdf", "epub"] to download these 12 | # uncomment these lines to add a link to github source and links to download 13 | # edit: https://github.com//bookdown-demo/edit/master/%s 14 | # Uncomment these lines if you want to make a pdf 15 | # bookdown::pdf_book: 16 | # includes: 17 | # in_header: preamble.tex 18 | # latex_engine: xelatex 19 | 20 | # To see the config options for HTML go to 21 | # https://bookdown.org/yihui/bookdown/html.html 22 | # citation_package: natbib 23 | # bookdown::epub_book: default 24 | -------------------------------------------------------------------------------- /docs/libs/gitbook-2.6.7/js/plugin-clipboard.js: -------------------------------------------------------------------------------- 1 | gitbook.require(["gitbook", "jQuery"], function(gitbook, $) { 2 | 3 | var copyButton = ''; 4 | var clipboard; 5 | 6 | gitbook.events.bind("page.change", function() { 7 | 8 | if (!ClipboardJS.isSupported()) return; 9 | 10 | // the page.change event is thrown twice: before and after the page changes 11 | if (clipboard) { 12 | // clipboard is already defined 13 | // we can deduct that we are before page changes 14 | clipboard.destroy(); // destroy the previous events listeners 15 | clipboard = undefined; // reset the clipboard object 16 | return; 17 | } 18 | 19 | $(copyButton).prependTo("div.sourceCode"); 20 | 21 | clipboard = new ClipboardJS(".copy-to-clipboard-button", { 22 | text: function(trigger) { 23 | return trigger.parentNode.textContent; 24 | } 25 | }); 26 | 27 | }); 28 | 29 | }); 30 | -------------------------------------------------------------------------------- /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 | -------------------------------------------------------------------------------- /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 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | This is a copy of the minimal example of a book from the **bookdown** (https://github.com/rstudio/bookdown) github page. Go to the [bookdown book](https://bookdown.org/yihui/bookdown) to read all about using the package. 2 | 3 | To build the book in RStudio, 4 | 5 | 1. Download the zip file and unzip. You can also fork the repository. 6 | 1. Create a project of the folder with the demo files. 7 | 2. The Build tab should appear with the option 'Build book'. If it does not 8 | - You don't have bookdown package installed. Install it. 9 | - You have not set the project in the right directory. The `.Rproj` file must be in the same directory as all the files for the book. 10 | 3. Click Build > Build book. 11 | 12 | To generate a PDF, 13 | 14 | 1. Make sure you have a LaTeX installation. If you don't have one, you can install the tinytex package. 15 | 16 | ``` 17 | install.packages('tinytex') 18 | tinytex::install_tinytex() 19 | ``` 20 | 21 | 2. Uncomment the lines in `_bookdown.yml` concerning PDF output. or 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. 22 | 23 | You can find the preview of this example at https://bookdown.org/yihui/bookdown-demo/. 24 | -------------------------------------------------------------------------------- /packages.bib: -------------------------------------------------------------------------------- 1 | @Manual{R-base, 2 | title = {R: A Language and Environment for Statistical Computing}, 3 | author = {{R Core Team}}, 4 | organization = {R Foundation for Statistical Computing}, 5 | address = {Vienna, Austria}, 6 | year = {2019}, 7 | url = {https://www.R-project.org/}, 8 | } 9 | @Manual{R-bookdown, 10 | title = {bookdown: Authoring Books and Technical Documents with R Markdown}, 11 | author = {Yihui Xie}, 12 | year = {2020}, 13 | note = {R package version 0.19}, 14 | url = {https://CRAN.R-project.org/package=bookdown}, 15 | } 16 | @Manual{R-knitr, 17 | title = {knitr: A General-Purpose Package for Dynamic Report Generation in R}, 18 | author = {Yihui Xie}, 19 | year = {2020}, 20 | note = {R package version 1.28}, 21 | url = {https://CRAN.R-project.org/package=knitr}, 22 | } 23 | @Manual{R-rmarkdown, 24 | title = {rmarkdown: Dynamic Documents for R}, 25 | 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 and Richard Iannone}, 26 | year = {2020}, 27 | note = {R package version 2.1}, 28 | url = {https://CRAN.R-project.org/package=rmarkdown}, 29 | } 30 | @Book{bookdown2016, 31 | title = {bookdown: Authoring Books and Technical Documents with {R} Markdown}, 32 | author = {Yihui Xie}, 33 | publisher = {Chapman and Hall/CRC}, 34 | address = {Boca Raton, Florida}, 35 | year = {2016}, 36 | note = {ISBN 978-1138700109}, 37 | url = {https://github.com/rstudio/bookdown}, 38 | } 39 | @Book{knitr2015, 40 | title = {Dynamic Documents with {R} and knitr}, 41 | author = {Yihui Xie}, 42 | publisher = {Chapman and Hall/CRC}, 43 | address = {Boca Raton, Florida}, 44 | year = {2015}, 45 | edition = {2nd}, 46 | note = {ISBN 978-1498716963}, 47 | url = {https://yihui.org/knitr/}, 48 | } 49 | @InCollection{knitr2014, 50 | booktitle = {Implementing Reproducible Computational Research}, 51 | editor = {Victoria Stodden and Friedrich Leisch and Roger D. Peng}, 52 | title = {knitr: A Comprehensive Tool for Reproducible Research in {R}}, 53 | author = {Yihui Xie}, 54 | publisher = {Chapman and Hall/CRC}, 55 | year = {2014}, 56 | note = {ISBN 978-1466561595}, 57 | url = {http://www.crcpress.com/product/isbn/9781466561595}, 58 | } 59 | @Book{rmarkdown2018, 60 | title = {R Markdown: The Definitive Guide}, 61 | author = {Yihui Xie and J.J. Allaire and Garrett Grolemund}, 62 | publisher = {Chapman and Hall/CRC}, 63 | address = {Boca Raton, Florida}, 64 | year = {2018}, 65 | note = {ISBN 9781138359338}, 66 | url = {https://bookdown.org/yihui/rmarkdown}, 67 | } 68 | -------------------------------------------------------------------------------- /docs/search_index.json: -------------------------------------------------------------------------------- 1 | [ 2 | ["index.html", "A Minimal Book Example Chapter 1 Prerequisites", " A Minimal Book Example Yihui Xie 2020-05-22 Chapter 1 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\\). The bookdown package can be installed from CRAN or Github: install.packages("bookdown") # or the development version # 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 XeLaTeX. You are recommended to install TinyTeX (which includes XeLaTeX): https://yihui.name/tinytex/. "], 3 | ["intro.html", "Chapter 2 Introduction", " Chapter 2 Introduction You can label chapter and section titles using {#label} after them, e.g., we can reference Chapter 2. If you do not manually label them, there will be automatic labels anyway, e.g., Chapter 4. Figures and tables with captions will be placed in figure and table environments, respectively. par(mar = c(4, 4, .1, .1)) plot(pressure, type = 'b', pch = 19) Figure 2.1: Here is a nice figure! Reference a figure by its code chunk label with the fig: prefix, e.g., see Figure 2.1. Similarly, you can reference tables generated from knitr::kable(), e.g., see Table 2.1. knitr::kable( head(iris, 20), caption = 'Here is a nice table!', booktabs = TRUE ) Table 2.1: Here is a nice table! Sepal.Length Sepal.Width Petal.Length Petal.Width Species 5.1 3.5 1.4 0.2 setosa 4.9 3.0 1.4 0.2 setosa 4.7 3.2 1.3 0.2 setosa 4.6 3.1 1.5 0.2 setosa 5.0 3.6 1.4 0.2 setosa 5.4 3.9 1.7 0.4 setosa 4.6 3.4 1.4 0.3 setosa 5.0 3.4 1.5 0.2 setosa 4.4 2.9 1.4 0.2 setosa 4.9 3.1 1.5 0.1 setosa 5.4 3.7 1.5 0.2 setosa 4.8 3.4 1.6 0.2 setosa 4.8 3.0 1.4 0.1 setosa 4.3 3.0 1.1 0.1 setosa 5.8 4.0 1.2 0.2 setosa 5.7 4.4 1.5 0.4 setosa 5.4 3.9 1.3 0.4 setosa 5.1 3.5 1.4 0.3 setosa 5.7 3.8 1.7 0.3 setosa 5.1 3.8 1.5 0.3 setosa You can write citations, too. For example, we are using the bookdown package (Xie 2020) in this sample book, which was built on top of R Markdown and knitr (Xie 2015). "], 4 | ["literature.html", "Chapter 3 Literature", " Chapter 3 Literature Here is a review of existing methods. "], 5 | ["methods.html", "Chapter 4 Methods", " Chapter 4 Methods We describe our methods in this chapter. "], 6 | ["applications.html", "Chapter 5 Applications 5.1 Example one 5.2 Example two", " Chapter 5 Applications Some significant applications are demonstrated in this chapter. 5.1 Example one 5.2 Example two "], 7 | ["final-words.html", "Chapter 6 Final Words", " Chapter 6 Final Words We have finished a nice book. "], 8 | ["references.html", "References", " References "] 9 | ] 10 | -------------------------------------------------------------------------------- /docs/libs/gitbook-2.6.7/css/plugin-bookdown.css: -------------------------------------------------------------------------------- 1 | .book .book-header h1 { 2 | padding-left: 20px; 3 | padding-right: 20px; 4 | } 5 | .book .book-header.fixed { 6 | position: fixed; 7 | right: 0; 8 | top: 0; 9 | left: 0; 10 | border-bottom: 1px solid rgba(0,0,0,.07); 11 | } 12 | span.search-highlight { 13 | background-color: #ffff88; 14 | } 15 | @media (min-width: 600px) { 16 | .book.with-summary .book-header.fixed { 17 | left: 300px; 18 | } 19 | } 20 | @media (max-width: 1240px) { 21 | .book .book-body.fixed { 22 | top: 50px; 23 | } 24 | .book .book-body.fixed .body-inner { 25 | top: auto; 26 | } 27 | } 28 | @media (max-width: 600px) { 29 | .book.with-summary .book-header.fixed { 30 | left: calc(100% - 60px); 31 | min-width: 300px; 32 | } 33 | .book.with-summary .book-body { 34 | transform: none; 35 | left: calc(100% - 60px); 36 | min-width: 300px; 37 | } 38 | .book .book-body.fixed { 39 | top: 0; 40 | } 41 | } 42 | 43 | .book .book-body.fixed .body-inner { 44 | top: 50px; 45 | } 46 | .book .book-body .page-wrapper .page-inner section.normal sub, .book .book-body .page-wrapper .page-inner section.normal sup { 47 | font-size: 85%; 48 | } 49 | 50 | @media print { 51 | .book .book-summary, .book .book-body .book-header, .fa { 52 | display: none !important; 53 | } 54 | .book .book-body.fixed { 55 | left: 0px; 56 | } 57 | .book .book-body,.book .book-body .body-inner, .book.with-summary { 58 | overflow: visible !important; 59 | } 60 | } 61 | .kable_wrapper { 62 | border-spacing: 20px 0; 63 | border-collapse: separate; 64 | border: none; 65 | margin: auto; 66 | } 67 | .kable_wrapper > tbody > tr > td { 68 | vertical-align: top; 69 | } 70 | .book .book-body .page-wrapper .page-inner section.normal table tr.header { 71 | border-top-width: 2px; 72 | } 73 | .book .book-body .page-wrapper .page-inner section.normal table tr:last-child td { 74 | border-bottom-width: 2px; 75 | } 76 | .book .book-body .page-wrapper .page-inner section.normal table td, .book .book-body .page-wrapper .page-inner section.normal table th { 77 | border-left: none; 78 | border-right: none; 79 | } 80 | .book .book-body .page-wrapper .page-inner section.normal table.kable_wrapper > tbody > tr, .book .book-body .page-wrapper .page-inner section.normal table.kable_wrapper > tbody > tr > td { 81 | border-top: none; 82 | } 83 | .book .book-body .page-wrapper .page-inner section.normal table.kable_wrapper > tbody > tr:last-child > td { 84 | border-bottom: none; 85 | } 86 | 87 | div.theorem, div.lemma, div.corollary, div.proposition, div.conjecture { 88 | font-style: italic; 89 | } 90 | span.theorem, span.lemma, span.corollary, span.proposition, span.conjecture { 91 | font-style: normal; 92 | } 93 | div.proof:after { 94 | content: "\25a2"; 95 | float: right; 96 | } 97 | .header-section-number { 98 | padding-right: .5em; 99 | } 100 | -------------------------------------------------------------------------------- /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 | -------------------------------------------------------------------------------- /docs/libs/gitbook-2.6.7/js/jquery.highlight.js: -------------------------------------------------------------------------------- 1 | gitbook.require(["jQuery"], function(jQuery) { 2 | 3 | /* 4 | * jQuery Highlight plugin 5 | * 6 | * Based on highlight v3 by Johann Burkard 7 | * http://johannburkard.de/blog/programming/javascript/highlight-javascript-text-higlighting-jquery-plugin.html 8 | * 9 | * Code a little bit refactored and cleaned (in my humble opinion). 10 | * Most important changes: 11 | * - has an option to highlight only entire words (wordsOnly - false by default), 12 | * - has an option to be case sensitive (caseSensitive - false by default) 13 | * - highlight element tag and class names can be specified in options 14 | * 15 | * Copyright (c) 2009 Bartek Szopka 16 | * 17 | * Licensed under MIT license. 18 | * 19 | */ 20 | 21 | jQuery.extend({ 22 | highlight: function (node, re, nodeName, className) { 23 | if (node.nodeType === 3) { 24 | var match = node.data.match(re); 25 | if (match) { 26 | var highlight = document.createElement(nodeName || 'span'); 27 | highlight.className = className || 'highlight'; 28 | var wordNode = node.splitText(match.index); 29 | wordNode.splitText(match[0].length); 30 | var wordClone = wordNode.cloneNode(true); 31 | highlight.appendChild(wordClone); 32 | wordNode.parentNode.replaceChild(highlight, wordNode); 33 | return 1; //skip added node in parent 34 | } 35 | } else if ((node.nodeType === 1 && node.childNodes) && // only element nodes that have children 36 | !/(script|style)/i.test(node.tagName) && // ignore script and style nodes 37 | !(node.tagName === nodeName.toUpperCase() && node.className === className)) { // skip if already highlighted 38 | for (var i = 0; i < node.childNodes.length; i++) { 39 | i += jQuery.highlight(node.childNodes[i], re, nodeName, className); 40 | } 41 | } 42 | return 0; 43 | } 44 | }); 45 | 46 | jQuery.fn.unhighlight = function (options) { 47 | var settings = { className: 'highlight', element: 'span' }; 48 | jQuery.extend(settings, options); 49 | 50 | return this.find(settings.element + "." + settings.className).each(function () { 51 | var parent = this.parentNode; 52 | parent.replaceChild(this.firstChild, this); 53 | parent.normalize(); 54 | }).end(); 55 | }; 56 | 57 | jQuery.fn.highlight = function (words, options) { 58 | var settings = { className: 'highlight', element: 'span', caseSensitive: false, wordsOnly: false }; 59 | jQuery.extend(settings, options); 60 | 61 | if (words.constructor === String) { 62 | words = [words]; 63 | // also match 'foo-bar' if search for 'foo bar' 64 | if (/\s/.test(words[0])) words.push(words[0].replace(/\s+/, '-')); 65 | } 66 | words = jQuery.grep(words, function(word, i){ 67 | return word !== ''; 68 | }); 69 | words = jQuery.map(words, function(word, i) { 70 | return word.replace(/[-[\]{}()*+?.,\\^$|#\s]/g, "\\$&"); 71 | }); 72 | if (words.length === 0) { return this; } 73 | 74 | var flag = settings.caseSensitive ? "" : "i"; 75 | var pattern = "(" + words.join("|") + ")"; 76 | if (settings.wordsOnly) { 77 | pattern = "\\b" + pattern + "\\b"; 78 | } 79 | var re = new RegExp(pattern, flag); 80 | 81 | return this.each(function () { 82 | jQuery.highlight(this, re, settings.element, settings.className); 83 | }); 84 | }; 85 | 86 | }); 87 | -------------------------------------------------------------------------------- /docs/libs/gitbook-2.6.7/js/plugin-sharing.js: -------------------------------------------------------------------------------- 1 | gitbook.require(["gitbook", "lodash", "jQuery"], function(gitbook, _, $) { 2 | var SITES = { 3 | 'github': { 4 | 'label': 'Github', 5 | 'icon': 'fa fa-github', 6 | 'onClick': function(e) { 7 | e.preventDefault(); 8 | var repo = $('meta[name="github-repo"]').attr('content'); 9 | if (typeof repo === 'undefined') throw("Github repo not defined"); 10 | window.open("https://github.com/"+repo); 11 | } 12 | }, 13 | 'facebook': { 14 | 'label': 'Facebook', 15 | 'icon': 'fa fa-facebook', 16 | 'onClick': function(e) { 17 | e.preventDefault(); 18 | window.open("http://www.facebook.com/sharer/sharer.php?u="+encodeURIComponent(location.href)); 19 | } 20 | }, 21 | 'twitter': { 22 | 'label': 'Twitter', 23 | 'icon': 'fa fa-twitter', 24 | 'onClick': function(e) { 25 | e.preventDefault(); 26 | window.open("http://twitter.com/intent/tweet?text="+document.title+"&url="+encodeURIComponent(location.href)+"&hashtags=rmarkdown,bookdown"); 27 | } 28 | }, 29 | 'linkedin': { 30 | 'label': 'LinkedIn', 31 | 'icon': 'fa fa-linkedin', 32 | 'onClick': function(e) { 33 | e.preventDefault(); 34 | window.open("https://www.linkedin.com/shareArticle?mini=true&url="+encodeURIComponent(location.href)+"&title="+encodeURIComponent(document.title)); 35 | } 36 | }, 37 | 'weibo': { 38 | 'label': 'Weibo', 39 | 'icon': 'fa fa-weibo', 40 | 'onClick': function(e) { 41 | e.preventDefault(); 42 | window.open("http://service.weibo.com/share/share.php?content=utf-8&url="+encodeURIComponent(location.href)+"&title="+encodeURIComponent(document.title)); 43 | } 44 | }, 45 | 'instapaper': { 46 | 'label': 'Instapaper', 47 | 'icon': 'fa fa-italic', 48 | 'onClick': function(e) { 49 | e.preventDefault(); 50 | window.open("http://www.instapaper.com/text?u="+encodeURIComponent(location.href)); 51 | } 52 | }, 53 | 'vk': { 54 | 'label': 'VK', 55 | 'icon': 'fa fa-vk', 56 | 'onClick': function(e) { 57 | e.preventDefault(); 58 | window.open("http://vkontakte.ru/share.php?url="+encodeURIComponent(location.href)); 59 | } 60 | } 61 | }; 62 | 63 | 64 | 65 | gitbook.events.bind("start", function(e, config) { 66 | var opts = config.sharing; 67 | if (!opts) return; 68 | 69 | // Create dropdown menu 70 | var menu = _.chain(opts.all) 71 | .map(function(id) { 72 | var site = SITES[id]; 73 | if (!site) return; 74 | return { 75 | text: site.label, 76 | onClick: site.onClick 77 | }; 78 | }) 79 | .compact() 80 | .value(); 81 | 82 | // Create main button with dropdown 83 | if (menu.length > 0) { 84 | gitbook.toolbar.createButton({ 85 | icon: 'fa fa-share-alt', 86 | label: 'Share', 87 | position: 'right', 88 | dropdown: [menu] 89 | }); 90 | } 91 | 92 | // Direct actions to share 93 | _.each(SITES, function(site, sideId) { 94 | if (!opts[sideId]) return; 95 | 96 | gitbook.toolbar.createButton({ 97 | icon: site.icon, 98 | label: site.label, 99 | title: site.label, 100 | position: 'right', 101 | onClick: site.onClick 102 | }); 103 | }); 104 | }); 105 | }); 106 | -------------------------------------------------------------------------------- /docs/libs/gitbook-2.6.7/js/plugin-fontsettings.js: -------------------------------------------------------------------------------- 1 | gitbook.require(["gitbook", "lodash", "jQuery"], function(gitbook, _, $) { 2 | var fontState; 3 | 4 | var THEMES = { 5 | "white": 0, 6 | "sepia": 1, 7 | "night": 2 8 | }; 9 | 10 | var FAMILY = { 11 | "serif": 0, 12 | "sans": 1 13 | }; 14 | 15 | // Save current font settings 16 | function saveFontSettings() { 17 | gitbook.storage.set("fontState", fontState); 18 | update(); 19 | } 20 | 21 | // Increase font size 22 | function enlargeFontSize(e) { 23 | e.preventDefault(); 24 | if (fontState.size >= 4) return; 25 | 26 | fontState.size++; 27 | saveFontSettings(); 28 | }; 29 | 30 | // Decrease font size 31 | function reduceFontSize(e) { 32 | e.preventDefault(); 33 | if (fontState.size <= 0) return; 34 | 35 | fontState.size--; 36 | saveFontSettings(); 37 | }; 38 | 39 | // Change font family 40 | function changeFontFamily(index, e) { 41 | e.preventDefault(); 42 | 43 | fontState.family = index; 44 | saveFontSettings(); 45 | }; 46 | 47 | // Change type of color 48 | function changeColorTheme(index, e) { 49 | e.preventDefault(); 50 | 51 | var $book = $(".book"); 52 | 53 | if (fontState.theme !== 0) 54 | $book.removeClass("color-theme-"+fontState.theme); 55 | 56 | fontState.theme = index; 57 | if (fontState.theme !== 0) 58 | $book.addClass("color-theme-"+fontState.theme); 59 | 60 | saveFontSettings(); 61 | }; 62 | 63 | function update() { 64 | var $book = gitbook.state.$book; 65 | 66 | $(".font-settings .font-family-list li").removeClass("active"); 67 | $(".font-settings .font-family-list li:nth-child("+(fontState.family+1)+")").addClass("active"); 68 | 69 | $book[0].className = $book[0].className.replace(/\bfont-\S+/g, ''); 70 | $book.addClass("font-size-"+fontState.size); 71 | $book.addClass("font-family-"+fontState.family); 72 | 73 | if(fontState.theme !== 0) { 74 | $book[0].className = $book[0].className.replace(/\bcolor-theme-\S+/g, ''); 75 | $book.addClass("color-theme-"+fontState.theme); 76 | } 77 | }; 78 | 79 | function init(config) { 80 | var $bookBody, $book; 81 | 82 | //Find DOM elements. 83 | $book = gitbook.state.$book; 84 | $bookBody = $book.find(".book-body"); 85 | 86 | // Instantiate font state object 87 | fontState = gitbook.storage.get("fontState", { 88 | size: config.size || 2, 89 | family: FAMILY[config.family || "sans"], 90 | theme: THEMES[config.theme || "white"] 91 | }); 92 | 93 | update(); 94 | }; 95 | 96 | 97 | gitbook.events.bind("start", function(e, config) { 98 | var opts = config.fontsettings; 99 | if (!opts) return; 100 | 101 | // Create buttons in toolbar 102 | gitbook.toolbar.createButton({ 103 | icon: 'fa fa-font', 104 | label: 'Font Settings', 105 | className: 'font-settings', 106 | dropdown: [ 107 | [ 108 | { 109 | text: 'A', 110 | className: 'font-reduce', 111 | onClick: reduceFontSize 112 | }, 113 | { 114 | text: 'A', 115 | className: 'font-enlarge', 116 | onClick: enlargeFontSize 117 | } 118 | ], 119 | [ 120 | { 121 | text: 'Serif', 122 | onClick: _.partial(changeFontFamily, 0) 123 | }, 124 | { 125 | text: 'Sans', 126 | onClick: _.partial(changeFontFamily, 1) 127 | } 128 | ], 129 | [ 130 | { 131 | text: 'White', 132 | onClick: _.partial(changeColorTheme, 0) 133 | }, 134 | { 135 | text: 'Sepia', 136 | onClick: _.partial(changeColorTheme, 1) 137 | }, 138 | { 139 | text: 'Night', 140 | onClick: _.partial(changeColorTheme, 2) 141 | } 142 | ] 143 | ] 144 | }); 145 | 146 | 147 | // Init current settings 148 | init(opts); 149 | }); 150 | }); 151 | 152 | 153 | -------------------------------------------------------------------------------- /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 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 | -------------------------------------------------------------------------------- /docs/libs/gitbook-2.6.7/js/plugin-search.js: -------------------------------------------------------------------------------- 1 | gitbook.require(["gitbook", "lodash", "jQuery"], function(gitbook, _, $) { 2 | var index = null; 3 | var $searchInput, $searchLabel, $searchForm; 4 | var $highlighted = [], hi, hiOpts = { className: 'search-highlight' }; 5 | var collapse = false, toc_visible = []; 6 | 7 | // Use a specific index 8 | function loadIndex(data) { 9 | // [Yihui] In bookdown, I use a character matrix to store the chapter 10 | // content, and the index is dynamically built on the client side. 11 | // Gitbook prebuilds the index data instead: https://github.com/GitbookIO/plugin-search 12 | // We can certainly do that via R packages V8 and jsonlite, but let's 13 | // see how slow it really is before improving it. On the other hand, 14 | // lunr cannot handle non-English text very well, e.g. the default 15 | // tokenizer cannot deal with Chinese text, so we may want to replace 16 | // lunr with a dumb simple text matching approach. 17 | index = lunr(function () { 18 | this.ref('url'); 19 | this.field('title', { boost: 10 }); 20 | this.field('body'); 21 | }); 22 | data.map(function(item) { 23 | index.add({ 24 | url: item[0], 25 | title: item[1], 26 | body: item[2] 27 | }); 28 | }); 29 | } 30 | 31 | // Fetch the search index 32 | function fetchIndex() { 33 | return $.getJSON(gitbook.state.basePath+"/search_index.json") 34 | .then(loadIndex); // [Yihui] we need to use this object later 35 | } 36 | 37 | // Search for a term and return results 38 | function search(q) { 39 | if (!index) return; 40 | 41 | var results = _.chain(index.search(q)) 42 | .map(function(result) { 43 | var parts = result.ref.split("#"); 44 | return { 45 | path: parts[0], 46 | hash: parts[1] 47 | }; 48 | }) 49 | .value(); 50 | 51 | // [Yihui] Highlight the search keyword on current page 52 | $highlighted = results.length === 0 ? [] : $('.page-inner') 53 | .unhighlight(hiOpts).highlight(q, hiOpts).find('span.search-highlight'); 54 | scrollToHighlighted(0); 55 | 56 | return results; 57 | } 58 | 59 | // [Yihui] Scroll the chapter body to the i-th highlighted string 60 | function scrollToHighlighted(d) { 61 | var n = $highlighted.length; 62 | hi = hi === undefined ? 0 : hi + d; 63 | // navignate to the previous/next page in the search results if reached the top/bottom 64 | var b = hi < 0; 65 | if (d !== 0 && (b || hi >= n)) { 66 | var path = currentPath(), n2 = toc_visible.length; 67 | if (n2 === 0) return; 68 | for (var i = b ? 0 : n2; (b && i < n2) || (!b && i >= 0); i += b ? 1 : -1) { 69 | if (toc_visible.eq(i).data('path') === path) break; 70 | } 71 | i += b ? -1 : 1; 72 | if (i < 0) i = n2 - 1; 73 | if (i >= n2) i = 0; 74 | var lnk = toc_visible.eq(i).find('a[href$=".html"]'); 75 | if (lnk.length) lnk[0].click(); 76 | return; 77 | } 78 | if (n === 0) return; 79 | var $p = $highlighted.eq(hi); 80 | $p[0].scrollIntoView(); 81 | $highlighted.css('background-color', ''); 82 | // an orange background color on the current item and removed later 83 | $p.css('background-color', 'orange'); 84 | setTimeout(function() { 85 | $p.css('background-color', ''); 86 | }, 2000); 87 | } 88 | 89 | function currentPath() { 90 | var href = window.location.pathname; 91 | href = href.substr(href.lastIndexOf('/') + 1); 92 | return href === '' ? 'index.html' : href; 93 | } 94 | 95 | // Create search form 96 | function createForm(value) { 97 | if ($searchForm) $searchForm.remove(); 98 | if ($searchLabel) $searchLabel.remove(); 99 | if ($searchInput) $searchInput.remove(); 100 | 101 | $searchForm = $('
    ', { 102 | 'class': 'book-search', 103 | 'role': 'search' 104 | }); 105 | 106 | $searchLabel = $('