33 |
34 | 这是一本 R 语言入门的教程书。它旨在为生物信息学相关方向的研究人员（包括学生）以及相关从业者提供 R 语言基础知识的学习指导。当然，由于本书内容的普适性，我相信对数据科学感兴趣的读者都能够从阅读中受益。如果读者已经掌握了一些 R 的编程知识，可以翻看目录挑选感兴趣的内容阅读；如果读者已经掌握的 R 编程基础知识，我推荐翻看本书的附录部分查找感兴趣的内容进一步深入学习。
35 |
36 | R 语言与知名的 C、Python 这类通用编程语言相比，它是一门领域特定语言（domain-specific language、DSL），专注于数据科学领域。由于 Python 的普及以及它在商业、科研分析中的流行，R 语言常常被用来与 Python 作比较。我在此无意做这样的比较，就我的个人使用经验来看，两者都有其独特和独到之处。作为一名数据科学家，我们常常需要掌握多门编程语言作为工具进行工作，其中主要包括 R、Python 和 Shell。R 和 Python 都是作为主要的数据探索、分析和可视化工具，读者任选其一熟练掌握即可。初学者同时学习 R 和 Python 是不可取，因为不同的编程语言都有相似的数据结构和运算控制逻辑，所以深度掌握一门语言能够更好地工作和更快地学习其他编程语言。另外，初学者往往困惑于 R 和 Python 两种语言中哪种更值得学习。就我的个人观点看，对于生物信息学方向的**大部分读者**，R 是更好的选择，有以下一些理由：
37 |
38 | - R 语言对于没有编程经验的读者更加友好，内置向量化运算机制和默认统计分析包可以快速开始分析和获取结果。
39 | - 由于 [Bioconductor](https://www.bioconductor.org/) 项目库和 [CRAN](https://cran.r-project.org/) 库中保存了上千个生物信息学软件包，涉及生物信息学领域的各个方面，读者在实际的研究工作中很难完全离开 R 语言环境。
40 | - [tidyverse 系列工具包](https://github.com/tidyverse/)的强力驱动让 R 在数据分析各个方面工作都非常强力。
41 |
42 | ## 内容简介 {-}
43 |
44 | 当前已经有不少 R 语言和数据分析相关的教程和书籍，本书无力像它们一样详尽地介绍 R 众多方面的内容，而是聚焦于指导读者学习和理解数据分析的核心要点，并能快速应用到自己实际的工作中。本书的创作哲学是结合必备基础知识的简要介绍与实际问题的讨论与方案。本书的核心内容包括 R 的基础语法和一系列数据分析编程知识，后者将根据 Hadley 在《R for Data Science》提供的数据分析流程概览图 \@ref(fig:r4ds-overview) 中指出的核心要点分别按章节进行介绍。最后，我们将通过一些 R 包学习 R 在生物信息学方向的应用。
45 |
46 | ```{r r4ds-overview, fig.align="center", echo=FALSE, fig.cap="数据分析概览 （图源：R for Data Science 第 1 章）"}
47 | knitr::include_graphics("fig/ch00-data-science.png")
48 | ```
49 |
50 | 本书的章节概要如下：
51 |
52 | - 第 \@ref(prepare) 章介绍 R 与相应编程环境的安装和使用。
53 | - 第 \@ref(base) 章介绍 R 基础编程语法，包括数据结构、控制流程等。
54 | - 第 \@ref(import) 章介绍如何使用 R 导入常见的数据文件格式。
55 | - 第 \@ref(clean) 章介绍数据清洗操作在 R 中的实现。
56 | - 第 \@ref(visualization) 章介绍数据可视化。
57 | - 第 \@ref(model) 章介绍 R 在统计建模方面的和实践。
58 | - 第 \@ref(report) 章介绍 R 怎样导出结果和生成分析报告。
59 | - 第 \@ref(bioapp) 章通过一些包的使用示例介绍 R 在生物信息学方向的应用。
60 |
61 | ## 许可 {-}
62 |
63 | 本网站（永久）免费阅读，以 [CC 署名-非商业性使用-禁止演绎 4.0 国际协议](https://creativecommons.org/licenses/by-nc-nd/4.0/deed.zh)发行。
64 |
65 | Copyright © 2020 王诗翔
66 |
67 | 
68 |
69 | ## 建议与反馈 {-}
70 |
71 | 这是我第一次编写比较系统的 R 语言教程，由于个人能力有限，难免存在错误和不当，恳请读者批评指正。**目前我在业余时间对本书内容进行积极的开发，如果读者有任何建议，欢迎到 [GitHub 仓库 Issue](https://github.com/ShixiangWang/geek-r-tutorial/issues) 中进行讨论**。
72 |
73 | ## 致谢 {-}
74 |
75 | 非常感谢谁谁以及谁谁对我的帮助。
76 |
77 | ```{block2, type='flushright', html.tag='p'}
78 | 王诗翔
79 | 于 上海
80 | ```
81 |
82 |
--------------------------------------------------------------------------------
/docs/libs/gitbook/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/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 |
--------------------------------------------------------------------------------
/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 = {2020},
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-data.table,
17 | title = {data.table: Extension of `data.frame`},
18 | author = {Matt Dowle and Arun Srinivasan},
19 | year = {2019},
20 | note = {R package version 1.12.8},
21 | url = {https://CRAN.R-project.org/package=data.table},
22 | }
23 | @Manual{R-dplyr,
24 | title = {dplyr: A Grammar of Data Manipulation},
25 | author = {Hadley Wickham and Romain François and Lionel Henry and Kirill Müller},
26 | year = {2020},
27 | note = {R package version 0.8.5},
28 | url = {https://CRAN.R-project.org/package=dplyr},
29 | }
30 | @Manual{R-ggplot2,
31 | title = {ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics},
32 | author = {Hadley Wickham and Winston Chang and Lionel Henry and Thomas Lin Pedersen and Kohske Takahashi and Claus Wilke and Kara Woo and Hiroaki Yutani and Dewey Dunnington},
33 | year = {2020},
34 | note = {R package version 3.3.0},
35 | url = {https://CRAN.R-project.org/package=ggplot2},
36 | }
37 | @Manual{R-knitr,
38 | title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
39 | author = {Yihui Xie},
40 | year = {2020},
41 | note = {R package version 1.28},
42 | url = {https://CRAN.R-project.org/package=knitr},
43 | }
44 | @Manual{R-readr,
45 | title = {readr: Read Rectangular Text Data},
46 | author = {Hadley Wickham and Jim Hester and Romain Francois},
47 | year = {2018},
48 | note = {R package version 1.3.1},
49 | url = {https://CRAN.R-project.org/package=readr},
50 | }
51 | @Manual{R-readxl,
52 | title = {readxl: Read Excel Files},
53 | author = {Hadley Wickham and Jennifer Bryan},
54 | year = {2019},
55 | note = {R package version 1.3.1},
56 | url = {https://CRAN.R-project.org/package=readxl},
57 | }
58 | @Manual{R-rmarkdown,
59 | title = {rmarkdown: Dynamic Documents for R},
60 | 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},
61 | year = {2020},
62 | note = {R package version 2.1},
63 | url = {https://CRAN.R-project.org/package=rmarkdown},
64 | }
65 | @Book{bookdown2016,
66 | title = {bookdown: Authoring Books and Technical Documents with {R} Markdown},
67 | author = {Yihui Xie},
68 | publisher = {Chapman and Hall/CRC},
69 | address = {Boca Raton, Florida},
70 | year = {2016},
71 | note = {ISBN 978-1138700109},
72 | url = {https://github.com/rstudio/bookdown},
73 | }
74 | @Book{ggplot22016,
75 | author = {Hadley Wickham},
76 | title = {ggplot2: Elegant Graphics for Data Analysis},
77 | publisher = {Springer-Verlag New York},
78 | year = {2016},
79 | isbn = {978-3-319-24277-4},
80 | url = {https://ggplot2.tidyverse.org},
81 | }
82 | @Book{knitr2015,
83 | title = {Dynamic Documents with {R} and knitr},
84 | author = {Yihui Xie},
85 | publisher = {Chapman and Hall/CRC},
86 | address = {Boca Raton, Florida},
87 | year = {2015},
88 | edition = {2nd},
89 | note = {ISBN 978-1498716963},
90 | url = {https://yihui.org/knitr/},
91 | }
92 | @InCollection{knitr2014,
93 | booktitle = {Implementing Reproducible Computational Research},
94 | editor = {Victoria Stodden and Friedrich Leisch and Roger D. Peng},
95 | title = {knitr: A Comprehensive Tool for Reproducible Research in {R}},
96 | author = {Yihui Xie},
97 | publisher = {Chapman and Hall/CRC},
98 | year = {2014},
99 | note = {ISBN 978-1466561595},
100 | url = {http://www.crcpress.com/product/isbn/9781466561595},
101 | }
102 | @Book{rmarkdown2018,
103 | title = {R Markdown: The Definitive Guide},
104 | author = {Yihui Xie and J.J. Allaire and Garrett Grolemund},
105 | publisher = {Chapman and Hall/CRC},
106 | address = {Boca Raton, Florida},
107 | year = {2018},
108 | note = {ISBN 9781138359338},
109 | url = {https://bookdown.org/yihui/rmarkdown},
110 | }
111 |
--------------------------------------------------------------------------------
/docs/libs/gitbook/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 = $book.find(".book-body");
85 |
86 | // Instantiate font state object
87 | fontState = gitbook.storage.get("fontState", {
88 | size: config.size || 2,
89 | family: FAMILY[config.family || "sans"],
90 | theme: THEMES[config.theme || "white"]
91 | });
92 |
93 | update();
94 | };
95 |
96 |
97 | gitbook.events.bind("start", function(e, config) {
98 | var opts = config.fontsettings;
99 | if (!opts) return;
100 |
101 | // Create buttons in toolbar
102 | gitbook.toolbar.createButton({
103 | icon: 'fa fa-font',
104 | label: 'Font Settings',
105 | className: 'font-settings',
106 | dropdown: [
107 | [
108 | {
109 | text: 'A',
110 | className: 'font-reduce',
111 | onClick: reduceFontSize
112 | },
113 | {
114 | text: 'A',
115 | className: 'font-enlarge',
116 | onClick: enlargeFontSize
117 | }
118 | ],
119 | [
120 | {
121 | text: 'Serif',
122 | onClick: _.partial(changeFontFamily, 0)
123 | },
124 | {
125 | text: 'Sans',
126 | onClick: _.partial(changeFontFamily, 1)
127 | }
128 | ],
129 | [
130 | {
131 | text: 'White',
132 | onClick: _.partial(changeColorTheme, 0)
133 | },
134 | {
135 | text: 'Sepia',
136 | onClick: _.partial(changeColorTheme, 1)
137 | },
138 | {
139 | text: 'Night',
140 | onClick: _.partial(changeColorTheme, 2)
141 | }
142 | ]
143 | ]
144 | });
145 |
146 |
147 | // Init current settings
148 | init(opts);
149 | });
150 | });
151 |
152 |
153 |
--------------------------------------------------------------------------------
/latex/template.tex:
--------------------------------------------------------------------------------
1 | \documentclass[$if(fontsize)$$fontsize$,$endif$$if(lang)$$babel-lang$,$endif$$if(papersize)$$papersize$paper,$endif$$for(classoption)$$classoption$$sep$,$endfor$]{$documentclass$}
2 | $if(beamerarticle)$
3 | \usepackage{beamerarticle} % needs to be loaded first
4 | $endif$
5 | $if(fontfamily)$
6 | \usepackage[$for(fontfamilyoptions)$$fontfamilyoptions$$sep$,$endfor$]{$fontfamily$}
7 | $else$
8 | \usepackage{lmodern}
9 | $endif$
10 | $if(linestretch)$
11 | \usepackage{setspace}
12 | \setstretch{$linestretch$}
13 | $endif$
14 | \usepackage{amssymb,amsmath}
15 | \usepackage{ifxetex,ifluatex}
16 | \usepackage{fixltx2e} % provides \textsubscript
17 | \ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
18 | \usepackage[$if(fontenc)$$fontenc$$else$T1$endif$]{fontenc}
19 | \usepackage[utf8]{inputenc}
20 | $if(euro)$
21 | \usepackage{eurosym}
22 | $endif$
23 | \else % if luatex or xelatex
24 | \ifxetex
25 | \usepackage{xltxtra,xunicode}
26 | \else
27 | \usepackage{fontspec}
28 | \fi
29 | \defaultfontfeatures{Ligatures=TeX,Scale=MatchLowercase}
30 | $for(fontfamilies)$
31 | \newfontfamily{$fontfamilies.name$}[$fontfamilies.options$]{$fontfamilies.font$}
32 | $endfor$
33 | $if(euro)$
34 | \newcommand{\euro}{€}
35 | $endif$
36 | $if(mainfont)$
37 | \setmainfont[$for(mainfontoptions)$$mainfontoptions$$sep$,$endfor$]{$mainfont$}
38 | $endif$
39 | $if(sansfont)$
40 | \setsansfont[$for(sansfontoptions)$$sansfontoptions$$sep$,$endfor$]{$sansfont$}
41 | $endif$
42 | $if(monofont)$
43 | \setmonofont[Mapping=tex-ansi$if(monofontoptions)$,$for(monofontoptions)$$monofontoptions$$sep$,$endfor$$endif$]{$monofont$}
44 | $endif$
45 | $if(CJKmainfont)$
46 | \usepackage{xeCJK}
47 | \setCJKmainfont[$for(CJKoptions)$$CJKoptions$$sep$,$endfor$]{$CJKmainfont$}
48 | $endif$
49 | \fi
50 | % use upquote if available, for straight quotes in verbatim environments
51 | \IfFileExists{upquote.sty}{\usepackage{upquote}}{}
52 | % use microtype if available
53 | \IfFileExists{microtype.sty}{%
54 | \usepackage{microtype}
55 | \UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
56 | }{}
57 | $if(geometry)$
58 | \usepackage[$for(geometry)$$geometry$$sep$,$endfor$]{geometry}
59 | $endif$
60 | \usepackage[unicode=true]{hyperref}
61 | $if(colorlinks)$
62 | \PassOptionsToPackage{usenames,dvipsnames}{color} % color is loaded by hyperref
63 | $endif$
64 | \hypersetup{
65 | $if(title-meta)$
66 | pdftitle={$title-meta$},
67 | $endif$
68 | $if(author-meta)$
69 | pdfauthor={$author-meta$},
70 | $endif$
71 | $if(keywords)$
72 | pdfkeywords={$for(keywords)$$keywords$$sep$, $endfor$},
73 | $endif$
74 | $if(colorlinks)$
75 | colorlinks=true,
76 | linkcolor=$if(linkcolor)$$linkcolor$$else$Maroon$endif$,
77 | citecolor=$if(citecolor)$$citecolor$$else$Blue$endif$,
78 | urlcolor=$if(urlcolor)$$urlcolor$$else$Blue$endif$,
79 | $else$
80 | pdfborder={0 0 0},
81 | $endif$
82 | breaklinks=true}
83 | \urlstyle{same} % don't use monospace font for urls
84 | $if(lang)$
85 | \ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
86 | \usepackage[shorthands=off,$for(babel-otherlangs)$$babel-otherlangs$,$endfor$main=$babel-lang$]{babel}
87 | $if(babel-newcommands)$
88 | $babel-newcommands$
89 | $endif$
90 | \else
91 | \usepackage{polyglossia}
92 | \setmainlanguage[$polyglossia-lang.options$]{$polyglossia-lang.name$}
93 | $for(polyglossia-otherlangs)$
94 | \setotherlanguage[$polyglossia-otherlangs.options$]{$polyglossia-otherlangs.name$}
95 | $endfor$
96 | \fi
97 | $endif$
98 | $if(natbib)$
99 | \usepackage{natbib}
100 | \bibliographystyle{$if(biblio-style)$$biblio-style$$else$plainnat$endif$}
101 | $endif$
102 | $if(biblatex)$
103 | \usepackage[$if(biblio-style)$style=$biblio-style$,$endif$$for(biblatexoptions)$$biblatexoptions$$sep$,$endfor$]{biblatex}
104 | $for(bibliography)$
105 | \addbibresource{$bibliography$}
106 | $endfor$
107 | $endif$
108 | $if(listings)$
109 | \usepackage{listings}
110 | $endif$
111 | $if(lhs)$
112 | \lstnewenvironment{code}{\lstset{language=Haskell,basicstyle=\small\ttfamily}}{}
113 | $endif$
114 | $if(highlighting-macros)$
115 | $highlighting-macros$
116 | $endif$
117 | $if(verbatim-in-note)$
118 | \usepackage{fancyvrb}
119 | \VerbatimFootnotes % allows verbatim text in footnotes
120 | $endif$
121 | $if(tables)$
122 | \usepackage{longtable,booktabs}
123 | % Fix footnotes in tables (requires footnote package)
124 | \IfFileExists{footnote.sty}{\usepackage{footnote}\makesavenoteenv{long table}}{}
125 | $endif$
126 | $if(graphics)$
127 | \usepackage{graphicx,grffile}
128 | \makeatletter
129 | \def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
130 | \def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi}
131 | \makeatother
132 | % Scale images if necessary, so that they will not overflow the page
133 | % margins by default, and it is still possible to overwrite the defaults
134 | % using explicit options in \includegraphics[width, height, ...]{}
135 | \setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
136 | $endif$
137 | $if(links-as-notes)$
138 | % Make links footnotes instead of hotlinks:
139 | \renewcommand{\href}[2]{#2\footnote{\url{#1}}}
140 | $endif$
141 | $if(strikeout)$
142 | \usepackage[normalem]{ulem}
143 | % avoid problems with \sout in headers with hyperref:
144 | \pdfstringdefDisableCommands{\renewcommand{\sout}{}}
145 | $endif$
146 | $if(indent)$
147 | $else$
148 | \IfFileExists{parskip.sty}{%
149 | \usepackage{parskip}
150 | }{% else
151 | \setlength{\parindent}{0pt}
152 | \setlength{\parskip}{6pt plus 2pt minus 1pt}
153 | }
154 | $endif$
155 | \setlength{\emergencystretch}{3em} % prevent overfull lines
156 | \providecommand{\tightlist}{%
157 | \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
158 | $if(numbersections)$
159 | \setcounter{secnumdepth}{$if(secnumdepth)$$secnumdepth$$else$5$endif$}
160 | $else$
161 | \setcounter{secnumdepth}{0}
162 | $endif$
163 | $if(subparagraph)$
164 | $else$
165 | % Redefines (sub)paragraphs to behave more like sections
166 | \ifx\paragraph\undefined\else
167 | \let\oldparagraph\paragraph
168 | \renewcommand{\paragraph}[1]{\oldparagraph{#1}\mbox{}}
169 | \fi
170 | \ifx\subparagraph\undefined\else
171 | \let\oldsubparagraph\subparagraph
172 | \renewcommand{\subparagraph}[1]{\oldsubparagraph{#1}\mbox{}}
173 | \fi
174 | $endif$
175 | $if(dir)$
176 | \ifxetex
177 | % load bidi as late as possible as it modifies e.g. graphicx
178 | $if(latex-dir-rtl)$
179 | \usepackage[RTLdocument]{bidi}
180 | $else$
181 | \usepackage{bidi}
182 | $endif$
183 | \fi
184 | \ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
185 | \TeXXeTstate=1
186 | \newcommand{\RL}[1]{\beginR #1\endR}
187 | \newcommand{\LR}[1]{\beginL #1\endL}
188 | \newenvironment{RTL}{\beginR}{\endR}
189 | \newenvironment{LTR}{\beginL}{\endL}
190 | \fi
191 | $endif$
192 |
193 | % set default figure placement to htbp
194 | \makeatletter
195 | \def\fps@figure{htbp}
196 | \makeatother
197 |
198 | $for(header-includes)$
199 | $header-includes$
200 | $endfor$
201 |
202 | $if(title)$
203 | \title{$title$$if(thanks)$\thanks{$thanks$}$endif$}
204 | $endif$
205 | $if(subtitle)$
206 | \providecommand{\subtitle}[1]{}
207 | \subtitle{$subtitle$}
208 | $endif$
209 | $if(author)$
210 | \author{$for(author)$$author$$sep$ \and $endfor$}
211 | $endif$
212 | $if(institute)$
213 | \providecommand{\institute}[1]{}
214 | \institute{$for(institute)$$institute$$sep$ \and $endfor$}
215 | $endif$
216 | \date{$date$}
217 |
218 | \begin{document}
219 | $if(title)$
220 | \maketitle
221 | $endif$
222 | $if(abstract)$
223 | \begin{abstract}
224 | $abstract$
225 | \end{abstract}
226 | $endif$
227 |
228 | $for(include-before)$
229 | $include-before$
230 |
231 | $endfor$
232 | $if(toc)$
233 | {
234 | \setcounter{tocdepth}{$toc-depth$}
235 | \tableofcontents
236 | }
237 | $endif$
238 | $if(lot)$
239 | \listoftables
240 | $endif$
241 | $if(lof)$
242 | \listoffigures
243 | $endif$
244 | $body$
245 |
246 | $if(natbib)$
247 | $if(bibliography)$
248 | $if(biblio-title)$
249 | $if(book-class)$
250 | \renewcommand\bibname{$biblio-title$}
251 | $else$
252 | \renewcommand\refname{$biblio-title$}
253 | $endif$
254 | $endif$
255 | \bibliography{$for(bibliography)$$bibliography$$sep$,$endfor$}
256 |
257 | $endif$
258 | $endif$
259 | $if(biblatex)$
260 | \printbibliography$if(biblio-title)$[title=$biblio-title$]$endif$
261 |
262 | $endif$
263 | $for(include-after)$
264 | $include-after$
265 |
266 | $endfor$
267 | \end{document}
268 |
--------------------------------------------------------------------------------
/docs/libs/gitbook/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 = $('