├── .DS_Store ├── .gitattributes ├── 0001-Introduction.md ├── 1001-base-ploting.md ├── 1001-base-ploting_files └── figure-html │ ├── unnamed-chunk-10-1.png │ ├── unnamed-chunk-10-2.png │ ├── unnamed-chunk-11-1.png │ ├── unnamed-chunk-12-1.png │ ├── unnamed-chunk-13-1.png │ ├── unnamed-chunk-14-1.png │ ├── unnamed-chunk-14-2.png │ ├── unnamed-chunk-15-1.png │ ├── unnamed-chunk-16-1.png │ ├── unnamed-chunk-17-1.png │ ├── unnamed-chunk-18-1.png │ ├── unnamed-chunk-18-2.png │ ├── unnamed-chunk-19-1.png │ ├── unnamed-chunk-20-1.png │ ├── unnamed-chunk-21-1.png │ ├── unnamed-chunk-23-1.png │ ├── unnamed-chunk-24-1.png │ ├── unnamed-chunk-25-1.png │ ├── unnamed-chunk-26-1.png │ ├── unnamed-chunk-26-2.png │ ├── unnamed-chunk-27-1.png │ ├── unnamed-chunk-28-1.png │ ├── unnamed-chunk-29-1.png │ ├── unnamed-chunk-3-1.png │ ├── unnamed-chunk-3-2.png │ ├── unnamed-chunk-30-1.png │ ├── unnamed-chunk-31-1.png │ ├── unnamed-chunk-32-1.png │ ├── unnamed-chunk-33-1.png │ ├── unnamed-chunk-34-1.png │ ├── unnamed-chunk-35-1.png │ ├── unnamed-chunk-35-2.png │ ├── unnamed-chunk-36-1.png │ ├── unnamed-chunk-4-1.png │ ├── unnamed-chunk-5-1.png │ ├── unnamed-chunk-7-1.png │ ├── unnamed-chunk-7-2.png │ ├── unnamed-chunk-8-1.png │ └── unnamed-chunk-8-2.png ├── 2001-ggplot-ploting.md ├── 2001-ggplot-ploting_files └── figure-html │ ├── unnamed-chunk-10-1.png │ ├── unnamed-chunk-10-2.png │ ├── unnamed-chunk-11-1.png │ ├── unnamed-chunk-11-2.png │ ├── unnamed-chunk-12-1.png │ ├── unnamed-chunk-12-2.png │ ├── unnamed-chunk-13-1.png │ ├── unnamed-chunk-14-1.png │ ├── unnamed-chunk-14-2.png │ ├── unnamed-chunk-16-1.png │ ├── unnamed-chunk-16-2.png │ ├── unnamed-chunk-17-1.png │ ├── unnamed-chunk-17-2.png │ ├── unnamed-chunk-17-3.png │ ├── unnamed-chunk-18-1.png │ ├── unnamed-chunk-19-1.png │ ├── unnamed-chunk-20-1.png │ ├── unnamed-chunk-21-1.png │ ├── unnamed-chunk-22-1.png │ ├── unnamed-chunk-23-1.png │ ├── unnamed-chunk-24-1.png │ ├── unnamed-chunk-25-1.png │ ├── unnamed-chunk-26-1.png │ ├── unnamed-chunk-28-1.png │ ├── unnamed-chunk-29-1.png │ ├── unnamed-chunk-3-1.png │ ├── unnamed-chunk-3-2.png │ ├── unnamed-chunk-30-1.png │ ├── unnamed-chunk-4-1.png │ ├── unnamed-chunk-5-1.png │ ├── unnamed-chunk-6-1.png │ ├── unnamed-chunk-8-1.png │ ├── unnamed-chunk-8-2.png │ ├── unnamed-chunk-8-3.png │ └── unnamed-chunk-9-1.png ├── 3001-Main-diagram-types.md ├── 3001-Main-diagram-types_files └── figure-html │ ├── unnamed-chunk-10-1.png │ ├── unnamed-chunk-12-1.png │ ├── unnamed-chunk-13-1.png │ ├── unnamed-chunk-14-1.png │ ├── unnamed-chunk-15-1.png │ ├── unnamed-chunk-16-1.png │ ├── unnamed-chunk-17-1.png │ ├── unnamed-chunk-18-1.png │ ├── unnamed-chunk-19-1.png │ ├── unnamed-chunk-2-1.png │ ├── unnamed-chunk-20-1.png │ ├── unnamed-chunk-23-1.png │ ├── unnamed-chunk-24-1.png │ ├── unnamed-chunk-25-1.png │ ├── unnamed-chunk-26-1.png │ ├── unnamed-chunk-27-1.png │ ├── unnamed-chunk-28-1.png │ ├── unnamed-chunk-29-1.png │ ├── unnamed-chunk-30-1.png │ ├── unnamed-chunk-31-1.png │ ├── unnamed-chunk-32-1.png │ ├── unnamed-chunk-35-1.png │ ├── unnamed-chunk-35-2.png │ ├── unnamed-chunk-37-1.png │ ├── unnamed-chunk-41-1.png │ ├── unnamed-chunk-42-1.png │ ├── unnamed-chunk-44-1.png │ └── unnamed-chunk-9-1.png ├── 4001-other-packages.md ├── 5001-interactive-ploting.md ├── 6001-some-examples.md ├── 6001-some-examples_files └── figure-html │ ├── unnamed-chunk-1-1.png │ ├── unnamed-chunk-10-1.png │ ├── unnamed-chunk-11-1.png │ ├── unnamed-chunk-12-1.png │ ├── unnamed-chunk-13-1.png │ ├── unnamed-chunk-16-1.png │ ├── unnamed-chunk-16-2.png │ ├── unnamed-chunk-17-1.png │ ├── unnamed-chunk-19-1.png │ ├── unnamed-chunk-2-1.png │ ├── unnamed-chunk-22-1.png │ ├── unnamed-chunk-23-1.png │ ├── unnamed-chunk-24-1.png │ ├── unnamed-chunk-25-1.png │ ├── unnamed-chunk-26-1.png │ ├── unnamed-chunk-26-2.png │ ├── unnamed-chunk-27-1.png │ ├── unnamed-chunk-28-1.png │ ├── unnamed-chunk-4-1.png │ ├── unnamed-chunk-5-1.png │ ├── unnamed-chunk-6-1.png │ └── unnamed-chunk-9-1.png ├── 7001-rmarkdown-base.md ├── 8001-rmarkdown-extended.md ├── 9000-appendix.md ├── 9990-references.md ├── CBook.pdf ├── CBook.tex ├── README.md ├── appendix.html ├── base-tutorial.html ├── causal.html ├── figure ├── 10.png ├── 11.png ├── 12.png ├── 13.png ├── 14.png ├── 16.png ├── 17.png ├── 18.png ├── 19.png ├── 2.png ├── 20.png ├── 22.png ├── 23.jpg ├── 24.png ├── 3.png ├── 4.png ├── 6.jpg ├── Rinstall.png ├── me.png └── vcode.jpg ├── ggplot2-plot.html ├── images ├── 38701658555592_.pic.jpg ├── 38711658555602_.pic.jpg ├── paste-020985AB.png ├── paste-09A826E7.png ├── paste-153F63DA.png ├── paste-17F40901.png ├── paste-1DBD1E6D.png ├── paste-20A9EA07.png ├── paste-224B4B25.png ├── paste-24B1DE88.png ├── paste-26331167.png ├── paste-39BF420C.png ├── paste-3AB25E87.png ├── paste-3B74BCEF.png ├── paste-3BB6003B.png ├── paste-3C23FCC2.png ├── paste-3E59C75E.png ├── paste-49E7FC6A.png ├── paste-4AB4302F.png ├── paste-5127AF6C.png ├── paste-5279D793.png ├── paste-533FDD15.png ├── paste-61B75CBE.png ├── paste-62C72EF4.png ├── paste-6EDE02D4.png ├── paste-720E8336.png ├── paste-7488C7A3.png ├── paste-7647DCE8.png ├── paste-7C36FD52.png ├── paste-8047133B.png ├── paste-80A658BA.png ├── paste-826D2A4B.png ├── paste-9D62CD2E.png ├── paste-AA57CB6A.png ├── paste-AEF2F3EB.png ├── paste-AF884A89.png ├── paste-C2B95842.png ├── paste-CAE96605.png ├── paste-D4893CD0.png ├── paste-DA97584B.png ├── paste-E2A98278.png ├── paste-E459B436.png ├── paste-E987C1F4.png └── paste-F27FC37A.png ├── index.html ├── index.md ├── interactive-ploting.html ├── libs ├── anchor-sections-1.1.0 │ ├── anchor-sections-hash.css │ ├── anchor-sections.css │ └── anchor-sections.js ├── crosstalk-1.2.0 │ ├── css │ │ └── crosstalk.min.css │ └── js │ │ └── crosstalk.min.js ├── datatables-binding-0.23 │ └── datatables.js ├── datatables-css-0.0.0 │ └── datatables-crosstalk.css ├── dt-core-1.11.3 │ ├── css │ │ ├── jquery.dataTables.extra.css │ │ └── jquery.dataTables.min.css │ └── js │ │ └── jquery.dataTables.min.js ├── gitbook-2.6.7 │ ├── css │ │ ├── fontawesome │ │ │ └── fontawesome-webfont.ttf │ │ ├── plugin-bookdown.css │ │ ├── plugin-clipboard.css │ │ ├── plugin-fontsettings.css │ │ ├── plugin-highlight.css │ │ ├── plugin-search.css │ │ ├── plugin-table.css │ │ └── style.css │ └── js │ │ ├── app.min.js │ │ ├── clipboard.min.js │ │ ├── jquery.highlight.js │ │ ├── plugin-bookdown.js │ │ ├── plugin-clipboard.js │ │ ├── plugin-fontsettings.js │ │ ├── plugin-search.js │ │ └── plugin-sharing.js ├── htmlwidgets-1.5.4 │ └── htmlwidgets.js ├── jquery-3.6.0 │ └── jquery-3.6.0.min.js ├── plotly-binding-4.10.0 │ └── plotly.js ├── plotly-htmlwidgets-css-2.5.1 │ └── plotly-htmlwidgets.css ├── plotly-main-2.5.1 │ └── plotly-latest.min.js └── typedarray-0.1 │ └── typedarray.min.js ├── main-diagram-types.html ├── other-packages.html ├── reference.html ├── rmarkdown-base.html ├── rmarkdown-extended.html ├── search_index.json ├── some-tips-alls.html └── tidyverse-tutorial.html 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-------------------------------------------------------------------------------- /4001-other-packages.md: -------------------------------------------------------------------------------- 1 | # 其他相关拓展包 {#other-packages} 2 | 3 | 4 | 5 | ## ggplot2 官网 109 种拓展包 6 | 7 | 该网站一共汇总了 109 种与ggplot2 包相关的[拓展包](https://exts.ggplot2.tidyverse.org/gallery/)，并且在不断更新中。拓展包与 ggplot2 包可以无缝连接，网站截图如下： 8 | 9 | ![](images/38711658555602_.pic.jpg) 10 | 11 | ![](images/38701658555592_.pic.jpg) 12 | 13 | ## 整理的相关扩展包 14 | 15 | 小编整理了些 R 语言可视化相关的拓展包。其中大部分是来自于 ggplot2 官网拓展包，也有部分不在这范围内，但是平常使用较多的包。 16 | 17 | > 这里给出各包介绍的链接，主要发布于公众号中，也有的内容转载与其他公众号。由于各个包都在不断更新，可能内部函数、功能存在一些变化。如果有能力的读者，建议去查阅最新的官方消息。 18 | 19 | 1. [ggvis 包--数据可视化交互](http://mp.weixin.qq.com/s?__biz=MzI1NjUwMjQxMQ==&mid=2247488405&idx=1&sn=271fc88b523e738a6a1d92504dbce330&chksm=ea24ec71dd5365671bb66cbb50afdb0b00762b7581b9d3e5060a4b59021485364093f1c8b963&scene=21#wechat_redirect) 20 | 21 | 2. [ggridges 包--峰峦图详细介绍](http://mp.weixin.qq.com/s?__biz=MzI1NjUwMjQxMQ==&mid=2247488248&idx=1&sn=6b71d7adba5ea796fdfe8f49fe232d94&chksm=ea24ed1cdd53640a1e30271584458097fce82a732f9d63ce2084dc63fbae6fb028fd7f813bb7&scene=21#wechat_redirect) 22 | 23 | 3. [esquisse 包--不写代码生成 ggplot 图](http://mp.weixin.qq.com/s?__biz=MzI1NjUwMjQxMQ==&mid=2247488200&idx=1&sn=3a058480b104165118975b2d908dff72&chksm=ea24ed2cdd53643a9deb58069cd8d0e9933fc165994a2bb7a6f7d4651c7796b839fc781ec86d&scene=21#wechat_redirect) 24 | 25 | 4. [calendR 包---私人定制专属日历](http://mp.weixin.qq.com/s?__biz=MzI1NjUwMjQxMQ==&mid=2247487814&idx=1&sn=aa58149b66ce8b6d1c6210ded418c71a&chksm=ea24eea2dd5367b4a24a670b9e78d377f1506399be8dd0d0a35230407e3dc131f6b07ab3d9ca&scene=21#wechat_redirect) 26 | 27 | 5. [corrplot 包：相关性矩阵可视化](http://mp.weixin.qq.com/s?__biz=MzI1NjUwMjQxMQ==&mid=2247487625&idx=1&sn=3102c4afb0cf97904d810579af386eb6&chksm=ea24ef6ddd53667b887d11e7013589f796c8ff4f9e1e9b6e8df817ea7b223baadbc19dfbaaa5&scene=21#wechat_redirect) 28 | 29 | 6. [cowplot 包：用 R 添加水印](http://mp.weixin.qq.com/s?__biz=MzI1NjUwMjQxMQ==&mid=2247486838&idx=2&sn=21ee1c8b683e7d27373f3e1f40901428&chksm=ea24f292dd537b843db330a88161ce6f89227418f64515164615c3f63721df6464b6d91a2b1a&scene=21#wechat_redirect) 30 | 31 | 7. [flexdashboard 包：用于 R 的简单交互式仪表盘](http://mp.weixin.qq.com/s?__biz=MzI1NjUwMjQxMQ==&mid=2247486237&idx=1&sn=571544510c7e3e48a280dd4d677656e5&chksm=ea24f4f9dd537defa493c419973f75943159316765ac61093a195b83fde314dd7fffe61349cd&scene=21#wechat_redirect) 32 | 33 | 8. [gghalves 包--你五毛我五毛](http://mp.weixin.qq.com/s?__biz=MzI1NjUwMjQxMQ==&mid=2247486214&idx=1&sn=7ff5d7375c615d20cffea6329cccff37&chksm=ea24f4e2dd537df4a5ebe66a441b2fb0ee0599a05a700e1d199f729c497a68857e8031cd2e61&scene=21#wechat_redirect) 34 | 35 | 9. [用 ggpubr 包制图](http://mp.weixin.qq.com/s?__biz=MzI1NjUwMjQxMQ==&mid=2247485615&idx=1&sn=47ac21f131bf2ac6c90c50fb9fb7966b&chksm=ea24f74bdd537e5d74f60919388f683dfe779fe8a2d11999e55e290d4bdb25c64e36cc74ccc1&scene=21#wechat_redirect) 36 | 37 | 10. 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[ggThemeAssist包：交互式修改图形主题](https://mp.weixin.qq.com/s/NvqznH9kA4E9c9qus0K-8g) 52 | -------------------------------------------------------------------------------- /5001-interactive-ploting.md: -------------------------------------------------------------------------------- 1 | # 认识交互式绘图工具{#interactive-ploting} 2 | 3 | 4 | 5 | 6 | 前面可视化的结果就是一个静态的图形，所有信息都一目了然地放在一张图上。 7 | 8 | 静态图形适合于分析报告等纸质媒介，而在网络时代，如果在网页上发布可视化，那么动态的、交互的图形则更有优势。 9 | 10 | 在R的环境中，动态交互图形的优势在于能和knitr，shiny等框架整合在一起，能迅速建立一套可视化原型系统。 11 | 12 | > 由于pdf不支持html有关的图形输出，这里只给代码，可以自行运行，查看结果。 13 | 14 | > 注意：提前安装好相应的包。 15 | 16 | htmlwidgets包，这是一个专为R语言打造的可视化JS库，只需要编写几行R语言代码便可生成交互式的可视化页面。目前已经有基于htmlwidgets制作的R包可供直接调用，具体名称及对应作用见表 17 | 18 | ![](figure/24.png) 19 | 20 | ## leaflet包 21 | 22 | 23 | ```r 24 | library(leaflet) 25 | leaflet()%>% 26 | addTiles()%>% 27 | addMarkers(lng=174.768,lat=-36.852,popup="ThebirthplaceofR") 28 | ``` 29 | 30 | ## dygraphs包 31 | 32 | 33 | ```r 34 | library(dygraphs) 35 | lungDeaths <- cbind(mdeaths, fdeaths) 36 | dygraph(lungDeaths) 37 | ``` 38 | 39 | ## plotly包 40 | 41 | 42 | ```r 43 | library(plotly) 44 | pal <- RColorBrewer::brewer.pal(nlevels(iris$Species), "Set1") 45 | plot_ly(data = iris, x = ~Sepal.Length, y = ~Petal.Length, color = ~Species, 46 | colors = pal, mode = "markers") 47 | ``` 48 | 49 | 50 | ```r 51 | p <- ggplot(iris, aes(x = Sepal.Length, y = Petal.Length, colour = Species))+ 52 | scale_color_brewer(palette = "Set1")+ 53 | geom_point() 54 | ggplotly(p) 55 | ``` 56 | 57 | ## DT包 58 | 59 | 60 | ```r 61 | library(DT) 62 | datatable(iris) 63 | ``` 64 | 65 | ## networkD3包 66 | 67 | 68 | ```r 69 | library(networkD3) 70 | src <- c("A","A","A","A","B","B","C","C","D") 71 | target <- c("B","C","D","J","E","F","G","H","I") 72 | networkData <- data.frame(src, target) 73 | simpleNetwork(networkData, zoom = T) 74 | ``` 75 | 76 | 77 | ```r 78 | data(MisLinks) 79 | data(MisNodes) 80 | forceNetwork(Links = MisLinks, Nodes = MisNodes, Source = "source", 81 | Target = "target", Value = "value", NodeID = "name", 82 | Group = "group", opacity = 0.8) 83 | ``` 84 | 85 | ## 利用Shiny包实现可交互的Web应用 86 | 87 | shiny的官网包含了非常多的内容，包括详细教程，案例等。网站地址如下： 88 | 89 | 90 | -------------------------------------------------------------------------------- /6001-some-examples.md: -------------------------------------------------------------------------------- 1 | # 常用案例 {#some-tips-alls} 2 | 3 | 4 | 5 | ## 绘制不同分布的 QQ 图 6 | 7 | 这里主要是用 qqplotr 包进行绘制，参考的博客：[An Introduction to qqplotr](https://cran.r-project.org/web/packages/qqplotr/vignettes/introduction.html)。 8 | 9 | ### 简单版本 10 | 11 | #### 绘制正态分布的 QQ 图 12 | 13 | 14 | ```r 15 | library(qqplotr) 16 | library(ggplot2) 17 | # 随机产生数据 18 | set.seed(0) 19 | smp <- data.frame(norm = rnorm(100)) 20 | # 绘制 21 | gg <- ggplot(data = smp, mapping = aes(sample = norm)) + 22 | stat_qq_band() + 23 | stat_qq_line() + 24 | stat_qq_point() + 25 | labs(x = "Theoretical Quantiles", y = "Sample Quantiles") 26 | gg 27 | ``` 28 | 29 | 30 | 31 | \begin{center}\includegraphics{6001-some-examples_files/figure-latex/unnamed-chunk-1-1} \end{center} 32 | 33 | 使用三种不同的置信带构造置信区间，其可以用参数 `bandType` 调整。 34 | 35 | 36 | ```r 37 | library(viridis) 38 | gg <- ggplot(data = smp, mapping = aes(sample = norm)) + 39 | geom_qq_band(bandType = "ks", mapping = aes(fill = "KS"), alpha = 0.9) + 40 | geom_qq_band(bandType = "ts", mapping = aes(fill = "TS"), alpha = 0.9) + 41 | geom_qq_band(bandType = "pointwise", mapping = aes(fill = "Normal"), alpha = 0.9) + 42 | geom_qq_band(bandType = "boot", mapping = aes(fill = "Bootstrap"), alpha = 0.9) + 43 | stat_qq_line() + 44 | stat_qq_point() + 45 | labs(x = "Theoretical Quantiles", y = "Sample Quantiles") + 46 | scale_fill_viridis(discrete = T,direction = -1) 47 | 48 | gg 49 | ``` 50 | 51 | 52 | 53 | \begin{center}\includegraphics{6001-some-examples_files/figure-latex/unnamed-chunk-2-1} \end{center} 54 | 55 | ### 进阶版本 56 | 57 | 读者绘制正态分布的 QQ 图，还是比较简单。但是如果是其他分布的情况呢？ 58 | 59 | > 这里以一个可靠性数据为例子，该数据来源于文献：Badar, M. G., Priest, A. M. (1982). Statistical aspects of fiber and bundle strength in hybrid composites. In: Hayashi, T., Kawata, K., Umekawa, S., eds. Progress in Science and Engineering Composites. Tokyo: ICCM-IV, pp. 1129--1136。 60 | 61 | 62 | ```r 63 | data = data.frame('y' = c(1.339, 1.434, 1.549, 1.574 ,1.589, 1.613, 1.746 ,1.753, 1.764 ,1.807, 1.812, 1.84, 1.852, 1.852, 1.862, 1.864, 1.931, 1.952, 1.974, 2.019, 2.051, 2.055, 2.058 ,2.088, 2.125, 2.162, 2.171, 2.172 ,2.18 ,2.194 ,2.211 ,2.27, 2.272, 2.28, 2.299, 2.308, 2.335 ,2.349 ,2.356 ,2.386, 2.39, 2.41, 2.43, 2.431, 2.458, 2.471, 2.497, 2.514 ,2.558, 2.577, 2.593, 2.601, 2.604, 2.62 ,2.633, 2.67, 2.682, 2.699, 2.705, 2.735, 2.785, 2.785,3.02, 3.042, 3.116, 3.174)) 64 | ``` 65 | 66 | #### 绘制指数分布的 QQ 图 67 | 68 | 这里我们绘制其指数分布的 QQ 图。根据指数函数参数拟合该数据之后，得到`rate =2.2867`，并将其保存到 list 中。 69 | 70 | > 具体如何拟合，读者自行搜索 R 包中的相关函数。 71 | 72 | 其他代码基本不变，主要是将 `stat_qq_line()` 和 `stat_qq_point()` 中的分布设定下，参数设定下。 73 | 74 | 75 | ```r 76 | # exponential distribution 77 | dp <- list(rate = 2.2867) 78 | di <- "exp" 79 | p1 = ggplot(data = data, mapping = aes(sample = y)) + 80 | stat_qq_band(distribution = di, dparams = dp) + 81 | stat_qq_line(distribution = di, dparams = dp) + 82 | stat_qq_point(distribution = di, dparams = dp) + 83 | labs(x = "Theoretical Quantiles", y = "Sample Quantiles") + 84 | theme_bw() + 85 | theme(panel.grid = element_blank()) 86 | p1 87 | ``` 88 | 89 | 90 | 91 | \begin{center}\includegraphics{6001-some-examples_files/figure-latex/unnamed-chunk-4-1} \end{center} 92 | 93 | #### 绘制威布尔分布的 QQ 图 94 | 95 | 同理，将该数据应用到威布尔分布中。结果如下： 96 | 97 | 98 | ```r 99 | # weibull distribution 100 | di <- "weibull" # exponential distribution 101 | dp <- list(shape=5.4766,scale=2.4113) 102 | p2 = ggplot(data = data, mapping = aes(sample = y)) + 103 | stat_qq_band(distribution = di, dparams = dp) + 104 | stat_qq_line(distribution = di, dparams = dp) + 105 | stat_qq_point(distribution = di, dparams = dp) + 106 | labs(x = "Theoretical Quantiles", y = "Sample Quantiles") + 107 | theme_bw() + 108 | theme(panel.grid = element_blank()) 109 | p2 110 | ``` 111 | 112 | 113 | 114 | \begin{center}\includegraphics{6001-some-examples_files/figure-latex/unnamed-chunk-5-1} \end{center} 115 | 116 | 可以看到该数据集，更适合使用 weibull分布进行拟合。 117 | 118 | 119 | ```r 120 | library(cowplot) 121 | plot_grid(p1, p2, ncol = 2, nrow = 1) 122 | ``` 123 | 124 | 125 | 126 | \begin{center}\includegraphics{6001-some-examples_files/figure-latex/unnamed-chunk-6-1} \end{center} 127 | 128 | ## 绘制混合密度函数图以及添加分位数线 129 | 130 | 主要使用 `ggridges` 包中的 `stat_density_ridges()`。参考的博客： 131 | 132 | ### 加载包 133 | 134 | 135 | ```r 136 | library(ggplot2) 137 | library(ggridges) 138 | ``` 139 | 140 | ### 产生数据集 141 | 142 | 假设数据来源于一个混合分布。 143 | 144 | 145 | ```r 146 | item <- 10000 147 | inds <- rbinom(1, item, 0.5) 148 | x <- c(rnorm(inds, 1, 1), rnorm(item - inds, 8, 1)) 149 | data <- data.frame("value" = x, "class" = rep(1, length(x))) 150 | ``` 151 | 152 | ### 绘制密度函数图并添加分位数线 153 | 154 | 155 | ```r 156 | # 绘图 157 | p1 <- ggplot(data, aes(x = value, y = class, fill = factor(stat(quantile)))) + 158 | stat_density_ridges( 159 | geom = "density_ridges_gradient", 160 | calc_ecdf = TRUE, 161 | quantiles = c(0.025, 0.975) 162 | ) + 163 | scale_fill_manual( 164 | name = "Probability", values = c("#E2EAF6", "#436FB0", "#E2EAF6") 165 | ) + 166 | theme_bw() + 167 | theme(legend.position = "none", panel.grid = element_blank()) + 168 | labs(x = "x", y = "Density") 169 | p1 170 | ``` 171 | 172 | 173 | 174 | \begin{center}\includegraphics{6001-some-examples_files/figure-latex/unnamed-chunk-9-1} \end{center} 175 | 176 | 177 | ```r 178 | p2 <- ggplot(data, aes(x = value, y = class, fill = factor(stat(quantile)))) + 179 | stat_density_ridges( 180 | geom = "density_ridges_gradient", 181 | calc_ecdf = TRUE, 182 | quantiles = c(0.005, 0.495, 0.51, 0.99) 183 | ) + 184 | scale_fill_manual( 185 | name = "Probability", values = c("#E2EAF6", "#436FB0", "#E2EAF6", "#436FB0", "#E2EAF6"), 186 | ) + 187 | theme_bw() + 188 | theme(legend.position = "none", panel.grid = element_blank()) + 189 | labs(x = "x", y = "Density") 190 | 191 | p2 192 | ``` 193 | 194 | 195 | 196 | \begin{center}\includegraphics{6001-some-examples_files/figure-latex/unnamed-chunk-10-1} \end{center} 197 | 198 | ### 合并两图（使用cowplot包） 199 | 200 | 201 | ```r 202 | library(cowplot) 203 | # pdf("plot_cow.pdf", width = 8, height = 4) 204 | plot_grid(p1, p2, ncol = 1, nrow = 2) 205 | ``` 206 | 207 | 208 | 209 | \begin{center}\includegraphics{6001-some-examples_files/figure-latex/unnamed-chunk-11-1} \end{center} 210 | 211 | ```r 212 | # dev.off() 213 | ``` 214 | 215 | ## 绘制不同参数的密度函数 216 | 217 | ### Beta 密度函数 218 | 219 | 绘制不同参数下的 Beta 密度函数。具体该分布的介绍可见： 220 | 221 | Beta函数如下： $$ 222 | B(a,b) = \int_{0}^{1} x^{a-1} {(1-x)}^{b-1} dx,\quad a,b>0 223 | $$ 224 | 225 | Beta 分布： 226 | 227 | 随机变量 X 的密度函数为： 228 | 229 | $$p(x) = \frac{1}{\mathrm{~B}(\alpha, \beta)} x^{\alpha-1}(1-x)^{\beta-1}$$ 230 | 231 | > **存在问题**：还未把各个密度函数的参数加入。 232 | 233 | 234 | ```r 235 | ## Beta Distribution 236 | library(ggplot2) 237 | library(reshape2) 238 | library(ggsci) 239 | item = 1000 240 | x <- seq(0,1,length = item) 241 | beta_dist <- data.frame(cbind(x,dbeta(x,0.5,0.5), dbeta(x,2,2), dbeta(x,0.5,2),dbeta(x,2,0.5),dbeta(x,1,5),dbeta(x,5,1),dbeta(x,1,1))) 242 | colnames(beta_dist) <- c("x","a=0.5,b=0.5","a=2,b=2","a=0.5,b=2", 243 | "a=2,b=0.5","a=1,b=5","a=5,b=1","a=1,b=1") 244 | beta_dist <- melt(beta_dist,x) 245 | beta_dist$"class" = c(rep(1:3,each = 2*item),rep(4,item)) 246 | g <- ggplot(beta_dist, aes(x,value, color=variable)) 247 | g + geom_line() + 248 | facet_wrap(vars(class),scales = "free_y") + 249 | labs(title="Beta Distribution", x="x", y="Probability") + 250 | scale_color_aaas() + 251 | theme_bw() + theme(panel.grid = element_blank(),legend.position = 'none') 252 | ``` 253 | 254 | 255 | 256 | \begin{center}\includegraphics{6001-some-examples_files/figure-latex/unnamed-chunk-12-1} \end{center} 257 | 258 | ## 散点图中加入第三变量的密度函数 259 | 260 | 261 | ```r 262 | ### Accept-reject algorithm 263 | ### beta(2.7,6.3) 264 | library(ggplot2) 265 | num <- 1000 266 | ys <- runif(num) 267 | us <- runif(num, 0, 2.67) 268 | xs <- dbeta(ys, 2.7, 6.3) 269 | data <- data.frame("x_rand" = ys, "Density" = us, "true_x" = xs) 270 | ggplot(data) + 271 | geom_point(aes(x_rand, Density), col = "#95E1D3") + 272 | geom_area(aes(x_rand, xs), 273 | fill = 4, alpha = 0.5, 274 | color = 1, # Line color 275 | lwd = 0.5, # Line width 276 | linetype = 1 277 | ) + 278 | annotate("text", x = 0.3, y = 0.5, label = "sum(xs>us)", size = 5) + 279 | labs(x = "x") + 280 | theme_bw() + 281 | theme(panel.grid = element_blank()) 282 | ``` 283 | 284 | 285 | 286 | \begin{center}\includegraphics{6001-some-examples_files/figure-latex/unnamed-chunk-13-1} \end{center} 287 | 288 | ## 绘制 Gamma 分布相关图形 289 | 290 | - 自定义主题 291 | 292 | 293 | ```r 294 | library(ggridges) 295 | # 自定义主题 296 | theme_manual = function(){ 297 | theme(panel.grid = element_blank(), 298 | panel.border = element_blank(), 299 | axis.text = element_blank(), 300 | axis.ticks = element_blank(), 301 | legend.position="none") 302 | } 303 | ``` 304 | 305 | - 数据模拟 306 | 307 | 308 | ```r 309 | library(DT) 310 | library(ggplot2) 311 | num = 100 312 | data = data.frame('id' = 1:num,'value' = rgamma(num,2,1),'class' = factor(gl(5,num/5))) 313 | datatable(data) 314 | ``` 315 | 316 | 317 | 318 | \begin{center}\includegraphics{6001-some-examples_files/figure-latex/unnamed-chunk-15-1} \end{center} 319 | 320 | - 绘图 321 | 322 | 323 | ```r 324 | p1 = ggplot(data,aes(id,value)) + 325 | geom_line() + 326 | geom_hline(yintercept = max(data$value)+0.2) + 327 | geom_hline(yintercept = min(data$value)-0.2) + 328 | theme_bw() + 329 | theme_manual() + xlab('') + ylab('') 330 | p1 331 | ``` 332 | 333 | 334 | 335 | \begin{center}\includegraphics{6001-some-examples_files/figure-latex/unnamed-chunk-16-1} \end{center} 336 | 337 | ```r 338 | ## 纵向密度函数图 339 | p2 = ggplot(data, aes(x = value, y =class, fill = class)) + 340 | geom_density_ridges(aes(),alpha = 0.2,scale = 1,bandwidth = 1) + 341 | coord_flip() + 342 | # scale_point_color_hue(l = 40) + 343 | # scale_discrete_manual(aesthetics = "point_shape", values = c(21, 22, 23,24,25)) + 344 | theme_bw() + 345 | theme_manual() + xlab('') + ylab('') 346 | p2 347 | ``` 348 | 349 | 350 | 351 | \begin{center}\includegraphics{6001-some-examples_files/figure-latex/unnamed-chunk-16-2} \end{center} 352 | 353 | - 合并图形 354 | 355 | 356 | ```r 357 | library(cowplot) 358 | plot_grid(p1,p2,ncol = 1) 359 | ``` 360 | 361 | 362 | 363 | \begin{center}\includegraphics{6001-some-examples_files/figure-latex/unnamed-chunk-17-1} \end{center} 364 | 365 | ## 纯手动复现密度图 366 | 367 | 老板觉得课件的图形太过模糊和单调，于是想让我用 [ggplot2](https://ggplot2.tidyverse.org/) 包复现一下结果，做的更加高清、精美些。于是我花将近一个小时复现了下面这个图形： 368 | 369 | ![](images/paste-224B4B25.png) 370 | 371 | 主要有两部分构成：1. 绘制密度函数曲线并填充分位数面积；2. 添加各种线段和文字。 372 | 373 | - 数据产生 374 | 375 | 376 | ```r 377 | # 数据产生 378 | set.seed(1) 379 | mu = c(2,5) 380 | std = c(1,1) 381 | num = 1000 382 | r1 = rnorm(num,mu[1],std[1]) 383 | r2 = rnorm(num,mu[2],std[2]) 384 | data = data.frame('value' = c(r1,rep(NA,num),r2,rep(NA,5*num)), 385 | 'class' = factor(rep(c(1:8),each= num))) 386 | knitr::kable(head(data)) 387 | ``` 388 | 389 | 390 | \begin{tabular}{r|l} 391 | \hline 392 | value & class\\ 393 | \hline 394 | 1.373546 & 1\\ 395 | \hline 396 | 2.183643 & 1\\ 397 | \hline 398 | 1.164371 & 1\\ 399 | \hline 400 | 3.595281 & 1\\ 401 | \hline 402 | 2.329508 & 1\\ 403 | \hline 404 | 1.179532 & 1\\ 405 | \hline 406 | \end{tabular} 407 | 408 | - 画图 409 | 410 | 文中还是使用前面自定义的主题。 411 | 412 | 413 | ```r 414 | # 画图 415 | ggplot(data, aes(x = value, y = class,fill = factor(stat(quantile)))) + 416 | # 添加密度函数图 417 | stat_density_ridges( 418 | geom = "density_ridges_gradient", 419 | calc_ecdf = TRUE,rel_min_height = 0.02, 420 | quantiles = c(0.025, 0.975), 421 | alpha = 1,scale = 0.6,bandwidth = 1 422 | ) + 423 | scale_fill_manual( 424 | name = "Probability", values = c("#FF0000A0", "white", "#FF0000A0"), #"#0000FFA0" 425 | labels = c("(0, 0.025]", "(0.025, 0.975]", "(0.975, 1]") 426 | ) + 427 | # 添加各种线段，文字 428 | annotate("segment", x = mu[1], xend = mu[1], y = 1, yend = 7,colour = "black") + 429 | annotate("segment", x = mu[2]-1, xend = mu[2]-1, y = 1, yend = 7,colour = "#0000FFA0",lty = "dashed") + 430 | annotate("segment", x = mu[1]-2.15, xend = mu[1]-2, y = 1, yend = 7,colour = "#0000FFA0",lty = "dashed") + 431 | annotate("segment", x = mu[2], xend = mu[2], y = 3-0.02, yend = 4.18,colour = "black") + 432 | annotate("segment", x = 0, xend = 10, y = 3, yend = 3,colour = "black") + 433 | annotate("segment", x = -3, xend = 7, y = 1, yend = 1,colour = "black") + 434 | annotate("text", x = mu[1], y = 0.7, label = expression(mu[T])) + 435 | annotate("text", x = mu[1]-2.15, y = 0.7, label = expression(alpha[1])) + 436 | annotate("text", x = mu[1]+2, y = 0.7, label = expression(alpha[2])) + 437 | annotate("text", x = mu[2], y = 2.8, label = expression(mu[T])) + 438 | annotate("text", x = 0.5, y = 3.9, label = expression(beta)) + 439 | annotate(geom = "line",x = c(0.8, 3.1), 440 | y = c(3.8, 3.2), 441 | arrow = arrow(angle = 20, length = unit(4, "mm"))) + 442 | annotate("text", x = mu[1], y = 7.3, label = "CL") + 443 | annotate("text", x = mu[2]-1, y = 7.4, label = "UCL") + 444 | annotate("text", x = mu[1]-2, y = 7.4, label = "LCL") + 445 | annotate("text", x = -1.3, y = 2.3, label = expression(alpha[1] + alpha[2] == alpha)) + 446 | coord_flip() + 447 | theme_bw() + 448 | theme_manual() + xlab('') + ylab('') 449 | ``` 450 | 451 | 452 | 453 | \begin{center}\includegraphics{6001-some-examples_files/figure-latex/unnamed-chunk-19-1} \end{center} 454 | 455 | 可以看到，现在得到的结果还是有点问题的。笔者能力有限，不能使用代卖复现的一模一样（也是为了省时间），于是我是用了 [AI](https://mp.weixin.qq.com/s/BkPAsH8qDZzQkcBRgMsOSw) 大法，对该图形进行了修改。最后得到： 456 | 457 | ![](images/paste-39BF420C.png) 458 | 459 | ## 绘制贝叶斯分析相关图形 460 | 461 | 主要使用 [bayesplot](https://github.com/stan-dev/bayesplot) 包进行绘制，对应的速查表网址为： 462 | 463 | 464 | ```r 465 | # 加载需要使用的包 466 | library(showtext) 467 | showtext_auto() #解决中文字体乱码问题 468 | library(bayesplot) 469 | library(rstanarm) 470 | options(mc.cores = parallel::detectCores()) 471 | library(ggplot2) 472 | library(dplyr) 473 | ``` 474 | 475 | ### 模型建模 476 | 477 | 为了展示贝叶斯图，我们将使用 `rstanarm::stan glm` 拟合线性回归，并始终使用这个模型。 478 | 479 | 480 | ```r 481 | model <- stan_glm(mpg~., data=mtcars, chains=4) 482 | posterior <- as.matrix(model) 483 | # head(posterior) 484 | ``` 485 | 486 | 展示你感兴趣参数的后验分布。 487 | 488 | 489 | ```r 490 | showtext_auto() 491 | mcmc_areas(posterior, pars = c("drat", "am", "wt"),prob = 0.8) + ggtitle("Posterior") 492 | ``` 493 | 494 | 495 | 496 | \begin{center}\includegraphics{6001-some-examples_files/figure-latex/unnamed-chunk-22-1} \end{center} 497 | 498 | 使用轨迹追踪图诊断收敛性 499 | 500 | 501 | ```r 502 | mcmc_trace(posterior, pars=c("sigma", "wt")) 503 | ``` 504 | 505 | 506 | 507 | \begin{center}\includegraphics{6001-some-examples_files/figure-latex/unnamed-chunk-23-1} \end{center} 508 | 509 | 使用`as.array`，可以提取每一个链的数据。这允许您查看每个链所选参数的跟踪图。 510 | 511 | 512 | ```r 513 | posterior_chains <- as.array(model) 514 | fargs <- list(ncol = 2, labeller = label_parsed) 515 | pars <- c("(Intercept)", "sigma") 516 | chains_trace <- mcmc_trace(posterior_chains, pars = pars, n_warmup = 300, facet_args = fargs) 517 | chains_trace 518 | ``` 519 | 520 | 521 | 522 | \begin{center}\includegraphics{6001-some-examples_files/figure-latex/unnamed-chunk-24-1} \end{center} 523 | 524 | 配对图有助于确定是否有任何高度相关的参数。 525 | 526 | 527 | ```r 528 | posterior_chains %>% mcmc_pairs(pars = c("(Intercept)", "wt", "sigma")) 529 | ``` 530 | 531 | 532 | 533 | \begin{center}\includegraphics{6001-some-examples_files/figure-latex/unnamed-chunk-25-1} \end{center} 534 | 535 | ### 后验预测检查 536 | 537 | 用后验预测密度来检查模型如何覆盖你的数据。 538 | 539 | 540 | ```r 541 | ppd <- posterior_predict(model, draws=500) 542 | ppd %>% 543 | ppc_intervals(y = mtcars$mpg, yrep = ., x = mtcars$wt, prob = 0.5) + 544 | labs(x = "Weight (1000 lbs)", y = "MPG", title = "") 545 | ``` 546 | 547 | 548 | 549 | \begin{center}\includegraphics{6001-some-examples_files/figure-latex/unnamed-chunk-26-1} \end{center} 550 | 551 | ```r 552 | ppd %>% ppc_stat_grouped(y = mtcars$mpg, 553 | group = mtcars$am, 554 | stat = "median", binwidth=0.5) 555 | ``` 556 | 557 | 558 | 559 | \begin{center}\includegraphics{6001-some-examples_files/figure-latex/unnamed-chunk-26-2} \end{center} 560 | 561 | ### 诊断 562 | 563 | Bayesplot 可以方便地检查 rstanarm 默认使用的NUTS采样方法的诊断。 564 | 565 | 566 | ```r 567 | mcmc_scatter(posterior, pars = c("wt", "sigma"), np = nuts_params(model$stanfit)) 568 | ``` 569 | 570 | 571 | 572 | \begin{center}\includegraphics{6001-some-examples_files/figure-latex/unnamed-chunk-27-1} \end{center} 573 | 574 | 575 | ```r 576 | np <- nuts_params(model$stanfit) 577 | mcmc_nuts_energy(np, binwidth=1) + 578 | ggtitle("NUTS Energy Diagnostic") 579 | ``` 580 | 581 | 582 | 583 | \begin{center}\includegraphics{6001-some-examples_files/figure-latex/unnamed-chunk-28-1} 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-------------------------------------------------------------------------------- /8001-rmarkdown-extended.md: -------------------------------------------------------------------------------- 1 | # 其他方式的文档沟通{#rmarkdown-extended} 2 | 3 | ## Typora 4 | 5 | markdown 的轻量级编辑器，非常推荐大家用它做笔记。教程从上到下进行拓展，首先了解 Typora 的特性，然后对其中存在的问题进行解决。这里包括：设置免费图床，使得Typora中的图同步到网上；给Typora中的字体变化颜色。当然，以后也会继续拓展。 6 | 7 | [R沟通｜markdown编辑器—Typora](http://mp.weixin.qq.com/s?__biz=MzI1NjUwMjQxMQ==&mid=2247491318&idx=1&sn=47128737582a34677926a9f64f03e4ed&chksm=ea24e112dd53680478ac90151554ebdde72ab122fcc84bae4da6e87e9c97b020275ecabc846c&scene=21#wechat_redirect) 8 | 9 | 10 | 11 | [R沟通 | 如何在Typora中设置免费的图床](http://mp.weixin.qq.com/s?__biz=MzI1NjUwMjQxMQ==&mid=2247492557&idx=1&sn=75024932a02364cb200873d069f79e29&chksm=ea271c29dd50953fbec48d64f7ac007893037bf2f89ecf023be5addff313eeefeb4ecae85b0b&scene=21#wechat_redirect) 12 | 13 | 14 | 15 | [R沟通｜Typora字体颜色设置](http://mp.weixin.qq.com/s?__biz=MzI1NjUwMjQxMQ==&mid=2247494584&idx=1&sn=bd9537620ad7c8895a37c10ba788a97c&chksm=ea27145cdd509d4acf4bbe867e4e50c6a995f57f70626c3798dab478dbd37f4f6c2a4247a312&scene=21#wechat_redirect) 16 | 17 | ## xaringan 幻灯片 18 | 19 | 强烈推荐使用这个包制作幻灯片，难度从上往下一步步晋升。认真学了这三期基本够用。小编带你装x，做出不一样的幻灯片。建议大家先把前面的入门教程过一遍，再往后学。 20 | 21 | 22 | 23 | [R沟通｜用xaringan包制作幻灯片](http://mp.weixin.qq.com/s?__biz=MzI1NjUwMjQxMQ==&mid=2247489685&idx=1&sn=aa5bccb2afe9c3882d415e4ed17c5b48&chksm=ea24e771dd536e6788cf8689009c469150998b58d4673c0453876f9c3b9854dbae385af33a2b&scene=21#wechat_redirect) 24 | 25 | [R沟通｜设置xaringan主题](http://mp.weixin.qq.com/s?__biz=MzI1NjUwMjQxMQ==&mid=2247489789&idx=1&sn=94e8b76d45743e85db57a2b0ef417fcf&chksm=ea24e719dd536e0fbec0d3ed94d4104f65e219ebd86f5a45a30d2ff2084cf5b0bddfe079852f&scene=21#wechat_redirect) 26 | 27 | [R沟通｜提升xaringan幻灯片的b格](http://mp.weixin.qq.com/s?__biz=MzI1NjUwMjQxMQ==&mid=2247495986&idx=1&sn=c0e47f57ddb341e581af7e96e8370e4a&chksm=ea270ed6dd5087c0c97adfad45988ae2ff53ff9519515e7fa503d9931d02f7268a572acf5a02&scene=21#wechat_redirect) 28 | 29 | ## 制作幻灯片 30 | 31 | 如果想要小编制作的 ppt 模板可以后台私聊。比起传统的 ppt，最大的优点就是能够将代码和结果直接输出到ppt中。 32 | 33 | [R沟通｜制作个性化ppt！](http://mp.weixin.qq.com/s?__biz=MzI1NjUwMjQxMQ==&mid=2247488738&idx=1&sn=b0d21bfe77d3c7c65d0c8df72c1694d0&chksm=ea24eb06dd536210b1d1ed44d2dcb5214d106a787ace6b437549a450a83300e84b052c595a5b&scene=21#wechat_redirect) 34 | 35 | ## Rbeamer 36 | 37 | 学术报告可以使用它，类似于 LaTeX 中的 Beamer 模板。小编基本都是使用它做讨论班的幻灯片（数学公式，代码，结果相结合）。 38 | 39 | [R沟通｜舍弃Latex，拥抱Rbeamer吧！](http://mp.weixin.qq.com/s?__biz=MzI1NjUwMjQxMQ==&mid=2247488659&idx=1&sn=738cd20bfccf8936b5d969483d4f6891&chksm=ea24eb77dd536261e9cc68eac635d66113ea2e296d3b5ed6280410771c0b956be1af64f52eee&scene=21#wechat_redirect) 40 | 41 | 42 | 43 | ## Dashboards 44 | 45 | 使用 markdown 语法构建可交互网站。非常容易入门，如果你对 shiny 一窍不通的话，建议先使用它来完成你的初步项目吧。 46 | 47 | [R文档沟通｜Dashboards入门（1）](http://mp.weixin.qq.com/s?__biz=MzI1NjUwMjQxMQ==&mid=2247494178&idx=1&sn=0580de258138d112e9362613ba0eb3c6&chksm=ea2715c6dd509cd030957d168648c428b5511b39dc850b49234790b0233ceba5ddcceb176eff&scene=21#wechat_redirect) 48 | 49 | 50 | 51 | [R文档沟通｜Dashboards入门（2）](http://mp.weixin.qq.com/s?__biz=MzI1NjUwMjQxMQ==&mid=2247494354&idx=1&sn=f2d9916c05c42e65b6cc75620deea8f3&chksm=ea271536dd509c20f2ef427b4dd547196a7d1338e678dda7b1484bdc832977bbfef98d04f81b&scene=21#wechat_redirect) 52 | 53 | 54 | 55 | [R文档沟通｜Dashboards入门（3）](http://mp.weixin.qq.com/s?__biz=MzI1NjUwMjQxMQ==&mid=2247494929&idx=1&sn=ac860a3a73a979e52a783e971d1bdda5&chksm=ea2712f5dd509be30bad6c1ff96ddd9c826d9d7d27ef3dfc13943d6794d9450f860f76fc7f4a&scene=21#wechat_redirect) 56 | 57 | 58 | 59 | ## shiny 60 | 61 | 该系列转自于公众号《生信技能树》，论shiny教程和功力，他们更优秀，我就不在出教程啦。我也是个小白，学习者。 62 | 63 | [基于R语言的shiny网页工具开发基础系列-01](http://mp.weixin.qq.com/s?__biz=MzI1NjUwMjQxMQ==&mid=2247490208&idx=1&sn=950d5ca8a3839346441096a0dcced3ae&chksm=ea24e544dd536c52590d0fa77c366adbb841eb93364d44276fb6ad8420e607a3e946360aaf65&scene=21#wechat_redirect) 64 | 65 | 66 | 67 | [基于R语言的shiny网页工具开发基础系列-02](http://mp.weixin.qq.com/s?__biz=MzI1NjUwMjQxMQ==&mid=2247490208&idx=2&sn=cdb9fee34dc815e08a9f28ff6dade73b&chksm=ea24e544dd536c52972cc1253ab620f2d44c5078abd4d3dec7a47ce206df8436ab00449229d3&scene=21#wechat_redirect) 68 | 69 | 70 | 71 | [基于R语言的shiny网页工具开发基础系列-03](http://mp.weixin.qq.com/s?__biz=MzI1NjUwMjQxMQ==&mid=2247490208&idx=3&sn=057a8c1b09c6ed8c107833b60f4ae372&chksm=ea24e544dd536c5264741399a66937849f76874f727e69ccc558073a9ee8398d2de249e67414&scene=21#wechat_redirect) 72 | 73 | 74 | 75 | [基于R语言的shiny网页工具开发基础系列-04](http://mp.weixin.qq.com/s?__biz=MzI1NjUwMjQxMQ==&mid=2247490960&idx=1&sn=a30971248a4c2c0e1ce413523f88ef63&chksm=ea24e274dd536b62a14f33a28571209187ceb122d31a7e7b97855aec190cbe1255a13a40b264&scene=21#wechat_redirect) 76 | 77 | 78 | 79 | [基于R语言的shiny网页工具开发基础系列-05](http://mp.weixin.qq.com/s?__biz=MzI1NjUwMjQxMQ==&mid=2247490960&idx=2&sn=12f795a5c8d8abf709d23d0563c0715c&chksm=ea24e274dd536b6204bcf38c40cdae43334b3b48fbe03e2ebe1c33f4df437158f5f8c6faadc0&scene=21#wechat_redirect) 80 | 81 | 82 | 83 | [基于R语言的shiny网页工具开发基础系列-06](http://mp.weixin.qq.com/s?__biz=MzI1NjUwMjQxMQ==&mid=2247491342&idx=1&sn=24db0123fdbb08a45dae3ddf422c1426&chksm=ea24e0eadd5369fc311057f6fd74ebed034e66009476ce141f2552247d4dfe1626ac29de8626&scene=21#wechat_redirect) 84 | 85 | 86 | 87 | [基于R语言的shiny网页工具开发基础系列-07](http://mp.weixin.qq.com/s?__biz=MzI1NjUwMjQxMQ==&mid=2247491342&idx=2&sn=3623e59373731ecd0e2bfdf9be6912c7&chksm=ea24e0eadd5369fc05627cdc90bb46bcf88439d5306aaa74e925f93aaa31c2f7e37e0c61f76f&scene=21#wechat_redirect) 88 | 89 | ## blogdown 90 | 91 | 使用 blogdown 搭建私人博客。基础版本推文已经在《统计之都》发送了，可见：[手把手带你搭建个人博客](https://mp.weixin.qq.com/s/S4B5KO_lc3RZNUOqTJjPNQ)。 92 | 93 | 94 | ## 制作简历 95 | 96 | 97 | [R沟通｜使用latex模板构建个人履历](http://mp.weixin.qq.com/s?__biz=MzI1NjUwMjQxMQ==&mid=2247493793&idx=1&sn=ac5653d10a318d71885e6b1ff3ed3a67&chksm=ea271745dd509e53173998508ab53dad55d4e2acb22c78afee57ea57bc9950503fdb22bc00d7&scene=21#wechat_redirect) 98 | 99 | ## bookdown 100 | 101 | 102 | [R沟通｜Bookdown中文书稿写作手册](https://zll-blog.netlify.app/2021/07/bookdown_tutoral/) 103 | 104 | 105 | [R沟通｜用bookdown制作图书(1)](http://mp.weixin.qq.com/s?__biz=MzI1NjUwMjQxMQ==&mid=2247492971&idx=1&sn=b342777e1f1bf1d4a85cff0f20735491&chksm=ea271a8fdd50939996772ee0a8e3bf1cb1f35b2361ef6c160011074464dc957a421e44cba1fe&scene=21#wechat_redirect) 106 | 107 | 108 | 109 | ## 小编有话说 110 | 111 | 1. 最近有空会把写过推文的教程录制成视频，并加入b站[**Rmarkdown从入门到精通**](https://www.bilibili.com/video/BV1ib4y1X7r9/)教程中。 112 | 2. 还会加入其他有关文档沟通的推文，**bookdown**，**blogdown**，**pagedown**等，以及对Rmarkdown做更加进一步的拓展。 113 | 3. 当然欢迎更多的读者提出宝贵的意见，或者有好的想法也欢迎和小编沟通交流。 114 | 115 | 116 | -------------------------------------------------------------------------------- /9000-appendix.md: -------------------------------------------------------------------------------- 1 | # 附录{#appendix} 2 | 3 | 为了方便初学者快速入门以及文稿的完整性，这里罗列了常用问题的介绍，包括：安装R和Rstudio，使用Rstudio可能遇到的问题以及如何获取帮助。 4 | 5 | **注：**该部分来源于[《数据科学中的 R 语言》](https://bookdown.org/wangminjie/R4DS/intro-R.html#%E5%A6%82%E4%BD%95%E8%8E%B7%E5%8F%96%E5%B8%AE%E5%8A%A9)。 6 | 7 | 8 | 9 | ## 安装R和Rstudio{-} 10 | 11 | R软件是一个自由、开源软件平台，具有统计分析、可视化和编程的强大功能。你可以从这里免费下载。为了更好的使用 R 软件，我推荐大家使用RStudio这个IDE。这里有个在线教程帮助我们熟悉 R 和 RStudio。 12 | 13 | ### 安装 R{-} 14 | 15 | 我们从官方网站http://cran.r-project.org下载, 网站界面感觉有点朴素: 16 | 17 | ![](figure/Rinstall.png) 18 | 19 | 20 | ### 安装RStudio{-} 21 | 22 | 安装完R， 还需要安装RStudio。有同学可能要问 R 与 RStudio 是什么关系呢？打个比方吧，R 就像汽车的发动机, RStudio 就是汽车的仪表盘。但我更觉得 R 是有趣的灵魂，而 Rstudio 是好看的皮囊。 23 | 24 | ![](figure/2.png) 25 | 26 | 同样，我们从官方网站下载并安装，如果你是苹果系统的用户，选择苹果系统对应的rstudio版本即可。 27 | 28 | - https://www.rstudio.com/download 29 | - 选择RStudio Desktop 30 | 31 | ![](figure/3.png) 32 | 33 | 34 | ![](figure/4.png) 35 | 36 | ## 可能的问题{-} 37 | 38 | - 问题1：如果下载速度太慢，可以选择国内镜像， 39 | 40 | ![选择国内镜像1](figure/16.png) 41 | 42 | ![选择国内镜像2](figure/17.png) 43 | 44 | 然后再输入命令`install.packages("tidyverse")`，或者直接指定清华大学镜像 45 | 46 | 47 | 48 | ``` 49 | install.packages("tidyverse", repos = "http://mirrors.tuna.tsinghua.edu.cn/CRAN") 50 | ``` 51 | 52 | - 问题2：如果遇到如下报错信息 53 | 54 | 55 | 56 | ``` 57 | Warning in install.packages : 58 | unable to access index for repository http://cran.rstudio.com/src/contrib: 59 | cannot open URL 'http://cran.rstudio.com/src/contrib/PACKAGES' 60 | ``` 61 | 62 | 输入下面命令后，再试试 63 | 64 | 65 | 66 | ``` 67 | options(download.file.method="libcurl") 68 | ``` 69 | 70 | 或者打开`D:\R\etc\Rprofile.site`，添加以下内容： 71 | 72 | 73 | 74 | ``` 75 | local({r <- getOption("repos") 76 | r["CRAN"] <- "http://mirrors.tuna.tsinghua.edu.cn/CRAN" 77 | options(repos=r)}) 78 | 79 | options(download.file.method="libcurl") 80 | ``` 81 | 82 | - 问题3：如果打开代码是乱码，可以试试修改如下设置 83 | 84 | ![代码是乱码](figure/18.png) 85 | 86 | - 问题4：如果每次打开Rstudio非常慢，可以在Rstudio里将这几个选项取消 87 | 88 | ![打开Rstudio非常慢](figure/19.png) 89 | 90 | - 问题5：如果 Rstudio 打开是空白 91 | 92 | 很大的可能是你的电脑用户名是中文的，修改用户名再试试 93 | 94 | - 问题6：安装过程中提示，我的系统不能兼容 64 位的 Rstudio。 95 | 96 | 可能你是低版本的windows系统，建议安装旧版本的Rstudio，可以在[这里](https://rstudio.com/products/rstudio/older-versions/)找到旧版本. 97 | 98 | 更多Rstudio的使用，可参考这里[introducing-the-rstudio](https://www.pipinghotdata.com/posts/2020-09-07-introducing-the-rstudio-ide-and-r-markdown/)。 99 | 100 | ## 如何获取帮助{-} 101 | 102 | - 记住和学习所有的函数几乎是不可能的 103 | - 打开函数的帮助页面(`Rstudio`右下面板的`Help`选项卡) 104 | 105 | 106 | 107 | ``` 108 | ?sqrt 109 | ?gather 110 | ?spread 111 | ?ggplot2 112 | ?scale 113 | ?map_dfr 114 | ``` 115 | 116 | 比如： 117 | 118 | ![help帮助](figure/20.png) 119 | 120 | ## R 语言社区{-} 121 | 122 | R 语言社区非常友好，可以在这里找到你问题的答案 123 | 124 | - twitter: https://twitter.com/ 125 | - R-Bloggers: https://www.r-bloggers.com/ 126 | - kaggle: https://www.kaggle.com/ 127 | - stackoverflow: https://stackoverflow.com/questions/tagged/r 128 | - rstudio: https://community.rstudio.com/ 129 | 130 | 131 | 132 | -------------------------------------------------------------------------------- /9990-references.md: -------------------------------------------------------------------------------- 1 | 2 | # 参考书籍{#reference} 3 | 4 | 这里书籍都有线上免费版本，可以点击**书籍名称跳转**。同时感谢**西京学院刘琦老师**对文稿提供的帮助。 5 | 6 | - [R语言基础教程——李东风](https://www.math.pku.edu.cn/teachers/lidf/docs/Rbook/html/_Rbook/graph.html) 7 | 8 | - [数据科学中的R语言——王敏杰](https://bookdown.org/wangminjie/R4DS/intro-R.html#%E5%AE%89%E8%A3%85-rstudio) 9 | 10 | - [ggplot2书](https://ggplot2-book.org/) 11 | 12 | - [ggplot2画廊](https://www.r-graph-gallery.com/ggplot2-package.html) 13 | 14 | - [R数据科学](https://r4ds.had.co.nz/) 15 | 16 | 其他有关**R语言**的书籍可在[**庄闪闪的R语言手册**](https://mp.weixin.qq.com/mp/profile_ext?action=home&__biz=MzI1NjUwMjQxMQ==&scene=124#wechat_redirect)(**可跳转**)命令窗口输入**“R”**获取。也欢迎**关注**我的个人公众号，和我一起学R，统计和数据科学。 17 | 18 | \begin{figure} 19 | 20 | {\centering \includegraphics[width=0.45\linewidth]{figure/vcode} 21 | 22 | } 23 | 24 | \caption{个人公众号：庄闪闪的R语言手册}(\#fig:unnamed-chunk-1) 25 | \end{figure} 26 | 27 | ![公众号内容：可视化，数据科学学习，有趣的R包，R基础视频教程](figure/me.png) 28 | **其他联系方式(可跳转)**： 29 | 30 | - [知乎](https://www.zhihu.com/people/zhuangshanshan) 31 | 32 | - [Github](https://github.com/liangliangzhuang "Github") 33 | 34 | - [CSDN](https://i.csdn.net/#/uc/profile "CSDN") 35 | 36 | - [b站](https://space.bilibili.com/226576305?share_medium=android&share_source=weixin&bbid=XYEE12AEF838D8A42E42282DBF81876CFC7CC&ts=1611217375878) 37 | 38 | 39 | 40 | -------------------------------------------------------------------------------- /CBook.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/liangliangzhuang/R-tutorial/df5f714cf9169b28bf08ecd4a0340ee5f380cb15/CBook.pdf -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # [庄闪闪的可视化笔记](https://liangliangzhuang.github.io/R-tutorial/index.html)（更新中） 2 | 3 | 4 | ## 目录 5 | 6 | ### 第一部分 R 语言基础 7 | 8 | #### 1 Base 系列（待） 9 | 10 | #### 2 Tidyverse 系列（待） 11 | 12 | ### 第二部分 R 语言可视化 13 | 14 | #### 3 [使用基础包绘图](https://liangliangzhuang.github.io/R-tutorial/causal.html) 15 | 16 | 3.1 绘制基本图形 17 | 18 | 3.2 修改图形参数 19 | 20 | 3.3 绘制组合图形 21 | 22 | 3.4 保存图形 23 | 24 | #### 4 [使用 ggplot2 包绘图](https://liangliangzhuang.github.io/R-tutorial/ggplot2-plot.html) 25 | 26 | 4.1 简介 27 | 28 | 4.2 qplot 29 | 30 | 4.3 ggplot2包图形语法 31 | 32 | 4.4 几何对象 33 | 34 | 4.5 统计变换 35 | 36 | 4.6 刻度scale 37 | 38 | 4.7 坐标系 39 | 40 | 4.8 分面 41 | 42 | 4.9 标题、标注、指南、拼接 43 | 44 | 4.10 保存图片 45 | 46 | 4.11 例子 47 | 48 | #### 5 [常用图形](https://liangliangzhuang.github.io/R-tutorial/main-diagram-types.html) 49 | 50 | 5.1 散点图 51 | 52 | 5.2 气泡图 53 | 54 | 5.3 线性图 55 | 56 | 5.4 相关系数图/热力图 57 | 58 | 5.5 条形图 59 | 60 | 5.6 箱线图 61 | 62 | 5.7 小提琴图 63 | 64 | 5.8 饼图 65 | 66 | 5.9 冲积图 67 | 68 | 5.10 系谱图 69 | 70 | 5.11 哑铃图 71 | 72 | 5.12 斜率图 73 | 74 | 5.13 堆叠面积图 75 | 76 | 5.14 棒棒糖图 77 | 78 | 5.15 树状图 79 | 80 | 5.16 瀑布图 81 | 82 | 5.17 双标图 83 | 84 | 5.18 雷达图/星图/蜘蛛图 85 | 86 | 87 | #### 6 [其他相关拓展包](https://liangliangzhuang.github.io/R-tutorial/other-packages.html) 88 | 89 | 6.1 ggplot2 官网 109 种拓展包 90 | 91 | 6.2 整理的相关扩展包 92 | 93 | 94 | ### 第三部分 R 语言文档沟通 95 | 96 | #### 7 [认识交互式绘图工具](https://liangliangzhuang.github.io/R-tutorial/interactive-ploting.html) 97 | 98 | 7.1 leaflet 包 99 | 100 | 7.2 dygraphs 包 101 | 102 | 7.3 plotly 包 103 | 104 | 7.4 DT 包 105 | 106 | 7.5 networkD3 包 107 | 108 | 7.6 利用 Shiny 包实现可交互的 Web 109 | 110 | #### 8 [常用案例](https://liangliangzhuang.github.io/R-tutorial/some-tips-alls.html) 111 | 112 | 8.1绘制不同分布的 QQ 图 113 | 114 | 8.2 绘制混合密度函数图以及添加 115 | 116 | 8.3 绘制不同参数的密度函数 117 | 118 | 8.4 散点图中加入第三变量的密度 119 | 120 | 8.5 绘制 Gamma 分布相关图形 121 | 122 | 8.6 纯手动复现密度图 123 | 124 | 8.7 绘制贝叶斯分析相关图形 125 | 126 | #### 9 [R Markdown 入门教程](https://liangliangzhuang.github.io/R-tutorial/rmarkdown-base.html) 127 | 128 | 9.1 Rmarkdown 简介 129 | 130 | 9.2 Rmarkdown 流程演示 131 | 132 | 9.3 Rmarkdown 的主题格式 133 | 134 | 9.4 总结一些常用技巧 135 | 136 | #### 10 [其他方式的文档沟通](https://liangliangzhuang.github.io/R-tutorial/rmarkdown-extended.html) 137 | 138 | 10.1 Typora 139 | 140 | 10.2 xaringan 幻灯片 141 | 142 | 10.3 制作幻灯片 143 | 144 | 10.4 Rbeamer 145 | 146 | 10.5 Dashboards 147 | 148 | 10.6 shiny 149 | 150 | 10.7 blogdown 151 | 152 | 10.8 制作简历 153 | 154 | 10.9 bookdown 155 | 156 | 10.10 小编有话说 157 | 158 | #### 11 [附录](https://liangliangzhuang.github.io/R-tutorial/appendix.html) 159 | 160 | 安装 R 和 Rstudio 161 | 162 | 可能的问题 163 | 164 | 如何获取帮助 165 | 166 | R 语言社区 167 | 168 | 169 | -------------------------------------------------------------------------------- /figure/10.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/liangliangzhuang/R-tutorial/df5f714cf9169b28bf08ecd4a0340ee5f380cb15/figure/10.png -------------------------------------------------------------------------------- /figure/11.png: -------------------------------------------------------------------------------- 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https://raw.githubusercontent.com/liangliangzhuang/R-tutorial/df5f714cf9169b28bf08ecd4a0340ee5f380cb15/images/paste-E987C1F4.png -------------------------------------------------------------------------------- /images/paste-F27FC37A.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/liangliangzhuang/R-tutorial/df5f714cf9169b28bf08ecd4a0340ee5f380cb15/images/paste-F27FC37A.png -------------------------------------------------------------------------------- /index.md: -------------------------------------------------------------------------------- 1 | --- 2 | title: "庄闪闪的可视化手册" 3 | author: "庄闪闪" 4 | date: "22/7/2022" 5 | description: "这是用R的bookdown功能制作中文图书的模板，输出格式为bookdown::gitbook和bookdown::pdf_book." 6 | documentclass: book 7 | biblio-style: apa 8 | bibliography: [mybib.bib] 9 | link-citations: yes 10 | --- 11 | 12 | 13 | 14 | # 简介 {-} 15 | 16 | 这本电子书是《庄闪闪的可视化笔记》。主要内容来自一次市场调查大赛公益课程的教学内容。 17 | 18 | 19 | 20 | 21 | 22 | 这个文稿主要是在一次公益课上整理出来的。经过一年的时候，小编在实践中添加了一些新的内容，希望能为各位科研人提供一些参考。对应的上课视频如下：[R语言可视化教程](https://www.bilibili.com/video/BV1MA411p7VR?spm_id_from=333.999.0.0)。 23 | 24 | 笔记还会持续更新，读者可以通过我的公众号[《庄闪闪的 R 语言手册》](https://zll-blog.netlify.app/images/wechat.png)了解最新的学习笔记。 25 | 26 | 我是庄闪闪，这是我的[个人博客](https://zll-blog.netlify.app/), 27 | 如果有什么问题，可以通过以下方式联系我： 28 | 29 | [GitHub](https://github.com/liangliangzhuang)、[B 站](https://space.bilibili.com/226576305)、[知乎](https://www.zhihu.com/people/zhuangshanshan)、[CSDN](https://blog.csdn.net/qq_37379316?spm=1011.2124.3001.5343)、[小红书](https://www.xiaohongshu.com/user/profile/597fbfc15e87e755ab15dc26?xhsshare=WeixinSession&appuid=597fbfc15e87e755ab15dc26&apptime=1627016124)、[掘金](https://juejin.cn/user/1689330843128008) 30 | 31 | 32 | 33 | 34 | 35 | 36 | -------------------------------------------------------------------------------- /libs/anchor-sections-1.1.0/anchor-sections-hash.css: -------------------------------------------------------------------------------- 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(max-width: 640px){.dataTables_wrapper .dataTables_length,.dataTables_wrapper .dataTables_filter{float:none;text-align:center}.dataTables_wrapper .dataTables_filter{margin-top:.5em}} 2 | -------------------------------------------------------------------------------- /libs/gitbook-2.6.7/css/fontawesome/fontawesome-webfont.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/liangliangzhuang/R-tutorial/df5f714cf9169b28bf08ecd4a0340ee5f380cb15/libs/gitbook-2.6.7/css/fontawesome/fontawesome-webfont.ttf -------------------------------------------------------------------------------- /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>*:last-child:after { 94 | content: "\25a2"; 95 | float: right; 96 | } 97 | .header-section-number { 98 | padding-right: .5em; 99 | } 100 | #header .multi-author { 101 | margin: 0.5em 0 -0.5em 0; 102 | } 103 | #header .date { 104 | margin-top: 1.5em; 105 | } 106 | -------------------------------------------------------------------------------- /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 | -------------------------------------------------------------------------------- /libs/gitbook-2.6.7/css/plugin-fontsettings.css: -------------------------------------------------------------------------------- 1 | /* 2 | * Theme 1 3 | */ 4 | .color-theme-1 .dropdown-menu { 5 | background-color: #111111; 6 | border-color: #7e888b; 7 | } 8 | .color-theme-1 .dropdown-menu .dropdown-caret .caret-inner { 9 | border-bottom: 9px solid #111111; 10 | } 11 | .color-theme-1 .dropdown-menu .buttons { 12 | border-color: #7e888b; 13 | } 14 | .color-theme-1 .dropdown-menu .button { 15 | color: #afa790; 16 | } 17 | .color-theme-1 .dropdown-menu .button:hover { 18 | color: #73553c; 19 | } 20 | /* 21 | * Theme 2 22 | */ 23 | .color-theme-2 .dropdown-menu { 24 | background-color: #2d3143; 25 | border-color: #272a3a; 26 | } 27 | .color-theme-2 .dropdown-menu .dropdown-caret .caret-inner { 28 | border-bottom: 9px solid #2d3143; 29 | } 30 | .color-theme-2 .dropdown-menu .buttons { 31 | border-color: #272a3a; 32 | } 33 | .color-theme-2 .dropdown-menu .button { 34 | color: #62677f; 35 | } 36 | .color-theme-2 .dropdown-menu .button:hover { 37 | color: #f4f4f5; 38 | } 39 | .book .book-header .font-settings .font-enlarge { 40 | line-height: 30px; 41 | font-size: 1.4em; 42 | } 43 | .book .book-header .font-settings .font-reduce { 44 | line-height: 30px; 45 | font-size: 1em; 46 | } 47 | 48 | /* sidebar transition background */ 49 | div.book.color-theme-1 { 50 | background: #f3eacb; 51 | } 52 | .book.color-theme-1 .book-body { 53 | color: #704214; 54 | background: #f3eacb; 55 | } 56 | .book.color-theme-1 .book-body .page-wrapper .page-inner section { 57 | background: #f3eacb; 58 | } 59 | 60 | /* sidebar transition background */ 61 | div.book.color-theme-2 { 62 | background: #1c1f2b; 63 | } 64 | 65 | .book.color-theme-2 .book-body { 66 | color: #bdcadb; 67 | background: #1c1f2b; 68 | } 69 | .book.color-theme-2 .book-body .page-wrapper .page-inner section { 70 | background: #1c1f2b; 71 | } 72 | .book.font-size-0 .book-body .page-inner section { 73 | font-size: 1.2rem; 74 | } 75 | .book.font-size-1 .book-body .page-inner section { 76 | font-size: 1.4rem; 77 | } 78 | .book.font-size-2 .book-body .page-inner section { 79 | font-size: 1.6rem; 80 | } 81 | .book.font-size-3 .book-body .page-inner section { 82 | font-size: 2.2rem; 83 | } 84 | .book.font-size-4 .book-body .page-inner section { 85 | font-size: 4rem; 86 | } 87 | .book.font-family-0 { 88 | font-family: Georgia, serif; 89 | } 90 | .book.font-family-1 { 91 | font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; 92 | } 93 | .book.color-theme-1 .book-body .page-wrapper .page-inner section.normal { 94 | color: #704214; 95 | } 96 | .book.color-theme-1 .book-body .page-wrapper .page-inner section.normal a { 97 | color: inherit; 98 | } 99 | .book.color-theme-1 .book-body .page-wrapper .page-inner section.normal h1, 100 | .book.color-theme-1 .book-body .page-wrapper .page-inner section.normal h2, 101 | .book.color-theme-1 .book-body .page-wrapper .page-inner section.normal h3, 102 | .book.color-theme-1 .book-body .page-wrapper .page-inner section.normal h4, 103 | .book.color-theme-1 .book-body .page-wrapper .page-inner section.normal h5, 104 | .book.color-theme-1 .book-body .page-wrapper .page-inner section.normal h6 { 105 | color: inherit; 106 | } 107 | .book.color-theme-1 .book-body .page-wrapper .page-inner section.normal h1, 108 | .book.color-theme-1 .book-body .page-wrapper .page-inner section.normal h2 { 109 | border-color: inherit; 110 | } 111 | .book.color-theme-1 .book-body .page-wrapper .page-inner section.normal h6 { 112 | color: inherit; 113 | } 114 | .book.color-theme-1 .book-body .page-wrapper .page-inner section.normal hr { 115 | background-color: inherit; 116 | } 117 | .book.color-theme-1 .book-body .page-wrapper .page-inner section.normal blockquote { 118 | border-color: #c4b29f; 119 | opacity: 0.9; 120 | } 121 | .book.color-theme-1 .book-body .page-wrapper .page-inner section.normal pre, 122 | .book.color-theme-1 .book-body .page-wrapper .page-inner section.normal code { 123 | background: #fdf6e3; 124 | color: #657b83; 125 | border-color: #f8df9c; 126 | } 127 | .book.color-theme-1 .book-body .page-wrapper .page-inner section.normal .highlight { 128 | background-color: inherit; 129 | } 130 | .book.color-theme-1 .book-body .page-wrapper .page-inner section.normal table th, 131 | .book.color-theme-1 .book-body .page-wrapper .page-inner section.normal table td { 132 | border-color: #f5d06c; 133 | } 134 | .book.color-theme-1 .book-body .page-wrapper .page-inner section.normal table tr { 135 | color: inherit; 136 | background-color: #fdf6e3; 137 | border-color: #444444; 138 | } 139 | .book.color-theme-1 .book-body .page-wrapper .page-inner section.normal table tr:nth-child(2n) { 140 | background-color: #fbeecb; 141 | } 142 | .book.color-theme-2 .book-body .page-wrapper .page-inner section.normal { 143 | color: #bdcadb; 144 | } 145 | .book.color-theme-2 .book-body .page-wrapper .page-inner section.normal a { 146 | color: #3eb1d0; 147 | } 148 | .book.color-theme-2 .book-body .page-wrapper .page-inner section.normal h1, 149 | .book.color-theme-2 .book-body .page-wrapper .page-inner section.normal h2, 150 | .book.color-theme-2 .book-body .page-wrapper .page-inner section.normal h3, 151 | .book.color-theme-2 .book-body .page-wrapper .page-inner section.normal h4, 152 | .book.color-theme-2 .book-body .page-wrapper .page-inner section.normal h5, 153 | .book.color-theme-2 .book-body .page-wrapper .page-inner section.normal h6 { 154 | color: #fffffa; 155 | } 156 | .book.color-theme-2 .book-body .page-wrapper .page-inner section.normal h1, 157 | .book.color-theme-2 .book-body .page-wrapper .page-inner section.normal h2 { 158 | border-color: #373b4e; 159 | } 160 | .book.color-theme-2 .book-body .page-wrapper .page-inner section.normal h6 { 161 | color: #373b4e; 162 | } 163 | .book.color-theme-2 .book-body .page-wrapper .page-inner section.normal hr { 164 | background-color: #373b4e; 165 | } 166 | .book.color-theme-2 .book-body .page-wrapper .page-inner section.normal blockquote { 167 | border-color: #373b4e; 168 | } 169 | .book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre, 170 | .book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code { 171 | color: #9dbed8; 172 | background: #2d3143; 173 | border-color: #2d3143; 174 | } 175 | .book.color-theme-2 .book-body .page-wrapper .page-inner section.normal .highlight { 176 | background-color: #282a39; 177 | } 178 | .book.color-theme-2 .book-body .page-wrapper .page-inner section.normal table th, 179 | .book.color-theme-2 .book-body .page-wrapper .page-inner section.normal table td { 180 | border-color: #3b3f54; 181 | } 182 | .book.color-theme-2 .book-body .page-wrapper .page-inner section.normal table tr { 183 | color: #b6c2d2; 184 | background-color: #2d3143; 185 | border-color: #3b3f54; 186 | } 187 | .book.color-theme-2 .book-body .page-wrapper .page-inner section.normal table tr:nth-child(2n) { 188 | background-color: #35394b; 189 | } 190 | .book.color-theme-1 .book-header { 191 | color: #afa790; 192 | background: transparent; 193 | } 194 | .book.color-theme-1 .book-header .btn { 195 | color: #afa790; 196 | } 197 | .book.color-theme-1 .book-header .btn:hover { 198 | color: #73553c; 199 | background: none; 200 | } 201 | .book.color-theme-1 .book-header h1 { 202 | color: #704214; 203 | } 204 | .book.color-theme-2 .book-header { 205 | color: #7e888b; 206 | background: transparent; 207 | } 208 | .book.color-theme-2 .book-header .btn { 209 | color: #3b3f54; 210 | } 211 | .book.color-theme-2 .book-header .btn:hover { 212 | color: #fffff5; 213 | background: none; 214 | } 215 | .book.color-theme-2 .book-header h1 { 216 | color: #bdcadb; 217 | } 218 | .book.color-theme-1 .book-body .navigation { 219 | color: #afa790; 220 | } 221 | .book.color-theme-1 .book-body .navigation:hover { 222 | color: #73553c; 223 | } 224 | .book.color-theme-2 .book-body .navigation { 225 | color: #383f52; 226 | } 227 | .book.color-theme-2 .book-body .navigation:hover { 228 | color: #fffff5; 229 | } 230 | /* 231 | * Theme 1 232 | */ 233 | .book.color-theme-1 .book-summary { 234 | color: #afa790; 235 | background: #111111; 236 | border-right: 1px solid rgba(0, 0, 0, 0.07); 237 | } 238 | .book.color-theme-1 .book-summary .book-search { 239 | background: transparent; 240 | } 241 | .book.color-theme-1 .book-summary .book-search input, 242 | .book.color-theme-1 .book-summary .book-search input:focus { 243 | border: 1px solid transparent; 244 | } 245 | .book.color-theme-1 .book-summary ul.summary li.divider { 246 | background: #7e888b; 247 | box-shadow: none; 248 | } 249 | .book.color-theme-1 .book-summary ul.summary li i.fa-check { 250 | color: #33cc33; 251 | } 252 | .book.color-theme-1 .book-summary ul.summary li.done > a { 253 | color: #877f6a; 254 | } 255 | .book.color-theme-1 .book-summary ul.summary li a, 256 | .book.color-theme-1 .book-summary ul.summary li span { 257 | color: #877f6a; 258 | background: transparent; 259 | font-weight: normal; 260 | } 261 | .book.color-theme-1 .book-summary ul.summary li.active > a, 262 | .book.color-theme-1 .book-summary ul.summary li a:hover { 263 | color: #704214; 264 | background: transparent; 265 | font-weight: normal; 266 | } 267 | /* 268 | * Theme 2 269 | */ 270 | .book.color-theme-2 .book-summary { 271 | color: #bcc1d2; 272 | background: #2d3143; 273 | border-right: none; 274 | } 275 | .book.color-theme-2 .book-summary .book-search { 276 | background: transparent; 277 | } 278 | .book.color-theme-2 .book-summary .book-search input, 279 | .book.color-theme-2 .book-summary .book-search input:focus { 280 | border: 1px solid transparent; 281 | } 282 | .book.color-theme-2 .book-summary ul.summary li.divider { 283 | background: #272a3a; 284 | box-shadow: none; 285 | } 286 | .book.color-theme-2 .book-summary ul.summary li i.fa-check { 287 | color: #33cc33; 288 | } 289 | .book.color-theme-2 .book-summary ul.summary li.done > a { 290 | color: #62687f; 291 | } 292 | .book.color-theme-2 .book-summary ul.summary li a, 293 | .book.color-theme-2 .book-summary ul.summary li span { 294 | color: #c1c6d7; 295 | background: transparent; 296 | font-weight: 600; 297 | } 298 | .book.color-theme-2 .book-summary ul.summary li.active > a, 299 | .book.color-theme-2 .book-summary ul.summary li a:hover { 300 | color: #f4f4f5; 301 | background: #252737; 302 | font-weight: 600; 303 | } 304 | -------------------------------------------------------------------------------- /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 | -------------------------------------------------------------------------------- /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 | -------------------------------------------------------------------------------- /libs/gitbook-2.6.7/js/clipboard.min.js: -------------------------------------------------------------------------------- 1 | /*! 2 | * clipboard.js v2.0.4 3 | * https://zenorocha.github.io/clipboard.js 4 | * 5 | * Licensed MIT © Zeno Rocha 6 | */ 7 | !function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return function(n){var o={};function r(t){if(o[t])return o[t].exports;var e=o[t]={i:t,l:!1,exports:{}};return n[t].call(e.exports,e,e.exports,r),e.l=!0,e.exports}return r.m=n,r.c=o,r.d=function(t,e,n){r.o(t,e)||Object.defineProperty(t,e,{enumerable:!0,get:n})},r.r=function(t){"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(t,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(t,"__esModule",{value:!0})},r.t=function(e,t){if(1&t&&(e=r(e)),8&t)return e;if(4&t&&"object"==typeof e&&e&&e.__esModule)return e;var n=Object.create(null);if(r.r(n),Object.defineProperty(n,"default",{enumerable:!0,value:e}),2&t&&"string"!=typeof e)for(var o in e)r.d(n,o,function(t){return e[t]}.bind(null,o));return n},r.n=function(t){var e=t&&t.__esModule?function(){return t.default}:function(){return t};return r.d(e,"a",e),e},r.o=function(t,e){return Object.prototype.hasOwnProperty.call(t,e)},r.p="",r(r.s=0)}([function(t,e,n){"use strict";var r="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(t){return typeof t}:function(t){return t&&"function"==typeof Symbol&&t.constructor===Symbol&&t!==Symbol.prototype?"symbol":typeof t},i=function(){function o(t,e){for(var n=0;n indicates arrow keys):', 82 | '/: navigate to previous/next page', 83 | 's: Toggle sidebar']; 84 | if (config.search !== false) info.push('f: Toggle search input ' + 85 | '(use //Enter in the search input to navigate through search matches; ' + 86 | 'press Esc to cancel search)'); 87 | if (config.info !== false) gitbook.toolbar.createButton({ 88 | icon: 'fa fa-info', 89 | label: 'Information about the toolbar', 90 | position: 'left', 91 | onClick: function(e) { 92 | e.preventDefault(); 93 | window.alert(info.join('\n\n')); 94 | } 95 | }); 96 | 97 | // highlight the current section in TOC 98 | var href = window.location.pathname; 99 | href = href.substr(href.lastIndexOf('/') + 1); 100 | // accentuated characters need to be decoded (#819) 101 | href = decodeURIComponent(href); 102 | if (href === '') href = 'index.html'; 103 | var li = $('a[href^="' + href + location.hash + '"]').parent('li.chapter').first(); 104 | var summary = $('ul.summary'), chaps = summary.find('li.chapter'); 105 | if (li.length === 0) li = chaps.first(); 106 | li.addClass('active'); 107 | chaps.on('click', function(e) { 108 | chaps.removeClass('active'); 109 | $(this).addClass('active'); 110 | gs.set('tocScrollTop', summary.scrollTop()); 111 | }); 112 | 113 | var toc = config.toc; 114 | // collapse TOC items that are not for the current chapter 115 | if (toc && toc.collapse) (function() { 116 | var type = toc.collapse; 117 | if (type === 'none') return; 118 | if (type !== 'section' && type !== 'subsection') return; 119 | // sections under chapters 120 | var toc_sub = summary.children('li[data-level]').children('ul'); 121 | if (type === 'section') { 122 | toc_sub.hide() 123 | .parent().has(li).children('ul').show(); 124 | } else { 125 | toc_sub.children('li').children('ul').hide() 126 | .parent().has(li).children('ul').show(); 127 | } 128 | li.children('ul').show(); 129 | var toc_sub2 = toc_sub.children('li'); 130 | if (type === 'section') toc_sub2.children('ul').hide(); 131 | summary.children('li[data-level]').find('a') 132 | .on('click.bookdown', function(e) { 133 | if (href === $(this).attr('href').replace(/#.*/, '')) 134 | $(this).parent('li').children('ul').toggle(); 135 | }); 136 | })(); 137 | 138 | // add tooltips to the 's that are truncated 139 | $('a').each(function(i, el) { 140 | if (el.offsetWidth >= el.scrollWidth) return; 141 | if (typeof el.title === 'undefined') return; 142 | el.title = el.text; 143 | }); 144 | 145 | // restore TOC scroll position 146 | var pos = gs.get('tocScrollTop'); 147 | if (typeof pos !== 'undefined') summary.scrollTop(pos); 148 | 149 | // highlight the TOC item that has same text as the heading in view as scrolling 150 | if (toc && toc.scroll_highlight !== false && li.length > 0) (function() { 151 | // scroll the current TOC item into viewport 152 | var ht = $(window).height(), rect = li[0].getBoundingClientRect(); 153 | if (rect.top >= ht || rect.top <= 0 || rect.bottom <= 0) { 154 | summary.scrollTop(li[0].offsetTop); 155 | } 156 | // current chapter TOC items 157 | var items = $('a[href^="' + href + '"]').parent('li.chapter'), 158 | m = items.length; 159 | if (m === 0) { 160 | items = summary.find('li.chapter'); 161 | m = items.length; 162 | } 163 | if (m === 0) return; 164 | // all section titles on current page 165 | var hs = bookInner.find('.page-inner').find('h1,h2,h3'), n = hs.length, 166 | ts = hs.map(function(i, el) { return $(el).text(); }); 167 | if (n === 0) return; 168 | var scrollHandler = function(e) { 169 | var ht = $(window).height(); 170 | clearTimeout($.data(this, 'scrollTimer')); 171 | $.data(this, 'scrollTimer', setTimeout(function() { 172 | // find the first visible title in the viewport 173 | for (var i = 0; i < n; i++) { 174 | var rect = hs[i].getBoundingClientRect(); 175 | if (rect.top >= 0 && rect.bottom <= ht) break; 176 | } 177 | if (i === n) return; 178 | items.removeClass('active'); 179 | for (var j = 0; j < m; j++) { 180 | if (items.eq(j).children('a').first().text() === ts[i]) break; 181 | } 182 | if (j === m) j = 0; // highlight the chapter title 183 | // search bottom-up for a visible TOC item to highlight; if an item is 184 | // hidden, we check if its parent is visible, and so on 185 | while (j > 0 && items.eq(j).is(':hidden')) j--; 186 | items.eq(j).addClass('active'); 187 | }, 250)); 188 | }; 189 | bookInner.on('scroll.bookdown', scrollHandler); 190 | bookBody.on('scroll.bookdown', scrollHandler); 191 | })(); 192 | 193 | // do not refresh the page if the TOC item points to the current page 194 | $('a[href="' + href + '"]').parent('li.chapter').children('a') 195 | .on('click', function(e) { 196 | bookInner.scrollTop(0); 197 | bookBody.scrollTop(0); 198 | return false; 199 | }); 200 | 201 | var toolbar = config.toolbar; 202 | if (!toolbar || toolbar.position !== 'static') { 203 | var bookHeader = $('.book-header'); 204 | bookBody.addClass('fixed'); 205 | bookHeader.addClass('fixed') 206 | .css('background-color', bookBody.css('background-color')) 207 | .on('click.bookdown', function(e) { 208 | // the theme may have changed after user clicks the theme button 209 | bookHeader.css('background-color', bookBody.css('background-color')); 210 | }); 211 | } 212 | 213 | }); 214 | 215 | gitbook.events.bind("page.change", function(e) { 216 | // store TOC scroll position 217 | var summary = $('ul.summary'); 218 | gs.set('tocScrollTop', summary.scrollTop()); 219 | }); 220 | 221 | var bookBody = $('.book-body'), bookInner = bookBody.find('.body-inner'); 222 | var chapterTitle = function() { 223 | return bookInner.find('.page-inner').find('h1,h2').first().text(); 224 | }; 225 | var saveScrollPos = function(e) { 226 | // save scroll position before page is reloaded 227 | gs.set('bodyScrollTop', { 228 | body: bookBody.scrollTop(), 229 | inner: bookInner.scrollTop(), 230 | focused: document.hasFocus(), 231 | title: chapterTitle() 232 | }); 233 | }; 234 | $(document).on('servr:reload', saveScrollPos); 235 | 236 | // check if the page is loaded in an iframe (e.g. the RStudio preview window) 237 | var inIFrame = function() { 238 | var inIframe = true; 239 | try { inIframe = window.self !== window.top; } catch (e) {} 240 | return inIframe; 241 | }; 242 | if (inIFrame()) { 243 | $(window).on('blur unload', saveScrollPos); 244 | } 245 | 246 | $(function(e) { 247 | var pos = gs.get('bodyScrollTop'); 248 | if (pos) { 249 | if (pos.title === chapterTitle()) { 250 | if (pos.body !== 0) bookBody.scrollTop(pos.body); 251 | if (pos.inner !== 0) bookInner.scrollTop(pos.inner); 252 | } 253 | } 254 | if ((pos && pos.focused) || !inIFrame()) bookInner.find('.page-wrapper').focus(); 255 | // clear book body scroll position 256 | gs.remove('bodyScrollTop'); 257 | }); 258 | 259 | }); 260 | -------------------------------------------------------------------------------- /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 | -------------------------------------------------------------------------------- /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 | -------------------------------------------------------------------------------- /libs/gitbook-2.6.7/js/plugin-search.js: -------------------------------------------------------------------------------- 1 | gitbook.require(["gitbook", "lodash", "jQuery"], function(gitbook, _, $) { 2 | var index = null; 3 | var fuse = null; 4 | var _search = {engine: 'lunr', opts: {}}; 5 | var $searchInput, $searchLabel, $searchForm; 6 | var $highlighted = [], hi, hiOpts = { className: 'search-highlight' }; 7 | var collapse = false, toc_visible = []; 8 | 9 | function init(config) { 10 | // Instantiate search settings 11 | _search = gitbook.storage.get("search", { 12 | engine: config.search.engine || 'lunr', 13 | opts: config.search.options || {}, 14 | }); 15 | }; 16 | 17 | // Save current search settings 18 | function saveSearchSettings() { 19 | gitbook.storage.set("search", _search); 20 | } 21 | 22 | // Use a specific index 23 | function loadIndex(data) { 24 | // [Yihui] In bookdown, I use a character matrix to store the chapter 25 | // content, and the index is dynamically built on the client side. 26 | // Gitbook prebuilds the index data instead: https://github.com/GitbookIO/plugin-search 27 | // We can certainly do that via R packages V8 and jsonlite, but let's 28 | // see how slow it really is before improving it. On the other hand, 29 | // lunr cannot handle non-English text very well, e.g. the default 30 | // tokenizer cannot deal with Chinese text, so we may want to replace 31 | // lunr with a dumb simple text matching approach. 32 | if (_search.engine === 'lunr') { 33 | index = lunr(function () { 34 | this.ref('url'); 35 | this.field('title', { boost: 10 }); 36 | this.field('body'); 37 | }); 38 | data.map(function(item) { 39 | index.add({ 40 | url: item[0], 41 | title: item[1], 42 | body: item[2] 43 | }); 44 | }); 45 | return; 46 | } 47 | fuse = new Fuse(data.map((_data => { 48 | return { 49 | url: _data[0], 50 | title: _data[1], 51 | body: _data[2] 52 | }; 53 | })), Object.assign( 54 | { 55 | includeScore: true, 56 | threshold: 0.1, 57 | ignoreLocation: true, 58 | keys: ["title", "body"] 59 | }, 60 | _search.opts 61 | )); 62 | } 63 | 64 | // Fetch the search index 65 | function fetchIndex() { 66 | return $.getJSON(gitbook.state.basePath+"/search_index.json") 67 | .then(loadIndex); // [Yihui] we need to use this object later 68 | } 69 | 70 | // Search for a term and return results 71 | function search(q) { 72 | let results = []; 73 | switch (_search.engine) { 74 | case 'fuse': 75 | if (!fuse) return; 76 | results = fuse.search(q).map(function(result) { 77 | var parts = result.item.url.split('#'); 78 | return { 79 | path: parts[0], 80 | hash: parts[1] 81 | }; 82 | }); 83 | break; 84 | case 'lunr': 85 | default: 86 | if (!index) return; 87 | results = _.chain(index.search(q)).map(function(result) { 88 | var parts = result.ref.split("#"); 89 | return { 90 | path: parts[0], 91 | hash: parts[1] 92 | }; 93 | }) 94 | .value(); 95 | } 96 | 97 | // [Yihui] Highlight the search keyword on current page 98 | $highlighted = $('.page-inner') 99 | .unhighlight(hiOpts).highlight(q, hiOpts).find('span.search-highlight'); 100 | scrollToHighlighted(0); 101 | 102 | return results; 103 | } 104 | 105 | // [Yihui] Scroll the chapter body to the i-th highlighted string 106 | function scrollToHighlighted(d) { 107 | var n = $highlighted.length; 108 | hi = hi === undefined ? 0 : hi + d; 109 | // navignate to the previous/next page in the search results if reached the top/bottom 110 | var b = hi < 0; 111 | if (d !== 0 && (b || hi >= n)) { 112 | var path = currentPath(), n2 = toc_visible.length; 113 | if (n2 === 0) return; 114 | for (var i = b ? 0 : n2; (b && i < n2) || (!b && i >= 0); i += b ? 1 : -1) { 115 | if (toc_visible.eq(i).data('path') === path) break; 116 | } 117 | i += b ? -1 : 1; 118 | if (i < 0) i = n2 - 1; 119 | if (i >= n2) i = 0; 120 | var lnk = toc_visible.eq(i).find('a[href$=".html"]'); 121 | if (lnk.length) lnk[0].click(); 122 | return; 123 | } 124 | if (n === 0) return; 125 | var $p = $highlighted.eq(hi); 126 | $p[0].scrollIntoView(); 127 | $highlighted.css('background-color', ''); 128 | // an orange background color on the current item and removed later 129 | $p.css('background-color', 'orange'); 130 | setTimeout(function() { 131 | $p.css('background-color', ''); 132 | }, 2000); 133 | } 134 | 135 | function currentPath() { 136 | var href = window.location.pathname; 137 | href = href.substr(href.lastIndexOf('/') + 1); 138 | return href === '' ? 'index.html' : href; 139 | } 140 | 141 | // Create search form 142 | function createForm(value) { 143 | if ($searchForm) $searchForm.remove(); 144 | if ($searchLabel) $searchLabel.remove(); 145 | if ($searchInput) $searchInput.remove(); 146 | 147 | $searchForm = $('
', { 148 | 'class': 'book-search', 149 | 'role': 'search' 150 | }); 151 | 152 | $searchLabel = $('