From c8fc9a8f4dc41f7b03b98dbadbb69aa812ad9df2 Mon Sep 17 00:00:00 2001 From: willferris30 <143441609+willferris30@users.noreply.github.com> Date: Fri, 23 Jan 2026 14:36:10 -0500 Subject: [PATCH] Add files via upload --- presentations/jan23pres.Rmd | 636 ++++++++++++++++++++++++ presentations/jan23pres.html | 920 +++++++++++++++++++++++++++++++++++ 2 files changed, 1556 insertions(+) create mode 100644 presentations/jan23pres.Rmd create mode 100644 presentations/jan23pres.html diff --git a/presentations/jan23pres.Rmd b/presentations/jan23pres.Rmd new file mode 100644 index 0000000..329a7d7 --- /dev/null +++ b/presentations/jan23pres.Rmd @@ -0,0 +1,636 @@ +--- +title: "Test slides" +subtitle: "⚔
with xaringan" +author: "Will Ferris" +institute: "RStudio, PBC" +date: "Jan 23, 2026 (updated: `r Sys.Date()`)" +output: + xaringan::moon_reader: + lib_dir: libs + nature: + highlightStyle: github + highlightLines: true + countIncrementalSlides: false +--- + +background-image: url(https://upload.wikimedia.org/wikipedia/commons/b/be/Sharingan_triple.svg) + +```{r setup, include=FALSE} +options(htmltools.dir.version = FALSE) +``` + +??? + +Image credit: [Wikimedia Commons](https://commons.wikimedia.org/wiki/File:Sharingan_triple.svg) + +--- +class: center, middle + +# This is a test presentation. + +### /ʃaː.'riŋ.ɡan/ + +--- +class: inverse, center, middle + +# Get Started + +--- + +# Hello World + +Install the **xaringan** package from [Github](https://github.com/yihui/xaringan): + +```{r eval=FALSE, tidy=FALSE} +remotes::install_github("yihui/xaringan") +``` + +-- + +You are recommended to use the [RStudio IDE](https://www.rstudio.com/products/rstudio/), but you do not have to. + +- Create a new R Markdown document from the menu `File -> New File -> R Markdown -> From Template -> Ninja Presentation`;1 + +-- + +- Click the `Knit` button to compile it; + +-- + +- or use the [RStudio Addin](https://rstudio.github.io/rstudioaddins/)2 "Infinite Moon Reader" to live preview the slides (every time you update and save the Rmd document, the slides will be automatically reloaded in RStudio Viewer. + +.footnote[ +[1] 中文用户请看[这份教程](https://slides.yihui.org/xaringan/zh-CN.html) + +[2] See [#2](https://github.com/yihui/xaringan/issues/2) if you do not see the template or addin in RStudio. +] + +--- +background-image: url(`r xaringan:::karl`) +background-position: 50% 50% +class: center, bottom, inverse + +# You only live once! + +--- + +# Hello Ninja + +As a presentation ninja, you certainly should not be satisfied by the "Hello World" example. You need to understand more about two things: + +1. The [remark.js](https://remarkjs.com) library; + +1. The **xaringan** package; + +Basically **xaringan** injected the chakra of R Markdown (minus Pandoc) into **remark.js**. The slides are rendered by remark.js in the web browser, and the Markdown source needed by remark.js is generated from R Markdown (**knitr**). + +--- + +# remark.js + +You can see an introduction of remark.js from [its homepage](https://remarkjs.com). You should read the [remark.js Wiki](https://github.com/gnab/remark/wiki) at least once to know how to + +- create a new slide (Markdown syntax* and slide properties); + +- format a slide (e.g. text alignment); + +- configure the slideshow; + +- and use the presentation (keyboard shortcuts). + +It is important to be familiar with remark.js before you can understand the options in **xaringan**. + +.footnote[[*] It is different with Pandoc's Markdown! It is limited but should be enough for presentation purposes. Come on... You do not need a slide for the Table of Contents! Well, the Markdown support in remark.js [may be improved](https://github.com/gnab/remark/issues/142) in the future.] + +--- +background-image: url(`r xaringan:::karl`) +background-size: cover +class: center, bottom, inverse + +# I was so happy to have discovered remark.js! + +--- +class: inverse, middle, center + +# Using xaringan + +--- + +# xaringan + +Provides an R Markdown output format `xaringan::moon_reader` as a wrapper for remark.js, and you can use it in the YAML metadata, e.g. + +```yaml +--- +title: "A Cool Presentation" +output: + xaringan::moon_reader: + yolo: true + nature: + autoplay: 30000 +--- +``` + +See the help page `?xaringan::moon_reader` for all possible options that you can use. + +--- + +# remark.js vs xaringan + +Some differences between using remark.js (left) and using **xaringan** (right): + +.pull-left[ +1. Start with a boilerplate HTML file; + +1. Plain Markdown; + +1. Write JavaScript to autoplay slides; + +1. Manually configure MathJax; + +1. Highlight code with `*`; + +1. Edit Markdown source and refresh browser to see updated slides; +] + +.pull-right[ +1. Start with an R Markdown document; + +1. R Markdown (can embed R/other code chunks); + +1. Provide an option `autoplay`; + +1. MathJax just works;* + +1. Highlight code with `{{}}`; + +1. The RStudio addin "Infinite Moon Reader" automatically refreshes slides on changes; +] + +.footnote[[*] Not really. See next page.] + +--- + +# Math Expressions + +You can write LaTeX math expressions inside a pair of dollar signs, e.g. $\alpha+\beta$ renders $\alpha+\beta$. You can use the display style with double dollar signs: + +``` +$$\bar{X}=\frac{1}{n}\sum_{i=1}^nX_i$$ +``` + +$$\bar{X}=\frac{1}{n}\sum_{i=1}^nX_i$$ + +Limitations: + +1. The source code of a LaTeX math expression must be in one line, unless it is inside a pair of double dollar signs, in which case the starting `$$` must appear in the very beginning of a line, followed immediately by a non-space character, and the ending `$$` must be at the end of a line, led by a non-space character; + +1. There should not be spaces after the opening `$` or before the closing `$`. + +1. Math does not work on the title slide (see [#61](https://github.com/yihui/xaringan/issues/61) for a workaround). + +--- + +# R Code + +```{r comment='#'} +# a boring regression +fit = lm(dist ~ 1 + speed, data = cars) +coef(summary(fit)) +dojutsu = c('地爆天星', '天照', '加具土命', '神威', '須佐能乎', '無限月読') +grep('天', dojutsu, value = TRUE) +``` + +--- + +# R Plots + +```{r cars, fig.height=4, dev='svg'} +par(mar = c(4, 4, 1, .1)) +plot(cars, pch = 19, col = 'darkgray', las = 1) +abline(fit, lwd = 2) +``` + +--- + +# Tables + +If you want to generate a table, make sure it is in the HTML format (instead of Markdown or other formats), e.g., + +```{r} +knitr::kable(head(iris), format = 'html') +``` + +--- + +# HTML Widgets + +I have not thoroughly tested HTML widgets against **xaringan**. Some may work well, and some may not. It is a little tricky. + +Similarly, the Shiny mode (`runtime: shiny`) does not work. I might get these issues fixed in the future, but these are not of high priority to me. I never turn my presentation into a Shiny app. When I need to demonstrate more complicated examples, I just launch them separately. It is convenient to share slides with other people when they are plain HTML/JS applications. + +See the next page for two HTML widgets. + +--- + +```{r out.width='100%', fig.height=6, eval=require('leaflet')} +library(leaflet) +leaflet() %>% addTiles() %>% setView(-93.65, 42.0285, zoom = 17) +``` + +--- + +```{r eval=require('DT'), tidy=FALSE} +DT::datatable( + head(iris, 10), + fillContainer = FALSE, options = list(pageLength = 8) +) +``` + +--- + +# Some Tips + +- Do not forget to try the `yolo` option of `xaringan::moon_reader`. + + ```yaml + output: + xaringan::moon_reader: + yolo: true + ``` + +--- + +# Some Tips + +- Slides can be automatically played if you set the `autoplay` option under `nature`, e.g. go to the next slide every 30 seconds in a lightning talk: + + ```yaml + output: + xaringan::moon_reader: + nature: + autoplay: 30000 + ``` + +- If you want to restart the play after it reaches the last slide, you may set the sub-option `loop` to TRUE, e.g., + + ```yaml + output: + xaringan::moon_reader: + nature: + autoplay: + interval: 30000 + loop: true + ``` + +--- + +# Some Tips + +- A countdown timer can be added to every page of the slides using the `countdown` option under `nature`, e.g. if you want to spend one minute on every page when you give the talk, you can set: + + ```yaml + output: + xaringan::moon_reader: + nature: + countdown: 60000 + ``` + + Then you will see a timer counting down from `01:00`, to `00:59`, `00:58`, ... When the time is out, the timer will continue but the time turns red. + +--- + +# Some Tips + +- The title slide is created automatically by **xaringan**, but it is just another remark.js slide added before your other slides. + + The title slide is set to `class: center, middle, inverse, title-slide` by default. You can change the classes applied to the title slide with the `titleSlideClass` option of `nature` (`title-slide` is always applied). + + ```yaml + output: + xaringan::moon_reader: + nature: + titleSlideClass: [top, left, inverse] + ``` + +-- + +- If you'd like to create your own title slide, disable **xaringan**'s title slide with the `seal = FALSE` option of `moon_reader`. + + ```yaml + output: + xaringan::moon_reader: + seal: false + ``` + +--- + +# Some Tips + +- There are several ways to build incremental slides. See [this presentation](https://slides.yihui.org/xaringan/incremental.html) for examples. + +- The option `highlightLines: true` of `nature` will highlight code lines that start with `*`, or are wrapped in `{{ }}`, or have trailing comments `#<<`; + + ```yaml + output: + xaringan::moon_reader: + nature: + highlightLines: true + ``` + + See examples on the next page. + +--- + +# Some Tips + + +.pull-left[ +An example using a leading `*`: + + ```r + if (TRUE) { + ** message("Very important!") + } + ``` +Output: +```r +if (TRUE) { +* message("Very important!") +} +``` + +This is invalid R code, so it is a plain fenced code block that is not executed. +] + +.pull-right[ +An example using `{{}}`: + +```` +`r ''````{r tidy=FALSE} +if (TRUE) { +*{{ message("Very important!") }} +} +``` +```` +Output: +```{r tidy=FALSE} +if (TRUE) { +{{ message("Very important!") }} +} +``` + +It is valid R code so you can run it. Note that `{{}}` can wrap an R expression of multiple lines. +] + +--- + +# Some Tips + +An example of using the trailing comment `#<<` to highlight lines: + +````markdown +`r ''````{r tidy=FALSE} +library(ggplot2) +ggplot(mtcars) + + aes(mpg, disp) + + geom_point() + #<< + geom_smooth() #<< +``` +```` + +Output: + +```{r tidy=FALSE, eval=FALSE} +library(ggplot2) +ggplot(mtcars) + + aes(mpg, disp) + + geom_point() + #<< + geom_smooth() #<< +``` + +--- + +# Some Tips + +When you enable line-highlighting, you can also use the chunk option `highlight.output` to highlight specific lines of the text output from a code chunk. For example, `highlight.output = TRUE` means highlighting all lines, and `highlight.output = c(1, 3)` means highlighting the first and third line. + +````md +`r ''````{r, highlight.output=c(1, 3)} +head(iris) +``` +```` + +```{r, highlight.output=c(1, 3), echo=FALSE} +head(iris) +``` + +Question: what does `highlight.output = c(TRUE, FALSE)` mean? (Hint: think about R's recycling of vectors) + +--- + +# Some Tips + +- To make slides work offline, you need to download a copy of remark.js in advance, because **xaringan** uses the online version by default (see the help page `?xaringan::moon_reader`). + +- You can use `xaringan::summon_remark()` to download the latest or a specified version of remark.js. By default, it is downloaded to `libs/remark-latest.min.js`. + +- Then change the `chakra` option in YAML to point to this file, e.g. + + ```yaml + output: + xaringan::moon_reader: + chakra: libs/remark-latest.min.js + ``` + +- If you used Google fonts in slides (the default theme uses _Yanone Kaffeesatz_, _Droid Serif_, and _Source Code Pro_), they won't work offline unless you download or install them locally. The Heroku app [google-webfonts-helper](https://google-webfonts-helper.herokuapp.com/fonts) can help you download fonts and generate the necessary CSS. + +--- + +# Macros + +- remark.js [allows users to define custom macros](https://github.com/yihui/xaringan/issues/80) (JS functions) that can be applied to Markdown text using the syntax `![:macroName arg1, arg2, ...]` or `![:macroName arg1, arg2, ...](this)`. For example, before remark.js initializes the slides, you can define a macro named `scale`: + + ```js + remark.macros.scale = function (percentage) { + var url = this; + return ''; + }; + ``` + + Then the Markdown text + + ```markdown + ![:scale 50%](image.jpg) + ``` + + will be translated to + + ```html + + ``` + +--- + +# Macros (continued) + +- To insert macros in **xaringan** slides, you can use the option `beforeInit` under the option `nature`, e.g., + + ```yaml + output: + xaringan::moon_reader: + nature: + beforeInit: "macros.js" + ``` + + You save your remark.js macros in the file `macros.js`. + +- The `beforeInit` option can be used to insert arbitrary JS code before `remark.create()`. Inserting macros is just one of its possible applications. + +--- + +# CSS + +Among all options in `xaringan::moon_reader`, the most challenging but perhaps also the most rewarding one is `css`, because it allows you to customize the appearance of your slides using any CSS rules or hacks you know. + +You can see the default CSS file [here](https://github.com/yihui/xaringan/blob/master/inst/rmarkdown/templates/xaringan/resources/default.css). You can completely replace it with your own CSS files, or define new rules to override the default. See the help page `?xaringan::moon_reader` for more information. + +--- + +# CSS + +For example, suppose you want to change the font for code from the default "Source Code Pro" to "Ubuntu Mono". You can create a CSS file named, say, `ubuntu-mono.css`: + +```css +@import url(https://fonts.googleapis.com/css?family=Ubuntu+Mono:400,700,400italic); + +.remark-code, .remark-inline-code { font-family: 'Ubuntu Mono'; } +``` + +Then set the `css` option in the YAML metadata: + +```yaml +output: + xaringan::moon_reader: + css: ["default", "ubuntu-mono.css"] +``` + +Here I assume `ubuntu-mono.css` is under the same directory as your Rmd. + +See [yihui/xaringan#83](https://github.com/yihui/xaringan/issues/83) for an example of using the [Fira Code](https://github.com/tonsky/FiraCode) font, which supports ligatures in program code. + +--- + +# CSS (with Sass) + +**xaringan** also supports Sass support via **rmarkdown**. Suppose you want to use the same color for different elements, e.g., first heading and bold text. You can create a `.scss` file, say `mytheme.scss`, using the [sass](https://sass-lang.com/) syntax with variables: + +```scss +$mycolor: #ff0000; +.remark-slide-content > h1 { color: $mycolor; } +.remark-slide-content strong { color: $mycolor; } +``` + +Then set the `css` option in the YAML metadata using this file placed under the same directory as your Rmd: + +```yaml +output: + xaringan::moon_reader: + css: ["default", "mytheme.scss"] +``` + +This requires **rmarkdown** >= 2.8 and the [**sass**](https://rstudio.github.io/sass/) package. You can learn more about **rmarkdown** and **sass** support in [this blog post](https://blog.rstudio.com/2021/04/15/2021-spring-rmd-news/#sass-and-scss-support-for-html-based-output) and in [**sass** overview vignette](https://rstudio.github.io/sass/articles/sass.html). + +--- + +# Themes + +Don't want to learn CSS? Okay, you can use some user-contributed themes. A theme typically consists of two CSS files `foo.css` and `foo-fonts.css`, where `foo` is the theme name. Below are some existing themes: + +```{r, R.options=list(width = 70)} +names(xaringan:::list_css()) +``` + +--- + +# Themes + +To use a theme, you can specify the `css` option as an array of CSS filenames (without the `.css` extensions), e.g., + +```yaml +output: + xaringan::moon_reader: + css: [default, metropolis, metropolis-fonts] +``` + +If you want to contribute a theme to **xaringan**, please read [this blog post](https://yihui.org/en/2017/10/xaringan-themes). + +--- +class: inverse, middle, center +background-image: url(https://upload.wikimedia.org/wikipedia/commons/3/39/Naruto_Shiki_Fujin.svg) +background-size: contain + +# Naruto + +--- +background-image: url(https://upload.wikimedia.org/wikipedia/commons/b/be/Sharingan_triple.svg) +background-size: 100px +background-position: 90% 8% + +# Sharingan + +The R package name **xaringan** was derived1 from **Sharingan**, a dōjutsu in the Japanese anime _Naruto_ with two abilities: + +- the "Eye of Insight" + +- the "Eye of Hypnotism" + +I think a presentation is basically a way to communicate insights to the audience, and a great presentation may even "hypnotize" the audience.2,3 + +.footnote[ +[1] In Chinese, the pronounciation of _X_ is _Sh_ /ʃ/ (as in _shrimp_). Now you should have a better idea of how to pronounce my last name _Xie_. + +[2] By comparison, bad presentations only put the audience to sleep. + +[3] Personally I find that setting background images for slides is a killer feature of remark.js. It is an effective way to bring visual impact into your presentations. +] + +--- + +# Naruto terminology + +The **xaringan** package borrowed a few terms from Naruto, such as + +- [Sharingan](https://naruto.fandom.com/wiki/Sharingan) (写輪眼; the package name) + +- The [moon reader](https://naruto.fandom.com/wiki/Moon_Reader) (月読; an attractive R Markdown output format) + +- [Chakra](https://naruto.fandom.com/wiki/Chakra) (查克拉; the path to the remark.js library, which is the power to drive the presentation) + +- [Nature transformation](https://naruto.fandom.com/wiki/Nature_Transformation) (性質変化; transform the chakra by setting different options) + +- The [infinite moon reader](https://naruto.fandom.com/wiki/Infinite_Tsukuyomi) (無限月読; start a local web server to continuously serve your slides) + +- The [summoning technique](https://naruto.fandom.com/wiki/Summoning_Technique) (download remark.js from the web) + +You can click the links to know more about them if you want. The jutsu "Moon Reader" may seem a little evil, but that does not mean your slides are evil. + +--- + +class: center + +# Hand seals (印) + +Press `h` or `?` to see the possible ninjutsu you can use in remark.js. + +![](https://upload.wikimedia.org/wikipedia/commons/7/7e/Mudra-Naruto-KageBunshin.svg) + +--- + +class: center, middle + +# Thanks! + +Slides created via the R package [**xaringan**](https://github.com/yihui/xaringan). + +The chakra comes from [remark.js](https://remarkjs.com), [**knitr**](https://yihui.org/knitr/), and [R Markdown](https://rmarkdown.rstudio.com). diff --git a/presentations/jan23pres.html b/presentations/jan23pres.html new file mode 100644 index 0000000..6c6b5a4 --- /dev/null +++ b/presentations/jan23pres.html @@ -0,0 +1,920 @@ + + + + Test slides + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +