R Markdown: The Definitive Guide

https://yihui.org/rmarkdown
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Comprehensive guide to R Markdown, covering dynamic document generation, authoring formats,...
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### Install TinyTeX for LaTeX

Source: https://yihui.org/rmarkdown/installation

Install the 'tinytex' R package and then use it to install the TinyTeX LaTeX distribution, recommended for PDF output.

```r
install.packages("tinytex")
tinytex::install_tinytex()  # install TinyTeX
```

--------------------------------

### Install rmdshower Package

Source: https://yihui.org/rmarkdown/shower-presentations

Install the rmdshower package from GitHub to enable Shower presentation creation.

```R
devtools::install_github("mangothecat/rmdshower")
```

--------------------------------

### Install sigma Package

Source: https://yihui.org/rmarkdown/htmlwidgets-sigma

Install the sigma package from GitHub using devtools. This is a prerequisite for using the sigma widget.

```R
devtools::install_github('jjallaire/sigma')
```

--------------------------------

### Install learnr Package

Source: https://yihui.org/rmarkdown/learnr-start

Install the learnr package to begin creating interactive tutorials. This is the first step before using the tutorial template in RStudio or setting up manually.

```r
install.packages("learnr")
```

--------------------------------

### Install htmlwidgets Package

Source: https://yihui.org/rmarkdown/htmlwidgets-create

Install the htmlwidgets package from CRAN. This is a prerequisite for creating custom widgets.

```R
install.packages("htmlwidgets")
```

--------------------------------

### Install bookdown Package

Source: https://yihui.org/rmarkdown/bookdown-start

Install the bookdown package from CRAN or the development version from GitHub.

```r
install.packages("bookdown")
```

```r
devtools::install_github("rstudio/bookdown")
```

--------------------------------

### Install GitHub R Package with devtools

Source: https://yihui.org/rmarkdown/template-share

Use this command to install an R package directly from GitHub, which is a common method for distributing templates.

```r
if (!requireNamespace("devtools")) install.packages("devtools")
devtools::install_github("username/packagename")
```

--------------------------------

### Enable reveal.js Notes and Search Plugins

Source: https://yihui.org/rmarkdown/reveal.js-plugins.html

Use `self_contained: false` and list desired plugins in `reveal_plugins`. This example enables the 'notes' and 'search' plugins.

```yaml
---
title: "Habits"
output:
  revealjs::revealjs_presentation:
    self_contained: false
    reveal_plugins: ["notes", "search"]
---
```

--------------------------------

### Install Blogdown Package

Source: https://yihui.org/rmarkdown/blogdown-start

Install the blogdown package from CRAN or the development version from GitHub using devtools.

```r
install.packages("blogdown")
```

```r
devtools::install_github("rstudio/blogdown")
```

--------------------------------

### Install revealjs Package

Source: https://yihui.org/rmarkdown/revealjs

Install the revealjs R package from CRAN to enable reveal.js presentation output.

```r
install.packages("revealjs")
```

--------------------------------

### Install xaringan Package

Source: https://yihui.org/rmarkdown/xaringan-start

Install the xaringan package from CRAN or GitHub. Use the CRAN version for stability or the development version from GitHub for the latest features.

```R
install.packages('xaringan')
```

```R
devtools::install_github('yihui/xaringan')
```

--------------------------------

### Install rsconnect Package

Source: https://yihui.org/rmarkdown/shiny-deploy

Install the 'rsconnect' R package, which is required for deploying Shiny documents to ShinyApps.io. Ensure you have the latest version.

```r
install.packages("rsconnect")
```

--------------------------------

### Use the Minimal Widget

Source: https://yihui.org/rmarkdown/htmlwidgets-create

Demonstrate the usage of a newly created minimal widget. This example shows how to load the widget package and call the widget function with a text argument.

```R
library(mywidget)
mywidget("hello, world")
```

--------------------------------

### Bookdown Chapter File Example

Source: https://yihui.org/rmarkdown/bookdown-project

An example of an Rmd file for a book chapter. Chapters should start with a first-level heading and do not require YAML metadata, as it is inherited from index.Rmd.

```markdown
# Introduction

This chapter is an overview of the methods that
we propose to solve an **important problem**.
```

```markdown
# Literature

Here is a review of existing methods.
```

--------------------------------

### Serve Book with bookdown::serve_book()

Source: https://yihui.org/rmarkdown/bookdown-edit

Start a live preview of your book. The book recompiles automatically upon saving Rmd files, and the preview updates reflect these changes, avoiding the need to manually re-run render or preview functions.

```r
bookdown::serve_book()
```

--------------------------------

### Skeleton Rmd with Output Format and Template

Source: https://yihui.org/rmarkdown/template-structure

The `skeleton.Rmd` file serves as a starting point for the R Markdown document. This example sets the default output format to `bookdown::html_document2` with table of contents and figure captions enabled, and specifies the 'flatly' template.

```rmarkdown
---
title: "Untitled"
author: "Your Name"
output:
  bookdown::html_document2:
    toc: true
    fig_caption: true
    template: flatly
---

## Introduction

## Analysis

## Conclusions

```

--------------------------------

### Install pkgdown Package

Source: https://yihui.org/rmarkdown/pkgdown-start

Install pkgdown from CRAN or its development version from GitHub. Ensure pkgdown is installed before proceeding.

```r
install.packages("pkgdown")
```

```r
# Or the development version
devtools::install_github("r-lib/pkgdown")
```

--------------------------------

### Build pkgdown Website

Source: https://yihui.org/rmarkdown/pkgdown-start

After installation, run `pkgdown::build_site()` in your package's root directory to generate the website in the `docs/` folder. This website can then be deployed using services like GitHub Pages or Netlify.

```r
pkgdown::build_site()
```

--------------------------------

### Build Entire R Markdown Site from Command Line

Source: https://yihui.org/rmarkdown/rmarkdown-site

Renders all Rmd and md files in the current directory into an R Markdown website. Assumes you are in the website's root directory.

```r
rmarkdown::render_site()
```

--------------------------------

### 2D Array Example

Source: https://yihui.org/rmarkdown/htmlwidgets-advanced

This is an example of a 2-dimensional array that might require transposition before being used by certain JavaScript libraries.

```json
[
  [5.1, 4.9, 4.7, 4.6, 5, 5.4],
  [3.5, 3, 3.2, 3.1, 3.6, 3.9],
  [1.4, 1.4, 1.3, 1.5, 1.4, 1.7],
  [0.2, 0.2, 0.2, 0.2, 0.2, 0.4],
  ["setosa", "setosa", "setosa", "setosa", "setosa", "setosa"]
]
```

--------------------------------

### Establish DBI Connection

Source: https://yihui.org/rmarkdown/language-engines

Set up a DBI connection to a database using `dbConnect()`. This connection object is then used in subsequent SQL chunks.

```r
library(DBI)
db = dbConnect(RSQLite::SQLite(), dbname = "sql.sqlite")
```

--------------------------------

### Load Custom Macros using beforeInit Option

Source: https://yihui.org/rmarkdown/some-tips

Configure 'beforeInit' under 'nature' to load external JavaScript files, such as custom macros, before remark.js initializes. This enables advanced customization and integration of external scripts.

```yaml
output:
  xaringan::moon_reader:
    nature:
      beforeInit: "macros.js"
```

--------------------------------

### Basic Shiny Dashboard Structure

Source: https://yihui.org/rmarkdown/shiny

This is a minimal example of a Shiny dashboard using flexdashboard. It includes YAML metadata, a global chunk for data loading, a sidebar for input controls, and a main column for rendering plots based on user input.

```yaml
---
title: "Old Faithful Eruptions"
output: flexdashboard::flex_dashboard
runtime: shiny
---
```

```r
```{r global, include=FALSE}
# load data in 'global' chunk so it can be shared
# by all users of the dashboard
library(datasets)
data(faithful)
```
```

```markdown
Column {.sidebar}
--------------------------------------------------

Waiting time between eruptions and the duration of the eruption
for the Old Faithful geyser in Yellowstone National Park,
Wyoming, USA.

```{r}
selectInput(
  "n_breaks", label = "Number of bins:",
  choices = c(10, 20, 35, 50), selected = 20
)

sliderInput(
  "bw_adjust", label = "Bandwidth adjustment:",
  min = 0.2, max = 2, value = 1, step = 0.2
)
```
```

```r
Column
--------------------------------------------------

### Geyser Eruption Duration

```{r}
renderPlot({
  erpt = faithful$eruptions
  hist(
    erpt, probability = TRUE, breaks = as.integer(input$n_breaks),
    xlab = "Duration (minutes)", main = "Geyser Eruption Duration",
    col = 'gray',
    border = 'white'
  )
  
  dens = density(erpt, adjust = input$bw_adjust)
  lines(dens, col = "blue", lwd = 2)
})
```
```

--------------------------------

### Install R Markdown Package

Source: https://yihui.org/rmarkdown/installation

Install the 'rmarkdown' package from CRAN or the development version from GitHub using the devtools package.

```r
# Install from CRAN
install.packages('rmarkdown')
```

```r
# Or if you want to test the development version,
# install from GitHub
if (!requireNamespace("devtools"))
  install.packages('devtools')
devtools::install_github('rstudio/rmarkdown')
```

--------------------------------

### Create bookdown Project Skeleton

Source: https://yihui.org/rmarkdown/bookdown-start

Create a skeleton project for bookdown in the current working directory.

```r
bookdown:::bookdown_skeleton(getwd())
```

--------------------------------

### R Exercise with Alternative Markdown Hint Syntax

Source: https://yihui.org/rmarkdown/learnr-exercises

An alternative syntax for Markdown hints using Pandoc's `:::` block, useful for Pandoc versions higher than 2.0. It achieves the same result as the `<div>` method.

```r
:::{#filter-hint}
**Hint:** You may want to use the dplyr `filter` function.
:::
```

--------------------------------

### Install rticles Package

Source: https://yihui.org/rmarkdown/rticles-start

Install the rticles package from CRAN or the development version from GitHub. The development version is recommended for the latest features and templates.

```r
install.packages("rticles")
```

```r
devtools::install_github("rstudio/rticles")
```

--------------------------------

### BibTeX Entry Example

Source: https://yihui.org/rmarkdown/markdown-syntax

Example of a BibTeX entry used for citations in R Markdown. Ensure your BibTeX file is specified in the YAML metadata.

```bibtex
@Manual{R-base,
  title = {R: A Language and Environment for Statistical
    Computing},
  author = {{R Core Team}},
  organization = {R Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = {2017},
  url = {https://www.R-project.org/},
}
```

--------------------------------

### Build Book with bookdown::render_book()

Source: https://yihui.org/rmarkdown/bookdown-edit

Use this function to build all Rmd files into a book. It respects settings in _output.yml and builds all specified formats.

```r
bookdown::render_book()
```

--------------------------------

### Install devtools Package

Source: https://yihui.org/rmarkdown/htmlwidgets-create

Install the devtools package from CRAN. This package is useful for creating and managing R packages, including scaffolding new widgets.

```R
install.packages("devtools")
```

--------------------------------

### Create a Basic Slidy Presentation

Source: https://yihui.org/rmarkdown/slidy-presentation

Use the `slidy_presentation` output format in the YAML header to generate a Slidy slideshow. Structure slides with `##` headings or `---` for new slides.

```yaml
---
title: "Habits"
author: John Doe
date: March 22, 2005
output: slidy_presentation
---

# In the morning

## Getting up

- Turn off alarm
- Get out of bed

## Breakfast

- Eat eggs
- Drink coffee

# In the evening

## Dinner

- Eat spaghetti
- Drink wine

---

```{r, cars, fig.cap="A scatterplot.", echo=FALSE}
plot(cars)
```

## Going to sleep

- Get in bed
- Count sheep
```

--------------------------------

### Enable Presenter Mode

Source: https://yihui.org/rmarkdown/ioslides-presentation

Append '?presentme=true' to the presentation URL to enable presenter mode, which opens a separate window for presenter notes and slide thumbnails.

```html
my-presentation.html?presentme=true

```

--------------------------------

### R Markdown YAML Metadata Example

Source: https://yihui.org/rmarkdown/compile

This is an example of YAML metadata for an R Markdown document specifying multiple output formats. The `rmarkdown::render()` function can target specific formats like 'pdf_document'.

```yaml
output:
  html_document:
    toc: true
  pdf_document:
    keep_tex: true
```
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