Markdown

Markdown allows us to concentrate on document structure and content. We can then worry about styling and presentation later.

RMarkdown

• Purpose: dynamically weave together text, data and analysis workflows.
• This is accomplished with the knitr package, an R package conveniently integrated into the R Studio UI.

Sample Markdown

# Top-level header

## Second-level header

This is a list:

* with some **bold** and 
* some *italic* text.

And a [hyperlink](https://bookdown.org/yihui/rmarkdown/) for good measure.

Basic formatting and structuring

RMarkdown: data-driven documents!

• Analysis can be integrated as R code into the document
• The analysis (i.e. the R code) is executed and the results updated when you knit the document.
• Text and code are interspersed.
• Code sections are included in code chunks like this.

The ‘YAML’ header

The YAML header must be placed at the beginning of a document and is enclosed by three dashes ---.

---
title: "Untitled"
output: html_document
date: '2022-12-16'
---

Above is the default YAML header when generating an RMarkdown file in R Studio.

Translating RMarkdown to HTML, PDF, Word etc

Turning RMarkdown into a shiny app

---
title: "Untitled"
output: html_document
date: '2022-12-16'
runtime: shiny
---

Now “knit” is replaced by “run”

And you need the “app logic”

Which will be included in the code chunks of the R Markdown document.

Create a sample interactive R Markdown document

In RStudio select: File > New File > R Markdown

Default example

Interactive code in the default example

```{r eruptions, echo=FALSE}
inputPanel(
  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)
)

renderPlot({
  hist(faithful$eruptions, probability = TRUE, breaks = as.numeric(input$n_breaks),
       xlab = "Duration (minutes)", main = "Geyser eruption duration")
  
  dens <- density(faithful$eruptions, adjust = input$bw_adjust)
  lines(dens, col = "blue")
})
```

Change the output format to flex_dashboard

Example

Change the layout

Dashboards are composed of rows and columns. Each output component is indicated by a level 3 header (i.e. ###).

• turn all sections into components
• change the flex_dashboard layout to vertical

---
title: "Untitled"
output: 
  flexdashboard::flex_dashboard:
    vertical_layout: scroll
date: "2022-12-16"
runtime: shiny
---

Example

Split input and output logic into different “components”

Example

Change the component layout

flexdashboard allows flexible layouts that are basically controlled through markdown section headers at three levels.

• create two separate dash board pages by adding a level 1 markdown section header above the first two and the last “components” respectively. Both the header variant # and =========================== will work.

Example

Create a nested layout for the first page

Place the “Inputs” and “Outputs” sections next to each other. This can be achieved by adding a level 2 markdown section header named Column above each of these sections. Both the header variant ## and ----------------------- will work.

Example

Change the dashboard theme and add

flexdashboard offers flexible styling of the output. Several built-in themes can be applied via the YAML header.

Example

and more options …

There is a broad range of styling options and components that can be controlled via the YAML header and standard R Markdown elements.

Example

Key Resources

• R Markdown
  • R Markdown: The Definitive Guide (Xie, Allaire, and Grolemund 2022)
  • Cheatsheet: Dynamic documents with rmarkdown cheatsheet
• Git/Github:
  • Happy Git and GitHub for the useR (Bryan 2021)
  • “Excuse me, do you have a moment to talk about version control?” (Bryan 2017)
  • Advanced git use: Pro Git book (Chacon and Straub 2014)
  • How to write a great commit message

References