Understanding Title Formatting in Pandoc and R Markdown

Introduction

Pandoc is a powerful document conversion tool that can be used to create documents in various formats, including R Markdown. R Markdown is a markup language developed by Hadley Wickham and Joeventer that allows users to write documents with code chunks that can be executed using various programming languages. However, when it comes to title formatting, Pandoc can be finicky.

Problems with Title Formatting

The question at hand involves using Pandoc to create an R Markdown document with title formatting issues. The issue arises when trying to use a cat command to print two titles in the same chunk of code, followed by another chunk of code that includes a plot function. However, only the first title is displayed correctly as a heading.

Here’s the problematic code snippet:

cat("##Title 1", "\n")
a=c(1,2,3)
b=c(2,2,5)
plot(a,b,type='l')
cat("##Title 2", "\n")

However, when we run this code, only “##Title 1” is displayed correctly as a heading. We are asked to figure out what’s going wrong and how to fix it.

Solution

The solution involves understanding the nuances of Pandoc’s title formatting requirements. In R Markdown documents created using Pandoc, titles must be separated by blank lines. This might seem counterintuitive at first, but it’s essential for proper rendering.

Here’s the corrected code:

cat("##Title 1", "\n")
a=c(1,2,3)
b=c(2,2,5)
plot(a,b,type='l')

cat("\n", "##Title 2", "\n")

By adding a blank line between the plot function and the second title, we ensure that Pandoc renders both titles correctly as headings.

What’s Going On?

So, what’s happening here? Let’s take a closer look at how Pandoc handles Markdown documents. When you create an R Markdown document, Pandoc converts your .md file into HTML. In this process, Pandoc also applies various formatting rules to your text and code chunks.

One of the key features of Pandoc is its support for ATX-style headings. These are Markdown headings that start with a # symbol followed by one or more spaces. For example:

# Heading 1

## Subheading 1

### Sub-subheading 1

Pandoc uses these styles to create HTML headings in the final document.

In our original code snippet, we’re using the cat function to print two titles directly into the Markdown document. However, this approach doesn’t work as expected because Pandoc requires a blank line between each title heading.

By separating the plot function from the second title and adding a blank line between them, we ensure that both titles are rendered correctly as headings in the final HTML document.

Why `echo=FALSE` and `results='asis'` Matter

In R Markdown documents created using Pandoc, there are two options you can use to customize how your code is rendered: echo=FALSE and results='asis'.

echo=FALSE: This option tells Pandoc not to display the output of any R commands in the final document. By default, Pandoc includes R outputs in the HTML document. However, if you use echo=FALSE, Pandoc will exclude these outputs.
results='asis': This option tells Pandoc to render your code chunks as ASCII art instead of executing them using a programming language. By default, Pandoc uses the rmarkdown::renderCode function to execute R code. However, if you use results='asis', Pandoc will preserve the original code without running it.

In our example, we’re using both options:

echo=FALSE: We want to exclude any R outputs from being displayed in the final document.
results='asis': We want to render our code chunks as ASCII art instead of executing them using a programming language.

By combining these two options, we can ensure that Pandoc renders our title formatting correctly without any R outputs getting in the way.

Best Practices for Title Formatting

So, how can you apply this knowledge to create better title formatting in your R Markdown documents? Here are some best practices:

Always use a blank line between each title heading. This ensures that Pandoc renders both titles as headings correctly.
Use echo=FALSE when working with R code chunks to exclude any R outputs from being displayed in the final document.
Consider using results='asis' to render your code chunks as ASCII art instead of executing them using a programming language.

Conclusion

Creating title formatting that works consistently in Pandoc can be finicky. However, by understanding how Pandoc handles Markdown documents and applying some best practices, you can create R Markdown documents with beautiful, readable titles. Remember to always use blank lines between each title heading, exclude R outputs from being displayed using echo=FALSE, and consider rendering code chunks as ASCII art using results='asis'.

Last modified on 2025-01-30