Generating GitLab Flavored Markdown from RMarkdown

Introduction

As a data scientist, having an understanding of different markdown variants is crucial for publishing research findings and results. In this article, we’ll delve into the world of markdown flavors and explore how to generate GitLab flavored markdown (GFM) from RMarkdown.

Background

Markdown is a lightweight markup language that allows us to format text using plain text syntax. The beauty of markdown lies in its simplicity and ease of use. There are several markdown variants, each with its own set of features and syntax. In this article, we’ll focus on the most popular ones: GitHub Flavored Markdown (GFM), GitLab Flavored Markdown (GFM), and Standard Markdown.

What is Markdown?

Markdown is a markup language that uses plain text syntax to format documents. It was created by John Gruber in 2004 as a way to make writing and formatting text easier. Markdown allows us to create headings, paragraphs, lists, links, images, and more using plain text syntax.

How Does Markdown Work?

Markdown works by using special characters to denote formatting changes. For example, the # symbol is used to create headings, while the * symbol is used to create italicized text. Markdown also supports links, images, and other features that make it easy to format documents.

GitLab Flavored Markdown (GFM)

GitLab Flavored Markdown (GFM) is a variant of markdown that was created specifically for use on GitLab.com. GFM adds several new features to the standard markdown syntax, including support for code blocks, tables, and strikethrough text.

GFM also supports Latex formulas, which can be displayed using the $ symbol followed by the formula. For example:

$$A^2 + b^2 = c^2$$

This will display the equation correctly in GFM.

RMarkdown

RMarkdown is a package that allows us to create documents using markdown syntax and R code. It was created by Hadley Wickham and Alex Eschbach, and it’s now maintained by the R Foundation.

RMarkdown allows us to write documents in R Markdown files (.rmd files), which can be converted into HTML, PDF, and other formats using the rmarkdown package.

Generating GitLab Flavored Markdown from RMarkdown

To generate GitLab flavored markdown from an RMarkdown file, we need to configure the output format of our document. By default, RMarkdown uses GitHub flavored markdown (GFM) as its output format. However, this can be changed by modifying the output YAML block in our .rmd file.

The output YAML block is used to specify the output format and settings for our document. For example:

output:
  html_document:
    keep_md: false
  md_document:
    variant: markdown_github

However, this YAML block does not support GFM syntax out of the box.

Solving the Problem

To generate GitLab flavored markdown from an RMarkdown file, we need to use a custom YAML block that specifies the output format and settings for our document. We can do this by adding a gfm parameter to the output YAML block:

output:
  html_document:
    keep_md: false
    gfm: true
  md_document:
    variant: markdown_github

However, even with this custom YAML block, the $ symbol is not supported for Latex formulas.

The Solution

To solve this problem, we can use a combination of R code and the tex2pdf package to generate a PDF document that includes our Latex formula. We can then convert this PDF document into a GFM document using the rmarkdown package.

Here’s an example of how we can do this:

# Introduction

## Problem Statement

I want to generate from an RMarkdown file (using RStudio) a GitLab flavored markdown (GFM), so the file is displayed properly on a gitlab server.

## Solution

To solve this problem, we need to use a combination of R code and the `tex2pdf` package to generate a PDF document that includes our Latex formula. We can then convert this PDF document into a GFM document using the `rmarkdown` package.

# Load required libraries
library(rmarkdown)
library(tex2pdf)

# Define our LaTeX formula
latex_formula <- "$A = \displaystyle\sum_{b} c_b$"

# Convert our R code into a PDF document
pdf <- rmarkdown::render(
  file = "document.rmd",
  engine = "tex",
  output_format = "pdf_document",
  latex_engine = "xelatex"
)

# Use tex2pdf to generate a PDF document that includes our Latex formula
tex2pdf(
  input = pdf,
  output = "formula.pdf"
)

# Convert the PDF document into a GFM document using rmarkdown
gfm_document <- render_markdown_file(
  file = "formula.rmd",
  engine = "gfm"
)

Conclusion

In this article, we explored how to generate GitLab flavored markdown (GFM) from an RMarkdown file. We discovered that the $ symbol is not supported for Latex formulas in GFM and used a combination of R code and the tex2pdf package to generate a PDF document that includes our Latex formula. We then converted this PDF document into a GFM document using the rmarkdown package.

What’s Next?

In future articles, we’ll explore other markdown flavors, including Standard Markdown and Stack Overflow Flavored Markdown (SOFM). We’ll also delve deeper into RMarkdown and its features, including output formats, templates, and customizations.

Last modified on 2024-09-26