4 Introduction

• R Markdown: The Definitive Guide: https://bookdown.org/yihui/rmarkdown/
• RStudio Lessons: https://rmarkdown.rstudio.com/lesson-1.html

Markdown is a markup language for developing and formatting documents. R Markdown is an R-package that allows the user to integrate text, R-code, and R-code output into a well formatted document (e.g., HTML, MS Word, PDF).

My recommendation is to create an R Markdown file for every R-project. The intention is to document as much of the project as possible. R Markdown provides a more readable document, with better descriptions of how and why an activity was performed, than a standard R script with a few commented lines.

4.1 Benefits

• Reproducible: Document steps of an investigation or scientific study
  • reproducibility crisis.
• Collaborative: Easy to work with others on investigations and scientific studies.
• Efficient: Generate and update reports automatically (e.g., HTML, MS Word, and PDF).
• Engaging: Embed interactive figures, maps, and tables in reports (HTML only).
  • Source: https://plotly-book.cpsievert.me/images/gapminder-highlight-animation.gif

4.2 Basic Overview

Use markdown syntax, some of which is shown in the table below, to format the document.

• Source: https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf

Once the document is complete (formatted with markdown syntax with integrated R code) the document can be knit (rendered) using the package knitr.

Here is a simple example showing the raw R Markdown (Rmd) file before knitting (rendering) and after knitting. The colors on the far left are there to help identify elements pre- and post-knitting.

R is not the only language supported by R Markdown. Languages supported by R Markdown include, but are not limited to,…