Chapter 5 Introduction to markdown

  • how does rmarkdown work? Advantages, disadvantages
  • rmarkdown syntax (examples)

5.1 Rmarkdown and usage

  • reproducible reporting with rmarkdown

  • dichotomizing Rmarkdown document content to (1) computation component and (2) narrative component (@MikeKane, Yale) collectively called as research compendia

  • Research Compedia: a container for the different elements that make up the document and its computations (i.e. text, code, data, …) and as a means for distributing, managing, and updating the collection.

5.2 Computation components

  • Objects to be presented: usually plots and tables
  • Reproducible code to visualize data

5.3 Narrative components

  • Provide backgrounds, goals
  • Contexualize computational components
  • Establish themes
  • Convey the results
  • Render in pdf, html, docx

5.4 Rproject set-up

  • Allows for integration of the two components (i.e. creation of Rmarkdowns with compuational components)
  • Integrates literate programming
  • Provide interpretability and facilitate reproducibility

5.5 Demo

  • End-to-end demonstration of a reproducible project
  • Please refer to Beaver.Rmd