04-rr-markdown.Rmd

---
title: "Markdown for reproducible research"
---

# Introduction to markdown

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

## 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.

## Computation components 


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

## Narrative components 

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

## 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

## Demo 
- End-to-end demonstration of a reproducible project
- Please refer to [Beaver.Rmd](Beavers.Rmd)