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Rmarkdown:
Improving reproducibility

RefReshing FRiday
09 April 2021

Sean Lucey

1 / 5

What is R Markdown

Simplified work flow that can aid in reproducibility by containing computer code and narrative in the same document

Can be used to generate:

  • Letters
  • Websites
  • Journal articles
  • Books
  • Presentations

Front cover of the R Markdown - The Definitive Guide book



Get the online version here

2 / 5

How does it work?

  • Uses the knitr package to embed R or other computer language in to markdown
    • Markdown is plain text that can be read by both humans and computers
  • Pandoc then converts the markdown into the output format of your choice
  • Output can be Word, PDF, html
  • Some features work better than others depending on what output you choose






Rmarkdown flow

3 / 5

Three basic components

Metadata

Text

  • Syntax is Markdown

Code

  • Can be incorporated in two ways
  • Inline using
  • Code chunk using 
---
  title: "Rmarkdown:<br /> Improving reproducibility"
subtitle: "RefReshing FRiday<br \> 09 April 2021"
author: "Sean Lucey"
output:
  xaringan::moon_reader:
  css: ["default", "libs/EDAB_theme3_508_SOE_16by9.css"]
---


This is how you make something **bold** or *italicized*

This is how you make something bold or italicized


`r 2+2`
```{r}
x <- 2
y <- 2
x + y
```
4 / 5

Packages that extend R Markdown

Rmarkdown family

5 / 5

What is R Markdown

Simplified work flow that can aid in reproducibility by containing computer code and narrative in the same document

Can be used to generate:

  • Letters
  • Websites
  • Journal articles
  • Books
  • Presentations

Front cover of the R Markdown - The Definitive Guide book



Get the online version here

2 / 5
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