Rmarkdown: Improving reproducibility

class: right, middle, my-title, title-slide

# Rmarkdown: Improving reproducibility
## RefReshing FRiday 09 April 2021
### Sean Lucey

---

.pull-left[

# 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

]

.pull-right[

.rotate20-left[
![:img Front cover of the R Markdown - The Definitive Guide book, 65%](EDAB_images/Rmarkdown_guide_cover.png)
]

[Get the online version here](https://bookdown.org/yihui/rmarkdown/)
]

---

# 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

.center[
![:img Rmarkdown flow](EDAB_images/rmarkdownflow.png)
]

---

# Three basic components

.pull-left[
## Metadata
- Written between the pair of three dashes ---
  - Syntax called YAML ([YAML Ain’t Markup Language](https://en.wikipedia.org/wiki/YAML))
- Indentation matters! 
  
## Text
- Syntax is Markdown

## Code
- Can be incorporated in two ways
- Inline using  
- Code chunk using   
  
]

.pull-right[

```
---
 title: "Rmarkdown: Improving reproducibility"
subtitle: "RefReshing FRiday 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
`r 2+2` 
```

````markdown
```{r}
x <- 2
y <- 2
x + y
```````
]

---

# Packages that extend R Markdown

.pull-left[
- bookdown - facilitates writing books and long-form articles/reports
  - [techdoc](https://github.com/NOAA-EDAB/tech-doc)
- linl - LaTeX letter template
  - [Response memo](https://github.com/NOAA-EDAB/memos)
- rticles - LaTeX journal article templates
  - [Rpath MSE manuscript](https://github.com/NOAA-EDAB/RPath_MSE)
- pkgdown - build a website for your package
  - [Survdat](https://noaa-edab.github.io/survdat/)
- xaringan - generate presentations
  - [This presentation]()
]

.pull-right[
![:img Rmarkdown family, 85%](EDAB_images/rmarkdownfamily.png)
]