Literature programming and RMarkdown

.title[
# Literature programming and RMarkdown
]
.subtitle[
## Introduction to Data Science (BIOL7800)
<a href="https://introdatasci.dlilab.com/" class="uri">https://introdatasci.dlilab.com/</a>
]
.author[
### Daijiang Li
]
.institute[
### LSU
]
.date[
### 2021/09/15
]

---

# Literature programming

.font200[
> Let us change our traditional attitude to the construction of programs:
> Instead of imagining that our main task is to instruct a computer what to do,
> let us concentrate rather on explaining to humans what we want the computer to
> do.
>
> .right[--- Donald E. Knuth, Literate Programming, 1984]

]

Literature programming weaves text (e.g., documentation, explanation, comments, etc.) in between machine executable code.

Need to _compile_ it to get a final report, not What You See Is What You Get (WYSIWYG, e.g., MS Word)
]

---

# R Markdown (https://rmarkdown.rstudio.com/)

### A powerful tool for combining analysis (in R, Python, Julia, or other programming languages) and reporting into the same document

![rmarkdown workflow](https://d33wubrfki0l68.cloudfront.net/61d189fd9cdf955058415d3e1b28dd60e1bd7c9b/9791d/images/rmarkdownflow.png)

```yaml
---
title: "Untitled"
author: "Daijiang Li"
date: "8/17/2021"
output: html_document
---
```

---

[.font300[Rmarkdown reference]](https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf)

---

# Open RStudio for demonstration

### https://github.com/daijiang/phyr_ms

---

# Reference books

## [R Markdown: The Definitive Guide](https://bookdown.org/yihui/rmarkdown/)

## [R Markdown Cookbook](https://bookdown.org/yihui/rmarkdown-cookbook/)