Markdown

• Markdown is a simple language to write documents.
• Markdown can be converted to many formats: html, pdf, docx, epub, …

R Markdown

• R Markdown is a way to embed R code within a Markdown document.
• R code can be run and its output part of the final document.

Under the hood (from rmarkdown.rstudio.com)

1. Easier to document an analysis.
2. Everything in one place: code, figures, comments.
3. Encourage better analysis, transparency and reproducibility
4. Speed up the "analysis-to-report" time.

Practical cases

1. Analysis report for you, your PI, or your lab-book/wiki. ^Markdown
2. Report to share with collaborators. ^{PDF HTML}
3. Code associated with a paper. ^Markdown
4. Tutorials/workshops. ^Markdown
5. Websites/blogs. ^Markdown

1. Write a Markdown document with your favorite editor/RStudio.
   • Header defines metadata and render parameters.
   • Text using Markdown syntax.
   • R code chunks that will be run.
2. Render the document:
   • In R, run the render function from the rmarkdown package.
   • In Rstudio, click on Knit

Defines the metadata of the document and parameters for the compilation.

---
title: "Introduction to R Markdown"
subtitle: "MonBUG Meeting"
author: "Jean Monlong"
date: May 9, 2018
output: ioslides_presentation
---

# Header 1

## Header 2

### Header 3

Some text with a **word in bold**, another *in italic* and 
a [link](https://rmarkdown.rstudio.com)

Some text with a word in bold, another in italic and a link

- Bullet item 1
    1. Ordered item 1
    1. Ordered item 2
- Bullet item 2
- Bullet item 3

• Bullet item 1
  1. Ordered item 1
  2. Ordered item 2
• Bullet item 2
• Bullet item 3

Note: 4 spaces to define sub-lists.

```{r histtest}
x = rnorm(1000)
hist(x)
```

Advice: Name your chunks.

• Used for figure names.
• Helps debugging.

x = rnorm(1000)
hist(x)

• eval=FALSE: don't run the code.
• echo=FALSE: don't show the output.
• message=FALSE: don't show the output messages.
• warning=FALSE: don't show the output warnings.
• include=FALSE: don't output anything (but code is run).
• fig.width=8: set the width of figures.
• cache=TRUE: cache the results of a chunk.
• tidy=TRUE: tidy the code.

At the beginning of the document. For example "no code" mode:

```{r include=FALSE}
knitr::opts_chunk$set(echo=FALSE, message=FALSE,
                      warning=FALSE, fig.width=10)
```

Or "code+output" mode:

```{r include=FALSE}
knitr::opts_chunk$set(echo=TRUE, message=FALSE,
                      warning=FALSE, fig.width=10, tidy=TRUE)
```

```{r cache=TRUE}
res = reallyLongComputation(x)
hist(res)
```

• Use with caution. Especially if it depends on other chunks.
• dependson can specify dependency but not very practical.

• Apparently autodep tries to understand dependencies.

• Caching manually is safer IMO.

df

##            time Rmarkdown.knowledge Rmarkdown.usage
## 1 Before MonBUG                3801       0.1123095
## 2  After MonBUG               11543       0.2234982

library(knitr)
kable(df)

kable(df, digits = 2, format.args = list(big.mark = ","), 
    col.names = c("Time", "RMarkdown knowledge", 
        "Rmarkdown usage"))

```{r, include=FALSE}
knitr::knit_hooks$set(resize = function(before, options, envir) {
    if (before) {
      return('\\resizebox{\\textwidth}{!}{')
    } else {
      return('}')
    }
})
```

## Wide table

```{r, resize=TRUE}
knitr::kable(df, format='latex')
```

---
output: md_document
---

For GitHub/Bitbucket pages or wikis.

---
output:
  md_document:
    variant: markdown_github
---

---
title: "Your title"
output:
  html_document:
    toc: true
---

Customizable themes and cool features:

• Table of Contents (toc).
• Floating Table of Contents (toc_float).
• Fold code chunks (code_folding).
• Tabs.

---
title: "Introduction to R Markdown"
subtitle: "MonBUG Meeting"
author: "Jean Monlong"
date: May 9, 2018
output: beamer_presentation
---

Trick: use PNG image types to reduce PDF size (sometimes).

output:
  beamer_presentation:
    dev: png

Remove navigation bar and add page numbers

---
output:
  beamer_presentation:
    includes:
      in_header: header.tex
---

And in header.tex:

\setbeamertemplate{navigation symbols}{}
\setbeamertemplate{footline}[page number]

• Single files
  • PDF
  • HTML have images embedded.
• On GitHub as Markdown files
  • .md file and _files folder (with images).
• On GitHub as HTML files
  • Name the file index.html and switch on GitHub Pages.
  • Use rawgit.com.
• On RPubs ("Publish" button in RStudio).

• R Markdown
• Chunk options from knitr's website
• R Markdown Cheatsheet (2 pages).
• R Markdown Reference Guide (5 pages).

• Bibliography from .bib files.
• Websites with the blogdown package.
• Dashboards, e.g. flexdashboard
• Interactive notebooks.
• Interactive graphs in HTML documents (example).