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191212_rladies_rmarkdown.html
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<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml" lang="" xml:lang="">
<head>
<title>Introduction to {rmarkdown}</title>
<meta charset="utf-8" />
<meta name="author" content="Sarah Bonnin" />
<meta name="date" content="2019-12-12" />
<link href="libs/remark-css-0.0.1/default.css" rel="stylesheet" />
<link href="libs/remark-css-0.0.1/rladies.css" rel="stylesheet" />
<link href="libs/remark-css-0.0.1/rladies-fonts.css" rel="stylesheet" />
<script src="libs/kePrint-0.0.1/kePrint.js"></script>
</head>
<body>
<textarea id="source">
class: center, middle, inverse, title-slide
# Introduction to {rmarkdown}
## R-ladies Barcelona
### Sarah Bonnin
### 2019-12-12
---
## What is Markdown ?
--
* **Lightweight markup language**
--
* **Easy-to-read** and **easy-to-write** plain text format
--
* Rendered as **HTML** document through [Blackfriday](https://gohugo.io/getting-started/configuration/)
---
## What is R Markdown ?
--
* Advanced version of "plain" Markdown: **embeds** and **executes R code**
--
* **Simple formatting syntax** for authoring **HTML, PDF, and MS Word** documents.
--
* Easy to **report** and **share** analysis.
--
* **Reproducibility** and **transparency**.
--
* Produce **high quality documents**.
--
<img src="https://bookdown.org/yihui/rmarkdown/images/hex-rmarkdown.png" width="30%" style="display: block; margin: auto;" />
---
## Install and load
{rmarkdown} package is **open-source** and can be installed and loaded as follows:
```r
install.packages("rmarkdown")
```
```r
library(rmarkdown)
```
---
## R Markdown Cheatsheet
R Markdown [Cheatsheet](https://rstudio.com/wp-content/uploads/2016/03/rmarkdown-cheatsheet-2.0.pdf)
---
## R Markdown (RMD) file
* Plain text file
--
* **.Rmd** extension
--
* Create, write and run from **R Studio**
---
## How does it work?
--
<img src="https://d33wubrfki0l68.cloudfront.net/61d189fd9cdf955058415d3e1b28dd60e1bd7c9b/b739c/lesson-images/rmarkdownflow.png" width="90%" style="display: block; margin: auto;" />
--
* **{rmarkdown}** feeds the input **.Rmd** file to **{knitr}**
--
* **{knitr}** creates a new **.md** file containing the output
--
* The **.md** file is then fed to **pandoc** that creates the final output
---
## R Markdown file and rendering
Example of a **source file** and its **rendering**:
<img src="images/RMD_knit.png" width="100%" style="display: block; margin: auto;" />
---
## Create an .Rmd file in R Studio
File -> New File -> R Markdown...
<img src="images/RMD_create.png" width="70%" style="display: block; margin: auto;" />
---
## Create an .Rmd file in R Studio
Choose output format:
<img src="images/RMD_choose_output.png" width="70%" style="display: block; margin: auto;" />
---
## Template .Rmd file
<img src="images/RMD_template.png" width="65%" style="display: block; margin: auto;" />
---
## First knit!
Knit the template **.Rmd** file to HTML!
<img src="images/RMD_knit_template.png" width="35%" style="display: block; margin: auto;" />
---
## First knit!
<img src="images/RMD_knit_template_output.png" width="60%" style="display: block; margin: auto;" />
---
## Blocks
* Header (optional) in **YAML** format surrounded by **3 dashes**
--
* R code chunks surrounded by **3 back ticks**
--
* (Formatted) text
---
## Header
The YAML header is surrounded by 3 dashes (**---**)
--
```r
---
title: "TEST"
author: "Sarah Bonnin"
date: "12/8/2019"
output: html_document
---
```
--
Add a table of content:
--
```r
---
title: "TEST"
author: "Sarah Bonnin"
date: "12/8/2019"
output:
html_document:
toc: true
---
```
---
## Format text
```r
*Italic* / _Italic_
**Bold** / __Bold__
***Bold + Italic*** / ___Bold + Italic___
superscript^2^
~~strikethrough~~
```
--
*Italic* / _Italic_
**Bold** / __Bold__
***Bold + Italic*** / ___Bold + Italic___
Superscript^2^
~~Strikethrough~~
---
## Format text
### Headers
````r
# Header 1
## Header 2
### Header 3
#### Header 4
````
--
# Header 1
## Header 2
### Header 3
#### Header 4
---
## Format text
### Headers
--
* Headers will be automatically organized in the **table of content** !
--
````r
# Section 1
## Subsection 1.1
Some text
## Subsection 1.2
More text
# Section 2
## Subsection 2.1
Text from section 2.1
## Subsection 2.2
Text from section 2.2
````
---
## Format text
### Headers
<img src="images/RMD_TOC_output.png" width="35%" style="display: block; margin: auto;" />
---
## Lists
### unordered
````
* first item
* second item
* first sub-item
* second sub-item
````
--
* first item
* second item
* first sub-item
* second sub-item
---
## Lists
### ordered
````r
1. first ordered item
2. second ordered item
+ first sub-item
+ second sub-item
````
--
1. first ordered item
2. second ordered item
+ first sub-item
+ second sub-item
---
## Code blocks
### Options
Customize the rendering with **options**:
--
<img src="images/RMD_options.png" width="95%" style="display: block; margin: auto;" />
---
## Code blocks
### Load packages in the background
--
* **.Rmd** files are "independent": packages you will need in your code should be loaded **in a code block inside the document** !
--
* If you want to show **no output** and **no message** but still **execute the code**, use the option **include = FALSE**
--
* Load the packages you will need to run the code of your analysis, **at the beginning of the .Rmd file**:
--
````r
```{r, include = FALSE}
library(ggplot2)
library(dplyr)
library(kableExtra)
```
````
---
## Code blocks: examples
The following code:
````r
```{r, eval=TRUE, echo=TRUE, message=TRUE}
ggplot(data=cars, aes(x=speed)) + geom_histogram()
```
````
--
Renders as:
```r
ggplot(data=cars, aes(x=speed)) + geom_histogram()
```
```
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
```
<!-- -->
---
## Code blocks: examples
The following code:
````r
```{r, eval=TRUE, echo=TRUE, message=TRUE, fig.height=3}
ggplot(data=cars, aes(x=speed)) + geom_histogram()
```
````
--
Renders as:
```r
ggplot(data=cars, aes(x=speed)) + geom_histogram()
```
```
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
```
<!-- -->
---
## Code blocks: examples
The following code:
````r
```{r, eval=TRUE, echo=TRUE, message=FALSE, fig.height=3}
ggplot(data=cars, aes(x=speed)) + geom_histogram()
```
````
--
Renders as:
```r
ggplot(data=cars, aes(x=speed)) + geom_histogram()
```
<!-- -->
---
## Code blocks: examples
The following code:
````r
```{r, eval=TRUE, echo=FALSE, message=FALSE, fig.height=3}
ggplot(data=cars, aes(x=speed)) + geom_histogram()
```
````
--
Renders as:
<!-- -->
---
## Code blocks: examples
The following code:
````r
```{r, eval=FALSE, echo=TRUE, message=FALSE, fig.height=3}
ggplot(data=cars, aes(x=speed)) + geom_histogram()
```
````
--
Renders as:
```r
ggplot(data=cars, aes(x=speed)) + geom_histogram()
```
---
## Code blocks: examples
The following code:
````r
```{r, eval=FALSE, echo=FALSE, message=FALSE, fig.height=3}
ggplot(data=cars, aes(x=speed)) + geom_histogram()
```
````
--
Renders as:
--
NOTHING! No code, no output, no message...
---
## Code blocks: examples (tidy)
The following code:
````r
```{r, eval=FALSE, echo=TRUE, message=FALSE, fig.height=3, tidy=TRUE}
ggplot(data=cars,aes(x=speed))+geom_histogram()
```
````
--
Renders as:
```r
ggplot(data = cars, aes(x = speed)) + geom_histogram()
```
---
## Code blocks
Include options globally:
````r
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, tidy = TRUE, message = FALSE)
```
````
---
## Code blocks: Python and bash
{rmarkdown} can also execute, for example, **bash** and **Python** blocks of code.
--
````bash
```{bash}
ls *
```
````
--
```bash
ls *
```
```
## 191212_rladies_rmarkdown.html
## 191212_rladies_rmarkdown.Rmd
## README.md
##
## 191212_rladies_rmarkdown_files:
## figure-html
##
## images:
## RMD_choose_output.png
## RMD_create.png
## RMD_knit.png
## RMD_knit_template_output.png
## RMD_knit_template.png
## RMD_options.png
## RMD_template.png
## RMD_TOC_output.png
##
## libs:
## kePrint-0.0.1
## remark-css-0.0.1
```
---
## Code blocks: Python and bash
{rmarkdown} can also execute, for example, **bash** and **Python** blocks of code.
--
````python
```{python}
x = 'Rladies Barcelona'
print(x.split(' '))
```
````
--
```python
x = 'Rladies Barcelona'
print(x.split(' '))
```
```
## ['Rladies', 'Barcelona']
```
---
## Code blocks: knitr language engines
{rmarkdown} can execute **many different languages!**
--
See this [knitr language engines guide](https://bookdown.org/yihui/rmarkdown/language-engines.html)
---
## Insert images
Recommended / easier to format way with **knitr::include_graphics**:
--
````r
```{r}
knitr::include_graphics("https://rladies.org/wp-content/uploads/2016/12/R-LadiesGlobal.png")
```
````
--
```r
knitr::include_graphics("https://rladies.org/wp-content/uploads/2016/12/R-LadiesGlobal.png")
```
<!-- -->
---
## Insert images
Recommended / easier to format way with **knitr::include_graphics**:
--
````r
```{r, out.width="50%", echo=FALSE, fig.align="center"}
knitr::include_graphics("https://rladies.org/wp-content/uploads/2016/12/R-LadiesGlobal.png")
```
````
--
<img src="https://rladies.org/wp-content/uploads/2016/12/R-LadiesGlobal.png" width="50%" style="display: block; margin: auto;" />
---
## Links
You can **link** web pages:
--
````r
Here is a [link]("https://rmarkdown.rstudio.com/")
to {rmarkdown} page on [R Studio](https://rstudio.com/) website.
````
--
Here is a [link]("https://rmarkdown.rstudio.com/")
to {rmarkdown} page on [R Studio](https://rstudio.com/) website.
---
## Create tables
You can create tables:
````r
Date | Workshop
----- | -----
12/12/2019 | R Markdown
21/01/2020 | Forecasting
````
--
Date | Workshop
----- | -----
12/12/2019 | R Markdown
21/01/2020 | Forecasting
---
## Show R objects as tables
Format tables with **knitr::kable** and [**{kableExtra}**](http://haozhu233.github.io/kableExtra/awesome_table_in_html.html) package.
````r
```{r}
knitr::kable(head(iris))
```
````
--
<table>
<thead>
<tr>
<th style="text-align:right;"> Sepal.Length </th>
<th style="text-align:right;"> Sepal.Width </th>
<th style="text-align:right;"> Petal.Length </th>
<th style="text-align:right;"> Petal.Width </th>
<th style="text-align:left;"> Species </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:right;"> 5.1 </td>
<td style="text-align:right;"> 3.5 </td>
<td style="text-align:right;"> 1.4 </td>
<td style="text-align:right;"> 0.2 </td>
<td style="text-align:left;"> setosa </td>
</tr>
<tr>
<td style="text-align:right;"> 4.9 </td>
<td style="text-align:right;"> 3.0 </td>
<td style="text-align:right;"> 1.4 </td>
<td style="text-align:right;"> 0.2 </td>
<td style="text-align:left;"> setosa </td>
</tr>
<tr>
<td style="text-align:right;"> 4.7 </td>
<td style="text-align:right;"> 3.2 </td>
<td style="text-align:right;"> 1.3 </td>
<td style="text-align:right;"> 0.2 </td>
<td style="text-align:left;"> setosa </td>
</tr>
<tr>
<td style="text-align:right;"> 4.6 </td>
<td style="text-align:right;"> 3.1 </td>
<td style="text-align:right;"> 1.5 </td>
<td style="text-align:right;"> 0.2 </td>
<td style="text-align:left;"> setosa </td>
</tr>
<tr>
<td style="text-align:right;"> 5.0 </td>
<td style="text-align:right;"> 3.6 </td>
<td style="text-align:right;"> 1.4 </td>
<td style="text-align:right;"> 0.2 </td>
<td style="text-align:left;"> setosa </td>
</tr>
<tr>
<td style="text-align:right;"> 5.4 </td>
<td style="text-align:right;"> 3.9 </td>
<td style="text-align:right;"> 1.7 </td>
<td style="text-align:right;"> 0.4 </td>
<td style="text-align:left;"> setosa </td>
</tr>
</tbody>
</table>
---
## Show R objects as tables
**Bold** columns
````r
```{r}
knitr::kable(head(iris)) %>%
column_spec(1:2, bold = TRUE)
```
````
--
<table>
<thead>
<tr>
<th style="text-align:right;"> Sepal.Length </th>
<th style="text-align:right;"> Sepal.Width </th>
<th style="text-align:right;"> Petal.Length </th>
<th style="text-align:right;"> Petal.Width </th>
<th style="text-align:left;"> Species </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:right;font-weight: bold;"> 5.1 </td>
<td style="text-align:right;font-weight: bold;"> 3.5 </td>
<td style="text-align:right;"> 1.4 </td>
<td style="text-align:right;"> 0.2 </td>
<td style="text-align:left;"> setosa </td>
</tr>
<tr>
<td style="text-align:right;font-weight: bold;"> 4.9 </td>
<td style="text-align:right;font-weight: bold;"> 3.0 </td>
<td style="text-align:right;"> 1.4 </td>
<td style="text-align:right;"> 0.2 </td>
<td style="text-align:left;"> setosa </td>
</tr>
<tr>
<td style="text-align:right;font-weight: bold;"> 4.7 </td>
<td style="text-align:right;font-weight: bold;"> 3.2 </td>
<td style="text-align:right;"> 1.3 </td>
<td style="text-align:right;"> 0.2 </td>
<td style="text-align:left;"> setosa </td>
</tr>
<tr>
<td style="text-align:right;font-weight: bold;"> 4.6 </td>
<td style="text-align:right;font-weight: bold;"> 3.1 </td>
<td style="text-align:right;"> 1.5 </td>
<td style="text-align:right;"> 0.2 </td>
<td style="text-align:left;"> setosa </td>
</tr>
<tr>
<td style="text-align:right;font-weight: bold;"> 5.0 </td>
<td style="text-align:right;font-weight: bold;"> 3.6 </td>
<td style="text-align:right;"> 1.4 </td>
<td style="text-align:right;"> 0.2 </td>
<td style="text-align:left;"> setosa </td>
</tr>
<tr>
<td style="text-align:right;font-weight: bold;"> 5.4 </td>
<td style="text-align:right;font-weight: bold;"> 3.9 </td>
<td style="text-align:right;"> 1.7 </td>
<td style="text-align:right;"> 0.4 </td>
<td style="text-align:left;"> setosa </td>
</tr>
</tbody>
</table>
---
## Show R objects as tables
**Colored** rows
````r
```{r}
knitr::kable(head(iris)) %>%
row_spec(1:3, color = "white", background = "red")
```
````
--
<table>
<thead>
<tr>
<th style="text-align:right;"> Sepal.Length </th>
<th style="text-align:right;"> Sepal.Width </th>
<th style="text-align:right;"> Petal.Length </th>
<th style="text-align:right;"> Petal.Width </th>
<th style="text-align:left;"> Species </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:right;color: white !important;background-color: red !important;"> 5.1 </td>
<td style="text-align:right;color: white !important;background-color: red !important;"> 3.5 </td>
<td style="text-align:right;color: white !important;background-color: red !important;"> 1.4 </td>
<td style="text-align:right;color: white !important;background-color: red !important;"> 0.2 </td>
<td style="text-align:left;color: white !important;background-color: red !important;"> setosa </td>
</tr>
<tr>
<td style="text-align:right;color: white !important;background-color: red !important;"> 4.9 </td>
<td style="text-align:right;color: white !important;background-color: red !important;"> 3.0 </td>
<td style="text-align:right;color: white !important;background-color: red !important;"> 1.4 </td>
<td style="text-align:right;color: white !important;background-color: red !important;"> 0.2 </td>
<td style="text-align:left;color: white !important;background-color: red !important;"> setosa </td>
</tr>
<tr>
<td style="text-align:right;color: white !important;background-color: red !important;"> 4.7 </td>
<td style="text-align:right;color: white !important;background-color: red !important;"> 3.2 </td>
<td style="text-align:right;color: white !important;background-color: red !important;"> 1.3 </td>
<td style="text-align:right;color: white !important;background-color: red !important;"> 0.2 </td>
<td style="text-align:left;color: white !important;background-color: red !important;"> setosa </td>
</tr>
<tr>
<td style="text-align:right;"> 4.6 </td>
<td style="text-align:right;"> 3.1 </td>
<td style="text-align:right;"> 1.5 </td>
<td style="text-align:right;"> 0.2 </td>
<td style="text-align:left;"> setosa </td>
</tr>
<tr>
<td style="text-align:right;"> 5.0 </td>
<td style="text-align:right;"> 3.6 </td>
<td style="text-align:right;"> 1.4 </td>
<td style="text-align:right;"> 0.2 </td>
<td style="text-align:left;"> setosa </td>
</tr>
<tr>
<td style="text-align:right;"> 5.4 </td>
<td style="text-align:right;"> 3.9 </td>
<td style="text-align:right;"> 1.7 </td>
<td style="text-align:right;"> 0.4 </td>
<td style="text-align:left;"> setosa </td>
</tr>
</tbody>
</table>
---
## Show R objects as tables
Change **font size**
````r
```{r}
knitr::kable(head(iris)) %>%
kable_styling(font_size = 10)
```
````
--
<table class="table" style="font-size: 10px; margin-left: auto; margin-right: auto;">
<thead>
<tr>
<th style="text-align:right;"> Sepal.Length </th>
<th style="text-align:right;"> Sepal.Width </th>
<th style="text-align:right;"> Petal.Length </th>
<th style="text-align:right;"> Petal.Width </th>
<th style="text-align:left;"> Species </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:right;"> 5.1 </td>
<td style="text-align:right;"> 3.5 </td>
<td style="text-align:right;"> 1.4 </td>
<td style="text-align:right;"> 0.2 </td>
<td style="text-align:left;"> setosa </td>
</tr>
<tr>
<td style="text-align:right;"> 4.9 </td>
<td style="text-align:right;"> 3.0 </td>
<td style="text-align:right;"> 1.4 </td>
<td style="text-align:right;"> 0.2 </td>
<td style="text-align:left;"> setosa </td>
</tr>
<tr>
<td style="text-align:right;"> 4.7 </td>
<td style="text-align:right;"> 3.2 </td>
<td style="text-align:right;"> 1.3 </td>
<td style="text-align:right;"> 0.2 </td>
<td style="text-align:left;"> setosa </td>
</tr>
<tr>
<td style="text-align:right;"> 4.6 </td>
<td style="text-align:right;"> 3.1 </td>
<td style="text-align:right;"> 1.5 </td>
<td style="text-align:right;"> 0.2 </td>
<td style="text-align:left;"> setosa </td>
</tr>
<tr>
<td style="text-align:right;"> 5.0 </td>
<td style="text-align:right;"> 3.6 </td>
<td style="text-align:right;"> 1.4 </td>
<td style="text-align:right;"> 0.2 </td>
<td style="text-align:left;"> setosa </td>
</tr>
<tr>
<td style="text-align:right;"> 5.4 </td>
<td style="text-align:right;"> 3.9 </td>
<td style="text-align:right;"> 1.7 </td>
<td style="text-align:right;"> 0.4 </td>
<td style="text-align:left;"> setosa </td>
</tr>
</tbody>
</table>
---
## Show R objects as tables