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<!DOCTYPE html>
<html lang="" xml:lang="">
<head>
<title> Extending Rmarkdown</title>
<meta charset="utf-8" />
<meta name="author" content=" Nicolas CASAJUS .inst[nicolas.casajus at fondationbiodiversite.fr]" />
<script src="libs/header-attrs-2.18/header-attrs.js"></script>
<link href="libs/font-awesome-6.2.0/css/all.min.css" rel="stylesheet" />
<link href="libs/font-awesome-6.2.0/css/v4-shims.min.css" rel="stylesheet" />
<link rel="stylesheet" href="css/xaringan-themer.css" type="text/css" />
<link rel="stylesheet" href="css/custom.css" type="text/css" />
</head>
<body>
<textarea id="source">
class: right, middle, title-slide
.title[
# <br /><code>Extending Rmarkdown</code>
]
.subtitle[
## <br />
]
.author[
### <br />Nicolas CASAJUS<br />.inst[nicolas.casajus at fondationbiodiversite.fr]
]
.date[
### .inst[Mardi 29 novembre 2022]
]
---
## Table of contents
.medium[
.pull-left[
1. Tips and Tricks
- Child
- `knitr::read_chunks()`
- params
- Figures & Tables
]
.pull-right[
**Output formats**
- Reports (`HTML`, `PDF`, `DOCX`, `GitHub Document`)
- Presentations (`xaringan`, `reveal.js`, `PPTX`)
- Scientific articles (`rticles`)
- Websites (`blogdown`, `distill`, `pkgdown`)
- Books (`bookdown`)
- Dashboards
- GitHub Pages (for HTML outputs)
**Bibliography**
- RStudio & Zotero
- Zotero styles
- `nocite: '@*'`
**Theming**
- Default themes
- Extensions
- Custom blocks
**Miscellaneous**
- Break list `<!-- end -->`
- Hard line break `\ `, `<br>`, `\newline`
]
]
---
## Chunks options
Usual way:
````r
```{r 'chunk-name', echo=FALSE, fig.width=10, fig.cap='This is a long long long long caption.'}
x <- 1 + 2
print(x)
```
````
```
## [1] 3
```
--
<br>
Alternatively:
````r
```{r}
#| 'chunk-name',
#| echo = FALSE,
#| fig.width = 10,
#| fig.cap = 'This is a long long
#| long long caption.'
x <- 1 + 2
print(x)
```
````
```
## [1] 3
```
.medium[<i class="far fa-hand-point-right" role="presentation" aria-label="hand-point-right icon"></i> Quarto uses this syntax]
---
## Global chunks options
Do not repeat same chunk options values across all chunks. Use instead a general
chunk that will provide default values for all chunks.
````r
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE, eval = TRUE, message = FALSE,
fig.width = 10, fig.height = 8, ...)
```
````
--
<br>
You will be able to change locally (for specific chunk) the default value:
````r
```{r 'chunk-name', echo = TRUE}
1 + 3
```
````
```r
1 + 3
```
```
## [1] 4
```
---
## Rmd with others languages
.pull-left[
**R code** - <i class="fab fa-r-project" role="presentation" aria-label="r-project icon"></i>
````r
```{r}
person <- "Jane Doe"
paste0("Hello, ", person, "!")
```
````
```
## [1] "Hello, Jane Doe!"
```
]
---
## Rmd with others languages
.pull-left[
**R code** - <i class="fab fa-r-project" role="presentation" aria-label="r-project icon"></i>
````r
```{r}
person <- "Jane Doe"
paste0("Hello, ", person, "!")
```
````
```
## [1] "Hello, Jane Doe!"
```
**Bash code** - <i class="fas fa-code" role="presentation" aria-label="code icon"></i>
````r
```{bash}
#| engine.path='/bin/bash'
person="Jane Doe"
echo "Hello"$person"!"
```
````
```
## Hello, Jane Doe!
```
]
.pull-right[
**Python code** - <i class="fab fa-python" role="presentation" aria-label="python icon"></i>
````r
```{python}
#| engine.path='/usr/local/bin/python3'
person <- "Jane Doe"
f"Hello, {person}!"
```
````
```
## 'Hello, Jane Doe!'
```
**Ruby on Rails code** - <i class="fas fa-code" role="presentation" aria-label="code icon"></i>
````r
```{ruby}
#| engine.path='/usr/bin/ruby'
person = "Jane Doe"
puts "Hello, " + person + "!"
```
````
```
## Hello, Jane Doe!
```
]
--
```r
Sys.which("python3") ## Locate the Python3 engine (binary)
```
```
## python3
## "/usr/local/bin/python3"
```
---
## Rmd with others languages
A smarter approach: use the global chunks options of `knitr`.
```r
## Global options ----
knitr::opts_chunk$set(engine.path = list(python = "/usr/local/bin/python3"))
```
--
<br/>
And then,
````r
```{python}
person <- "Jane Doe"
f"Hello, {person}!"
```
````
```
## 'Hello, Jane Doe!'
```
---
## Resources
.medium[
- [**R Markdown Advanced Tips**](https://www.youtube.com/watch?v=WkF7nqEYF1E)
<br/><i class="far fa-hand-point-right" role="presentation" aria-label="hand-point-right icon"></i> Video by **Tom Mock**
- [**Meta RMarkdown - Taxonomy and Use cases**](https://themockup.blog/posts/2020-07-25-meta-rmarkdown/)
<br/><i class="far fa-hand-point-right" role="presentation" aria-label="hand-point-right icon"></i> Blogpost by **Tom Mock**
- [**R Markdown Cookbook**](https://bookdown.org/yihui/rmarkdown-cookbook/)
<br/><i class="far fa-hand-point-right" role="presentation" aria-label="hand-point-right icon"></i> Online book by **Yihui Xie et al.**
- [**R Markdown: The Definitive Guide**](https://bookdown.org/yihui/rmarkdown/)
<br/><i class="far fa-hand-point-right" role="presentation" aria-label="hand-point-right icon"></i> Online book by **Yihui Xie et al.**
- [**Dynamic Documents with R and knitr**](https://duhi23.github.io/Analisis-de-datos/Yihue.pdf)
<br/><i class="far fa-hand-point-right" role="presentation" aria-label="hand-point-right icon"></i> Online book by **Yihui Xie**
- [**blogdown: Creating Websites with R Markdown**](https://bookdown.org/yihui/blogdown/)
<br/><i class="far fa-hand-point-right" role="presentation" aria-label="hand-point-right icon"></i> Online book by **Yihui Xie et al.**
- [**bookdown: Authoring Books and Technical Documents with R Markdown**](https://bookdown.org/yihui/bookdown/)
<br/><i class="far fa-hand-point-right" role="presentation" aria-label="hand-point-right icon"></i> Online book by **Yihui Xie**
]
---
## Custom blocks
.pull-left[
**In the `.Rmd` file**
```
::: {.box-info}
Lorem ipsum dolor sit amet, consectetur adipiscing
elit. Suspendisse at mattis libero. Vestibulum
ante ipsum primis in faucibus...
:::
```
]
.pull-right[
**CSS style**
```css
div.box-info p {
padding: 1em;
margin: 20px 0;
background: #DDECF6;
border: 1px solid #CEE9F2;
border-radius: 10px;
color: #487997;
border-left: 5px solid #487997;
}
```
]
<br>
.center[]
.medium[Example: <**https://github.com/rdatatoolbox/rmd-examples/custom-blocks/index.Rmd**>]
</textarea>
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