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---
title: "Quarto"
subtitle: "Recherche reproductible en écologie numérique"
author:
- name: "François Guilhaumon"
url: https://fguilhaumon.github.io/
orcid: "0000-0003-4707-8932"
affiliations: "IRD (ENTROPIE)"
date: "2023-11-21"
date-format: long
format:
revealjs:
theme: night
transition: slide
background-transition: fade
scrollable: true
css: assets/custom.css
chalkboard: true
slide-number: true
self-contained: false
footer: "Quarto -- CESAB Data Toolbox -- 2023-11-21"
smaller: false
---
# Notebooks
##
RMarkdown & Jupyter Notebook
::: columns
::: {.column width="33%"}
[![](https://bookdown.org/yihui/rmarkdown/images/cover.png)](https://bookdown.org/yihui/rmarkdown/)
:::
::: {.column width="33%"}
[![](https://bookdown.org/yihui/rmarkdown-cookbook/images/cover.png)](https://bookdown.org/yihui/rmarkdown-cookbook/)
:::
::: {.column width="33%"}
[![](https://github.com/ipython-books/cookbook-2nd/raw/master/cover-cookbook-2nd.png)](http://ipython-books.github.io/)
:::
:::
## RMarkdown
With time, RMarkdown gathered an entire ecosystem of R packages
![](https://mine.quarto.pub/hello-quarto/images/1-share/rmd_ecosystem.png){style="text-align: center;" fig-align="center" width="80%"}
## Quarto: Next gen R Markdown
![](https://media1.giphy.com/media/v1.Y2lkPTc5MGI3NjExZDY5N2Y5MzY0NGI2ZDNkMWM4ZjU0YzNlNWVmZDg1OTg2ZjIyMmMyMyZjdD1n/XgE4LlECZjw6k/giphy.gif){style="text-align: center;" fig-align="center;" width="20%"}
#### Quarto *unifies* and *extends* the R Markdown ecosystem {.centered}
## {auto-animate=true}
Quarto is a new, open-source, scientific and technical publishing system
![](https://cdn.myportfolio.com/45214904-6a61-4e23-98d6-b140f8654a40/c2ef45f1-4a68-4c7a-a43f-bdcf0f90e104.png?h=57404b88e9bf43eea2d2b57c71b13303)
## {auto-animate=true}
Quarto is a new, open-source, scientific and technical publishing system
![](https://cdn.myportfolio.com/45214904-6a61-4e23-98d6-b140f8654a40/c2ef45f1-4a68-4c7a-a43f-bdcf0f90e104.png?h=57404b88e9bf43eea2d2b57c71b13303)
Quarto is a software (command line interface) that renders plain text formats such as `.qmd`, `.rmd`, `.md` into static PDF/Word/HTML reports, books, websites, presentations and more
## Quarto CLI orchestrates each step of rendering
![](https://cdn.myportfolio.com/45214904-6a61-4e23-98d6-b140f8654a40/b5217f2a-f129-4bf9-90dc-c5b9783d0ea8_rw_1920.png?h=0d8c9fc177975359270821bcba83986c)
## Quarto basics
This is a Quarto file -- a plain text file that has the extension `.qmd`:
```{r echo = FALSE, comment = ""}
cat(readr::read_file("diamond-sizes.qmd"))
```
## Quarto basics
It contains three important types of content:
::: incremental
1. An (optional) **YAML header** surrounded by `---`s.
2. **Chunks** of R code surrounded by ```` ``` ````.
3. Text mixed with simple text formatting like `# heading` and `_italics_`.
:::
## Quarto basics
```{r echo = FALSE, comment = ""}
cat(readr::read_file("diamond-sizes.qmd"))
```
##
For example, **Quarto** powers [Computo](https://computo.sfds.asso.fr/)
<br/>
[![A journal of the French Statistical Society SFdS - ISSN 2824-7795](https://computo.sfds.asso.fr/assets/img/logo_text_vertical.svg){width="30%" fig-align="center"}](https://computo.sfds.asso.fr/)
# Quarto VS Rmarkdown
## Decoupling from R
::: incremental
- Quarto is multi-core and multi-engine
- Dedicated CLI
- Unlike Rmd / Jupyter notebooks (Python), Quarto is not tied to a language ([You can use Python in Rmd within Rstudio and R in Jupyter notebooks but few people do]{.small})
- Compatible with your editor (Jupyter Lab, Neovim, VS Code, RStudio, etc ...), *with many visual edition modes available*
- Makes collaboration easier
:::
# Quarto highlights
##
<br/>
::: incremental
- Consistent implementation of features across outputs: (tabsets, code-folding, syntax highlighting)
- More accessible defaults, better support for accessibility
- Guardrails, particularly helpful for new learners: (YAML completion, informative syntax errors)
- Support for other languages like Python, Julia, Observable, ...
:::
## Citations / cross-references
::: incremental
- citations: bibliography files (bibtex), bibliography style (csl)
::: fragment
``` yaml
---
title: "My Document"
bibliography: references.bib
csl: nature.csl
---
She said "[...] but you can't stop the future" [@Sp231992].
```
:::
- cross-references for figures (`fig-`), tables (`tbl-`), sections (`sec-`), equations (`eq-`), (`thm-`), etc
::: fragment
``` yaml
## Introduction {#sec-introduction}
See @sec-introduction for additional context.
```
:::
:::
## Extensions
::: incremental
- [`include-code-files`](https://github.com/quarto-ext/include-code-files) : code from source files
- [`fontawesome`](https://github.com/quarto-ext/fontawesome), [`academicons`](https://github.com/schochastics/academicons), ... : Use icons {{< fa thumbs-up >}} {{< fa folder >}} {{< fa chess-pawn >}} {{< ai open-access }} {{< ai dataverse >}} {{< ai moodle >}} {{< ai sci-hub >}}
- [`collapse-social-embeds`](https://github.com/sellorm/quarto-social-embeds) : include social items.
- [Journal Articles Template](https://quarto.org/docs/extensions/listing-journals.html)
- [`quarto-inrae-extension`](https://github.com/davidcarayon/quarto-inrae-extension) : INRAE formats for HTML, PDF, Docx, Revealjs, and Beamer, thanks to [\@david_carayon](https://twitter.com/david_carayon)
- ... [Quarto Extensions](https://quarto.org/docs/extensions/)
:::
## Moving between formats is straightforward {.centered}
::: columns
::: {.column width="33%"}
::: fragment
Document HTML
::: {.code-file .sourceCode .cell-code}
{{< fa file >}} lesson-1.qmd
:::
``` yaml
title: "Lesson 1"
format: html
```
:::
::: fragment
Document PDF
::: {.code-file .sourceCode .cell-code}
{{< fa file >}} lesson-1.qmd
:::
``` yaml
title: "Lesson 1"
format: pdf
```
:::
:::
::: {.column width="33%"}
::: fragment
Presentation
::: {.code-file .sourceCode .cell-code}
{{< fa file >}} lesson-1.qmd
:::
``` yaml
title: "Lesson 1"
format: revealjs
```
:::
::: fragment
Book
::: {.code-file .sourceCode .cell-code}
{{< fa file >}} \_quarto.yml
:::
``` yaml
project:
type: book
output-dir: _book
```
:::
:::
::: {.column width="33%"}
::: fragment
Website
::: {.code-file .sourceCode .cell-code}
{{< fa file >}} \_quarto.yml
:::
``` yaml
project:
type: website
website:
navbar:
left:
- lesson-1.qmd
```
:::
:::
:::
::: aside
And more in the [Gallery](https://quarto.org/docs/gallery/) ...
:::
## RStudio integration
![](https://quarto.org/docs/get-started/hello/images/rstudio-hello.png)
# Presentations
## Easy presentations
::: {layout="[1, 20]"}
![](https://quarto.org/docs/presentations/revealjs/demo/images/presentation-menu.png){width="41"}
Toggle the slide menu with the menu button to go to other slides and access presentation tools. Some other tools like **PDF Export** in this settings.
:::
. . .
::: {layout="[1, 20]"}
![](https://quarto.org/docs/presentations/revealjs/demo/images/presentation-chalkboard.png){width="41"}
Use the chalkboard button to toggle the chalkboard.
:::
. . .
::: {layout="[1, 20]"}
![](https://quarto.org/docs/presentations/revealjs/demo/images/presentation-notes-canvas.png){width="41"}
Use the notes canvas button to toggle drawing on top of the current slide.
:::
## Callout-blocks
``` yaml
::: {.callout-note}
Five types of callouts: `note`, `warning`,
`important`, `tip`, and `caution`.
:::
```
<br/><br/>
::: callout-note
Five types of callouts: **`note`**, `warning`, `important`, `tip` and `caution`.
:::
::: callout-tip
Five types of callouts: `note`, `warning`, `important`, **`tip`** and `caution`.
:::
## Diagrams
````
```{{mermaid}}
flowchart LR
A[Hard edge] --> B(Round edge)
B --> C{Decision}
C --> D[Result one]
C --> E[Result two]
```
````
<br/><br/>
```{mermaid}
flowchart LR
A[Hard edge] --> B(Round edge)
B --> C{Decision}
C --> D[Result one]
C --> E[Result two]
```
## Videos
``` {.default shortcodes="false"}
{{< video https://www.youtube.com/watch?v=KPXFs2YU3F4>}}
```
[{{< video https://www.youtube.com/watch?v=KPXFs2YU3F4 width="700" height="500" title="Future Maore Reefs" start="423">}}]{.center}
## Widgets
Native support for [JupyterWidgets](https://quarto.org/docs/interactive/widgets/jupyter.html) (Jupyter) and [htmlwidgets](https://quarto.org/docs/interactive/widgets/htmlwidgets.html) (R/knitr)
::: {style="font-size: 0.9em"}
```{r}
#| echo: fenced
#| output-location: column-fragment
library(leaflet)
leaflet(width = "480px") %>%
addTiles() %>%
addMarkers(
lat=43.61270525357229,
lng=3.8733237524215443,
popup="We are here!"
)
```
:::
## Transitions {.smaller}
Use `. . .` to indicate a break at an arbitrary location
. . .
::: {style="font-size: 0.9em"}
````
Let's have a look at `iris`
. . .
```{{r}}
head(iris) |> knitr::kable()
```
````
:::
. . .
Let's have a look at `iris`
. . .
```{r}
head(iris) |> knitr::kable()
```
## Fragments
::: columns
::: {.column width="60%"}
::: {style="font-size: 0.75em"}
```
::: {.fragment}
Fade in
:::
::: {.fragment .fade-out}
Fade out
:::
::: {.fragment .strike}
Strike text
:::
::: {.fragment .fade-in-then-out}
Fade in, then out
:::
::: {.fragment .fade-up}
Slide up while fading in
:::
```
:::
:::
::: {.column width="40%"}
::: fragment
Fade in
:::
::: {.fragment .fade-out}
Fade out
:::
::: {.fragment .strike}
Strike text
:::
::: {.fragment .fade-in-then-out}
Fade in, then out
:::
::: {.fragment .fade-up}
Slide up while fading in
:::
:::
:::
## Column output
::: {style="font-size: 0.8em"}
```{r}
#| echo: fenced
#| code-line-numbers: "|3"
#| output-location: column
library(ggplot2)
ggplot(mtcars, aes(hp, mpg)) +
geom_point() +
geom_smooth(formula = y ~ x, method = "loess")
```
:::
. . .
::: {style="font-size: 0.8em"}
```{r}
#| echo: fenced
#| code-line-numbers: "|3"
#| output-location: column-fragment
ggplot(mtcars, aes(hp, mpg)) +
geom_point() +
geom_smooth(formula = y ~ x, method = "loess")
```
:::
## Tabset output {.smaller}
::: panel-tabset
### Code
```{r}
#| echo: fenced
p <- ggplot(mtcars, aes(hp, mpg)) +
geom_point() +
geom_smooth(formula = y ~ x, method = "loess")
```
### Plot
```{r}
p
```
### Under the hood
::: {style="font-size: 0.8em"}
````
::: {.panel-tabset}
### Plot code
```{{r}}
#| echo: fenced
p <- ggplot(mtcars, aes(hp, mpg)) +
geom_point() +
geom_smooth(formula = y ~ x, method = "loess")
```
### Plot
```{{r}}
p
```
:::
````
:::
:::
## Easy layouts {.smaller}
::: panel-tabset
### Code
- Use negative values for white space
::: {style="font-size: 0.8em"}
```{r}
#| echo: fenced
#| eval: false
#| fig-subcap:
#| - "boring 🥱"
#| - "boooring 🥱🥱"
#| - "boooriiing 🥱🥱🥱"
#| fig-height: 2
#| layout: [[40,-20,40], [100]]
p
p
p
```
:::
### Plot
```{r}
#| fig-subcap:
#| - "boring 🥱"
#| - "boooring 🥱🥱"
#| - "boooriiing 🥱🥱🥱"
#| fig-height: 2
#| layout: [[40,-20,40], [100]]
p
p
p
```
:::
## RMarkdown {auto-animate="true"}
```` markdown
```{{r setup, include=FALSE}}
knitr::opts_chunk$set(echo = TRUE)
library(tidyverse)
library(DT)
library(ggimage)
```
````
## Quarto {auto-animate="true"}
```` markdown
```{{r}}
#| label: "setup"
#| include: false
knitr::opts_chunk$set(echo = TRUE)
library(tidyverse)
library(DT)
library(ggimage)
```
````
Options are moved to within the code chunk using `#|` (hash-pipe) for each line
## How to move to Quarto {.smaller}
::: incremental
1. [Install Quarto](https://quarto.org/docs/get-started/)
2. Start a Quarto Project
3. Convert your Rmarkdown Documents
- Change your `output:` to the corresponding `format:` in your YAML
- Use `knitr::convert_chunk_header()` to convert your code blocks (outputs a `.qmd` file)
4. Render your files
5. For websites: edit your `_quarto.yml` file if necessary
6. Publish
:::
## Take Home Messages
::: incremental
- Quarto is a new, open-source, scientific and technical publishing system
- Quarto supports multiple languages / IDEs
- Quarto standardizes a lot of outputs
- Does a better job of one document, many outputs than Rmd
- Lots of publishing features (references, figures, etc.)
- Very well documented
:::
# Ressources
## Ressources
<br/><br/>
- [Quarto documentation](https://quarto.org/)
- [Hadley's intro to Quarto](https://r4ds.hadley.nz/quarto)
- [Awesome Quarto](https://github.com/mcanouil/awesome-quarto)
- [La présentation originale de Cédric Midoux](https://cedric.midoux.pages.mia.inra.fr/slides/posts/2023-04-13_quarto)