Requirements

• You must have installed quarto: https://quarto.org/docs/get-started/
• Download the dataframe_fishi.csv
• Have the necessary packages been installed?

# fishi
devtools::install_github("https://github.com/OB7-IRD/fishi", INSTALL_opts=c("--no-multiarch"))

# other packages
pkg_list <- c(
  "quarto", "rmarkdown", "kableExtra", "ggplot2", "dplyr"
  )
install.packages(pkg_list, repos="http://cran.us.r-project.org")

Great, let’s get started!

The basics

Composition of a Quarto script :

• IDE Studio

• YAML header

• Anatomy of a document

  • Titles
  • The syntax
  • Adding an image
  • Creating two columns

The basics - IDE Studio

1. Create a quarto file

1.  File > New File > Quarto document

2.  Details : Titre / Auteur / HTML

3.  Create

The basics - IDE Studio

1. Create a quarto file

1.  File > New File > Quarto document

2.  Details : Titre / Auteur / HTML

3.  Create

2. IDE Studio

The basics - IDE Studio

1. Create a quarto file

1.  File > New File > Quarto document

2.  Details : Titre / Auteur / HTML

3.  Create

2. IDE Studio

The basics - IDE Studio

1. Create a quarto file

1.  File > New File > Quarto document

2.  Details : Titre / Auteur / HTML

3.  Create

2. IDE Studio

The basics - IDE Studio

1. Create a quarto file

1.  File > New File > Quarto document

2.  Details : Titre / Auteur / HTML

3.  Create

2. IDE Studio

The basics - IDE Studio

The basics - YAML header

 ---
title: "formation-quarto"
author:
  - name: Clara Lerebourg
    orcid: 0000-0003-0589-8932
    email: Clara.Lerebourg@ird.fr
    institution: IRD/MARBEC/OB7
  - name: Mathieu Depetris
    orcid: 0000-0001-8080-0531
    email: Clara.Lerebourg@ird.fr
    institution: IRD/MARBEC/OB7
  - name: Julien Lebranchu
    orcid: 0000-0002-7759-0534
    email: Julien.Lebranchu@ird.fr
    institution: IRD/MARBEC/OB7
toc: true
number-sections: true
format: 
  html :
    code-fold: true
prefer-html: true
---

• toc : if true add a table of content

• Formats : html, pdf, docx

• code-fold : hide r code

• prefer-html : displays images when saving in word and pdf format

The basics - Anatomy of the document

Titles

# Header 1

## Header 2

### Header 3

#### Header 4

##### Header 5

###### Header 6

The basics - Anatomy of the document

Syntax

*italics* and **bold**

superscript^2^ / subscript~2~

~~strikethrough~~

`verbatim code`

The basics - Anatomy of the document

Add a picture

![](image/polar-axis.png){.absolute left="350" top="175" width="80%"}

The basics - Anatomy of the document

Add two columns

::: columns
::: {.column width="50%}
Colonne 1
:::

::: {.column width="50%}
Colonne 2
:::

:::

Your Turn

• Create a document Quarto qmd
• Write the Yaml
• Write a texte with syntax and headers
• Add a picture and center it in the middle of the doc
• Create two colomns

What we are going to see

Deepening our knowledge:

• Libraries and dataframe

• Figures

• Tables

• Text

• List

Libraries and dataframes

Like in every script you need to start with the libraries

library(ggplot2)
library(dplyr)
library(kableExtra)
library(tidyverse)
library(fishi)

Use the dataframe for fishi

dataframe <- read_csv("dataframe_fishi.csv")

Figures

fishing_capacity(dataframe = dataframe)

Figures

#| label: fig-fishing-capacity
#| fig-cap: "Annual changes in the number of vessels"
#| fig-width: 10
#| fig-height: 10

fishing_capacity(dataframe = dataframe)

Figures

#| fig-height: 7
#| fig-width: 7
#| label: fig-fishing-capacity-2
#| fig-cap: "Annual changes in the number of vessels"
#| fig-subcap:
#|   - "Color by number of cylinders“
#|   - "Color by engine displacement, in liters“
#| layout-ncol: 2

fishi::fishing_capacity(dataframe = dataframe)
fishi::fishing_capacity(dataframe = dataframe)

Tables

#| label: table-mpg

mpg

# A tibble: 234 × 11
   manufacturer model      displ  year   cyl trans drv     cty   hwy fl    class
   <chr>        <chr>      <dbl> <int> <int> <chr> <chr> <int> <int> <chr> <chr>
 1 audi         a4           1.8  1999     4 auto… f        18    29 p     comp…
 2 audi         a4           1.8  1999     4 manu… f        21    29 p     comp…
 3 audi         a4           2    2008     4 manu… f        20    31 p     comp…
 4 audi         a4           2    2008     4 auto… f        21    30 p     comp…
 5 audi         a4           2.8  1999     6 auto… f        16    26 p     comp…
 6 audi         a4           2.8  1999     6 manu… f        18    26 p     comp…
 7 audi         a4           3.1  2008     6 auto… f        18    27 p     comp…
 8 audi         a4 quattro   1.8  1999     4 manu… 4        18    26 p     comp…
 9 audi         a4 quattro   1.8  1999     4 auto… 4        16    25 p     comp…
10 audi         a4 quattro   2    2008     4 manu… 4        20    28 p     comp…
# ℹ 224 more rows

Tables

#| label: table-mpg-1

kable(mpg) %>% 
 kable_classic(c("hover", 
                 "condensed"),
               font_size = 14)

Text

The plots in @fig-fishing-capacity show the annual changes 
in the number of purse seiners by tonnage categories and total carrying capacity

The plots in Figure 1 show the annual changes in the number of purse seiners by tonnage categories and total carrying capacity

Text

mean_cty <- round(mean(mpg$cty), 2) 
mean_hwy <- round(mean(mpg$hwy), 2)

 
 There are `r nrow(mpg)` observations in our data. The average city mileage of the cars in our data is `r mean_cty` and the average highway mileage is `r mean_hwy`.

Text

mean_cty <- round(mean(mpg$cty), 2) 
mean_hwy <- round(mean(mpg$hwy), 2)

 
 There are `r nrow(mpg)` observations in our data. The average city mileage of the cars in our data is `r mean_cty` and the average highway mileage is `r mean_hwy`.

There are 234 observations in our data.
The average city mileage of the cars in our data is 16.86 and the average highway mileage is 23.44.  

List

Made list - Incremental

::: {.incremental}

- Eat spaghetti
- Drink wine

:::

List

Made list - Non incremental

::: {.nonincremental}

- Eat spaghetti
- Drink wine

:::

Your Turn

• Display a fishi figure : Add a title and define the size
• Display a table
• Write a text using the values in the mpg table

Create a presentation

1. Create a quarto presentation

1.  File > New File > Quarto presentation

2.  Details : Titre / Auteur / HTML

3.  Create

Create a presentation

2. Create slides

Slides are defined by level 1 titles (#) for a title on a page, or level 2 (##) :

Create a presentation

2. Create slides

Slides are defined by level 1 titles (#) for a title on a page, or level 2 (##) :

---
title: "Habits"
author: "John Doe"
format: revealjs
---

# In the morning

## Getting up

- Turn off alarm
- Get out of bed

## Breakfast

- Eat eggs
- Drink coffee

Code animation

For animation : Title and {auto-animate=“true”}

For smaller slide : Title and {.smaller}

Your Turn

• Create a presentation Quarto qmd
• Write the Yaml
• Create multiple slides
  • One with a picture in the middle
  • One with fragments
  • One with animations
  • One with the code on the left and a fishi figure on the right

Advanced class

More informations :

• References
• How to change the theme ?
• Notes, warning and comments

References

Write /ci in the quarto document and select “Citation… Reference to a source”.

References

Write /ci in the quarto document and select “Citation… Reference to a source”.

Change theme

HTML documents rendered with Quarto use Bootstrap 5 by default. This can be disabled or customized via the theme option:

theme: default # bootstrap 5 default
theme: cosmo   # cosmo bootswatch theme
theme: pandoc  # pandoc default html treatment
theme: none    # no theme css added to document

Quarto includes 25 themes from the Bootswatch project (for example, the website uses the cosmo theme) : https://bootswatch.com/

Change theme

HTML documents rendered with Quarto use Bootstrap 5 by default. This can be disabled or customized via the theme option:

theme: default # bootstrap 5 default
theme: cosmo   # cosmo bootswatch theme
theme: pandoc  # pandoc default html treatment
theme: none    # no theme css added to document

Quarto includes 25 themes from the Bootswatch project (for example, the website uses the cosmo theme) : https://bootswatch.com/

Use of any of these themes via the theme option. For example:

format:
  html:
    theme: united

Notes, warnings and comments

:::{.callout-note}
Note that there are five types of callouts, including: 
`note`, `tip`, `warning`, `caution`, and `important`.
:::

Quarto Extension

Quarto have multiple extensions that you can integrate in your documents:

For example:

• fontawesome Use Font Awesome icons in HTML and PDF documents.
• quarto-nes-theme NES.css format for Revealjs
• …

More details on

• https://quarto.org/docs/extensions/
• Quarto Awesome

Ob7 extensions

You can use our own extension/theme:

• Theme for presentation with RevealJS : quarto-farquhar-revealjs
• Theme for letter : quarto-ob7-letter-extension
• Theme for report : quarto-ob7-report
  • Only document in Word and HTML format.
  • PDF is still under development.