Create a Quarto File in a project we already have in our computer
Create a New Quarto Project
General folder structure in a Quarto Project
Quarto file general structure
Visual mode vs Source mode
Visual mode shortcuts
Insert Code Chuncks
Code cuncks options
Code Chuncks Options
You can add Quarto options to code cells by adding a #| comment to the top, followed by the option in YAML syntax. For example, adding the echo option with the value true would look like this:
The echo option describes whether the code is included in the rendered article. If you make this change and save index.qmd, you’ll see this code now appears in the article.
apply journal styles to your outputs with Quarto extensions
orchestrate multiple inputs and outputs with embedded computing using a new Quarto project type: manuscript
produce manuscripts in multiple formats (including LaTeX or MS Word formats required by journals), and give readers easy access to all of the formats through a website
publish computations from one or more notebooks alongside the manuscript, allowing readers to dive into your code and view it or interact with it in a virtual environment
publish to GitHub Pages, Netlify, and more
Journals vs Manuscripts
In Quarto, a journal refers to a single document, potentially with embedded computations and visualizations, designed for publication in a journal format.
A manuscript, on the other hand, represents a collection of Quarto documents, potentially including multiple chapters, that are intended to be assembled into a book-like structure.
Journals
Intsalling the templates from your terminal
How does the journal template file looks like
Rendering a Journal paper
Getting started with a manuscript: create a manuscript project
Start from scratch
in your terminal write quarto create project manuscript <name>
Learn how to Track your project with Git and host on GitHub for happy publishing.
Your Turn! Option 1
If you already have a peper of your own (with differnt r files with code) go to your RStudio Terminal and create a new project from scratch
Terminal
quarto create project manuscript indo-rctCreating project at /Users/mine/indo-rct:- Created _quarto.yml- Created index.qmd- Created references.bib? Open Withvscode❯ rstudio(don't open)
Your Turn! Option 2
If you wanna follow along the same structure we are going to you can copy the repo from github repo
The basic workflow for writing a manuscript in Quarto is to make changes to your article content (the index.qmd if you are following the example), preview the changes with Quarto, and repeat.
How does it look like once render?
Your Turn: Render your first qmd manuscript
Open index.qmd.
Render and preview the manuscript by hitting the Render button located in the menu bar of the editor
You’ll see some output from Quarto in the Background Jobs pane and then a live preview will appear in the Viewer pane.
Change the title of your index.qmd
Save the file, re-render, and you’ll see the preview update.
title: La Palma Earthquakesauthor:-name: Steve Purvesorcid: 0000-0002-0760-5497corresponding:trueemail: steve@curvenote.comroles:- Investigation- Project administration- Software- Visualizationaffiliations:- Curvenote-name: Rowan Cockettorcid: 0000-0002-7859-8394corresponding:falseroles:[]affiliations:- Curvenotekeywords:- La Palma- Earthquakesabstract: | In September 2021, a significant jump in seismic activity on the island of La Palma (Canary Islands, Spain) signaled the start of a volcanic crisis that still continues at the time of writing. Earthquake data is continually collected and published by the Instituto Geográphico Nacional (IGN). ...plain-language-summary: | Earthquake data for the island of La Palma from the September 2021 eruption is found ...key-points:- A web scraping script was developed to pull data from the Instituto Geogràphico Nacional into a machine-readable form for analysis- Earthquake events on La Palma are consistent with the presence of both mantle and crustal reservoirs.date: last-modifiedbibliography: references.bibcitation:container-title: Earth and Space Sciencenumber-sections:true---
Using computations in the body of youtr text
You can use computed values directly in your article text using the syntax `{r} expr`. For example, consider this line in index.qmd:
Based on data up to and including 1971, eruptions on La Palma happen every `{r} round(avg_years_between_eruptions, 1)` years on average.
When rendered, it displays as:
Based on data up to and including 1971, eruptions on La Palma happen every 79.8 years on average.
Code chuncks for computations using the lable and fig- options
```{r}#| label: fig-timeline#| fig-cap: Timeline of recent earthquakes on La Palma#| fig-alt: An event plot of the years of the last 8 eruptions on La Palma.#| fig-height: 1.5#| fig-width: 6par(mar =c(3, 1, 1, 1) +0.1)plot( eruptions, rep(0, n_eruptions), pch ="|", axes =FALSE)axis(1)box()```
Citations
references.bib
@article{marrero2019, author = {Marrero, Jos{\' e} and Garc{\' i}a, Alicia and Berrocoso, Manuel and Llinares, {\' A}ngeles and Rodr{\' i}guez-Losada, Antonio and Ortiz, R.}, journal = {Journal of Applied Volcanology}, year = {2019}, month = {7}, pages = {},title = {Strategies for the development of volcanic hazard maps in monogenetic volcanic fields: the example of {La} {Palma} ({Canary} {Islands})}, volume = {8}, doi = {10.1186/s13617-019-0085-5},}
Citations
Studies of the magma systems feeding the volcano, such as @marrero2019, have proposed ...
When rendered, it displays as:
Studies of the magma systems feeding the volcano, such as Marrero et al. (2019), have proposed
Citations
… and when hovering over the citation text it reveals the full reference details allowing reader to click on the citation and take it to the reference in the References section at the end of the article:
Citations
Another common style is to place the citation within parentheses at the end of a sentence. You can achieve this by enclosing the citation syntax in square brackets [. For example,
A prior study of the magma systems feeding the volcano proposed that there are two main magma reservoirs feeding the Cumbre Vieja volcano [@marrero2019].
When rendered, it displays as:
A prior study of the magma systems feeding the volcano proposed that there are two main magma reservoirs feeding the Cumbre Vieja volcano (Marrero et al. 2019).
Citations
Tip
Quarto support differnt syntax variotions to include page numbers, chapters, exclude author names and other cool posibilities. You can learn more about it the Citation documentation at https://quarto.org/docs/authoring/citations.html
Your Turn! Add a citation to your bib file and use it
Go to your bib file and add a citation
Go back to your index.qmd file and use the citation
Render your file and chevck the changes
Your turn!: Redy steady go!
👍 Please sign me with when you are ready.
Cross References
Labeled as…
@fig-timeline
Should be use used as
Eight eruptions have been recorded since the late 1400s (@fig-timeline).
And will look something like
Eight eruptions have been recorded since the late 1400s (Figure 1).
Cross References element and prefix
Figure fig- and will render as Figure 1
Table tbl- and will render as Table 1
Equation eq- and will render as Equation 1
Section sec- and will render as Section 1
Warning
To cross reference sections your document YAML header must also include number-sections: true You can add a label to a section heading in curly braces after the heading, e.g ## Data & Methods {#sec-data-methods} and the you can then reference this section in the text by adding the text and the @ reference like Data and methods are discussed in @sec-data-methods.
Cross Reference in visual mode
Static Figues and images
To include a figure from a file, the markdown syntax looks like:
By using #fig-name-of-image inside curly braces following the image path you can provide the reader a label for cross references. For eg.
{#fig-map fig-alt="A map of the Canary Islands. The second most west island, La Palma, is highlighted."}
Tip
It is recomended to store your in an folder named images/. Your images can be anywhere inside your manuscript project directory, just make sure you include the full path to the image, relative to the location of index.qmd.
{fig-align = “center”}
{fig-align = “center”}
