Quarto

— enables you to weave together content and executable code into a finished document —

CAPRO

We specialize in data processing and capture of large life science data for social sciences and humanities

CAPRO

• Data flow and processing

• Data capture

• Project data management

• Registry data handling

• HPC analyses

Next generation R Markdown

Quarto is a multi-language, next-generation version of R Markdown from Posit, and includes dozens of new features and capabilities while at the same being able to render most existing Rmd files without modification.

Multi-lingual

• Create dynamic content with Python, R, Julia, and Observable.

• Author documents as plain text markdown or Jupyter notebooks.

• Publish high-quality articles, reports, presentations, websites, blogs, and books in HTML, PDF, MS Word, ePub, and more.

• Author with scientific markdown, including equations, citations, crossrefs, figure panels, callouts, advanced layout, and more.

IDE agnostic

• RStudio integrated

• Vs Code extensions

• Jupyter notebooks

• Text editor

Quarto Extensions

Extensions are a powerful way to modify and extend the behavior of Quarto.

• Shortcodes for icons etc.

• Presentation themes

• Journal article templates

Comprehensive online docs

• User guide

• Reference list

• Gallery of examples

• Blog with updates and show-cases

This workshop

Outline

• Elements of a qmd ( ~ 45 minutes)

• Making our first html report ( ~ 45 minutes)

• Citations & cross-references ( ~ 45 minutes)

• Lunch ( ~ 60 minutes)

• Making our first pdf report (~ 45 minutes)

• Making our first presentation ( ~ 45 minutes)

Tools

Being taught

• Quarto

• RStudio

Not taught

• R

• python / julia / js

• vscode / jupyter

Using these tools, you will be able to follow along everything I do, and I can help when things go wrong

If you choose another setup, you are very welcome to that. But I will not be able to help as easily (or set aside time to do so), and you will need to think of your own code examples in other languages.

Markdown flavours

Markdown type	file extension	code chunks
Plain markdown	.md	no
R markdown	.Rmd	yes
Quarto markdown	.qmd	yes

What are code chunks?

Pieces of code that will be execute on report rendering to include output in the report.

``` {{r}}
#| label: code-example

hist(mtcars$mpg)
```

What are code chunks?

These could also be inline code for incorporation into the text parts of a report.

R Markdown | Quarto

Number of observations: `r nrow(mtcars)` . 

Output

Number of observations: 32

How does that work?

R markdown vs. Quarto

Code chunks can be provided inside the code chunk

```{r echo = TRUE, message = FALSE ```

```{r}

#| echo: true

#| message: false

```