.

Outline

• Introduction to Quarto

• Quarto document elements

• Exercise: generating report

• Improving report

Introduction to Quarto

Reproducibility

Reproducibility

• Obtaining computational results using the same input data, computational steps, methods, code and conditions of analysis.

Replicability

• Obtaining consistent results across studies aimed at answering the same scientific question, each of which has obtained its own data.

Source: National Academies of Sciences, Engineering, and Medicine. 2019. Reproducibility and Replicability in Science. Washington, DC: The National Academy Press, https://doi.org/10.17226/25303

What is reproducibility and replicability in research?

Reproducibility

• same procedures

• same data

• same code

Replicability

• same procedures

• new data

• new code

Source: Baker, M. (2016). 1,500 scientists lift the lid on reproducibility. Nature, 533(7604), Article 7604. https://doi.org/10.1038/533452a

Source: Baker, M. (2016). 1,500 scientists lift the lid on reproducibility. Nature, 533(7604), Article 7604. https://doi.org/10.1038/533452a

Quarto document elements

Quarto document elements

Quarto document elements

Renderring or knitting file

YAML

• YAML header

• Output types

• adding and formatting date

YAML

Yet Another Markup Language

• refers to the metadata at the top of the document

• define the structure, appearance, and behavior

• enclosed by 3 dashes ---

---
title: "My Analysis Report"
author: "John Doe"
date: "2024-09-21"
format: html
editor: visual
---

YAML

Yet Another Markup Language

• title: title of the document

• author: author of the document

• date: date of the document

• format: output format

• editor: editor used to create the document

---
title: "My Analysis Report"
author: "John Doe"
date: "2024-09-21"
format: html
editor: visual
---

Code chunk

• adding code chunk

• adding code comments

Code chunk

• section of executable code embedded in the document

• enable to run code and display output

• enclosed by three back ticks and curly braces

Text

• adding and formatting texts

• adding headers

• adding sentences

• inline code

• including links and images

Text

• Quarto supports various fomatting elements to create rich content.

• Headers, paragraphs, lists, and inline code are some of the elements that can be used to create content.

Text

Headers

Text

Bold and italics

This is **bold** and *italic* text.

This is bold and italic text.

Text

Lists

• Unordered lists: use - or * for bullet points.

• Ordered lists: use numbers followed by periods.

- Item 1
- Item 2


1. First
2. Second

• Item 1

• Item 2

1. First

2. Second

Text

Links and images

• Links: [Link text](https://example.com)

• Images: ![Alt text](path/to/image.png)

[Quarto website](https://quarto.org)

![Sample Image](images/example.png)

Quarto website

Sample Image