x05-Creation of Reports with Quarto

Applied Statistics – A Practical Course

Thomas Petzoldt

2025-09-16

About these slides

The slides were created with Quarto using Rstudio and R.

Use cursor keys for navigation, press O for a slide Overview

Markdown, RMarkdown and Quarto

Markdown .md

” … is a lightweight markup language for creating formatted text using a plain-text editor” (Wikipedia, 2022).
Can be written with any text editor, less perfect than Latex, but much easier.
Markdown supported by many programs and services (e.g. Github, StackOverflow, Matrix, RStudio, …)

RMarkdown .Rmd

is an extension of markdown that can embed R code.
superseeded by Quarto

Quarto .qmd

is an extension of Markdown that can embed R, Python, Julia and Observable code.
improved capabilities to create reports, slides, websites, papers, books.

Why Markdown or Quarto

Quick note taking (documentation of ideas, experiments, SOPs, …)
Documentation of statistical analyses (Quarto + R)
Clearly structured documents (outline clearly visible)
Easy literature referencing
Much easier than LaTeX
Widely used technology, useful for Stackoverflow, Github or Matrix

Software

You can use any text editor, e.g. Notepad++, your mail client
… or even Word

Better: use an editor with Markdown support
- RStudio
- PanWriter, a basic writing program with an almost empty screen
  $\rightarrow$ distraction free writing
- Joplin, a note taking program with cloud connectivity and encryption
- many online services: Github, Gitlab, StackOverflow, Matrix
- and more

Many Markdown Programs Available, e.g. Panwriter

Panwriter with live preview

Let’s use RStudio. Supports Markdown and Quarto

RStudio

Example

Section titles are introduced with one or several hash symbols #, ##, praragraphs with empty lines, italic and bold face are indicated with one or two starts before and after a phrase, bullet points with a leading dash - or a star *. Weblinks are automatically activated. Here an example:

    # First level

    Text can be written with any editor, that can be formatted, e.g. *slanted*, **boldface**,
    `verbatim text` weblinks: https://tu-dresden.de or bullet points:

    * point 1
    * point 2

    Section titles start with one or more hash tags
    
    
    ## Second level
    
    ### Third level

There are of course more formatting options, found in the docs or explained later.

YAML Header

Quarto and markdown documents can have a few special lines on top, enclosed within three dashes ---. This so called “YAML header” is used to set text settings and formatting options:

    ---
    title: "Test"
    author: "Who wrote this"
    date: '2024-11-12'
    format: html
    ---
    
    # First Section

    Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy
    eirmod tempor invidunt ut labore et dolore magna aliquyam erat.
    
    At vero eos et accusam et justo duo dolores et ea rebum.
    
    # Second Section
     
    Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum 
    dolor sit amet.

YAML: yet another markup language. A list format coming from the python world.

Layout and format conversion

User can concentrate on writing, formatting is done automatically.
Several tools exist to convert markdown to other document formats.
One of the most popular is pandoc. It is built-in in Rstudio.

Rendering is done with the pandoc utility to convert Quarto or Markdown text to
HTML for web pages, pdf for printing, or Word for further editing.

What is Pandoc?

Pandoc is a universal text conversion tool
It is said to be the “swiss-army knife” to convert between formats
Open Source licensed: GPL 2.0 resp. MIT license
Available from: https://pandoc.org/
… or embedded in RStudio

Exercise

Write your first Quarto document in RStudio.
Render it to HTML and Word

Optional without warranty

Create PDF output
Needs LaTeX type setting system installed
Can be done with R’s tinytex package:

::: {.cell}

:::

… or by installing tinytex from the Terminal of RStudio

quarto install tinytex

and then include format: pdf in the YAML header

title: "My document"
format: pdf

See more at: https://quarto.org/docs/output-formats/pdf-basics.html

Section Titles

Section titles can be formatted with hashtags or by underlining:

# A Section

## A subsection

or:

A Section
=========

A Subsection
------------

Automatic numbering can optionally be enabled in the YAML header:

---
title: "My document"
format:
  html:
    toc: true
    number-sections: true
---

Weblinks

Formatted weblinks

[further reading](https://rmarkdown.rstudio.com)

is then formatted as: further reading

Example

The [*Markdown Wikipedia page*](https://de.wikipedia.org/wiki/Markdown) contains examples.

The Markdown Wikipedia page contains examples.

Images

Images are similar to weblinks, but with a leading !

![figure title](mushrooms.jpg)

figure title

Verbatim Text

Verbatim text can be created with several methods:

Inline: enclose text within single backticks `verbatim text` $\rightarrow$ verbatim text
Indentation by 4 spaces
Use so-called fencing with ``` before and after a tect or code block.

```
Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy
eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam
voluptua.
```

appears as:

Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy
eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam
voluptua.

Tables

Source code:

| Right | Left | Default | Center |
|------:|:-----|---------|:------:|
|    12 | 34   |   56    |   78   |
| this  | is   |   a     | table  |

HTML Output:

Right	Left	Default	Center
12	34	56	78
this	is	a	table

PDF output:

Style similar to a scientific paper.

Bigger or more complex tables: create the table in Excel or LibreOffice and add markdown formatting, or use R and kable to create the table from data.

Citations

Create database file in `.bib`-format, e.g. `references.bib`

can be exported from Zotero
put bibliography file to the document folder

Use `@bib_key`-syntax

textual citation: American Psychological Association (2020b) $\leftarrow$ @APA2020b
parenthetical citation: (American Psychological Association, 2020a) $\leftarrow$ [@APA2020a]

Declare bibliography in YAML header

bibliography: references.bib
csl: apa

and optionally a .csl-style e.g. apa.csl, that is copied to the folder of the document
csl styles can be found here: https://citationstyles.org/authors/

Mathematical Formulae

Markdown and Quarto support a subset of the LaTeX formula syntax

Inline formula

$s_x = \frac{\sum_{i=1}^{N} (x_i - \bar{x})^2}{N-1}$ $\quad \rightarrow \qquad s_x = \frac{\sum_{i=1}^{N} (x_i - \bar{x})^2}{N-1}$

#### Display formula

$$s_x = \frac{\sum_{i=1}^{N} (x_i - \bar{x})^2}{N-1}$$

\[s_x = \frac{\sum_{i=1}^{N} (x_i - \bar{x})^2}{N-1}\]

Mathematical symbols

$\rightarrow, \le, \approx, \mu, \delta, \int, \infty, \mathrm{m^3s^{-1}}$

More maths and chemistry

\[\begin{align} \frac{dX_1}{dt} &= k_1 \cdot X_1 - k_2 X_1 X_2 \\ \frac{dX_2}{dt} &= - k_4 \cdot X_2 + k_3 X_1 X_2 \\ \end{align}\]

\begin{align}
\frac{dX_1}{dt} &=  k_1 \cdot X_1 -  k_2 X_1 X_2 \\
\frac{dX_2}{dt} &=  k_3 X_1 X_2 - k_4 \cdot X_2 \\
\end{align}

\[\rm 6CO_2 + 6H_2O \rightarrow C_6H_{12}O_6 + 6O_2 \quad \Delta H^0 = +2870 kJ mol^{-1}\]

$$\rm 6CO_2 + 6H_2O \rightarrow C_6H_{12}O_6 + 6O_2 \quad \Delta H^0 = +2870 kJ mol^{-1}$$

Embedding of R in Quarto Documents

Create a Quarto template from the File menu in RStudio. Then make your changes and click the Render button. Then, a document will be generated that includes both content as well as the output of any embedded R code chunks.

Then embed your own R code chunks like this:

```{r iris_summary}
summary(iris)
```

To show both, the code and the output

  Sepal.Length    Sepal.Width     Petal.Length    Petal.Width   
 Min.   :4.300   Min.   :2.000   Min.   :1.000   Min.   :0.100  
 1st Qu.:5.100   1st Qu.:2.800   1st Qu.:1.600   1st Qu.:0.300  
 Median :5.800   Median :3.000   Median :4.350   Median :1.300  
 Mean   :5.843   Mean   :3.057   Mean   :3.758   Mean   :1.199  
 3rd Qu.:6.400   3rd Qu.:3.300   3rd Qu.:5.100   3rd Qu.:1.800  
 Max.   :7.900   Max.   :4.400   Max.   :6.900   Max.   :2.500  
       Species  
 setosa    :50  
 versicolor:50  
 virginica :50

Tables from R

If you want to include real tables, you can create the table in R and then format it with knitr::kable

```{r iris_table}
knitr::kable(iris[1:4, ])
```

Sepal.Length	Sepal.Width	Petal.Length	Petal.Width	Species
5.1	3.5	1.4	0.2	setosa
4.9	3.0	1.4	0.2	setosa
4.7	3.2	1.3	0.2	setosa
4.6	3.1	1.5	0.2	setosa

The kable function has several functions for configuring table layout, see kable help page for details.

Include Plots

You can also embed plots, for example:

```{r iris_sepal}
plot(Sepal.Width ~ Sepal.Length, data=iris, pch=16, col=Species)
```

Suppress Code

The code chunks can be modified with additional options. In the following example the figure size is adjusted and an option echo = FALSE was added to prevent printing of the R code that generated the plot.

```{r iris_sepal3, fig.width=3, fig.height=3, echo=FALSE}
plot(Sepal.Width ~ Sepal.Length, data=iris, pch=16, col=Species)
```

Shows the plot without the code:

Flowcharts and graphs

… can be created with the DiagrammeR package that supports the graphviz language.

R code of the flowchart

library("DiagrammeR")
grViz("digraph pandoc {
         graph [rankdir = LR]
           node [shape = 'box']
                Markdown HTML PDF Word
           node [shape = cds]
             pandoc
           node [shape = oval]
             figs bib
           edge [penwidth=2]
             Markdown -> pandoc
             {figs bib} -> {pandoc}
             pandoc -> {HTML PDF Word}
}")

More at: https://graphviz.org/

References

American Psychological Association. (2020a). Concise guide to APA style: The official APA style guide for students (7th ed.).

American Psychological Association. (2020b). Publication manual of the American Psychological Association: The official guide to APA style. (7th ed.).

R Core Team. (2024). R: A language and environment for statistical computing. R Foundation for Statistical Computing. https://www.R-project.org/

RStudio Team. (2021). RStudio: Integrated development environment for R. RStudio, PBC. http://www.rstudio.com/

The Quarto Dev Team. (2024). Quarto. An open-source scientific and technical publishing system. https://quarto.org

Wikipedia. (2022). Markdown. Wikipedia. https://en.wikipedia.org/w/index.php?title=Markdown&oldid=1079645429

Xie, Y. (2015). Dynamic documents with R and knitr (2nd ed.). Chapman; Hall/CRC. https://yihui.org/knitr/

x05-Creation of Reports with Quarto

About these slides

Markdown, RMarkdown and Quarto

Why Markdown or Quarto

Software

Many Markdown Programs Available, e.g. Panwriter

Let’s use RStudio. Supports Markdown and Quarto

Example

YAML Header

Layout and format conversion

What is Pandoc?

Exercise

Optional without warranty

Section Titles

Weblinks

Formatted weblinks

Example

Images

Verbatim Text

Tables

Citations

Create database file in .bib-format, e.g. references.bib

Use @bib_key-syntax

Declare bibliography in YAML header

Mathematical Formulae

Inline formula

Mathematical symbols

More maths and chemistry

Embedding of R in Quarto Documents

Tables from R

Include Plots

Suppress Code

Flowcharts and graphs

R code of the flowchart

Further reading

References

Create database file in `.bib`-format, e.g. `references.bib`

Use `@bib_key`-syntax