Writing reports in Quarto (or R markdown)

Basics: Quarto and Rmarkdown

  • Quarto and R Markdown a special kind of scripts where text and computer code can be combined to generate reports.
  • Under the hood, a report generator is converting code and plain text to an output format such as html, pdf or docx (more formats are available).
  • Quarto is a new, well documented format that gives extra flexibility, but also requires installation of extra software.
  • R Markdown is also, see e.g. R Markdown, R Markdown: The Definitive Guide

Code execution and the environment

  • When a quarto or Rmarkdown file is “knitted” or compiled, the source file looks for additional files in the same directory as the source file is saved.
  • Working in a RStudio projects makes it easy to work with the report interactively as you can use relative paths.
  • RStudio has an excellent guide to its project feature

RStudio projects

  • A projects is a collection of settings together with a root directory.
  • This means that you will be able to work with relative paths.
  • If reading a csv file using relative paths, your code will look like this from a project.
dat <- read_csv("./data/my-data.csv")

Absolute paths

  • If your are using absolute paths, reaching the same operation could look like this
dat <- read_csv("C:/Users/Daniel/Dropbox/Some-folder/a-project/data/my-data.csv")

A basic structure for projects

  • RStudio projects helps you create good habits for reproducible analysis as all analyses are conducted within a stand-alone folder structure. Your data and scripts can be shared.

  • Use a basic structure for all projects:

My-project
        |
        |-.Rproj        (The project settings)
        |--/data        (Contains all data needed for your analysis)
        |--/R           (Contains all scripts/R-files)
        |--/output      (Collection of all output files)

Writing in Quarto/R Markdown

  • The basic syntax in quarto/R Markdown files is markdown. Markdown makes it easy to format text without point-and-click as all formatting can be added with syntax, example:
This text is an example of the markdown syntax which includes **bold**, *italic*,
^super^ and ~subscript~ and ~~striketrough~~

Resulting in:

This text is an example of the markdown syntax which includes bold, italic, super and subscript and striketrough

Markdown - More on text formatting (html)



We can also use html for <sub>subscripts</sub>
and <sup>superscript</sup>

We can also use html for subscripts and superscript

Markdown - More on text formatting (latex)


Mathematical formulas can be added inline with $y_i \sim \operatorname{Normal}(\mu_i, \sigma)$

or as a block, using

$$
y = \beta_0 + \beta_1 \times x_1 + \epsilon
$$

Mathematical formulas can be added inline with \(y_i \sim \operatorname{Normal}(\mu_i, \sigma)\)

or as a block, using

\[ y = \beta_0 + \beta_1 \times x_1 + \epsilon \]

Markdown lists

A list can be unordered and ordered

* Item A
    + Item x

    
1. Item 1
2. Item 2
    i) Item i

A list can be unordered and ordered

  • Item A
    • Item x


  1. Item 1
  2. Item 2
    1. Item i

Markdown tables


| Left |Center|Right| 
| :--- |:---: |---:|
|Text | Text| Text| 
|35| 3| 999|

: A table caption
A table caption
Left Center Right
Text Text Text
35 3 999

Adding images

![](img/inn-logo.svg)

Cross-referencing

  • With cross-referencing it is possible to reference images, tables, equations etc.
  • A cross reference requires an identifier
![](img/inn-logo.svg){#fig-inn}

See [@fig-inn] for an example ...

Figure 1: Høgskolen i Innlandet logo

See Figure 1 for an example …

Code chunk options

  • Output from code chunks can be tables, figures or text used in the report.
  • Code chunk options lets you specify, for example
    • Figure captions, figure short-captions
    • If code, messages or warnings should be shown
    • Labels used for cross-referencing
    • Caching (saving computations of a code block if unchanged)

Code chunk options syntax


#| echo: false
#| message: false
#| warning: false
#| label: fig-example
#| fig-cap: "An example figure"


library(exscidata); library(tidyverse)

cyclingstudy %>%
        ggplot(aes(weight.T1, height.T1)) + geom_point()

Figure 2: An example figure

Inline code

  • Code may be included inline to include code generated outputs
a_variable <- 3.14
  • To include the variable in the text:
The variable will be displayed here `r a_variable`

Bibliographies

  • Bibliographies/Citations may be added to reports using a external bibliography file. A simple format is bibtex
  • Pubmed entries can be searched using TexMed
  • In the visual editor, bibliographies can be easily created
---
title: "My document"
bibliography: "resources/bibliography.bib"
---

Where to find help?

See the.