Producing Reports With Quarto

Overview

Questions

• How can I integrate software and reports?

Objectives

• Understand the value of writing reproducible reports
• Learn how to recognise and compile the basic components of an Quarto file
• Become familiar with R code chunks, and understand their purpose, structure and options
• Demonstrate the use of inline chunks for weaving R outputs into text blocks, for example when discussing the results of some calculations
• Be aware of alternative output formats to which a Quarto file can be exported

Data analysis reports

---

Data analysts tend to write a lot of reports, describing their analyses and results, for their collaborators or to document their work for future reference.

Many new users begin by first writing a single R script containing all of their work, and then share the analysis by emailing the script and various graphs as attachments. But this can be cumbersome, requiring a lengthy discussion to explain which attachment was which result.

Writing formal reports with Word or LaTeX can simplify this process by incorporating both the analysis report and output graphs into a single document. But tweaking formatting to make figures look correct and fixing obnoxious page breaks can be tedious and lead to a lengthy “whack-a-mole” game of fixing new mistakes resulting from a single formatting change.

Creating a report as a web page (which is an html file) using Quarto makes things easier. The report can be one long stream, so tall figures that wouldn’t ordinarily fit on one page can be kept at full size and easier to read, since the reader can simply keep scrolling. Additionally, the formatting of a Quarto document is simple and easy to modify, allowing you to spend more time on your analyses instead of writing reports.

Callout

You might also have heard about R Markdown as a literate programming tool. In a lot of ways, Quarto is the next-generation version of R Markdown with more advanced features and multi-language support. However, at its core, Quarto still works the same as R Markdown when it comes to R-based documents and R Markdown files (.Rmd) are still compatible with Quarto. Much of what we cover in this episode is thus also valid for traditional R Markdown files.

Literate programming

---

Ideally, such analysis reports are reproducible documents: If an error is discovered, or if some additional subjects are added to the data, you can just re-compile the report and get the new or corrected results rather than having to reconstruct figures, paste them into a Word document, and hand-edit various detailed results.

The key R package here is knitr. It allows you to create a document that is a mixture of text and chunks of code. When the document is processed by knitr, chunks of code will be executed, and graphs or other results will be inserted into the final document.

This sort of idea has been called “literate programming”.

When rendering a document, knitr will execute the R code in each chunk and creates a new markdown (.md) document, which will include both the regular text and output from the executed code chunks. This markdown file is then converted to the final output format with pandoc. This whole process is handled for you by the Render button in the RStudio IDE.

Creating a Quarto document

---

Within RStudio, click File → New File → Quarto document... and you’ll get a dialog box like this:

You can stick with the default (HTML output), but give it a title.

Basic components of R Markdown

---

The initial chunk of text (header) contains instructions for Quarto to specify what kind of document will be created, and the options chosen. You can use the header to give your document a title, author, date, and tell it what type of output you want to produce. In this case, we’re creating an html document.

YAML

---
title: "My Quarto document"
author: "John Doe"
format: html
editor: visual
---

You can delete any of those fields if you don’t want them included. The double-quotes aren’t strictly necessary in this case. They’re mostly needed if you want to include a colon in the title.

RStudio creates the document with some example text to get you started. Note below that there are chunks like

{verbatim} ```{r} 1 + 1 ```

These are chunks of R code that will be executed by knitr and replaced by their results. More on this later.

Markdown

---

Markdown is a system for writing web pages by marking up the text much as you would in an email rather than writing html code. The marked-up text gets converted to html, replacing the marks with the proper html code.

For now, let’s delete all of the stuff that’s there and write a bit of markdown.

You make things bold using two asterisks, like this: **bold**, and you make things italics by using underscores, like this: _italics_.

You can make a bulleted list by writing a list with hyphens or asterisks with a space between the list and other text, like this:

MARKDOWN

A list:

* bold with double-asterisks
* italics with underscores
* code-type font with backticks

or like this:

MARKDOWN

A second list:

- bold with double-asterisks
- italics with underscores
- code-type font with backticks

Each will appear as:

• bold with double-asterisks
• italics with underscores
• code-type font with backticks

You can use whatever method you prefer, but be consistent. This maintains the readability of your code.

You can make a numbered list by just using numbers. You can even use the same number over and over if you want:

MARKDOWN

1. bold with double-asterisks
1. italics with underscores
1. code-type font with backticks

This will appear as:

1. bold with double-asterisks
2. italics with underscores
3. code-type font with backticks

You can make section headers of different sizes by initiating a line with some number of # symbols:

MARKDOWN

# Title

## Main section

### Sub-section

#### Sub-sub section

You compile the R Markdown document to an html webpage by clicking the “Render” button in the upper-left. Or using the keyboard shortcut Shift+Ctrl+K on Windows and Linux, or Shift+Cmd+K on Mac.

Challenge 1

Create a new Quarto document. Delete all of the R code chunks and write a bit of Markdown (some sections, some italicized text, and an itemized list).

Convert the document to a webpage.

Solution to Challenge 1

In RStudio, select File > New file > Quarto Document...

Delete the placeholder text and add the following:

MARKDOWN

# Introduction

## Background on Data

This report uses the *gapminder* dataset, which has columns that include:

* country
* continent
* year
* lifeExp
* pop
* gdpPercap

## Background on Methods

Then click the ‘Render’ button on the toolbar to generate an html document (webpage).

A bit more Markdown

---

You can make a hyperlink like this: [Carpentries Home Page](https://carpentries.org/).

You can include an image file like this: ![The Carpentries Logo](https://carpentries.org/assets/img/TheCarpentries.svg)

You can do subscripts (e.g., F₂) with F~2~ and superscripts (e.g., F²) with F^2^.

If you know how to write equations in LaTeX, you can use $ $ and $$ $$ to insert math equations, like $E = mc^2$ and

$$y = \mu + \sum_{i=1}^p \beta_i x_i + \epsilon$$

which will show as

\[y = \mu + \sum_{i=1}^p \beta_i x_i + \epsilon\]

You can review Markdown syntax by navigating to the “Markdown Quick Reference” under the “Help” field in the toolbar at the top of RStudio.

R code chunks

---

The real power of Quarto comes from mixing markdown with chunks of code. When processed, the R code will be executed; if they produce figures, the figures will be inserted in the final document.

The main code chunks look like this:

{verbatim} ```{r} #| label: load_data gapminder <- read.csv("gapminder.csv") ```

That is, you place a chunk of R code between ```{r} and ```. You should give each chunk a unique name, by inserting the line #| label: label_name as they will help you to fix errors and, if any graphs are produced, the file names are based on the name of the code chunk that produced them. You can create code chunks quickly in RStudio using the shortcuts Ctrl+Alt+I on Windows and Linux, or Cmd+Option+I on Mac.

Code chunk options in R Markdown

In R Markdown, you add chunk labels by including them within the ```{r} line like so:

{verbatim} ```{r label_data} gapminder <- read.csv("gapminder.csv") ```

Challenge 2

Add code chunks to:

• Load the ggplot2 package
• Read the gapminder data
• Create a plot

Solution to Challenge 2

{verbatim} ```{r} #| label: libraries library(ggplot2) ```

{verbatim} ```{r} #| label: load-gapminder-data gapminder <- read.csv("gapminder.csv") ```

{verbatim} ```{r} #| label: make-plot plot(lifeExp ~ year, data = gapminder) ```

How things get compiled

---

When you press the “Render” button, the Quarto document is processed by knitr and a plain Markdown document is produced (as well as, potentially, a set of figure files): the R code is executed and replaced by both the input and the output; if figures are produced, links to those figures are included.

The Markdown and figure documents are then processed by the tool pandoc, which converts the Markdown file into an html file, with the figures embedded.

Chunk options

---

There are a variety of options to affect how the code chunks are treated. Here are some examples:

• Use echo=FALSE to avoid having the code itself shown.
• Use results="hide" to avoid having any results printed.
• Use eval=FALSE to have the code shown but not evaluated.
• Use warning=FALSE and message=FALSE to hide any warnings or messages produced.
• Use fig.height and fig.width to control the size of the figures produced (in inches).

So you might write:

{verbatim} ```{r} #| label: load_libraries #| echo: false #| message: false library(dplyr) library(ggplot2) ```

Often there will be particular options that you’ll want to use repeatedly; for this, you can set global chunk options in the files YAML header like so:

YAML

---
...
knitr:
  opts_chunk:
    message: false
    warning: false
    echo: false
    results: "hide"
    fig.path: "Figs/
    fig.width: 11
---

The fig.path option defines where the figures will be saved. The / here is really important; without it, the figures would be saved in the standard place but just with names that begin with Figs.

If you have multiple R Markdown files in a common directory, you might want to use fig.path to define separate prefixes for the figure file names, like fig.path="Figs/cleaning-" and fig.path="Figs/analysis-".

Challenge 3

Use chunk options to control the size of a figure and to hide the code.

Solution to Challenge 3

{verbatim} ```{r} #| label: faitful-plot #| echo: false #| fig.width: 3 plot(faitful) ```

You can review all of the R chunk options by navigating to the “R Markdown Cheat Sheet” under the “Cheatsheets” section of the “Help” field in the toolbar at the top of RStudio.

Inline R code

---

You can make every number in your report reproducible. Use `r and ` for an in-line code chunk, like so: ``r "r round(some_value, 2)"``. The code will be executed and replaced with the value of the result.

Don’t let these in-line chunks get split across lines.

Perhaps precede the paragraph with a larger code chunk that does calculations and defines variables, with include=FALSE for that larger chunk (which is the same as echo=FALSE and results="hide").

Challenge 4

Try out a bit of in-line R code.

Solution to Challenge 4

Here’s some inline code to determine that 2 + 2 = r 2+2:

{verbatim} Here's some inline code to determine that 2 + 2 = `r 2+2`:

Other output options

---

You can also convert R Markdown to a PDF or a Word document. Change the format: field in the YAML header to pdf or docx. For an overview of all the available output formats, see the Quarto documentation

Parameterised reports

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Literate programming with tools like Quarto and R Markdown is very powerful in that it allows you to generate analysis reports in a reproducible manner. This makes it very easy to update your work and alter the input parameters within the report You can take this one step further, by parametrising the reports themselves. This is very useful in a number of cases, for example:

• Running the same analysis on different datasets
• Generating multiple reports for different groups of the data (e.g. geographic location or time periods)
• Controlling the knitr options; e.g. you might want to show the code in some reports but not in others

Including parameters in a Quarto document

Including parameters in a Quarto document (or R Markdown, which follows the same syntax) can be done by adding the params field to they YAML header. This field can hold a list of multiple parameters.

For example, imagine we want to analyse the life expectancy of different countries, using the gapminder dataset, but we want a separate report for each country. To achieve this, we set the YAML header for our Quarto document as follows:

YAML

---
title: "Life Expectancy Report"
format: html
execute:
  echo: false
  warning: false
  message: false
params:
  country: "Afghanistan"
---

We can then reference this parameter anywhere in the R code in our report by accessing the params object. To calculate the life expectancy for just the country defined by the params, we can do:

`{verbatim}{r} library(tidyverse) library(gapminder)

```{r}
life_expectancy <-
  gapminder |>
  select(country, year, lifeExp) |>
  filter(country == params$country)

The last line in the code chunk above uses the `params` object to filter the `gapminder` dataset.
Note that we can also `params` in inline R code snippets. So we can generate a heading that will
change based on the country parameter:

````{verbatim}
## Life Expectancy in `r params$country`

```{r}
#| label: !expr paste0("life-expectancy-plot", params$country)
ggplot(life_expectancy, aes(year, lifeExp)) +
  geom_line() +
  theme_minimal()
```

In fact, we can even use this in the main document title in the YAML header, as it also accepts R code expressions:

YAML

---
title: "Life Expectancy Report for `r params$country`"
...

Rendering Quarto documents from within R

Of course, manually editing the YAML header every time you want to generate a report isn’t much better than manually editing the report itself. The real power of parameterised reports is when we render them programmatically. This can be done using the {quarto} R package, which provides the quarto_render() function. This function takes a Quarto file and any execution parameters as input.

So to generate the life expectancy report for Afghanistan, we can write a script with the following code:

R

# render-report.R
library(quarto)
quarto_render("life_expectancy_report.qmd", execute_params = list(country = "Afghanistan"))

And now for the real magic, we can modify our script to render a report for a list of countries of interest from the gapminder dataset.

{r} # render-all-reports.R library(quarto) countries <- c("Afghanistan", "Belgium", "India", "United Kingdom") for (country in countries) { quarto_render( input = "life_expectancy_report.qmd", output_file = paste0("life_expectancy_", country, ".html"), execute_params = list(country = country) ) }

After running this script, we should have the following files in our working directory:

.
├── life_expectancy_Afghanistan.html
├── life_expectancy_Belgium.html
├── life_expectancy_India.html
├── life_expectancy_United Kingdom.html
├── life_expectancy_report.qmd
└── life_expectancy_report_files

Callout

WARNING: although this will work and generate the correct output files, you might notice that each report will show the exact same plot, which is unexpected. This is an issue with the Quarto R package.

With R Markdown we don’t have this issue, to render we would use the following code:

R

rmarkdown::render(
  input = "life_expectency_report.Rmd",
  output_file = paste0("life_expectancy_", country, ".html"),
  params = list(country = country)
)

Tip: Creating PDF documents

Creating .pdf documents may require installation of some extra software. The R package tinytex provides some tools to help make this process easier for R users. With tinytex installed, run tinytex::install_tinytex() to install the required software (you’ll only need to do this once) and then when you knit to pdf tinytex will automatically detect and install any additional LaTeX packages that are needed to produce the pdf document. Visit the tinytex website for more information.

Tip: Visual markdown editing in RStudio

RStudio versions 1.4 and later include visual markdown editing mode. In visual editing mode, markdown expressions (like **bold words**) are transformed to the formatted appearance (bold words) as you type. This mode also includes a toolbar at the top with basic formatting buttons, similar to what you might see in common word processing software programs. You can turn visual editing on and off by pressing the button in the top right corner of your R Markdown document.

Resources

---

• Knitr in a knutshell tutorial
• Dynamic Documents with R and knitr (book)
• R Markdown documentation
• R Markdown cheat sheet
• Getting started with R Markdown
• R Markdown: The Definitive Guide (book by Rstudio team)
• Reproducible Reporting
• The Ecosystem of R Markdown
• Introducing Bookdown

Key Points

• Mix reporting written in R Markdown with software written in R.
• Specify chunk options to control formatting.
• Use knitr to convert these documents into PDF and other formats.