Documents

OST-HS23: Open Science Tools
authoring and publishing workflows for collaborative scientific writing

Lars Schöbitz

October 17, 2023

Anatomy of a Quarto document

Components

1. Metadata: YAML

2. Text: Markdown

3. Code: Executed via knitr or jupyter

Weave it all together, and you have beautiful, powerful, and useful outputs!

Literate programming

Literate programming is writing out the program logic in a human language with included (separated by a primitive markup) code snippets and macros.

---
title: "ggplot2 demo"
date: "5/23/2023"
format: html
---

## MPG

There is a relationship between city and highway mileage.

```{r}
#| label: fig-mpg

library(ggplot2)

ggplot(mpg, aes(x = cty, y = hwy)) + 
  geom_point() + 
  geom_smooth(method = "loess")
```

Source: https://en.wikipedia.org/wiki/Literate_programming

Metadata

YAML

“Yet Another Markup Language” or “YAML Ain’t Markup Language” is used to provide document level metadata.

---
key: value
---

Output options

---
format: something
---

---
format: html
---

---
format: pdf
---

---
format: revealjs
---

Output option arguments

Indentation matters!

---
format: 
  html:
    toc: true
    code-fold: true
---

YAML validation

• Invalid: No space after :

---
format:html
---

• Invalid: Read as missing

---
format:
html
---

YAML validation

There are multiple ways of formatting valid YAML:

• Valid: There’s a space after :

format: html

• Valid: format: html with selections made with proper indentation

format: 
  html:
    toc: true

Quarto linting

Lint, or a linter, is a static code analysis tool used to flag programming errors, bugs, stylistic errors and suspicious constructs.

Source: https://en.wikipedia.org/wiki/Lint_(software)

Quarto YAML Intelligence

RStudio + VSCode provide rich tab-completion - start a word and tab to complete, or Ctrl + space to see all available options.

Your turn

• Open hello-penguins.qmd in your exercises project in RStudio on Posit Cloud.
• In the YAML header, try Ctrl + space to see the available YAML options.
• Try out the tab-completion of any options you remember.
• You can use the HTML reference as needed.

05:00

List of valid YAML fields

• Many YAML fields are common across various outputs

• But also each output type has its own set of valid YAML fields and options

• Definitive list: quarto.org/docs/reference/formats/html

Text

Text Formatting

Markdown Syntax	Output
*italics* and **bold**	italics and bold
superscript^2^ / subscript~2~	superscript2 / subscript2
~~strikethrough~~	strikethrough
`verbatim code`	verbatim code

Headings

Markdown Syntax	Output
# Header 1	Header 1
## Header 2	Header 2
### Header 3	Header 3
#### Header 4	Header 4
##### Header 5	Header 5
###### Header 6	Header 6

Links

There are several types of “links” or hyperlinks.

Markdown

You can embed [named hyperlinks](https://quarto.org/),
direct urls like <https://quarto.org/>, and links to 
[other places](#quarto-anatomy) in 
the document. The syntax is similar for embedding an
inline image: 
![Penguins playing with ball](images/penguins-quarto-ball.png).

Output

You can embed named hyperlinks, direct urls like https://quarto.org/, and links to other places in the document. The syntax is similar for embedding an inline image: .

Lists

Unordered list:

Markdown:

-   unordered list         
    -   sub-item 1         
    -   sub-item 1         
        -   sub-sub-item 1 

Output

• unordered list
  • sub-item 1
    
  • sub-item 1
    • sub-sub-item 1

Ordered list:

Markdown:

1. ordered list            
2. item 2                  
    i. sub-item 1          
         A.  sub-sub-item 1

Output

1. ordered list
   
2. item 2
   1. sub-item 1
      1. sub-sub-item 1

Quotes

Markdown:

> Let us change our traditional attitude to the construction of programs: Instead of imagining that our main task is to instruct a computer what to do, let us concentrate rather on explaining to human beings what we want a computer to do. 
> - Donald Knuth, Literate Programming

Output:

Let us change our traditional attitude to the construction of programs: Instead of imagining that our main task is to instruct a computer what to do, let us concentrate rather on explaining to human beings what we want a computer to do. - Donald Knuth, Literate Programming

Knuth (1984)

Your turn

• Open markdown-syntax.qmd in RStudio.
• Use the source editor mode
• Follow the instructions in the document, then exchange one new thing you’ve learned with your neighbor.

05:00

Callouts

::: callout-note
Note that there are five types of callouts, including: 
`note`, `tip`, `warning`, `caution`, and `important`.
:::

Note that there are five types of callouts, including: note, tip, warning, caution, and important.

More callouts

Callouts provide a simple way to attract attention, for example, to this warning.

Danger, callouts will really improve your writing.

Here is something under construction.

Caption

Tip with caption.

Your turn

• Open callout-boxes.qmd and render the document.
• Using the visual editor mode, change the type of the first callouts box and then re-render. Also play with the options to change its appearance.
• Add a caption to the second callout box.
• Make the third callout box collapsible. Then, switch over to the source editor to inspect the markdown code.
• Change the format to PDF and re-render.

10:00

Footnotes

Pandoc supports numbering and formatting footnotes.

Inline footnotes

Here is an inline note.^[Inlines notes are easier to write,
since you don't have to pick an identifier and move down to
type the note.]

Here is an inline note.¹

1. Inline notes are easier to write, since you don’t have to pick an identifier and move down to type the note.

Inline footnotes

Here is a footnote reference[^1]

[^1]: This can be easy in some situations when you have a really long note or
don't want to inline complex outputs.

Here is a footnote reference¹

Notice in both situations that the footnote is placed at the bottom of the page in presentations, whereas in a document it would be hoverable or at the end of the document.

1. This can be easy in some situations when you have a really long note or don’t want to inline complex outputs.

Code

Anatomy of a code chunk

```{r}
#| label: car-stuff
#| message: false

library(tidyverse)
library(palmerpenguins)

penguins |> 
  distinct(species)
```

# A tibble: 3 × 1
  species  
  <fct>    
1 Adelie   
2 Gentoo   
3 Chinstrap

• Has 3x backticks on each end
• Engine (r) is indicated between curly braces {r}
• Options stated with the #| (hashpipe): #| option1: value

Code, who is it for?

• The way you display code is very different for different contexts.
• In a teaching scenario like today, I really want to display code.
• In a business, you may want to have a data-science facing output which displays the source code AND a stakeholder-facing output which hides the code.

Showing and hiding code with echo

• The echo option shows the code when set to true and hides it when set to false.

Tables and figures

• In reproducible reports and manuscripts, the most commonly included code outputs are tables and figures.

• So they get their own special sections in our deep dive!

Tables

Markdown tables

Markdown:

| Right | Left | Default | Center |
|------:|:-----|---------|:------:|
|   12  |  12  |    12   |    12  |
|  123  |  123 |   123   |   123  |
|    1  |    1 |     1   |     1  |

Output:

Right	Left	Default	Center
12	12	12	12
123	123	123	123
1	1	1	1

Grid tables

Markdown:

+---------------+---------------+--------------------+
| Fruit         | Price         | Advantages         |
+===============+===============+====================+
| Bananas       | $1.34         | - built-in wrapper |
|               |               | - bright color     |
+---------------+---------------+--------------------+
| Oranges       | $2.10         | - cures scurvy     |
|               |               | - tasty            |
+---------------+---------------+--------------------+

: Sample grid table.

Grid tables

Output:

Sample grid table.

Fruit	Price	Advantages
Bananas	$1.34	built-in wrapper bright color
Oranges	$2.10	cures scurvy tasty

Grid tables: Alignment

• Alignments can be specified as with pipe tables, by putting colons at the boundaries of the separator line after the header:

+---------------+---------------+--------------------+
| Right         | Left          | Centered           |
+==============:+:==============+:==================:+
| Bananas       | $1.34         | built-in wrapper   |
+---------------+---------------+--------------------+

Grid tables: Authoring

• Note that grid tables are quite awkward to write with a plain text editor because unlike pipe tables, the column indicators must align.

• The Visual Editor can assist in making these tables!

Tables from code

The knitr package can turn data frames into tables with knitr::kable():

library(knitr)

head(penguins) |> 
  kable()

species	island	bill_length_mm	bill_depth_mm	flipper_length_mm	body_mass_g	sex	year
Adelie	Torgersen	39.1	18.7	181	3750	male	2007
Adelie	Torgersen	39.5	17.4	186	3800	female	2007
Adelie	Torgersen	40.3	18.0	195	3250	female	2007
Adelie	Torgersen	NA	NA	NA	NA	NA	2007
Adelie	Torgersen	36.7	19.3	193	3450	female	2007
Adelie	Torgersen	39.3	20.6	190	3650	male	2007

Tables from code

If you want fancier tables, try the gt package and all that it offers!

library(gt)

head(penguins) |> 
  gt() |>
  tab_style(
    style = list(
      cell_fill(color = "pink"),
      cell_text(style = "italic")
      ),
    locations = cells_body(
      columns = bill_length_mm,
      rows = bill_length_mm > 40
    )
  )

species	island	bill_length_mm	bill_depth_mm	flipper_length_mm	body_mass_g	sex	year
Adelie	Torgersen	39.1	18.7	181	3750	male	2007
Adelie	Torgersen	39.5	17.4	186	3800	female	2007
Adelie	Torgersen	40.3	18.0	195	3250	female	2007
Adelie	Torgersen	NA	NA	NA	NA	NA	2007
Adelie	Torgersen	36.7	19.3	193	3450	female	2007
Adelie	Torgersen	39.3	20.6	190	3650	male	2007

Figures

Markdown figures

![Penguins playing with a Quarto ball](images/penguins-quarto-ball.png)

Penguins playing with a Quarto ball

Subfigures

Markdown:

::: {#fig-penguins layout-ncol=2}

![Blue penguin](images/blue-penguin.png){#fig-blue width="250px"}

![Orange penguin](images/orange-penguin.png){#fig-orange width="250px"}

Two penguins

:::

Subfigures

Output:

(a) Blue penguin

(b) Orange penguin

Figure 1: Two penguins

Finding the figures to include

In places like markdown, YAML, or the command line/shell/terminal, you’ll need to use absolute or relative file paths:

• Absolute = BAD: "/Users/lars/exercises" - Whose computer will this work on?

• Relative = BETTER:

  • "../ = up one directory, ../../ = up two directories, etc.
  • /.. or / = start from root directory of your current computer

Figures with code

```{r}
#| fig-width: 4
#| fig-align: right

knitr::include_graphics("images/penguins-quarto-ball.png")
```

Referencing paths in R code

Use the here package to reference the project root, as here::here() always starts at the top-level directory of a .Rproj:

here::here()

[1] "/Users/lschoebitz/Documents/gitrepos/gh-org-ost-hs23/website"

Figures from code

```{r}
#| fig-width: 6
#| fig-asp: 0.618

ggplot(penguins, aes(x = species, fill = species)) +
  geom_bar(show.legend = FALSE)
```

Cross references

Cross references

• Help readers to navigate your document with numbered references and hyperlinks to entities like figures and tables.

• Cross referencing steps:

  • Add a caption to your figure or table.
  • Give an ID to your figure or table, starting with fig- or tbl-.
  • Refer to it with @fig-... or @tbl-....

Figure cross references

The presence of the caption (Blue penguin) and label (#fig-blue-penguin) make this figure referenceable:

Markdown:

See @fig-blue-penguin for a cute blue penguin.
![Blue penguin](images/blue-penguin.png){#fig-blue-penguin}

Output:

See Figure 2 for a cute blue penguin.

Figure 2: Blue penguin

Table cross references

The presence of the caption (A few penguins) and label (#tbl-penguins) make this table referenceable:

Markdown:

See @tbl-penguins for data on a few penguins.
```{r}
#| label: tbl-penguins
#| tbl-cap: A few penguins

head(penguins) |> 
  gt()
```

Output:

See Table 1 for data on a few penguins.

head(penguins) |> 
  gt()

Table 1:

A few penguins

species	island	bill_length_mm	bill_depth_mm	flipper_length_mm	body_mass_g	sex	year
Adelie	Torgersen	39.1	18.7	181	3750	male	2007
Adelie	Torgersen	39.5	17.4	186	3800	female	2007
Adelie	Torgersen	40.3	18.0	195	3250	female	2007
Adelie	Torgersen	NA	NA	NA	NA	NA	2007
Adelie	Torgersen	36.7	19.3	193	3450	female	2007
Adelie	Torgersen	39.3	20.6	190	3650	male	2007

Our turn

• Open tables-figures.qmd.
• Follow along with me and the instructions in the document, then exchange one new thing you’ve learned with your neighbor.

10:00

Learn more

quarto.org/docs/authoring/markdown-basics.html

References

Knuth, D. E. 1984. “Literate Programming.” The Computer Journal 27 (2): 97–111. https://doi.org/10.1093/comjnl/27.2.97.