Quarto, anatomy

1. Metadata: YAML

2. Text: Markdown

3. Code: knitr or jupyter

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. - Wikipedia

---
title: "ggplot2 demo"
date: "5/22/2021"
format: html
---

## Air Quality

There is a relationship between temperature and the ozone level.

```{r}
#| label: fig-airquality
library(ggplot2)
ggplot(airquality, aes(Temp, Ozone)) + 
  geom_point() + 
  geom_smooth(method = "loess"
)
```

Metadata: YAML

“Yet Another Markup Language” or “YAML Ain’t Markup Language”

---
key: value
---

Output Options

---
format: something
---

---
format: html
---

---
format: pdf
---

---
format: revealjs
---

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

---
format: 
  html:
    option1: text
    option2: logical
---

YAML for format: html

YAML is sensitive

---
format:html # invalid, no space between
---

---
format: # invalid, read as missing
html
---

---
format: 
  html: # valid but needs next object
---

format: html # valid - there's a space

format:
  html # valid - there's 2x spaces on a new line and no trailing :

# valid - format = HTML with selections made
format: 
  html:
    toc: true

Why YAML?

To avoid manually typing out all the options, every time!

quarto render document.qmd --to html

quarto render document.qmd --to html -M code fold:true

quarto render document.qmd --to html -M code-fold:true -P alpha:0.2 -P ratio:0.3

Quarto workflow

Executing the Quarto Render button in RStudio will call Quarto render in a background job - this will prevent Quarto rendering from cluttering up the R console, and gives you and easy way to stop.

Rendering

1. Render in RStudio, starts a background job and previews the output

quarto render document.qmd # defaults to html
quarto render document.qmd --to pdf
quarto render document.qmd --to docx

library(quarto)
quarto_render("document.qmd") # defaults to html
quarto_render("document.qmd", output_format = "pdf")

Quarto linting

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

Quarto YAML Intelligence

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

HTML options

quarto.org/docs/reference/formats/html

You can use the HTML reference if needed.

Text Formatting

*italics* and **bold**

superscript^2^ / subscript~2~

~~strikethrough~~

`verbatim code`

Headings

# Header 1

## Header 2

### Header 3

#### Header 4

##### Header 5

###### Header 6

Links

• There are several types of “links” or hyperlinks.

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: ![Boston terrier](images/howard-gentleman.jpeg){fig-alt="A boston terrier's dressed up like a victorian gentleman"}.

Tables

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

Tables from code

knitr itself can turn R dataframes into tables with knitr::kable()

A very simple table generator, and it is simple by design. It is not intended to replace any other R packages for making tables. . . .

head(mtcars) |> 
  knitr::kable()

Quotes

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 ¹

> 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

> I like dogs
> And I like cats

Anatomy of a code chunk

```{r}
#| label: car-stuff
#| echo: false
mtcars %>% 
  distinct(cyl)
```

Divs and Spans

Pandoc and therefore Quarto can parse “fenced Div blocks”

::: {.border}
This content can be styled with a border
:::

This is text with [special]{style="color:red;"} formatting.

::: {.unnumbered .unlisted}
Text
:::

<div style="font-size: 200px;">Text</div>

Callout Blocks

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

Callout markdown syntax

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


:::{.callout-tip}
## Tip With Caption

This is an example of a callout with a caption.
:::

:::{.callout-caution collapse="true"}
## Expand To Learn About Collapse

This is an example of a 'folded' caution callout that can be expanded by the user. You can use `collapse="true"` to collapse it by default or `collapse="false"` to make a collapsible callout that is expanded by default.
:::

Figures

Basic markdown syntax:

![Boston Terrier](images/boston-terrier.png)

Boston Terrier

Figures w/ code

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

knitr::include_graphics("images/howard-gentleman.jpeg")
```

Fragments/spans

![Boston terrier](images/boston-terrier.png){fig-align="left"}

![](images/boston-terrier.png){fig-align="right" fig-alt="A photo a Boston Terrier."}

Subfigures fenced div class

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

![Excited](images/boston-terrier.png){#fig-boston width="250px"}

![Sleeping](images/boston-sleep.png){#fig-sleep width="250px"}

Two states of Howard

:::

Subfigures

Subfigures

Subfigures

::: {#fig-bostons layout-nrow=2}

![Excited](images/boston-terrier.png){#fig-boston width="250px"}

![Sleeping](images/boston-sleep.png){#fig-sleep width="250px"}

![Still Excited](images/boston-terrier.png){#fig-boston width="250px"}

![Still sleeping](images/boston-sleep.png){#fig-sleep width="250px"}

:::

Subfigures

Two states of Howard, twice

Subfigures

::: {layout-ncol="2"}
![Excited](images/boston-terrier.png){width="250px"}

![Sleeping](images/boston-sleep.png){width="250px"}

![Still Excited](images/boston-terrier.png){width="250px"}

![Still sleeping](images/boston-sleep.png){width="250px"}

Two states of Howard, twice
:::

Diagrams w/ mermaid

flowchart LR
  A[Hard edge] --> B(Round edge)
  B --> C{Decision}
  C --> D[Result one]
  C --> E[Result two]