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Chapter 29 revisions #148

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Chapter 29 revisions
jonthegeek Jul 19, 2024
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Disable broken scraping example
jonthegeek Jul 19, 2024
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Disable another broken scraping example
jonthegeek Jul 19, 2024
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8 changes: 6 additions & 2 deletions 24-web_scraping.Rmd
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Expand Up @@ -45,7 +45,9 @@ HTML = **H**yper**T**ext **M**arkup **L**anguage

[IMDB data from the Internet Archive](https://web.archive.org/web/20220201012049/https://www.imdb.com/chart/top/)

```{r web_scraping-tables, eval=TRUE}
(currently times out, disabled for now; next cohort should revise!)

```{r web_scraping-tables, eval=FALSE}
url <- "https://web.archive.org/web/20220201012049/https://www.imdb.com/chart/top/"
html <- read_html(url)
html |>
Expand All @@ -62,7 +64,9 @@ html |>

## Example: Specific table {-}

```{r web_scraping-html_element, eval=TRUE}
(See "Example: Table" slide above; fix that then this)

```{r web_scraping-html_element, eval=FALSE}
html |>
html_element("table") |>
html_table()
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185 changes: 87 additions & 98 deletions 29-quarto_formats.Rmd
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Expand Up @@ -2,160 +2,149 @@

**Learning objectives:**

- Give a brief overview of some options for communicating your results with Quarto, from static and interactive documents to presentations to websites and books.
- Render Quarto documents to different formats.
- Set output options for Quarto documents in different formats.
- Render documents in various formats from Quarto documents.
- Render presentations in various formats from Quarto documents.
- Create interactive web pages with Quarto.
- Group Quarto documents together into websites and books.
- Find information about other Quarto formats.

## Setting output type {-}

## Setting output type
2 ways to set qmd output format:

There are two ways to set the output of a document:
1. YAML header:


1. Modify the YAML header:
```{r eval=FALSE}
```{yaml}
title: "Diamond sizes"
format: html
```

2. Call quarto::quarto_render() by hand:
2. `quarto::quarto_render()`:

```{r eval=FALSE}

quarto::quarto_render("diamond-sizes.qmd", output_format = c("docx", "pdf"))
```

Note: You can produce multiple types of output since the `output_format` argument can take a list of values

## Output options

- You can find the complete list of Quarto output formats at <https://quarto.org/docs/output-formats/all-formats.html>
- Many formats share some output options, but others have options that are format specific.
- Ex. including a table of content vs. code folding
- To render to all formats specified in the YAML of a document, you can use `output_format = "all"`.

```{r eval=FALSE}
quarto::quarto_render("diamond-sizes.qmd", output_format = "all")
```

## Documents
Note: `output_format` can have multiple values

- There are several basic variations off HTML for generating different types of documents. To name a few, examples are:
- `pdf` makes a PDF with LaTeX
## Output options {-}

- `docx` for Microsoft Word (.docx) documents.
- [Quarto output formats](https://quarto.org/docs/output-formats/all-formats.html)
- Some options shared (`toc: true`)
- Some format-specific (`code-fold: true` for `format: html`)
- `default` to use defaults for format

- `gfm` for a GitHub Flavored Markdown (.md) document.

- `ipynb` for Jupyter Notebooks (.ipynb).


```{r eval=FALSE}
```{yaml}
format:
html:
toc: true #include table of contents
toc_float: true #make table of contents floating
toc: true
toc_float: true
pdf: default
docx: default
```

Note: use special syntax (i.e. `pdf: default`) if you don’t want to override any default options.
- `output_format = "all"` for all specified formats

## Presentations
## Documents {-}

- When using Quarto to produce presentations, you get less visual control than with a tool like PowerPoint, but the upside is you can automatically insert the results of your R code into your presentation.
- Presentations work by dividing your content into slides, with a new slide beginning at each second (`##`) level header.
- First (`#`) level headers indicate the beginning of a new section with a section title slide.
- Quarto supports a variety of presentation formats, including:
Document formats:

- `revealjs` - HTML presentation with revealjs

- `pptx` - PowerPoint presentation

- `beamer` - PDF presentation with LaTeX Beamer.
- `pdf` = PDF with LaTeX
- `docx` = Microsoft Word
- `gfm` = GitHub Flavored Markdown
- `ipynb` = Jupyter Notebooks

- You can read more about creating presentations with Quarto at <https://quarto.org/docs/presentations>.
## Presentations {-}

## Interactivity
- `#` = new section, `##` = new slide

- HTML documents created with Quarto can contain interactive components as well.
- Two example options for including interactivity in your Quarto documents are htmlwidgets and Shiny.
- **htmlwidgets** are R functions that produce interactive HTML visualizations
- `Shiny` is a package that allows you to create interactivity using R code
Presentation formats:

## htmlwidgets
- `revealjs` = HTML presentation with revealjs
- `pptx` = PowerPoint presentation
- `beamer` = PDF presentation with LaTeX Beamer

- htmlwidgets provide client-side interactivity, meaning all the interactivity happens in the browser, independently of R.
- You don’t need to know anything about HTML or JavaScript to use them because all the details are wrapped inside the package.
- There are many packages that provide htmlwidgets, including:
- [`leaflet`](https://rstudio.github.io/leaflet/) for interactive map
- [`dygraphs`](https://rstudio.github.io/dygraphs) for interactive time series visualizations.

- [`DT`](https://rstudio.github.io/DT/) for interactive tables.

- [`threejs`](https://bwlewis.github.io/rthreejs) for interactive 3d plots.

- [`DiagrammeR`](https://rich-iannone.github.io/DiagrammeR) for diagrams (like flow charts and simple node-link diagrams).
More at [quarto.org/docs/presentations](https://quarto.org/docs/presentations)

- To learn more about htmlwidgets and see a complete list of packages that provide them visit <https://www.htmlwidgets.org>.
## Interactivity {-}

## Shiny
`format: html` support interactivity

- Shiny interactions occur on the server-side, meaning you can write interactive apps without knowing JavaScript, but you need a server to run them on.
- {htmlwidgets} = pure client-side interactivity
- {shiny} = complex interactivity with server-side processing
- {shinylive} (not in book) = complex interactivity without server

- To call Shiny code from a Quarto document, add `server: shiny` to the YAML header:
```{r eval=FALSE}
## htmlwidgets {-}

- Handles HTML & JavaScript for you
- Many packages provide {htmlwidgets}:
- [{leaflet}](https://rstudio.github.io/leaflet/) = maps
- [{dygraphs}](https://rstudio.github.io/dygraphs) = time series visualizations
- [{DT}](https://rstudio.github.io/DT/) = tables
- [{threejs}](https://bwlewis.github.io/rthreejs) = 3d plots
- [{DiagrammeR}](https://rich-iannone.github.io/DiagrammeR) = flow charts, node-link diagrams, etc
- More at [htmlwidgets.org](https://www.htmlwidgets.org)

## Shiny {-}

```{yaml}
title: "Shiny Web App"
format: html
server: shiny
```

- Then you can use the “input” functions to add interactive components to the document:

```{r eval=FALSE}
library(shiny)

textInput("name", "What is your name?")
numericInput("age", "How old are you?", NA, min = 0, max = 150)
```

- And you also need a code chunk with chunk option `context: server` which contains the code that needs to run in a Shiny server.
- Code chunk with `#| context: server` for server-side code

## Websites and books
## ShinyLive {-}

- With a bit of additional infrastructure, you can use Quarto to generate a complete website or book:
- Uses [WebR](https://docs.r-wasm.org/webr/latest/)
- No server side
- Can't (yet?) communicate with internet
- Can't hide secrets from user

- Put your `.qmd` files in a single directory. `index.qmd` will become the home page.

- Add a YAML file named `_quarto.yml` that provides the navigation for the site. In this file, set the project type to either `book` or `website`, e.g.:

```{r eval=FALSE}
project:
type: book
```
[quarto-ext.github.io/shinylive](https://quarto-ext.github.io/shinylive/)

## Websites and books {-}

- Read more at <https://quarto.org/docs/websites> about Quarto websites and <https://quarto.org/docs/books> about books.
Quarto projects can group `.qmd`s into websites or books

- Note: [R4DS 2E](r4ds.hadley.nz) is itself a quarto book. You can find the code to render it on your own here: <https://github.com/hadley/r4ds/>. The [Quarto website](https://quarto.org/) itself was made with Quarto. You can find the code here: <https://github.com/quarto-dev/quarto-web>.
- Put `.qmd` files in single directory (confirm)
- `index.qmd` = home page
- `_quarto.yml` specifies structure

## Other formats
```{yaml}
project:
type: book
```

- Quarto offers even more output formats. For example:
- More at [quarto.org](https://quarto.org):
- [/docs/websites](https://quarto.org/docs/websites)
- [/docs/books](https://quarto.org/docs/books)

- You can write journal articles using Quarto Journal Templates: <https://quarto.org/docs/journals/templates.html>.

- You can output Quarto documents to Jupyter Notebooks with `format: ipynb`: <https://quarto.org/docs/reference/formats/ipynb.html>.
## Other formats {-}

- See <https://quarto.org/docs/output-formats/all-formats.html> for a list of even more formats.
- [Quarto Journal Templates](https://quarto.org/docs/journals/templates.html)
- [More at quarto.org](https://quarto.org/docs/output-formats/all-formats.html)

## Resources
## Resources {-}

- [Quarto Pub](https://quartopub.com/): Create documents, websites, presentations, books, and blogs in Quarto, then securely publish them to the web with the Quarto CLI, the easiest way to publish and share on the web.
- [Awesome Quarto](https://github.com/mcanouil/awesome-quarto): A curated list of Quarto talks, tools, examples & articles!
- Quarto documentation: <https://quarto.org/>
- Quarto GitHub repo: <https://github.com/quarto-dev>
- [quarto.pub](https://quartopub.com/): Quarto publishing platform
- [github.com/mcanouil/awesome-quarto](https://github.com/mcanouil/awesome-quarto): Awesome Quarto (Quarto talks, tools, etc)
- [quarto.org](https://quarto.org/): Quarto documentation
- [github.com/quarto-dev](https://github.com/quarto-dev)

## Meeting Videos
## Meeting Videos {-}

### Cohort 5
### Cohort 5 {-}

`r knitr::include_url("https://www.youtube.com/embed/2MGp74nb2ig")`

Expand Down Expand Up @@ -187,7 +176,7 @@ project:
```
</details>

### Cohort 6
### Cohort 6 {-}

`r knitr::include_url("https://www.youtube.com/embed/qQrnNef9fkM")`

Expand All @@ -213,7 +202,7 @@ https://exts.ggplot2.tidyverse.org/gallery/
</details>


### Cohort 7
### Cohort 7 {-}

`r knitr::include_url("https://www.youtube.com/embed/vkjYlBK9-9c")`

Expand All @@ -230,7 +219,7 @@ https://exts.ggplot2.tidyverse.org/gallery/
</details>


### Cohort 8
### Cohort 8 {-}

`r knitr::include_url("https://www.youtube.com/embed/7kW7DEWPVZ8")`

Expand Down