Quarto

Misc

  • Packages

    • {quarto}
    • {{brand_yml}} - Create reports, apps, dashboards, plots and more that match your company’s brand guidelines with a single _brand.yml file
      • For Quarto dashboards, websites, reports, etc.
      • For Python shiny, seaborn, matplotlib, etc.
      • For R shiny, ggplot2, plot, RMarkdown
    • {froggeR} - Reusable templates and project structures
      • Enhanced Quarto Project Creation
        • Creates skeleton of project files. These files can also be created with individual functions (See below)
      • Reusable YAML Headers
      • Templated Documents
      • .gitignore, SCSS, RProj, README templates
    • {litedown} - A lightweight version of R Markdown
      • Control number of rows printed (source)

        • Global

          options(xfun.md_table.limit = N)
          • Where N is the number of the maximum number of rows you want printed.

        • Chunk

          ```{r print.args = list(data.frame = list(limit = N)}
# stuff
```
          • You can substitute ‘data.frame’ with the class of your data object to be printed
    • {cocoon} - Extract, Format, and Print Statistical Output into inline Rmd/qmd documents

  • Resources

  • Tools

    • qvm - Quarto Version Manager

  • quarto --version - Must be in RStudio Terminal

  • quarto check - Must be in RStudio Terminal - versions and engine checks

    $ quarto check
[>] Checking versions of quarto binary dependencies...
      Pandoc version 3.1.1: OK
      Dart Sass version 1.55.0: OK
[>] Checking versions of quarto dependencies......OK
[>] Checking Quarto installation......OK
      Version: 1.3.340
      Path: C:\Users\tbats\AppData\Local\Programs\Quarto\bin
      CodePage: 1252
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....OK
      Version: 3.8.1 (Conda)
      Path: C:/Users/tbats/Miniconda3/python.exe
      Jupyter: 4.9.1
      Kernels: python3
(\) Checking Jupyter engine render....2023-04-28 10:18:15,018 - traitlets - WARNING - Kernel
Provisioning: The 'local-provisioner' is not found.  This is likely due to the presence of multiple jupyter_client distributions and a        previous distribution is being used as the source for entrypoints - which does not include 'local-provisioner'.  That distribution should     be removed such that only the version-appropriate distribution remains (version >= 7).  Until then, a 'local-provisioner' entrypoint will     be automatically constructed and used.
The candidate distribution locations are: ['C:\\Users\\tbats\\Miniconda3\\lib\\site-packages\\jupyter_client-5.3.4.dist-info',                'C:\\Users\\tbats\\Miniconda3\\lib\\site-packages\\jupyter_client-7.0.6.dist-info']
[>] Checking Jupyter engine render....OK
[>] Checking R installation...........OK
      Version: 4.2.3
      Path: C:/PROGRA~1/R/R-42~1.3
      LibPaths:
        - C:/Users/tbats/AppData/Local/R/win-library/4.2
        - C:/Program Files/R/R-4.2.3/library
      knitr: 1.42
      rmarkdown: 2.20
[>] Checking Knitr engine render......OK

  • CLI

    • quarto render to compile a document
    • quarto preview to render a live preview that automatically updates when the source files are saved

  • Using a development verison of Quarto

    • First Usage

      • Change directories to where you want to store the dev version

      • Clone repo and change to the cloned directory

        git clone https://github.com/quarto-dev/quarto-cli
cd quarto-cli

      • Disable Anti-Virus

      • Run Configuration Script

        • Windows Command Prompt

          cmd /k configure.cmd
          • \k keeps the window open in case it errors

        • Powershell

          Invoke-Item configure.cmd

        • Linux/MacOS

          ./configure.sh

        • This will take a minute or two as it checks versions, installs dependencies like pandoc, etc.

      • Add path to quarto.cmd to PATH

        • After the configuration file runs, it will output the path you need to put on PATH, e.g. "C:\Users\erc\Documents\Quarto\quarto-cli\package\dist\bin"

      • Enable Anti-Virus

      • Should be able to use in RStudio

        • I was not able to use the RStudio terminal for quarto commands (e.g. quarto check) though.
        • To find the version, I just opened powershell and ran quarto –version just to make sure it was running and on PATH.
          • Not sure if they use this every time but it was 99.9.9 instead of the verion in the changelog.
        • I also rendered a qmd file using quarto-cmd from the root directory of quarto-cli to see if it matched the output from RStudio. (cd qmd then quarto preview forecasting-statistical.qmd --to html --no-watch-inputs --no-browse)
    • Subsequent Development Versions
      • Change directory to quarto-cli and git pull

  • Shortcuts

    • New R chunk: ctrl + alt + i
    • Build whole book: ctrl+shift b
    • Render page and preview book: ctrl+shift k

  • Using yaml style for chunk options

  • Convert Rmd chunk options to Quarto: knitr::convert_chunk_header("doc.rmd", "doc.qmd")

  • Anchor Link - A link, which allows the users to flow through a website page. It helps to scroll and skim-read easily. A named anchor can be used to link to a different part of the same page (like quickly navigating) or to a specific section of another page.

    • This is the “#sec-moose” id that can be added to headers which it allows to be referenced within the document or in other documents.

  • MathJax commands

    • Font Size: \tiny{ }, \scriptsize{ }, \small{ }, \normal{ }, \large{ }, \Large{ }, \LARGE{ }, \huge{ }, \Huge{ }

  • Lightbox

    • Docs
    • Grouping images for lightbox carousel: ![A Lovely Image](mv-1.jpg){group="my-gallery"}

  • Foldable (non-executable) Code Blocks

    • HTML Tags

      ![](image.png)

<details>

<summary>Code: My non-executable code</summary>

``` r
# code
```

</details>

  • Add an animated gif

    ```{r, echo = FALSE}
knitr::include_graphics("man/figures/clusterpermute_animation.gif", 
                        error = FALSE)
```

  • Using variables and highlighting text

    ```{epoxy, .data=text_data_chunk_1_3}
In {year}, measles elimination was <span class = "txt-navy">achieved</span> in {nb_achieved} countries in the WHO region, while it was <span class = "txt-yellow">re-established</span> in ...
```

Syntax

  • Inline code

    -   Total number of counties: **`{r} polling_places |> filter(state == "Alabama") |> distinct(county_name) |> count()`**
-   Total number of polling places: **`{r} polling_places |> filter(state == "Alabama") |> count()`**
-   Election Day: **`{r} polling_places |> filter(state == "Alabama") |> pull(election_date) |> unique()`**

    • To escape backticks in inline code, you have to use double-backticks instead of single backticks

      • Example: To get "`"\$(\$file.FullName)`""

        `` "`"\$(\$file.FullName)`"" ``

  • Align code chunk under bullet and add indented comment below chunk

    -   [Example]{.ribbon-highlight} (using a SQL Query; method 1)

    ``` r
    # open dataset
    ds <- arrow::open_dataset(dir_out, partitioning = "species")
    # open connection to DuckDB
    con <- dbConnect(duckdb::duckdb())
    # register the dataset as a DuckDB table, and give it a name
    duckdb::duckdb_register_arrow(con, "my_table", ds)
    # query
    dbGetQuery(con, "
      SELECT sepal_length, COUNT(*) AS n
      FROM my_table
      WHERE species = 'species=setosa'
      GROUP BY sepal_length
    ")

    # clean up
    duckdb_unregister(con, "my_table")
    dbDisconnect(con)
    ```

    -   filtering using a partition, the WHERE format is '\<partition_variable\>=\<partition_value\>'
    • Space between bullet and top ticks
    • Space between bottom ticks and bullet
    • Note alignment of text

  • Add Code Annotations

    -   [Partition a large file and write to arrow format]{.underline}

    ``` r
    lrg_file <- open_dataset(<file_path>, format = "csv") # <1>
    lrg_file %>%
        group_by(var) %>% # <2>
        write_dataset(<output_dir>, format = "feather") # <3>
    ```

    1.  Pass the file path to `open_dataset()`

    2.  Use `group_by()` to partition the Dataset into manageable chunks

    3.  Use `write_dataset()` to write each chunk to a separate Parquet file---all without needing to read the full CSV file into R

    -   `open_dataset` is fast because it only reads the metadata of the file system to determine how it can construct queries

  • Footnote

    words [^1]

[^1]: Data from https://github.com/rfordatascience/tidytuesday

  • For PDF output, you need pagebreaks:

    {{< pagebreak >}}

  • Include shortcode to copy/paste the content of another quarto document (Docs)

    {{< include _content.qmd >}}
    • Relative references (links, images, etc.) inside the included file resolve based on the directory of the main file not the included file
    • Need to appear by themselves in a line, and they need to be surrounded by empty lines. This means that you cannot use an include shortcode inside markdown syntax (such as an item in a bulleted list).
    • Use cases: block of text, code cells

  • Reference Figure

    1 See polling place locations in @fig-statemap.

YAML

  • Set global chunk options in yaml

    • For code cells

      execute:
  echo: false
  message: false
  warning: false

  • Enable Margin Notes

    ---
# YAML front matter
reference-location: margin
---

  • !expr to render code within chunk options

    • e.g. figure caption: #| fig-cap: !expr glue::glue("The mean temperature was {mean(airquality$Temp) |> round()}")

  • column: screen-inset yaml markup is used to show a very wide table

  • If you haven’t set your Quarto document to be self-contained, then the images have also already been saved for you - probably in a folder called documentname_files/figure-html/

    format: 
  html:
    embed-resources: true

  • Date first published and date modified using the current date:

    ---
date: 2024-01-01
date-modified: today
---

  • YAML Examples

    • Example

  • For Standalone HTML Documents with htmlwidgets, make sure to set embed-resources: true

    ---
format:
  html:
    embed-resources: true
---

Chunk Options

  • Graphics

    • Code Chunk

      #| label: "fig-statemap"
#| dpi: 300
#| fig.height: 7.2
#| fig.width: 3.6
#| dev: "png"
#| echo: false
#| warning: false
#| message: false
      • Example shows settings for a graph for mobile
      • fig.height and fig.width are always given in inches

    • Set Figure Height and Width Dynamically

      ```{r}
if(params$country == "Somalia") {
  map_width <- 5
  map_height <- 4
} else {
  ...
}
```
stuff and more stuff

```{r}
|# fig-width: !expr map_width + .5
|# fig-height: !expr map_height
```

  • Dynamic Fig Captioning (via rmflight)

    ```{r}
#| label: fig-each
#| fig-cap: !expr glue::glue('Number of things in {multi}.')
#| fig-keep: all
purrr::walk(multi, \(in_item){
    tmp = big_df |>
               dplyr::filter(value %in% in_item)
    print(ggplot(tmp, aes()) + geom_point())
})
```

  • Conditional Code Chunk Evaluation

    • Example: document output type

      • Set value in a code chunk

        ```{r setup}
# Include in first chunk of .qmd
# Get output file type
out_type <- knitr::opts_knit$get("rmarkdown.pandoc.to")
```

      • Use !expr sytax to determine evaluation status

        • Example: eval chunk based on output type

          ```{r}
#| eval: !expr out_type == "html"

# code to create interactive {plotly}
```

```{r}
#| eval: !expr out_type == "docx"

# code to create static {ggplot2}
```

    • Example: Use parameterization to set value

      ---
title: "test"
format: html
params:
  my_value: false
---
      • my_value can then be used throughout the document to determine chunk evaluation status

  • Knitr Hooks

    • Notes from Writing knitr hooks
      • Also has a knitr hook example that alters cell output (e.g. only prints 4 lines of a vector)
    • Chunk Hooks

      • Chunk hooks get called twice: once before knitr executes the code in the chunk, and once again afterwards

      • The function can take up to four arguments, all of which are optional:

        • before: A logical value indicating whether the function is being called before or after the code chunk is executed
        • options: The list of chunk options
        • envir: The environment in which the code chunk is executed
        • name: The name of the code chunk option that triggered the hook function

      • The chunk hook is called for its side effects not the return value. However, if it returns a character output, knitr will add that output to the document output as-is.

      • Example: Chunk Timer

        • Code

          create_timer_hook <- function() {
  start_time <- NULL
  function(before, options) {
    if (before) {
      start_time <<- Sys.time()
    } else {
      stop_time <- Sys.time()
      elapsed <- difftime(stop_time, start_time, units = "secs")
      paste(
        "<div style='font-size: 70%; text-align: right'>",
        "Elapsed time:", 
        round(elapsed, 2), 
        "secs",
        "</div>"
      )
    }
  }
}
knitr::knit_hooks$set(timer = create_timer_hook())
          • The hook is triggered the first time (with before = TRUE) to record the system time somewhere (e.g., in a variable called start_time). Then, when the hook is triggered the second time (with before = FALSE), it records the system time again (e.g., as stop_time), and computes the difference in time.

        • Use in a cell

          ```{r}
#| timer: true
runif(10000)
```

        • Output

R and Python

  • If only R or R and Python, the notebook is rendered by {knitr}

  • If only Python, the notebook is rendered by jupyter

  • Set-up

    • {reticulate} automatically comes loaded in Quarto and it knows to use it when it sees a python block, so you don’t need to load the package
    • Quarto will select a version of Python using the Python Launcher on Windows or system PATH on MacOS and Linux. You can override the version of Python used by Quarto by setting the QUARTO_PYTHON environment variable.
      • In CLI on Windows, type py is see which version the Python Launcher , and therefore Quarto, is using and py –list to see which versions are installed.

  • R

    ```{r}
#| label: read-data
#| echo: true
#| message: false
#| cache: true
lemurs <- readr::read_csv('https://raw.githubusercontent.com/rfordatascience/tidytuesday/master/data/2021/2021-08-24/lemur_data.csv')
```

  • Python

    ```{python}
#| label: modelling 
#| echo: true 
#| message: false

lemur_data_py = r.lemur_data 
import statsmodels.api as sm 
y = lemur_data_py[["Weight"]] 
x = lemur_data_py[["Age"]] 
x = sm.add_constant(x) 
mod = sm.OLS(y, x).fit() 
lemur_data_py["Predicted"] = mod.predict(x) 
lemur_data_py["Residuals"] = mod.resid`
```
    • Use r. to access the data in the R chunk
    • The first execution of a python cell starts reticulate::repl_python() in the terminal

  • (back to) R

    ```{r}
#| label: plotting 
#| echo: true 
#| output-location: slide 
#| message: false 
#| fig-align: center 
#| fig-alt: "Scatter plot of predicted and residual values for the fitted linear model." 

library(reticulate) 
library(ggplot2) 
lemur_residuals <- py$lemur_data_py 
ggplot(data = lemur_residuals, aes(x = Predicted, y = Residuals)) +
  geom_point(colour = "#2F4F4F") +
  geom_hline(yintercept = 0,
            colour = "red") +
  theme(panel.background = element_rect(fill = "#eaf2f2", colour = "#eaf2f2"),
        plot.background = element_rect(fill = "#eaf2f2", colour = "#eaf2f2"))
```
    • Use py$ to access the data in the Python chunk *
    • Must call library(reticulate) in order for Quarto to recognize py$

Layouts

  • 2 cols (1 col: text, 1 col: image)

    ::: {layout="[50,50]"}

::: column
Every Quarto project starts with a Quarto file that has the extension `.qmd`.


This particular one analyzes children's early words, but every `.qmd` includes the same three basic elements inside:


- A block of metadata at the top, between two fences of `---`s. This is written in [YAML](https://learnxinyminutes.com/docs/yaml/). 
- Narrative text, written in [Markdown](https://commonmark.org/help/tutorial/). 
- Code chunks in gray between two fences of ```` ``` ````, written with R or another programming language.


You can use all three elements to develop your code and ideas in one reproducible document.
:::

![](img/01-source.png)
:::

  • 2 figures, 2 columns (i.e. side-by-side) with captions at the top

    ---
fig-cap-location: top
---

-   Words
    -   Predictions of Standard RF vs Oblique RF

        ::: {layout-ncol="2"}
        ![Standard Random Forest](_resources/Regression,_Survival.resources/ml-rf-obl-vs-axis-axpred-1.png){fig-align="left" width="432"}

        ![Oblique Random Forest](_resources/Regression,_Survival.resources/ml-rf-obl-vs-axis-oblpred-1.png){fig-align="left" width="432"}
        :::

        -   Words
    • fig-cap-location: bottom is default;
    • fig-cap-location: margin is buggy, at least in for project type book. Captions are added to the margins but bullet points mysteriously disappear during rendering to html

  • 2 charts side-by-side extending past body margins

    ```{r}
#| label: my-figure
#| layout-ncol: 2
#| column: page
ggplot() + ...
ggplot() + ...
```
    • “layout-ncol” says 2 side-by-side columns
    • “column: page” says extend column width to the width of the page

  • Tabs

    -   Stuff
    -   More Stuff

::: panel-tabset
## tab title 1

``` r
# code
```

## tab title 2

words

``` r
# other code
```
-  Thoughts
:::

-   Stuff

  • Nested Tabs

  • Callout Blocks

    • Resources

    • Example: Todo

      ::: {.callout-note collapse="true"}
## todo

1.  Finish video
    -   Currently working on: multinomial
2.  Figure out exactly what $e$ is in the weight formula
3.  Organize note
4.  Transfer PS Matching section from econometrics-general
:::

    • Example: Caution

      ::: callout-caution
This note is unfinished. I still have more to add, and the concepts need to be organized.
:::

Automation

  • Misc

    • Using External R FIles (source)

      • Use source

        ```{r}
source("../code/functions.R")
```

      • Chunk Option

        ```{r}
#| file: R/functions.R
```
        • The file path should be relative to where your Quarto document is, and you need to make sure you set eval: true either in the code block, or document-wide.

    • Using External Quarto Files (Docs):

      {{< include file.qmd >}}

    • Use dataframes as parameter inputs

      • Not recommended. Should used files (e.g. csvs) instead.

      • Using serialization

      • Using get

        ---
title: "Data as a parameter"
params:
  dataset: "mtcars"
---

```{r}
head(get(params$dataset))
```
  • Iteration and Parameterization

    • Misc

      • Notes from

      • Might need to use fs::file_move to move processed reports to another folder.

        • You can also use Quarto Project and its _quarto.yml file to specify a directory

          project:
  output-dir: "Outputs"
          • If you’re publishing your document on GitHub Pages (but not using GitHub Actions to render the documents), then setting output-dir: "docs" will make for easier set up.

      • Check the number of pages generated is correct (source)

        purrr::walk(list.files("generated_reports/", full.names = TRUE),
            function (x) {
              pdf_length <- pdftools::pdf_length(x)
              if (pdf_length != 6) {
                print(paste0(x, " reports ERROR"))
              } else {
                print("All reports have correct number of pages")
              }
            })

      • Plot Bug During Iteration (source, github issue)

        • When using walk, plots get overwritten in the loop and either none show up or only the last one shows up in the document.

        • Solution: Set Embed Resources in YAML

          ---
format:
  html:
    embed-resources: true
---

    • It involves having a “child” document as a template and running it repeatedly with different parameters

    • The “main” document includes the output from the child document

    • Rendering Options

      • CLI: e.g. quarto render polling-places-report.qmd -P state:'California'

      • {quarto}:

        quarto::quarto_render(
  input = here::here("polling-places-report.qmd"),
  execute_params = list(state = "California")
  # execute_params = yaml::yaml.load_file("params.yml")
)
        • YAML files can be used to deliver parameter values

    • Example: Create a report for each parameter value. In each report, use the parameter value (e.g. state) to iterate through a template file that makes a tables (1 for each county) based on that value.

    • Main Report Document

      ---
title: "Polling Places Report - `r params$state`"
params:
  state: "California"
---

```{r}
#| results: hide

library(dplyr)

counties <- polling_places |> 
  filter(state == params$state) |> 
  distinct(county_name) |> 
  pull()

expanded_child <- 
  counties |> 
    purrr::map(\(county) {
      knitr::knit_expand("../_template.qmd", 
                         current_county = county))
      }|> 
    purrr::flatten()

parsed_child <- knitr::knit_child(text = unlist(expanded_child))
```

`{{r}} parsed_child`
      • The document that gets published, emailed, etc.
      • params specified in YAML
        • Value can also be used in the title of the document via inline R code
      • Each county is iterated through the child document (_template.qmd) via current_county variable and knit_expand
      • parsed_child is a list of the template file outputs.
      • Then, parsed_child is converted to a character vector by unlist and all the results are printed in the document by the inline R code

    • Child Document (i.e. Template)

      ### {{current_county}} COUNTY

-   Total Polling Places: `{r} polling_places |> filter(state == params$state, county_name == "{{current_county}}") |> count()`
-   Example Locations:

```{r}
polling_places |> 
  filter(state == params$state, 
         county_name == "{{current_county}}") |> 
  head(6) |> 
  select(name, address.x) |> 
  kbl(format = "markdown")
```
      • Parameter value is used to get county data and create tables for each.
      • No YAML is necessary in child document
        • params values are automatically available through knitr::knit_expand that’s executed in the Main document
      • The county variable is utilized by the template file using the double curly braces, {{current_county}}
      • kbl outputs in markdown format so the table is correctly rendered in the Main document.

    • Rendering Script

      • Example

        polling_places <-
  readr::read_csv(here::here("data", "geocoded_polling_places.csv"))

# create quarto::render arguments df
polling_places_reports <-
  polling_places |>
  dplyr::distinct(state) |>
  dplyr::slice_head(n = 5) |>
  dplyr::mutate(
    output_format = "html",
    output_file = paste0(tolower(state),
                         "-polling-places"),
    execute_params = purrr::map(state,
                                \(state) list(state = state))
  ) |>
  # default output is html, so that variable not selected
  dplyr::select(output_file, execute_params) 

# iterate through args and create reports
purrr::pwalk(
  .l = polling_places_reports,
  .f = quarto::quarto_render,
  input = here::here("main_report_document.qmd"),
  .progress = TRUE
)
        • Creates a report for each params value (e.g. state)
        • Generates a dataframe for each set of arguments to be fed to quarto::quarto_render.

      • Example

        gapminder_params <- expand.grid(
  years = unique(gapminder$year),
  continents = unique(gapminder$continent)
)


walk2(
  .x = gapminder_params$years,
  .y = gapminder_params$continents,
  .f = ~quarto_render(
    input = "example.qmd",
    output_file = glue("report_{.x}_{.y}_{Sys.Date()}.html"),
    execute_params = list(
      choose_year = .x,
      choose_continent = .y
    )
  )
)

Typst

  • Alternative to LaTeX for formatting pdfs

  • Resources

  • Notes from

  • Comparison with LaTeX

    • LaTeX

      \usepackage{geometry}
\usepackage{eso-pic}
\usepackage{xcolor}
\geometry{a4paper, total={170mm,257mm}, left=20mm, top=20mm, bottom=20mm, right=50mm}
\definecolor{light}{HTML}{E6E6FA}
\AddToShipoutPicture{% 
  \AtPageLowerLeft{% 
      \put(\LenToUnit{\dimexpr\paperwidth-3cm},0){% 
          \color{light}\rule{3cm}{\LenToUnit\paperheight}}%
   }%
}%
      • Advantages
        • You want to include equations (currently easier in LaTeX)
        • (Currently) more flexibility with images and tables

    • Typst

      set page(
  margin: (left: 2cm, right: 1.5cm, top: 2cm, bottom: 2cm),
  background: place(right + top, rect(
    fill: rgb("#E6E6FA"),
    height: 100%,
    width: 3cm,
  ))
)

      • Advantages

        • Easier to learn
        • More informative error messages
        • No extra installations
        • Speed

  • Font

    ---
title: "My document"
format: 
  typst:
    mainfont: "Cascadia Code"
---

  • Template

    • Example 1

      • YAML

        ---
title: "My document"
format:
  typst:
      template-partials:
        - typst-template.typ
        - typst-show.typ
---

        • typst-show.typ takes the variables from the quarto document and passes them to typst

        • typst-template.typ - Once typst has the quarto variables, it creates this template which is used to create the pdf

      • Show

        #show: article.with(
$if(title)$
  title: "$title$",
$endif$
)

# another example with a param town in quarto yaml
#show: psc-report.with(
  $if(title)$
    title: "$title$",
  $endif$
  $if(params.town)$
    town: "$params.town$",
  $endif$
)
        • Says if there’s a title in the qmd, then create a variable, title, with its value

      • Template

        #let article(
  // The document title.
  title: "Some title",
  // The document content.
  body
) = {

  // Set document metadata.
  set document(title: title)

  // Links should be purple.
  show link: set text(rgb("#800080"))

  // Title.
  text(weight: 800, upper(title))
    • Example 2 (source)

      • Show

        #show: psc-report.with(
  $if(title)$
    title: "$title$",
  $endif$
  $if(params.town)$
    town: "$params.town$",
  $endif$
)
        • Sets variables for title metadata and town param from quarto YAML

      • Template

        Code

         
        #let psc-report(
  title: "title",
  town: "town",
  body,
) = {

  // text style for whole report
  set text(
   font: "Open Sans",
   size: 12pt,
  )


  set page(

    // dimensions of document
    "us-letter", // or "a4"
    margin: (left: 1in, 
             right: 1in, 
             top: 0.7in, 
             bottom: 1in),

    // places blue rectangle in header
    background: 
      place(top, 
            rect(fill: rgb("15397F"), // hex-code for color
                 width: 100%, 
                 height: 0.5in
            )
      ),

    // creates layout for text in header rectangle
    header: align(
      horizon,
      grid(
        columns: (80%, 20%), // div sizes for title, town text
        // title text properties
        align(left, 
              text(size: 20pt, 
                   fill: white, 
                   weight: "bold", 
                   title)),
        // town text properties
        align(right, 
              text(size: 12pt, 
                   fill: white, 
                   weight: "bold", 
                   town)
        )
      )
    ),

    // page number, image
    footer: align(
      grid(
        columns: (40%, 60%), // page number, graphic
        align(horizon, 
              text(fill: rgb("15397F"), 
              size: 12pt, 
              counter(page).display("1"))), // sets page number
        align(right, 
              image("assets/psclogo.svg", 
                    height: 300%)
        )
      )
    )

 body
}

  • Extensions

    • Installing the extension downloads a .typ file with some styling
    • Usage

      • Example: dept-news extension

        ---
title: "Chemistry Department"
format:
  dept-news-typst: default
---

WebR

  • Set-Up

    • Install the extension alongside your blog post by running quarto add coatless/quarto-webr
    • Add the extension to your blog by adding filters: ["webr"] to your post’s frontmatter
    • Instead of {r} code chunks, use {webr-r} ones

  • Install CRAN packages on page load

    filters:
  - "webr"
webr:
  packages:
  - "dplyr"
  - "tidyr"
  - "purrr"
  - "tibble"
  - "crayon"
    • Add to frontmatter

  • Install R-Universe Package

    ```{webr-r}
#| context: setup
webr::install("collateral", repos = c("https://jimjam-slam.r-universe.dev"))
```
    • R-Universe packages must be installed in code cells

Extensions

  • Resources
  • Commands
    • Extension Install: quarto add username/repository
    • List exensions in a project: quarto list extensions
    • Remove: quarto remove username/repository
    • Update: quarto update username/repository
  • sverto - Lets you seamlessly write and include Svelte components, like charts and other visuals, in your Quarto website and documents.
    • It’s like adding shiny inputs and charts with just some js code.
  • closeread (video) - Scrollytelling
  • Icons
  • animate (library) - CSS text animations
  • elevator (library)- Adds a back-to-the-top button at the bottom of the page. Can add a .mp3 to play a sound while the page returns to the top
  • nutshell - Opens a window that includes only the snippet you need, not the whole page. Plus, instead of being lost in a jungle of new tabs, your reader stays on one page, keeping their flow of reading
  • social-share - Add buttons to share articles on various social media platforms
  • custom-callout - Allows you to customize callouts through yaml settings instead of inside the callout code or through css/scss.

Dashboards

  • Misc

    • Resources
    • Notes from Velasquez talk
    • Both interactive JavaScript-based plots and standard raster based plots are supported.
    • Deployment Types
      • Static: Rendered a single time (e.g.when underlying data won’t ever change)
      • Scheduled: Rendered on a schedule (e.g. via cron job) to accommodate changing data.
      • Parameterized: Variations of static or scheduled dashboards based on parameters.
      • Interactive: Fully interactive dashboard using Shiny (requires a server for deployment).

  • YAML

    • Basic

      ---
title: "My first Quarto dashboard"
format: dashboard
---

    • Logo and Nav-Buttons

      ---
title: "My first Quarto dashboard"
format: 
  dashboard:
    logo: images/car.png
    nav-buttons:
      - reddit
      - icon: gitlab
        href: https://gitlab.com/ivelasq
---

    • Add Shiny Interactivity

      ---
title: "My first Quarto dashboard"
format: 
  dashboard:
    orientation: rows
server: shiny
---

    • Bootswatch Themes

      ---
title: "My first Quarto dashboard"
format: 
  dashboard:
    theme: united
server: shiny
---

    • CSS and SCSS files

      ---
title: "My first Quarto dashboard"
format: 
  dashboard:
    theme: style.scss
server: shiny
---

  • Layouts

    • Using the YAML: Rows or Columns

      ---
title: "My first Quarto dashboard"
format: 
  dashboard:
    orientation: rows
---

```{r}
#| title: "Plot 1"
plot(mtcars)
```

```{r}
#| title: "Plot 2"
plot(mtcars)
```
      • orientation: columns for columns format

    • Using Headings: Multiple Rows

      ---
title: "My first Quarto dashboard"
format: dashboard
---

## Row

Here is my dashboard:

## Row

```{r}
#| title: "Plot 1"
plot(mtcars)
```

```{r}
#| title: "Plot 2"
plot(mtcars$mpg)
```

    • Using Headings: Rows and Columns

      ---
title: "My first Quarto dashboard"
format: dashboard
---

## Row

Here is my dashboard:

## Row

### Column

```{r}
#| title: "Plot 1"
plot(mtcars)
```

```{r}
#| title: "Plot 2"
plot(mtcars)
```

### Column

```{r}
#| title: "Plot 3"
plot(mtcars)
```
      • 2 rows where the second row has 2 columns and the 1st column has 2 plots
      • Sub-layouts determined by h2 and h3 headers

  • Tabsets

    ### Column {.tabset}

```{r}
#| title: "Plot 1"
plot(mtcars)
```

```{r}
#| title: "Plot 2"
plot(mtcars$mpg)
```

  • Pages

    ---
title: "My first Quarto dashboard"
format: dashboard
---

## Row

Here is my dashboard:

# Page 1

```{r}
#| title: "Plot 1"
plot(mtcars)
```

```{r}
#| title: "Plot 2"
plot(mtcars$mpg)
```

# Page 2

```{r}
#| title: "Plot 3"
plot(mtcars$hp)
```
    • Pages syntax uses h1 headers
    • h2 row specification at the top means that row is present in both pages

  • Text

    • Only-Text

      ::: {.card}
This text will be displayed within a card
:::

    • With Cell

      ::: {.card}
```{r}
plot(mtcars)
```

Above is my plot.
:::

  • Value Boxes

    ## Row

::: {.valuebox color="#F52A32"}
Last updated:

`{{r}} Sys.Date()`
:::

```{r}
#| content: valuebox
#| title: "Spam per day"
n <- mtcars |> tibble::as_tibble() |> dplyr::count() |> dplyr::pull(n)

list(
  icon = "trash",
  color = "#F52A32",
  value = n
)
```

  • Inputs

    • Sidebar

      ## {.sidebar}

Sidebar text here!

    • Add Shiny interactivity

      ```{r}
#| context: setup
library(ggplot2)
```

## {.sidebar}

```{r}
selectInput(
    "variableChoice",
    "Choose a variable:",
    choices = names(mtcars)
  )
```

## Column

### Row

Here is my dashboard:

### Row

```{r}
#| title: "Plot 2"
plotOutput("variablePlot")
```

```{r}
#| context: server

output$variablePlot <- renderPlot({
  yVar <- mtcars[[input$variableChoice]]
  plot(mtcars$index, yVar)
})
```
```
      • Need server: shiny in the YAML (See YAML section)