Quarto • soils

If you’re new to Quarto, first check out the Hello, Quarto tutorial and explore the documentation.

This primer is not a comprehensive introduction to Quarto. Instead, it provides a brief reference for workflows and features used in {soils}.

File paths

soils::create_soils(path = "soils-demo") creates an RStudio Project called “soils-demo” with the template Quarto (.qmd) files, example data, R script, images, style sheets, and the .Rproj file that designates the directory as an RStudio Project. All template files use relative paths instead of absolute paths to ensure the file paths work on anyone’s computer.

Absolute vs relative paths

❌ Absolute paths start with the root directory and provide the full path to a specific file or folder (C:/Users/jryan/Documents/R/projects/soils-demo/data/washi-data.csv). This path will not work on anyone’s computer unless the operating system, user, directory structure, and folder names match exactly.

✅ Relative paths are relative to the working directory, or the project’s home (data/washi-data.csv). When working in a RStudio project, the default working directory is always the root project directory (where the .Rproj file is). This path will work on anyone’s computer with this project directory.

{here} package

When a Quarto file renders, its default current working directory is where the .qmd file lives. To make code more robust, the {here} package builds relative file paths and takes care of the backslashes or forward slashes so the path will work no matter the operating system.

For example, in our new {soils} project, 01_producer-report.qmd imports data using read.csv(here::here("data/washi-data.csv")).

Parameterized reporting

{soils} uses Quarto to help you generate parameterized reports for each participant in your survey from the same template file.

Parameterized reports are like complex functions where the function is the .qmd template, the input are the parameters, and the output are the reports.

To learn more about parameterized reporting, see the materials for Jadey Ryan’s 20-minute presentation, follow along with her 2-hour code-along workshop, or read the Quarto parameters documentation.

Quarto specific features

{soils} uses several intermediate to advanced Quarto features, listed below with references for further reading.

Shortcodes

Shortcodes are special markdown directives that generate various types of content. The markdown syntax uses the shortcode name and attributes inside angle brackets that are nested inside double curly braces {{< shortcode >}}. Read more in the Shortcodes article.

Pagebreak

pagebreak inserts native page breaks into a document regardless of the report format (e.g., HTML, MS Word). Read more in the Pagebreaks article.

{{< pagebreak >}}

Include

include embeds content from a separate .qmd file into the main report. This shortens the number of lines in the main .qmd file and makes the markdown and code of the project more modular. Read more in the Includes article.

Examples found in 01_producer-report.qmd are shown below.

{{< include 03_project-summary.qmd >}}

{{< include 04_soil-health-background.qmd >}}

`knitr::knit_child()`

The include shortcode is limited and cannot generate dynamic sections from an “included” Quarto file. {soils} uses the knitr::knit_child() function as a workaround, thanks to Quishi Yan’s blog post.

For each measurement group results section, 02_section-template.qmd is used as a template to generate each section’s header, table, plot, and page break.

The below code is in the create-measurement-group-sections code chunk of 01_producer-report.qmd.

sections <- purrr::map_chr(measurement_groups, \(group) {     # <1>
  knitr::knit_child(
    input = "02_section-template.qmd",
    envir = rlang::env(),
    quiet = TRUE
  )
})

cat(sections, sep = "\n")                                     # <2>

purrr::map_chr() loops over each measurement group to generate its section as a child document.
With the chunk option #| output: asis and the cat(sections, sep = "\n") line, the child documents are embedded within the main producer report.

Divs and spans

Add classes and attributes to regions of content with divs and spans.

Divs

Divs start and end with a fence containing at least three consecutive colons (:::). The div should be separated by blank lines from preceding and following blocks.

Divs may or may not use curly braces {} around the class and attributes. In the below example, columns is a standalone class, while .column width="50%" is a class with an attribute.

Divs may also be nested, as shown below. Optionally, more than three consecutive colons to distinguish nested divs from their parents.

:::: columns

::: {.column width="50%"}
Left column
:::

::: {.column width="50%"}
Right column
:::

::::

Spans

Bracketed text immediately followed by a class or attributes in curly braces {} will be treated as a span.

[Purple]{style="color:purple;font-weight: bold;font-size: x-large;"} is my favorite color.

is rendered as: Purple is my favorite color.

Read more in the Divs and Spans documentation.

Conditional Content

Conditional content classes and attributes control whether content is or is not displayed in a given format. For example, to control visibility for HTML formats, use a div with the .content-visible class and the when-format="html" OR unless-format="html" attribute. Read more in the Conditional Content article.

::: {.content-visible when-format="html"}
This interactive content will ONLY appear in HTML reports.
:::

::: {.content-visible unless-format="html"}
This static content will appear in all reports EXCEPT in HTML reports.
:::

Tabsets

Tabsets work only in HTML documents and are created with the ::: panel-tabset div. Each top-level heading within the div creates a new tab. Read more in the Tabsets article.

The below example shows how 04_soil-health-background.qmd uses include shortcodes, nested divs, conditional content, and a tabset to include a tabset only for HTML reports.

::: {.content-visible when-format="html"}
:::: panel-tabset
{{< include 05_physical-measurements.qmd >}}

{{< include 06_biological-measurements.qmd >}}

{{< include 07_chemical-measurements.qmd >}}
::::
:::

::: {.content-visible unless-format="html"}
{{< include 05_physical-measurements.qmd >}}

{{< include 06_biological-measurements.qmd >}}

{{< include 07_chemical-measurements.qmd >}}
:::