Add cognitive domain findings to Luria Voice reports

Cognitive domain findings in Luria Voice are not written inline inside template.qmd. Instead, each cognitive domain lives in its own .qmd partial file — a self-contained fragment of Quarto markdown that holds prose, R code, score tables, and figures for that domain. The report assembles these partials at render time through a single include file called _domains_to_include.qmd. This modular structure makes it easy to add, remove, or reuse domain sections across different report types.

How partial includes work in Quarto

Quarto’s {{< include >}} shortcode pastes the contents of another .qmd file directly into the parent document before rendering. It is equivalent to writing all that content inline, but stored in a separate file. In template.qmd, the cognitive domain section looks like this:

{{< include _domains_to_include.qmd >}}

And _domains_to_include.qmd is itself just a list of further includes:

{{< include _neurocognitive.qmd >}}
{{< include _verbal-memory.qmd >}}
{{< include _attention.qmd >}}
{{< include _executive.qmd >}}

When Quarto renders the report, it recursively expands all includes in order before passing anything to Typst. The final PDF contains all domain sections in the sequence they appear in _domains_to_include.qmd.

Create `_domains_to_include.qmd`

The template scaffolds a starter _domains_to_include.qmd for you. Open it and edit the list to match the domains you actually assessed.

Manual selection
Full battery
cingulate pipeline

List only the domains relevant to this evaluation. Remove or comment out any domains not administered.

{{< include _neurocognitive.qmd >}}
{{< include _verbal-memory.qmd >}}
{{< include _attention.qmd >}}

For a comprehensive evaluation including all standard domains:

{{< include _neurocognitive.qmd >}}
{{< include _verbal-memory.qmd >}}
{{< include _visual-memory.qmd >}}
{{< include _attention.qmd >}}
{{< include _executive.qmd >}}
{{< include _language.qmd >}}
{{< include _visuospatial.qmd >}}
{{< include _academics.qmd >}}
{{< include _adaptive.qmd >}}
{{< include _emotional.qmd >}}

If you are using the cingulate R package pipeline, it can generate _domains_to_include.qmd automatically based on the tests detected in your data. Run the pipeline first, then render the report without manually editing the include file.

library(cingulate)
# Generate domain include file from scored data
generate_domain_includes(data_dir = "data/")

Check the generated _domains_to_include.qmd before rendering to confirm the correct domains were detected.

Every file referenced in _domains_to_include.qmd must exist in your project directory. Quarto will error out at render time if a referenced partial is missing. Either create the missing file or remove its {{< include >}} line.

Anatomy of a domain partial file

Each domain partial follows the same structure: a section heading, optional narrative prose, and one or more R code chunks that load data and produce output using the cingulate package. Here is a complete example for the neurocognitive functioning domain. A domain partial starts with a section heading, optional narrative prose, and R code chunks. Section heading and narrative prose (_neurocognitive.qmd):

## Neurocognitive Functioning

Maria's overall neurocognitive profile showed relative strengths in processing
speed and working memory, with more variable performance across measures of
novel problem-solving and cognitive flexibility.

Score table chunk (add after the narrative):

#| label: neurocog-table
#| echo: false
#| message: false
library(cingulate)

# Load processed score data for this domain
neurocog_data <- load_domain_data("neurocognitive")

# Render a formatted score table
render_score_table(neurocog_data)

Score visualization chunk (add after the table):

#| label: neurocog-plot
#| echo: false
#| fig-width: 7
#| fig-height: 3

# Render a ggplot2 score visualization
plot_domain_scores(neurocog_data)

Key conventions

Section heading: Use ## (H2) so the domain appears as a top-level section in the report’s table of contents.
chunk labels: Give every code chunk a unique label. Duplicate labels across partials will cause a render error.
echo: false: Always set this so raw R code does not appear in the PDF output.
Data loading: Use cingulate::load_domain_data() with the domain name matching your data directory conventions.

Create a new domain partial from scratch

If the template does not include a partial for a domain you need, create one manually.

Create the file

Create a new .qmd file in your project directory. Use the naming convention _DOMAIN-NAME.qmd, for example _processing-speed.qmd.

touch _processing-speed.qmd

Add the section heading and narrative

Open the file and add a ## heading and your clinical narrative for this domain.

## Processing Speed

Performance on timed measures of processing speed fell within the average
range, consistent with age-referenced norms.

Add R code chunks for score data

Add code chunks that load and visualize the score data using cingulate. In your .qmd partial, add an R chunk like the following:

#| label: processing-speed-table
#| echo: false
#| message: false
library(cingulate)

ps_data <- load_domain_data("processing_speed")
render_score_table(ps_data)

Add an include line to _domains_to_include.qmd at the position where you want this domain to appear in the report.

{{< include _neurocognitive.qmd >}}
{{< include _processing-speed.qmd >}}
{{< include _attention.qmd >}}

Render and verify

Run quarto render and confirm the new domain section appears in the correct position in the PDF.

quarto render template.qmd --to neurotyp-adult-typst

Using the cingulate pipeline to auto-generate includes

The cingulate package can inspect your scored data directory and automatically produce a _domains_to_include.qmd that lists only the domains for which data is present.

library(cingulate)

# Point to the directory containing your scored CSV or RDS files
generate_domain_includes(
  data_dir  = "data/",
  output    = "_domains_to_include.qmd"
)

Auto-generation does not create the domain partial files themselves — only the include list. You still need a corresponding _[domain].qmd file for each domain detected. The template provides starters for all standard domains; the pipeline only selects which ones to activate.

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Add cognitive domain findings to Luria Voice reports

How partial includes work in Quarto

Create `_domains_to_include.qmd`

Anatomy of a domain partial file

Key conventions

Create a new domain partial from scratch

Using the cingulate pipeline to auto-generate includes

​How partial includes work in Quarto

​Create _domains_to_include.qmd

​Anatomy of a domain partial file

​Key conventions

​Create a new domain partial from scratch

​Using the cingulate pipeline to auto-generate includes

How partial includes work in Quarto

Create `_domains_to_include.qmd`

Anatomy of a domain partial file

Key conventions

Create a new domain partial from scratch

Using the cingulate pipeline to auto-generate includes