> ## Documentation Index
> Fetch the complete documentation index at: https://docs.brainworkup.org/llms.txt
> Use this file to discover all available pages before exploring further.

# Use modular section partials in report templates

> Use Quarto include shortcodes and domain-specific partial files to include only the cognitive domain sections relevant to each patient's evaluation.

Luria Voice reports are modular by design. Rather than a single long `template.qmd` that contains every possible section, the master template pulls in domain-specific partial files using Quarto's `include` shortcode. You control which sections appear in a given report by editing a single file: `_domains_to_include.qmd`.

## How the include pattern works

Quarto's `include` shortcode inserts the full contents of another `.qmd` file at the point where the shortcode appears. The syntax is:

```markdown theme={null}
{{< include _filename.qmd >}}
```

The leading underscore (`_`) is a Quarto convention: files prefixed with `_` are treated as partials and are not rendered as standalone documents. They are only processed when included by another file.

In a Luria Voice project, `template.qmd` includes `_domains_to_include.qmd` at the point in the report where cognitive domain sections should appear:

```markdown theme={null}
{{< include _domains_to_include.qmd >}}
```

You then populate `_domains_to_include.qmd` with the domain partials for this specific patient.

## The `_domains_to_include.qmd` file

This is the only file you edit to add or remove sections from a report. Each line includes one domain partial.

```markdown theme={null}
{{< include _neurocognitive.qmd >}}
{{< include _memory.qmd >}}
{{< include _executive_function.qmd >}}
{{< include _attention.qmd >}}
```

To exclude a domain, delete or comment out its line. To reorder sections, change the order of the lines. The rendered PDF reflects the order in this file exactly.

<Tip>
  Keep a reference `_domains_to_include.qmd` with all available domains listed
  and commented out. For each patient, uncomment only the relevant ones. This
  makes it easy to see at a glance which sections are active.
</Tip>

## Common domain partials

The table below lists the partial files typically available in a Neurotyp project. Create any that are missing for your practice's standard assessment battery.

| File                      | Domain                                         |
| ------------------------- | ---------------------------------------------- |
| `_neurocognitive.qmd`     | General neurocognitive overview / intelligence |
| `_attention.qmd`          | Attention and concentration                    |
| `_memory.qmd`             | Learning and memory                            |
| `_executive_function.qmd` | Executive function                             |
| `_language.qmd`           | Language and verbal abilities                  |
| `_visuospatial.qmd`       | Visuospatial and perceptual abilities          |
| `_processing_speed.qmd`   | Processing speed                               |
| `_social_cognition.qmd`   | Social cognition and emotional processing      |
| `_validity.qmd`           | Performance and symptom validity               |
| `_sirf.qmd`               | Summary, impressions, and recommendations      |

## Writing a domain partial

A domain partial is a standard `.qmd` file that contains the prose, R code chunks, and Markdown for one cognitive domain section. It can include anything that is valid in a Quarto document.

The following example shows a memory domain partial that uses the `cingulate` R package to generate a score summary visualisation.

```markdown theme={null}
## Learning and Memory

Jane Doe's performance on measures of verbal and visual learning and memory
was within normal limits overall, with relative weakness on delayed free
recall tasks compared to recognition memory.

\`\`\`{r memory-plot}
#| label: fig-memory
#| fig-cap: "Learning and memory domain scores"
#| echo: false
#| warning: false

library(cingulate)

# Generate a domain-level score summary plot

plot_domain_scores(
domain = "memory",
patient = params$name,
scores = memory_scores
)
\`\`\`

_Table 3_ summarises the scores from verbal and visual memory tasks administered
during the evaluation.
```

<Note>
  Each partial file is inserted verbatim into the report at render time,
  including all R code chunks. Variables and objects defined in earlier partials
  are available to later ones because all partials share the same Quarto
  rendering session.
</Note>

## Including or excluding sections per patient

The power of the partial pattern is that you tailor each report to what was actually assessed. A standard adult evaluation might include six domains; a focused attention evaluation might include only two.

**For a comprehensive adult evaluation:**

```markdown theme={null}
{{< include _neurocognitive.qmd >}}
{{< include _attention.qmd >}}
{{< include _memory.qmd >}}
{{< include _executive_function.qmd >}}
{{< include _language.qmd >}}
{{< include _processing_speed.qmd >}}
{{< include _validity.qmd >}}
{{< include _sirf.qmd >}}
```

**For a focused attention evaluation:**

```markdown theme={null}
{{< include _neurocognitive.qmd >}}
{{< include _attention.qmd >}}
{{< include _validity.qmd >}}
{{< include _sirf.qmd >}}
```

## Nesting partials

You can include partials within partials. For example, a `_memory.qmd` partial could itself include subtest-level partials:

```markdown theme={null}
## Learning and Memory

{{< include _memory_verbal.qmd >}}
{{< include _memory_visual.qmd >}}
```

Use nesting sparingly. One level of nesting — domain partials included by `_domains_to_include.qmd` — is enough for most evaluations.

<Warning>
  Quarto does not detect circular includes. If partial A includes partial B and
  partial B includes partial A, the render will hang or fail. Keep the include
  hierarchy strictly one-directional.
</Warning>