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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.

The _quarto.yml file at the root of your project controls how Quarto builds your report. Luria Voice requires this file to be present in the same directory from which you run quarto render. If Quarto cannot find _quarto.yml in the current directory, it will not resolve the neurotyp-adult extension and rendering will fail.

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Project type

_quarto.yml
project:
  type: default
Set type to default for single-document neuropsychological reports. Use type: book only if you are building a multi-document project such as a training manual — standard evaluation reports do not need book mode.

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Format settings

_quarto.yml
format:
  neurotyp-adult-typst:
    toc: false
    keep-typ: false
FieldDefaultDescription
tocfalseTable of contents. Keep false for clinical reports — sections are short and a TOC adds visual clutter.
keep-typfalseRetain the intermediate .typ file after rendering. Set to true when debugging Typst layout issues.
The format key neurotyp-adult-typst tells Quarto to use the neurotyp-adult extension’s Typst output format. This key must match exactly. The extension must be installed in your project (run quarto add brainworkup/neurotyp-adult from your project root if it is missing).

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Using multiple formats

You can define additional formats in the same _quarto.yml if you need to output both PDF and HTML for the same source document:
_quarto.yml
format:
  neurotyp-adult-typst:
    toc: false
    keep-typ: false
  html:
    theme: default
    toc: true
Run quarto render template.qmd to produce both outputs at once, or target a specific format with --to: 
quarto render template.qmd --to neurotyp-adult-typst

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Knitr chunk options

_quarto.yml
knitr:
  opts_chunk:
    echo: false
    warning: false
    message: false
These global chunk options suppress all R source code, warnings, and package startup messages from the rendered PDF. This is the correct default for clinical reports — patients and referring clinicians should not see R output in their evaluation document.
OptionValueEffect
echofalseHides R source code from output
warningfalseSuppresses R warnings
messagefalseSuppresses package messages (e.g., tidyverse loading messages)
Override these defaults for a specific chunk by setting options inline: #| echo: true. This is useful when you want to show a table-generating command during development without changing the global defaults.

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Render on save

_quarto.yml
editor:
  render-on-save: true
When render-on-save is true, supported editors (VS Code with the Quarto extension, RStudio) automatically re-render the document each time you save. This gives you a live preview loop without manually running quarto render.
Render-on-save re-runs all R code on every save. If your report calls slow computations or hits an external API (such as Ollama for AI narratives), disable this option and render manually to avoid long waits on each keystroke.

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Full example

_quarto.yml
project:
  type: default

format:
  neurotyp-adult-typst:
    toc: false
    keep-typ: false

knitr:
  opts_chunk:
    echo: false
    warning: false
    message: false

editor:
  render-on-save: true

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Extension resolution

Quarto resolves the neurotyp-adult extension by looking for an _extensions/neurotyp-adult/ directory relative to your project root (the folder containing _quarto.yml). Always run quarto render, quarto add, and quarto update from that same root directory. Running these commands from a subdirectory or a different path will cause extension-not-found errors.
Last modified on May 20, 2026