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PARC TOX Template User Guide

This repository contains the Quarto code for rendering the PARC TOX Template User guide, which you can consult by clicking the link at the top-left of this GitHub page or going to https://eu-parc.github.io/tox-template-guide directly.

For instructions on how to edit the guide, see below.

Editing

To edit this book, you can directly edit the files on GitHub and commit your changes, a GitHub action will then render the updated guide (Recommended).

Alternatively (not recommended if you've never worked with R/RStudio), you can clone this repository and make changes locally, which will give you an (almost instant) preview of your changes. To do so, follow the instructions in the Quarto documentation to set up the required Quarto tools.

Quarto Markdown

This project is a Quarto book. Add chapters by creating a new .qmd file and listing it in the chapters section of _quarto.yml in the desired order. In the _quarto.yml you can also edit the authors and formatting of the book.

To write/edit Quarto Markdown (.qmd), please see the Quarto Authoring documentation.

Workbook tables

The workbook tables in the guide are generated from the CSV files in the data directory. The description column can be formatted using Markdown, see the documentation linked above for the options (NB: you can add paragraph breaks by using <br><br>).

More complex (e.g., conditional) formatting of the tables can be achieved using the gt package (https://gt.rstudio.com/). For example, we make the text red if the value is "Mandatory" using the following code in the data_as_gt_tables() function in R/utils.R:

tab_style(
    locations = cells_body(
        columns = value,
        rows = value == "Mandatory"
    ),
    style = list(cell_text(color = 'red'))
) 

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Guide to help fill the PARC In-Vitro Toxicity Meta(data) Reporting Template.

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