UCL-ARC / r-amr-epidemiology

R for Reproducible Scientific Analysis
http://github-pages.arc.ucl.ac.uk/r-amr-epidemiology/
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Update RMarkdown episode to use Quarto and add section on parametrised reports #19

Closed milanmlft closed 3 months ago

milanmlft commented 3 months ago

Parametrised reports

[!WARNING] There seems be an issue with quarto::quarto_render() when generating parameterised reports in that it will overwrite the output figures, so the rendered reports will all show the exact same plot...

See https://github.com/quarto-dev/quarto-r/issues/205 for more info

This kind of renders the whole gapminder example useless, but I left it in with a callout and some notes about how to get the same with R Markdown. With a bit of luck, the issue gets fixes soonish 🤞

Fixes #5

github-actions[bot] commented 3 months ago

Thank you!

Thank you for your pull request :smiley:

:robot: This automated message can help you check the rendered files in your submission for clarity. If you have any questions, please feel free to open an issue in {sandpaper}.

If you have files that automatically render output (e.g. R Markdown), then you should check for the following:

Rendered Changes

:mag: Inspect the changes: https://github.com/UCL-ARC/r-amr-epidemiology/compare/md-outputs..md-outputs-PR-19

The following changes were observed in the rendered markdown documents:

 22-knitr-markdown.md => 22-quarto.md               | 370 +++++++++++++++------
 config.yaml                                        |  94 +++---
 ...-markdown-rendered-rmd_to_html_fig-1.png (gone) | Bin 7382 -> 0 bytes
 fig/New_Quarto_Document.png (new)                  | Bin 0 -> 55936 bytes
 md5sum.txt                                         |   4 +-
 5 files changed, 326 insertions(+), 142 deletions(-)
What does this mean? If you have source files that require output and figures to be generated (e.g. R Markdown), then it is important to make sure the generated figures and output are reproducible. This output provides a way for you to inspect the output in a diff-friendly manner so that it's easy to see the changes that occur due to new software versions or randomisation.

:stopwatch: Updated at 2024-08-20 17:22:13 +0000