add libraries (ggplot2, epidemics, webshot) to episode

[avallecam]

Fix #1

[github-actions[bot]]

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: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:

• :dart: correct output
• :framed_picture: correct figures
• :question: new warnings
• :bangbang: new errors

Rendered Changes

:mag: Inspect the changes: https://github.com/epiverse-trace/tutorials-late/compare/md-outputs..md-outputs-PR-2

The following changes were observed in the rendered markdown documents:

 compare-interventions.md                           |   32 +-
 config.yaml (gone)                                 |   84 -
 ...erventions-rendered-unnamed-chunk-6-1.png (new) |  Bin 0 -> 23754 bytes
 fig/introduction-rendered-unnamed-chunk-5-1.png    |  Bin 50697 -> 51455 bytes
 fig/model-choices-rendered-unnamed-chunk-3-1.png   |  Bin 20234 -> 16678 bytes
 fig/model-choices-rendered-unnamed-chunk-4-1.png   |  Bin 9243 -> 9015 bytes
 fig/simulating-transmission-rendered-plot-1.png    |  Bin 16367 -> 16147 bytes
 md5sum.txt                                         |   30 +-
 renv.lock (gone)                                   | 2201 --------------------
 9 files changed, 27 insertions(+), 2320 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 2024-03-11 12:20:33 +0000

[avallecam]

hi @Bisaloo , brief review request.

Also, an opportunity to ask, how to put "Rebase and merge" as the default for merge? should this change after merging this or we can set this up in the Settings of the repo?

[avallecam]

@Bisaloo also, while looking at the md-output for compare-interventions, the section that generates a diagram with {DiagrammeR} generates a weird output. Can you see it? This is the first time I've noticed this in this episode.

the simulating-transmission episode, that also uses {DiagrammeR} seems to deploy ok.

In order to make the printing of {DiagrammeR} visible on the workbench, we are using webshot::install_phantomjs(force = TRUE). Please see this comment and reference link

{webshot} is present in simulating-transmission but not in compare-interventions, should we try to add it there to see if this fix the md output?

[Bisaloo]

Also, an opportunity to ask, how to put "Rebase and merge" as the default for merge? should this change after merging this or we can set this up in the Settings of the repo?

The default is user-specific and it corresponds to the latest setting you used in a specific repo. We cannot set it for all the users.

[Bisaloo]

{DiagrammeR} generates a weird output. Can you see it? This is the first time I've noticed this in this episode.

the simulating-transmission episode, that also uses {DiagrammeR} seems to deploy ok.

In order to make the printing of {DiagrammeR} visible on the workbench, we are using webshot::install_phantomjs(force = TRUE). Please see this comment and reference link

{webshot} is present in simulating-transmission but not in compare-interventions, should we try to add it there to see if this fix the md output?

My understanding is that it will still work fine on main because all episodes are re-rendered and webshot will already be loaded + phanthomjs already installed. We can also add it to simulation-transmission to make sure that PR previews look good as well.

[avallecam]

@Bisaloo I confirm that adding {webshot} within the Rmd file (https://github.com/epiverse-trace/tutorials-late/pull/2/commits/1b09850cdf8fbd7d52a14958f6d2e6a1d8476d62) allows us to have clean md-outputs when using {Diagrammer} as in compare-interventions episode. (this may not be visible after merging, so you need to trust me, heh)

My take-home message is that each episode is independent with respect to the package dependencies loaded. For this reason, we got issues with {epidemics} and {ggplot} in this episode only.

Ready to rebase and merge 🚀