Remove {i2extras}

[Degoot-AM]

This PR completely removes the usage of {i2extras} from tutorials, and thus addressing issue #71. It also add section for calculating and visualizing the cumulative cases, and peak estimation.

[github-actions]

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🤖 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}.

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Rendered Changes

🔍 Inspect the changes: https://github.com/epiverse-trace/tutorials-early/compare/md-outputs..md-outputs-PR-86

The following changes were observed in the rendered markdown documents:

 config.yaml                                        |   2 +-
 describe-cases.md                                  |  55 ++++-
 fig/describe-cases-rendered-unnamed-chunk-7-1.png  | Bin 9500 -> 9477 bytes
 ...ribe-cases-rendered-unnamed-chunk-8-1.png (new) | Bin 0 -> 6284 bytes
 ...-analysis-rendered-unnamed-chunk-1-1.png (gone) | Bin 21079 -> 0 bytes
 ...-analysis-rendered-unnamed-chunk-2-1.png (gone) | Bin 20476 -> 0 bytes
 ...-analysis-rendered-unnamed-chunk-5-1.png (gone) | Bin 22930 -> 0 bytes
 ...-analysis-rendered-unnamed-chunk-6-1.png (gone) | Bin 20947 -> 0 bytes
 md5sum.txt                                         |   5 +-
 simple-analysis.md (gone)                          | 229 ---------------------
 10 files changed, 55 insertions(+), 236 deletions(-)

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⏱️ Updated at 2024-06-24 11:18:56 +0000

[avallecam]

thanks! I'll start the review today

[avallecam]

Thanks for this update! Brief edit suggestions and typos to incorporate. Some additional comments are below:

I think we can later use the simple-analysis.Rmd file to still showcase the log-linear model more explicitly with all the assumptions and limitations before introducing EpiNow2. Assumptions and limitations and deciding why to choose a model are easier to interiorize than methods and possibly a more useful message. Filled as issue #87

Also, I would suggest that for the following PRs, try not to commit the renv.lock file. First, check if the GH workflow check passes or not. We should prefer to update renv files in isolated PRs only unless checks do not pass due to package versions. For this it seems not to break anything, so let's keep it.

[avallecam]

in further versions, we can add a callout explanation or simulation to understand the bootstrapping method.

[avallecam]

ready to merge 🚀