add mpox data cleaning pipeline

[Karim-Mane]

This PR is created to add the Mpox data cleaning pipeline to the tutorials.

I added both the Rmd and md files for reviewers to decide which one to keep.

[github-actions]

Thank you!

Thank you for your pull request 😃

🤖 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:

• 🎯 correct output
• 🖼️ correct figures
• ❓ new warnings
• ‼️ new errors

Rendered Changes

🔍 Inspect the changes: https://github.com/epiverse-trace/tutorials-early/compare/md-outputs..md-outputs-PR-197

The following changes were observed in the rendered markdown documents:

 cache/__packages (new)                             |     4 +
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 ...k-10_bd1ffbc2aff69a3954dcbe76452428ed.rdb (new) |   Bin 0 -> 199497 bytes
 ...k-10_bd1ffbc2aff69a3954dcbe76452428ed.rdx (new) |   Bin 0 -> 184 bytes
 ...11_91314f7094ad4c8568cce7f65ab6ef13.RData (new) |   Bin 0 -> 2894 bytes
 ...k-11_91314f7094ad4c8568cce7f65ab6ef13.rdb (new) |     0
 ...k-11_91314f7094ad4c8568cce7f65ab6ef13.rdx (new) |   Bin 0 -> 125 bytes
 ...-2_019f65e3ee6e7cfa41ee6accfa09a0ab.RData (new) |   Bin 0 -> 3048 bytes
 ...nk-2_019f65e3ee6e7cfa41ee6accfa09a0ab.rdb (new) |   Bin 0 -> 200124 bytes
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 ...-4_04320ce64d80f3f3c68776b240360c4b.RData (new) |   Bin 0 -> 2971 bytes
 ...nk-4_04320ce64d80f3f3c68776b240360c4b.rdb (new) |     0
 ...nk-4_04320ce64d80f3f3c68776b240360c4b.rdx (new) |   Bin 0 -> 125 bytes
 ...-5_2d1d6cf0d41298025ac774de8a674c3b.RData (new) |   Bin 0 -> 2757 bytes
 ...nk-5_2d1d6cf0d41298025ac774de8a674c3b.rdb (new) |   Bin 0 -> 701 bytes
 ...nk-5_2d1d6cf0d41298025ac774de8a674c3b.rdx (new) |   Bin 0 -> 151 bytes
 ...-6_732feb044ab921922343f4dcde90c448.RData (new) |   Bin 0 -> 4343 bytes
 ...nk-6_732feb044ab921922343f4dcde90c448.rdb (new) |   Bin 0 -> 1137 bytes
 ...nk-6_732feb044ab921922343f4dcde90c448.rdx (new) |   Bin 0 -> 224 bytes
 ...-7_e92be1e32836449d1b74d26bf048ea9f.RData (new) |   Bin 0 -> 2795 bytes
 ...nk-7_e92be1e32836449d1b74d26bf048ea9f.rdb (new) |   Bin 0 -> 194792 bytes
 ...nk-7_e92be1e32836449d1b74d26bf048ea9f.rdx (new) |   Bin 0 -> 150 bytes
 ...-8_4e335ff1d89a595858337e896e21f779.RData (new) |   Bin 0 -> 3786 bytes
 ...nk-8_4e335ff1d89a595858337e896e21f779.rdb (new) |   Bin 0 -> 481 bytes
 ...nk-8_4e335ff1d89a595858337e896e21f779.rdx (new) |   Bin 0 -> 209 bytes
 ...-9_9f789bd5ac672ad0334605325a9c9de6.RData (new) |   Bin 0 -> 2792 bytes
 ...nk-9_9f789bd5ac672ad0334605325a9c9de6.rdb (new) |   Bin 0 -> 199001 bytes
 ...nk-9_9f789bd5ac672ad0334605325a9c9de6.rdx (new) |   Bin 0 -> 147 bytes
 config.yaml (gone)                                 |    83 -
 data/cleaned_data.csv                              | 29998 +++++++++----------
 ...g_pipeline-rendered-unnamed-chunk-2-1.png (new) |   Bin 0 -> 10283 bytes
 ...g_pipeline-rendered-unnamed-chunk-4-1.png (new) |   Bin 0 -> 10289 bytes
 md5sum.txt                                         |    36 +-
 mpox_data_cleaning_pipeline.md (new)               |   908 +
 renv.lock (gone)                                   |  6116 ----
 35 files changed, 15930 insertions(+), 21215 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.

⏱️ Updated at 2025-07-09 22:53:36 +0000