Fix read describe cases

[Degoot-AM]

This PR aims at addressing existing conflicts with origin before get more complicated. This issues specifically arise from
including the development version of {cleanepi} package. It also adds the following episodes:

1. Read case data
2. Clean and validate data
3. Aggregate and visualize
4. Early analysis

This PR addresses issues #21 and #22.

[github-actions]

Thank you!

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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}.

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-39

The following changes were observed in the rendered markdown documents:

 clean-data.md (new)                                |   415 +
 config.yaml (gone)                                 |    86 -
 data/Marburg.zip (new)                             |   Bin 0 -> 1581 bytes
 data/ebola_line_cases.csv (new)                    | 15001 +++++++++++++++++++
 data/simulated_ebola_2.csv (new)                   | 15001 +++++++++++++++++++
 delays-functions.md                                |    16 +-
 describe-cases.md (new)                            |   292 +
 ...elays-functions-rendered-unnamed-chunk-16-1.png |   Bin 50804 -> 50427 bytes
 ...elays-functions-rendered-unnamed-chunk-17-1.png |   Bin 52299 -> 50974 bytes
 ...unctions-rendered-unnamed-chunk-19-1.png (gone) |   Bin 52727 -> 0 bytes
 ...elays-functions-rendered-unnamed-chunk-20-1.png |   Bin 51477 -> 51959 bytes
 ...elays-functions-rendered-unnamed-chunk-21-1.png |   Bin 33204 -> 33142 bytes
 ...unctions-rendered-unnamed-chunk-23-1.png (gone) |   Bin 51632 -> 0 bytes
 ...ys-reuse-rendered-unnamed-chunk-14-1.png (gone) |   Bin 11595 -> 0 bytes
 ...ribe-cases-rendered-unnamed-chunk-6-1.png (new) |   Bin 0 -> 5791 bytes
 ...ribe-cases-rendered-unnamed-chunk-7-1.png (new) |   Bin 0 -> 9266 bytes
 ...ransmissibility-rendered-unnamed-chunk-17-1.png |   Bin 31489 -> 31431 bytes
 ...ransmissibility-rendered-unnamed-chunk-18-1.png |   Bin 30336 -> 29836 bytes
 ...ransmissibility-rendered-unnamed-chunk-21-1.png |   Bin 83577 -> 83259 bytes
 fig/report_demo.png (new)                          |   Bin 0 -> 81199 bytes
 ...e-analysis-rendered-unnamed-chunk-1-1.png (new) |   Bin 0 -> 21079 bytes
 ...e-analysis-rendered-unnamed-chunk-2-1.png (new) |   Bin 0 -> 20476 bytes
 ...e-analysis-rendered-unnamed-chunk-5-1.png (new) |   Bin 0 -> 22930 bytes
 ...e-analysis-rendered-unnamed-chunk-6-1.png (new) |   Bin 0 -> 20947 bytes
 md5sum.txt                                         |    30 +-
 quantify-transmissibility.md                       |   124 +-
 read-cases.md (new)                                |   157 +
 reference.md                                       |     2 +
 renv.lock (gone)                                   |  2703 ----
 simple-analysis.md (new)                           |   178 +
 30 files changed, 31137 insertions(+), 2868 deletions(-)

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⏱️ Updated at 2024-04-29 19:51:25 +0000

[avallecam]

@Degoot-AM thank you for requesting a review, I'll be able to do this next week on Friday. Hope this works for you.

[avallecam]

given that all checks have passed, the workbench workflows created a preview branch with the number of the PR:

• md-outputs-PR-39 👍

[avallecam]

Using library with package::function() will cause lintr to raise a warning and block merging. I would suggest to use loadNamespace instead. What do you think @avallecam

Yes, just recall that. Actually, we fixed this in c9954bc to avoid warnings. Try keeping this warning in the local version, and pushing this to GitHub. It should pass.

[avallecam]

Nice arrangement of episodes covering a good diversity of packages within this task. My general suggestions go to add spaces within code chunks and brief comments in each action.

The md-output shows and error, so we need to solve this before merging this branch. I suggest to prioritize comments and create issues from other that may not be so relevant or may require more time. I think it would be possible to merge this PR at the end of this week.

Then, we may need to find how to rearrange the episodes later given that the describe-cases episode already uses epiparameter.

[Degoot-AM]

first submit for early tutorials.

[avallecam]

This PR is now ready to merge 🚀

I fixed the errors visible in the md-outputs-PR in this commit 1f956a0 I followed the template in this previous reading step

tutorials-early/episodes/delays-functions.Rmd

Lines 559 to 570 in fabe4f0

	```{r,eval=TRUE,echo=FALSE,message=FALSE}
	# read data from the tutorial repository R project
	ebola_confirmed <-
	read_csv(file.path("data", "ebola_cases.csv"))
	```
	```{r,eval=FALSE,echo=TRUE}
	# read data
	# e.g.: if path to file is data/raw-data/ebola_cases.csv then:
	ebola_confirmed <-
	read_csv(here::here("data", "raw-data", "ebola_cases.csv"))

We should not use here::here() to read data in the workbench, instead we use file.path(), but we can suggest the reader to use it.

A way to verify this is by running the chunks locally, getting outputs like these

With error:

Fixed: