Add new per-check documentation pages and check severity parameter

[katy-sadowski]

This pull request contains the following changes:

• A new severity parameter is added to the check descriptions file and to check documentation, as decided in the Fall 2023 DQD Hackathon. This parameter is not used for anything yet, but in the future we will add the ability to specify which severity level(s) to execute in a DQD run
• A new dropdown menu and individual check documentation pages have been added to the DQD website. Docs for 8 checks have been added so far - those with finalized DQD Hackathon worksheets (see here)
• Related updates to documentation configuration files, as well as some cleanups to our vignette headers

Notes for reviewers:

• You may of course ignore all auto-generated files
• I'd recommend to pull down my branch and run pkgdown::build_site() so you can review the actual webpage rather than the markdown files
• So far, I only populated the severity parameter for the 8 checks we finalized worksheets for. As we complete the worksheets for more checks, we can open new PRs to add the docs and populate severity in the check description files. (@MaximMoinat I'm thinking you can add docs for your 3 new checks, once we agree on the format here and merge in this PR 😄)
• For now, I'm keeping the original Check Type Descriptions documentation page - we can keep this around until we have docs for all the checks

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (c065c84) 85.00% compared to head (9c166f8) 84.59%.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #518      +/-   ##
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- Coverage    85.00%   84.59%   -0.41%     
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  Files           16       16              
  Lines          907      909       +2     
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- Hits           771      769       -2     
- Misses         136      140       +4     

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[clairblacketer]

This looks great, thank you Katy for putting these together!

[MaximMoinat]

Very nice work. I only have some small suggestions for the template, see inline comments on the fkClass page.

[MaximMoinat]

@katy-sadowski I have applied a new markdown template to the existing checks, and instantiated the template for all other checks as well.
Other changes:

• check description files moved to vignettes/checks
• the template is under extras/checkDescriptionTemplate.Rmd, which is instantiated with createCheckDoc.R
• completely rebuild the docs folder, which removes some redundant files (e.g. the _docs folder)

[katy-sadowski]

Thank you so much for these additions @MaximMoinat ! The template looks great and is super useful. I left some minor suggestions on the plausible after birth doc.

As mentioned in Teams I will wait to merge this until @dimshitc 's new checks are merged in, to save him merge conflict grief 😄

[katy-sadowski]

i think we were calling this "Characterization"?

[katy-sadowski]

also i put emojis next to the other 2 statuses (a skull for fatal and a warning sign for CDM convention). feel free to choose and add one for characterization 😄

[MaximMoinat]

So about the emojis. I looked for one but did not find a good one. I added a ✔ ✔. But I am not really convinced about the need for them for this purpose (although in general I love using emojis everywhere). Let's discuss next meeting.

[katy-sadowski]

Haha, they are definitely not necessary. I was thinking maybe in the new report view we build eventually, having some visual marker for the severity could be helpful, but that's something to be discussed later on as we think through the UI.

[katy-sadowski]

maybe should also add the option of leaving as-is, i.e. for prenatal or other observations where the date is actually valid.

[MaximMoinat]

I actually like that better for the conservative strategy. Modifying the event date might create other issues. Either it is correct and you leave it as is, or you don't trust the record and remove it, or you don't trust the person and remove it.

[katy-sadowski]

@MaximMoinat thanks for the fixes! Just 2 more minor things.