Closes #111 dataset contents ref pages

[vbshuliar]

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[github-actions]

Package	Line Rate	Health
pharmaversesdtm	0%	❌
Summary	0% (0 / 41)	❌

[bundfussr]

• A comment should be added to the R/*.R that these are generated and shouldn't be edited manually.
• README.md should be updated to describe the new documentation process.

[manciniedoardo]

• A comment should be added to the R/*.R that these are generated and shouldn't be edited manually.
• README.md should be updated to describe the new documentation process.

@vbshuliar once you update README.md could you also do the same in pharmaverseadam as we are now following the same process across both packages? thanks

[vbshuliar]

@manciniedoardo @bundfussr Please take a look at the updated version.

[manciniedoardo]

Thanks @vbshuliar - I tested the actual process and looks great. I've added a couple of comments.

In addition to the above I also tried rendering the site. Looks good, but can you please restructure the reference page so that it mentions datasets and not functions:

Edit: get_terms() should still be under functions.

[vbshuliar]

I updated the layout as you requested. Please, proceed with the rereview @manciniedoardo

[bundfussr]

I'm not sure if we should turn off lintr completely for all files in R and data-raw.

@manciniedoardo , what do you think?

[manciniedoardo]

ideally not completely, is there a more granular approach?

[bundfussr]

I would keep the old setting for data-raw where we just turn off the undesirable function lintr.

For the R folder I would not turn off anything. To avoid issues with the line length I would wrap the lines with stringr::str_wrap() and enclose lines which are too long after that with # nolint start: line_length_linter and # nolint end.

[vbshuliar]

@manciniedoardo @bundfussr What if I set the exclusion to only the line length parameter in the generated files, instead of ignoring everything? This approach would be more specific and still allow us to track important inconsistencies.

[manciniedoardo]

that's a good idea

[manciniedoardo]

LGTM - @bundfussr please add your review when you can so that I can then do a release.

[bundfussr]

The metadata for vs_peds was lost. It is available at https://pharmaverse.github.io/pharmaversesdtm/reference/vs_peds.html but in this branch I get

Warning message:
No metadata found for vs_peds - using default values. 

when calling create_sdtms_data.R.

[bundfussr]

Looks good now.

@vbshuliar , thanks for your great work and patience!

[vbshuliar]

@bundfussr @manciniedoardo
Thanks you both for the opportunity to contribute to pharmaverse. I really enjoyed it and gained lots of valuable experience!