51 documentation updates v01

[edgar-manukyan]

Thank you for your Pull Request! We have developed this task checklist from the Development Process Guide to help with the final steps of the process. Completing the below tasks helps to ensure our reviewers can maximize their time on your code as well as making sure the oak codebase remains robust and consistent.

Please check off each taskbox as an acknowledgment that you completed the task or check off that it is not relevant to your Pull Request. This checklist is part of the Github Action workflows and the Pull Request will not be merged into the devel branch until you have checked off each task.

• [ ] Place Closes # into the beginning of your Pull z Request Title (Use Edit button in top-right if you need to update)
• [ ] Code is formatted according to the tidyverse style guide. Run styler::style_file() to style R and Rmd files
• [ ] Updated relevant unit tests or have written new unit tests, which should consider realistic data scenarios and edge cases, e.g. empty datasets, errors, boundary cases etc. - See Unit Test Guide
• [ ] If you removed/replaced any function and/or function parameters, did you fully follow the deprecation guidance?
• [ ] Update to all relevant roxygen headers and examples, including keywords and families. Refer to the categorization of functions to tag appropriate keyword/family.
• [ ] Run devtools::document() so all .Rd files in the man folder and the NAMESPACE file in the project root are updated appropriately
• [ ] Address any updates needed for vignettes and/or templates
• [ ] Update NEWS.md if the changes pertain to a user-facing function (i.e. it has an @export tag) or documentation aimed at users (rather than developers)
• [ ] Build oak site pkgdown::build_site() and check that all affected examples are displayed correctly and that all new functions occur on the "Reference" page.
• [ ] Address or fix all lintr warnings and errors - lintr::lint_package()
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[github-actions[bot]]

Package	Line Rate	Health
sdtm.oak	88%	✔
Summary	88% (786 / 894)	✔

[rammprasad]

@edgar-manukyan @galachad @ramiromagno - I think all checks passed in the pipeline. But it is not showing up. Can you help me resolve this? From a content perspective, everything is complete.

[ramiromagno]

The DT package is in Suggests but should be in Imports because it's used in dataset_oak_vignette().

[ramiromagno]

Also, with R version 4.4 and more recent packages, I am also getting:

Using an external vector in selections was deprecated in tidyselect 1.1.0.
i Please use `all_of()` or `any_of()` instead.
  # Was:
  data %>% select(.after)

  # Now:
  data %>% select(all_of(.after))

These warnings come from the functions implemented in the branch with conditioned data frames, and I know I have fixed them before we merged into main. So I guess this branch does not yet have the most up-to-date version of main integrated into it...?

[rammprasad]

I have merged the latest main to this branch. Not sure what is going on. It doesn't show any differences.