Closes #2415 replaced hard coding of expr(USUBJID, STUDYID) or expr(USUBJID) with …

[ProfessorP-beep]

…!!!get_admiral_option("subject_keys") to allow for flexibility in using the function. There is an error in the bds_exposure.Rmd markdown on line 361, chunk 22 that needs to be fixed.

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[github-actions[bot]]

Package	Line Rate	Health
admiral	96%	✔
Summary	96% (4883 / 5082)	✔

[bms63]

Looking nice @ProfessorP-beep! Can you just run styler on your code

[ProfessorP-beep]

I'm still getting the error with pkgdown::build_site(), but everything else, including running the .Rmd checks out. It's running again right now after merging an update.

[bms63]

I'm still getting the error with pkgdown::build_site(), but everything else, including running the .Rmd checks out. It's running again right now after merging an update.

I will see if I can build site on my end

[bms63]

I was able to build website - I will review PR. @manciniedoardo can you also help with review please.

[manciniedoardo]

@ProfessorP-beep sorry, would it be possible to please update the occasions where we have exprs(get_admiral_option("subject_keys") to just say get_admiral_option("subject_keys")? I believe that would be the right syntax. thanks

[ProfessorP-beep]

@manciniedoardo Already done. I realized my mistake after that last push. New one coming as soon as the checks are done.

[ProfessorP-beep]

Sorry, hold off on reviewing on minute. Some of the changes weren't pushed through.

[ProfessorP-beep]

Hey @manciniedoardo, sorry about that. The latest pull is ready for review.

[rossfarrugia]

@bms63 any user could hardcode the subject identifiers instead if they were only ever going to use STUDYID, USBUJID here, but for our package to follow our own instructions at https://pharmaverse.github.io/admiral/reference/#admiral-options we have to follow the more generic way, otherwise an option that we ourselves advertise for users doesn't actually consistently work across the package.

[bms63]

@bms63 any user could hardcode the subject identifiers instead if they were only ever going to use STUDYID, USBUJID here, but for our package to follow our own instructions at https://pharmaverse.github.io/admiral/reference/#admiral-options we have to follow the more generic way, otherwise an option that we ourselves advertise for users doesn't actually consistently work across the package.

Okay! I understand how options work :) I feel like I'm not making myself very clear with my concerns...so maybe my concerns for the users is moot! :) If you all think this update makes sense for the users, then full steam ahead!!

[bms63]

and thanks @ProfessorP-beep for seeing this through!! This is how it works on the team :) We do PRs and I get a little huffy and puffy and ask funny questions - which usually are me being paranoid.

[rossfarrugia]

Thanks @bms63 - all fair questions, but i guess these all would have been discussed when we first added this option. Now that we have it offered in the package, we just need to make sure it works :)

[ProfessorP-beep]

and thanks @ProfessorP-beep for seeing this through!! This is how it works on the team :) We do PRs and I get a little huffy and puffy and ask funny questions - which usually are me being paranoid.

No problem! I'm also learning a lot more so this is cool. I'm looking through the discussion now.

[bms63]

@bundfussr @rossfarrugia @manciniedoardo - This update isn't critical to me for 1.1. Can we implement for 1.2 as it is actually quite large and seems to be opening lots of questions?

[manciniedoardo]

@bundfussr @rossfarrugia @manciniedoardo - This update isn't critical to me for 1.1. Can we implement for 1.2 as it is actually quite large and seems to be opening lots of questions?

Ok, let's leave until 1.2 to ensure we do this right and don't have to come back to it later. I still think it's an important update to make, and we can definitely still leverage all the work done by @ProfessorP-beep in this PR, but what we have now is not wrong per se, just a bit inconsistent.

[bms63]

Hi @ProfessorP-beep, we can talk about this tomorrow, but going to pause on this PR until after we ship 1.1 release. This will be our first PR into 1.2!

[ProfessorP-beep]

Hi @ProfessorP-beep, we can talk about this tomorrow, but going to pause on this PR until after we ship 1.1 release. This will be our first PR into 1.2!

Sounds good, I'm just gonna push the additional changes I've done since then. There is probably still some review to be done to make sure all cases are addressed.

[github-actions[bot]]

This Pull Request is stale because it has not been worked on in 15 days.

[github-actions[bot]]

This Pull Request is stale because it has not been worked on in 15 days.