Documentation & Templates: Make subject keys consistently flexible

[rossfarrugia]

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User Guides

Let us know where something needs a refresh or put your idea here!

There's some examples in the vignettes and the templates where STUDYID or USUBJID are still being called usually in by_vars instead of get_admiral_option("subject_keys"). See https://pharmaverse.github.io/admiral/reference/#admiral-options.

For example see inst/templates/ad_adoe.R or vignettes/advfq.Rmd.

Also in assertion check call in R/derive_var_bcvacritxfl.R.

FYI @manciniedoardo

[aldrichsalva]

I added set_admiral_options() right below the library functions in each of the templates based on the example in https://pharmaverse.github.io/admiral/reference/set_admiral_options.html.

Would the placement of the function be the same for vignettes?

Also, what would be the placement in the functions? Thanks!

[rossfarrugia]

@aldrichsalva the admiral package already defaults to these values so you don't need to ever set them in the templates (unless a user ever wanted to change these). you could follow this PR to guide on the updates needed, but bear in mind its still in progress so see the review comments: pharmaverse/admiral#2452

[manciniedoardo]

thanks @rossfarrugia - @aldrichsalva I believe for admiralophtha you'd just have to replace any mentions like this:

  derive_vars_merged(
    dataset_add = adsl,
    new_vars = adsl_vars,
    by_vars = exprs(STUDYID, USUBJID)
  )

with something like this:

  derive_vars_merged(
    dataset_add = adsl,
    new_vars = adsl_vars,
    by_vars = get_admiral_options("subject_keys")
  )

with the code a little more complex in the case that the by_vars encompass more variables than just the subject keys. See the PR that Ross linked for some examples there.

[rossfarrugia]

I made a similar PR for admiralonco earlier for this as FYI: https://github.com/pharmaverse/admiralonco/pull/285/files - there's a couple of minor other pieces updated there too, but in the most part its examples like Edoardo shared above. To find the impacts I used a search on the github repo for USUBJID and then worked from there.

[rossfarrugia]

Also I realised that for the admiralroche (closed source) templates we did choose to include the set_admiral_options() call so that might have caused confusion here. I guess that decision was as we have one team using this tool that do likely need to change this option so we made it more visible there as a reminder, but the same wasn't deemed needed in admiral core so better we keep the open source packages consistent.

[manciniedoardo]

@aldrichsalva any chance you can take a stab at this today, so that we can release tomorrow? otherwise i can take over form you.

[aldrichsalva]

@manciniedoardo apologies for the delay! Please take over if that is ok.