Documentation: Rehab the Reference Page

[bms63]

Please select a category the issue is focused on?

Function Documentation

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

As we push to 1.0 we are trying to reduce the number of functions visible in our documentation that are not helpful for users.

For theses eleven functions: 8 will be completely removed and 3 will be exported but have keywords/family changed to internal.

• Remove: We no longer should export this functions and so @export is removed and keywords and family removed
• Export, but change keyword to internal: These functions should still be exported, but their keyword and family changed to internal so they no longer appear on our reference page.

assert_db_requirements() - Remove
assert_terms() - Remove
assert_valid_queries() - Remove
extend_source_datasets() - Remove
filter_date_sources() - Remove
format(<basket_select>) - Export, but change keyword to internal
validate_basket_select() - Remove
validate_query() - Remove
chr2vars() - Remove
signal_duplicate_records() - Export, but change keywords to internal
extract_duplicate_records() - Export, but change keywords to internal

Definition of Done

• All 11 functions documentation updated
• Check vignettes and templates are NOT using the 11 functions
• Update to News to list out what we have removed/suppressed - no need to do any deprecation process.
• Check that no extension packages might be using these 11 functions.
• Proceed with normal PR.

Hi @pharmaverse/admiral another nice one!!

[bundfussr]

@bms63 , should we create an issue in admiraldev to update the programming strategy?

[bms63]

Yes! Good call. I will make an issue

[bms63]

@bms63 , should we create an issue in admiraldev to update the programming strategy?

@bundfussr pharmaverse/admiraldev#346

[sophie-gem]

I can pick this up and do this tomorrow morning.

[sophie-gem]

Note to self: 4 templates (from ADPP) and vignettes left to check.

[sophie-gem]

Hi @bms63 , @bundfussr , in terms of checking the admiral extension packages for this...have I remembered all below:

• admiraloptha
• admiralonco
• admiralvaccine

Also, is anyone able to check your company specific admiral packages: admiralroche, admiralgsk, etc?

[bundfussr]

Hi @bms63 , @bundfussr , in terms of checking the admiral extension packages for this...have I remembered all below:

• admiraloptha
• admiralonco
• admiralvaccine

Also, is anyone able to check your company specific admiral packages: admiralroche, admiralgsk, etc?

@sophie-gem , you remembered the extensions packages correctly.

I have checked admiralroche. It uses chr2vars() and signal_duplicates_records().

[bms63]

Hi @bms63 , @bundfussr , in terms of checking the admiral extension packages for this...have I remembered all below:

• admiraloptha
• admiralonco
• admiralvaccine

Also, is anyone able to check your company specific admiral packages: admiralroche, admiralgsk, etc?

@sophie-gem , you remembered the extensions packages correctly.

I have checked admiralroche. It uses chr2vars() and signal_duplicates_records().

Then we should still export chr2vars but use internal? @bundfussr

[bundfussr]

Hi @bms63 , @bundfussr , in terms of checking the admiral extension packages for this...have I remembered all below:

• admiraloptha
• admiralonco
• admiralvaccine

Also, is anyone able to check your company specific admiral packages: admiralroche, admiralgsk, etc?

@sophie-gem , you remembered the extensions packages correctly.
I have checked admiralroche. It uses chr2vars() and signal_duplicates_records().

Then we should still export chr2vars but use internal? @bundfussr

I would export both and also list them on the reference page.

[sophie-gem]

So given what @bundfussr said above, I will retract the changes to chr2vars() and signal_duplicates_records() and check the 3 admiral extensions (R functions, templates, and vignettes) for any of these functions.

[bms63]

Awesome thanks @sophie-gem !!

[sophie-gem]

Note to self: No templates contain these functions. Rest of vignettes left to check from bds_finding onwards.

[bms63]

Hey @sophie-gem can you finish this by the end of the week?

[sophie-gem]

Ah, so sorry - dropped off the planet again! Yes, I will aim to get this done by EOB Friday. Is that ok?

[bms63]

Ah, so sorry - dropped off the planet again! Yes, I will aim to get this done by EOB Friday. Is that ok?

yes no problem!