Closes #2897 ADAB Vignette

[Kcdahn]

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[github-actions]

Package	Line Rate	Health
admiral	100%	✔
Summary	100% (6070 / 6083)	✔

[Copilot]

Pull request overview

This PR adds a comprehensive vignette for creating Anti-Drug Antibody (ADA) ADaM datasets (ADAB). The vignette provides detailed guidance on processing immunogenicity data from SDTM IS and EX domains into a parameter-based ADaM structure, covering both baseline and post-baseline ADA assessments as well as neutralizing antibody (NAB) status.

Key Changes

• New ADAB vignette (vignettes/adab.Rmd) demonstrating the complete workflow for creating an Anti-Drug Antibody ADaM dataset with 1,583 lines of comprehensive documentation and code examples
• Updated package documentation (_pkgdown.yml) to include navigation link to the new ADAB vignette
• Coverage of both SDTM v1.x and v2.0 standards with guidance on handling differences in variable naming conventions

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 20 comments.

File	Description
vignettes/adab.Rmd	Comprehensive vignette providing step-by-step guidance for creating ADAB datasets, including data staging, parameter derivation, baseline/post-baseline flagging, treatment-emergent categorization, and final dataset assembly
_pkgdown.yml	Added navigation entry for the new ADAB vignette in the articles section

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[Fanny-Gautier]

Same comments as in the template to be implemented here.

[Fanny-Gautier]

Thank you for providing such a detailed vignette on the complex ADA dataset derivation!
Please find my comments from the first review. Feel free to implement them as you see fit.

[bms63]

I'm a little confused here

IS_ADA is a product of the pharmaverse IS_ADA data. ??

what does that mean?

[Kcdahn]

I'll update this. I had copied part of the verbiage from another vignette.

[Kcdahn]

I just updated it, take a look.

[bms63]

@Kcdahn - I'm happy to get this merged in today if you can fix the "verbiage". I did a quick read and looks great! A little over my head but wow so much to learn!! Thanks for driving and putting together!!

[Kcdahn]

@bms63 What about my updates due to Jeff's derive_var_nfrlt() I have to add code and verbiage for that function but it doesn't work or test yet from my vignette branch. We could merge this to Main now then update it again in Jeff's NFRLT branch. Up to you.

[bms63]

@bms63 What about my updates due to Jeff's derive_var_nfrlt() I have to add code and verbiage for that function but it doesn't work or test yet from my vignette branch. We could merge this to Main now then update it again in Jeff's NFRLT branch. Up to you.

Okay - I requested the experimental badges be added to those two functions. I only glanced at the functions but they look great to me. The tests are really thorough.

[bms63]

@Kcdahn functions are merged in - please proceed.

[bms63]

Looks like Code Styler actions is failing on the vignette

[Kcdahn]

I added the main adab.R template code updates related to derive_var_nfrlt() updates and added/changed some related verbiage.
The Styler issue was some dataset_vignette() adds needed styling.

[bms63]

Just a couple of additions to spelling wordlist and then I think we are good!?!

[bms63]

Brilliant job all! I think it has been a while since we had a new vignette and template. maybe a year since Jeff did the PC ones??