Questions and Comments (Agenda for the Bi-Weekly admiral meetings)

[bms63]

To help simplify, we are moving the Question and Comments Agenda from the Phuse Teams to GitHub. This agenda drives our discussion for the bi-weekly admiral meetings.

You can find the old agenda here

• For each bi-weekly meeting please start a new thread with date of meeting at the top
• Remember if you create an issue from a Topic, then please make sure it has context as well as a Definition of Done

[bms63]

October 18th, 2023 Agenda

• admiraldiscovery and its unveiling
• staged.dependencies and remotes

[bms63]

Some notable notes of note

• Stefan has a blog post coming on floating points/binary representation from our struggles in admiral
• Zelos is doing an admiral presentation at CDISC Conference this week!
• Jeff is doing a pk-admiral presentation at R/Pharma
• We got 8 issues that need to be worked on!!

ACTIONS

• Separate meeting to be set up to discuss scope and functionality for admiraldiscovery - @ddsjoberg to set up. (Meeting set for Nov 2)
• DESCRIPTION file will have remotes field enabled which will allow us to reduce footprint in the README around installing dev version of the package. Further discussion will be needed with CI team to see how we can remove staged.dependencies from the CI workflows and reduce complexity. However, remotes and stage.dependencies can co-exist in harmony and love

@pharmaverse/admiral Short but great meeting! Trying out the new agenda/note-taking replacement.

[bms63]

November 15th, 2023 Agenda

• Let's begin using usethis::use_release_issue() to prepare CRAN releases. It has a few benefits that would have helped with the last round of releases: checking on the CRAN Windows devel version, RHub Debian checks, etc.
• Updates on new CI processes
• Investigate devel issues in CI check

@pharmaverse/admiral don't forget to fill out the agenda here for this week's meeting.

[bms63]

Some notable notes of note

• Currently some errors are occurring in the r-devel CI workflow. This might be a problem at release.
• admiraldiscovery is looking very nice
• Potential issue of un-released templates being available to users on the website as main is our development branch now.
• renv is being abandoned post-1.0. We will need to think on how to approach reproducibility around failing workflows - this was an issue in the past and why we adopted renv.
• derive_vars_period has some unexpected behavior

ACTIONS

• Ben to look into submitting the package to CRAN to check that admiral is working on windows r-devel
• If anyone has some time - do check on Edoardo's cheat sheet and provide feedback.
• Ben to make issue on updating User Guides to point to use_ad_template() rather than link to actual template.
• Ben to make a call to slack for someone to investigate the Bug: derive_vars_period() errors unexpectedly when dataset_ref has unused variables #2231
• Daniel to re-open admiraldev PR and make a few of the suggested changes

[bms63]

@pharmaverse/admiral trying to jot down a few notes for our meetings going forward. anything of note please add. also for folks who did not attend some brief notes for you.!!

[bms63]

November 29th, 2023 Agenda

• Roche verification before release to CRAN
• dependency package releases (sdtm, dev)
• 2.0/1.1 Roadmap and inviting the community to the meeting
• Retrospective
• https://github.com/pharmaverse/admiral/pull/2246/files new packages in the DESCRIPTION file
• pharmaverse/admiral-community-team

[bms63]

Notable notes of note

• Light discussion on the difference between 2.0 and 1.1 and how a 2.0 might not be needed.
• Interest in a Roadmap meeting for 1.1 with a focus on resourcing, release cadence, features (to happen after Retrospective)
• Not everything has to be a vignette - we can make more of them into articles which means they are not checked by CRAN and can head off any nastiness from CRAN checks (TBD more in new year).
• Reduced meeting in the new year!!
• Community Team - how to get folks interested in admiral from the community and work on small issues for us. Formation of a pharmaverse community team.

ACTIONS

• @manciniedoardo to discuss with @millerg23 on doing admiralroche checks before we submit to CRAN
• @zdz2101 to set up the Retrospective Meeting and Board (mid January)
• @bms63 to create a pharmaverse admiral community team so he can tag folks
• @ddsjoberg to look into failing r-devel actions and if we need to do anything about it.

@pharmaverse/admiral anything else of note we want to put here?

[bms63]

December 13th 2023 Agenda

• Superseded functions that are used in our Imported Packages (General Issue: dplyr::transmute() is superseded #2274)
• Review of upcoming meeting schedules (Retrospective, Road Map, Core Meetings)
• Cleaning up all repos in admiral-land (template, ci, dev, data packages)

[bms63]

Notable notes of note

• Okay given on updating superseded function from dplyr. However, no special task force will be assembled to investigate other superseded functions as these will be around for a long time...so no rush on updating admiral codebase. If folks spot potential superseded functions in the wild that are in admiral, then please bring to our attention .
• Please try your best to make it to our two hour Retro/Road Map meeting (January 17th). We do want to minimize the number of meetings and conscious of folks' time, but this one will be a good one for us!!
• Please prioritize adding issues to the board from all the different repos. This ensures that nothing is getting stale and work is identified for others

ACTIONS

• For everyone - check schedule to make sure you can make it to January 17th meeting. Please prioritize!!
• Add issues from all admiral-focused repos to the board.

@pharmaverse/admiral Hi all. 2023's last meeting was short and sweet. For those in attendance, let me know if I missed anything, for those missed - please check out notes and many thanks again for all your hard work to this project!

[bms63]

PS - Be sure to check out the Retro Board and fill out! https://phuseaccount.sharepoint.com/:w:/r/sites/Pharmaverse-admiral/Shared%20Documents/Dev[…]=wd069c12df36f405bb684e38aff2db2ea&csf=1&web=1&e=UXaQma

[bms63]

Road Map January 17th 2024

[bms63]

Intros

• New Joiners from Cytel!

Retrospective

See Board: https://phuseaccount.sharepoint.com/:w:/r/sites/Pharmaverse-admiral/Shared%20Documents/Dev[…]=wd069c12df36f405bb684e38aff2db2ea&csf=1&web=1&e=UXaQma for seeing what went, what went poorly and how we can improve.

A possible list of things to look into more:

• How to set up Reminder around checking cheatsheet before a release/PR
• How do help detect issues in upcoming releases? UAT period?
• Do we need a temperature check for contribution to make sure we are okay on resources? How can we get to 1.1/2.0 with current folks
• What is the best development model to build a package?!? Do we need a write-up on guidance/possibilities/hitches/lessons learned for other folks to have?!?
• Time limits for issues at the time of release?? See Board?
• How to best optimize the admiral functions for large datasets?

Road Map

See Lucid Board: https://lucid.app/lucidchart/e0cdbe11-c3ee-4fd6-9753-5f4fcbb66c6e/edit?invitationId=inv_7e6fc110-ddc5-4335-a8ba-0c5538f2e7d0&referringApp=slack&page=0_0#

Focus Areas

• How to improve user experience with error/warning messages
• How to improve the Reference Page for users?
• How to improve Developer Setup (Youtube, renv, Posit Cloud)
• Balancing feedback from Users, Developers over time and incorporating
• Regulatory filings and reviewers using admiral should be kept
• Mid-Year Road Map Meeting (TBD)
• How to improve functions (big datasets) without upsetting users
• Increase use of blog and example site to bring awareness

Major Challenges

• Retaining developers
• onboarding new devs
• Use of admiral by regulatory agencies
• Bugs are going to be harder to sovle

Specific Issues

• Did not really have time for. See Board for list of tiems

How would you like to work

• Continue with fortnightly meetings
• Increased engagement on slack

[bms63]

January 24th, 2024 Meeting

Errors, Warnings and Messages...oh my!!

• @ddsjoberg to look into and lead an Error/warning message elite squad of folks
• Focus on admiraldev and the assert functions
• Possible adoption of CLI package as depedency - https://cli.r-lib.org/index.html
• Proposal to have a document for team to review before next meeting (uncertain)
  • List of functions to update
  • Style we want to use
• Use of Core meetings to discuss Error messaging at the end of the agenda

Deprecation/Superseded Strategy

• There is some confusion on team on the strategy of using Deprecation/Superseded

• Currently not following the superseded strategy that is used in the tidyverse

• It sounds like some folks think we are never deprecating any functions versus some folks thinking a few might be deprecated down the road.

• @bms63 to summarize current strategy from his understanding in a Discussion Thread

  • When do we supersede and scenarios
  • When do we deprecate and scenarios
  • Once strategy is clarified in Discussion we can codify in the Programming Strategy
  • Hopefully, reduces need to revisit Strategy going forward

  Big Data Big Problems

  • How does admiral perform on big data?
    • One user reports that at 7 million rows admiral fails
    • Team member reports that left_join also has similar problem and had to use a workaround
  • Is this a focus for admiral team?

• @bms63 to look into setting up some experiments to compare performance of dplyr join functions and admiral derive_vars_join function

Timing is everything

• @zdz2101 brought up the cyclomatic complexity of our date/time functions. We have adjusted our lintr checks to allow for more complexity - which is a bit of a no no.
• @zdz2101 to investigate the parttime package as a possible solution to reduce the cyclomatic complexity of the datetime functions
• Necrod the discussion - Feature Request: Partial Date-Time objects #2051

[bms63]

@pharmaverse/admiral Hi all - I made some notes. Apologies I'm not the best at taking notes and participating. My brains hurts.

Please fill any gaps or ask questions and I or others can help clarify.

[bms63]

February 7th 2024

Agenda

• Round Robin Check-in
• Report back on Error Messaging (@ddsjoberg)
• Report back on parttime (@zdz2101)
• Report back on Deprecation/Superseded Strategy (@bms63) (Deprecation 2.0 #2329 (comment))
• hotfix 1.0.1 release
• decision for derive_var_trtemfl() enhancement
• lintr versus stlyer CI issues

Notable Notes

Briefs from the Check-in

• hotfix released around derive_vars_query
• pharmaverseadam is being utilized in nest templates. this has surfaced some interesting issues for us to work on! thanks @kaz462
• Fanny and Alex are working through the onboarding issue
• We need some bit of gudiance for getting up and running since renv has been purged.
  • @bms63 to make an use

Error Messaging

• Daniel presented on the cli package and showcased many of the awesome features available.
• information on cli - https://cli.r-lib.org/index.html
• slides from master class from Wickham on using adopting cli into another package Daniel is working on - https://www.danieldsjoberg.com/ARD-onboarding/05-cli-conditions.html
• Daniel will ping slack channel and assemble a small breakout group to identify functions that could benefit adoption of cli messaging.

Parttime

• Zelos presented on his review of the parttime package` as a way to reduce cyclomatic complexity in our date/time functions
• Link to package parttime - https://github.com/dgkf/parttime
• Very powerful, but is missing some key pieces that could introduce other issues into our current approach/functions
• Recommendation is for us not to use parttime.
• Zelos, Gordon and Ben to look into "mindmapping" the date/time functions to help with breakout into smaller functions and reduce complextiy
• Daniel recommends that add additional unit tests before embarking on working on the functions to try and head off any pesky bugs. Hopefully mindmap will give us some more leads for tests.

Actions

• Ben to make issue for dev guidance on installing all packages for dev work (Documentation: setup of developer environment admiraldev#362)
• Daniel to gather team for using cli to enhance error messaging in admiraldev/admiral
• Zelos, Gordon and Ben to spearhead the mindmapping of cyclometric doom
• Ben to follow up on other issues not discussed in today's meeting and cajole, bribe, beg and barter them into completion.

[bms63]

@pharmaverse/admiral great meeting today everyone!! Lot's of interesting discussion. Sorry that we couldn't hit on every topic.

Here are my notes - please feel free to add or clarify to them.

Anything that we missed - be sure that I will pursue.

[bms63]

February 21st 2024

• Round Robin Check-in
• Report back on Deprecation/Superseded Strategy (@bms63) (Deprecation 2.0 #2329 (comment))
• hotfix 1.0.1 release
• potential hotfix 1.0.2 release - Bug: derive_param_tte() fails if dataset and by_vars is specified #2336
• decision for Enhancing derive_var_trtemfl() to deal with AEs recorded on multiple lines #2302
• lintr versus stlyer CI issues
• Report back on Error Messaging (@ddsjoberg)
• Report back on parttime (@zdz2101)

Notable Notes of Note

• lintr structure() issue still seems to flare up, otherwise the lintr/styler issue should resolve on its own
• potential build_site() issue that may need to be investigated
• datetime/date c.c. stuff is starting to churn along
• admiralpeds kicked off

Actions

• Ben to set up meeting with Fanny and Lina to discuss pkgdown issue
• Ben will summarize proposed deprecation strategy
• Gordon will start looking into Bug: derive_param_tte() fails if dataset and by_vars is specified #2336

[bms63]

March 6th, 2024

Agenda

• Go arounds (how was Phuse!?!)
• Revisit PR Template and Changelog item (https://pharmaverse.slack.com/archives/C028SJ83KM1/p1708958804204549)
• Report back on Error Messaging Group
• Report back on date/time cyclomatic complexity group
• Hotfix 1.0.2 lessons learned (website)
• Proposed changes in admiral for GSK
• User-defined baselines in ADLB, ADVS, ADEG, etc (Time-matched, visit-matched, etc)
• Building sites (window machines?)

Notable Notes of Note

• Lots of folks attended Phuse US Connect!! admiral and general R hype was abound
• At Phuse folks from Eli Lily and AZ are looking at ways to use admiral, metatools/metacore to drive their ADaM building (way cool!)
  • Be cool to reach out to them and get them involved with the project more
• Cyclo and Error messaging groups are proceeding quite well driven by the ever-amazing and indefatigable Zelos and Daniel respectively.
  • Questions regarding alerting users to these under the hood changes
  • For Error messaging that will get it's own news blurb in the News section
  • For other developer updates, we will have a new Developer Notes section in the changelog
    • Large under the hood changes should get placed here (but not everything!)
• Website versions and package number has been impacted during latest changes
  • Dinakar is looking into fixing/maintaining website versions as this part is not working as expected
  • Unsure on package number as the color has changed and is difficult to read
• Check out discussion on Proposed GSK changes if interested - admiral's use within GSK's ADaM metadata driven system #2349
• Gordon brought up some interesting User-defined baselines in ADLB, ADVS, ADEG, etc (Time-matched, visit-matched, etc) and will make discussion around it (seems very niche, but might be some nice updates for admiral)
• The building of the website locally can get wonky (there are some troubleshooting fixes presented, but it is a bit of a mystery)

Actions

• Edoardo to make news blurb in admiral around new Error Messaging paradigm to alert users
• Ben to make update for PR Template and Changelog section for tracking Developer updates
• Gordon to make discussion on user-defined baselines
• Eric to make update to lintr issue around stlyer doing indentation and suspending check for linter indentation
  - [ ] Ben to update Remotes in Description for in admiral to get updates going on in admiraldev

[bms63]

@millerg23 do you mind making a discussion thread for the basetype stuff? Helpful if we can make some simple examples.

[bms63]

March 20th, 2024

Agenda

• First ten minutes: discussion about how to manage and fix website versions for the main package (@cicdguy joining the call for this discussion)
• Go arounds
• Awareness of Prog Docs - https://pharmaverse.slack.com/archives/C028SJ83KM1/p1710769679010549
• Report back on Error Messaging Group
• Report back on date/time cyclomatic complexity group
• derive_vars_dt(preserve) removing this argument
• User-defined baselines in ADLB, ADVS, ADEG, etc (Time-matched, visit-matched, etc)
• Snapshot unit tests not being run on our customs checks - should we use the posit one?
• Testing of non-exported functions (@nord?)
• Issues in Backlog

Notable Notes of Note

• Reverting the website back to multi-version so that insightsengineering can maintain one set of workflows for all packages
• Fanny is working on version number coloring on pkgdown site - paused while Dinakar works on deploying fix for multiversion
• Proposal to remove the preserve argument from the dt/dtm functions. Will NOT implement as admiralroche templates make use of this argument. Cyclomatic complexity group will try and improve the code around this argument.
• Discussion on non-exported functions not being tested. seems like some issue with testthat - Daniel to look into
• Few outstanding issues form late 2023 were discussed. Sophie to take on dplyr update Feature Request: Use dplyr::left_join(relationship) argument #2247. Gordon was "volunteered" for Feature Request: Enable passing additional arguments to get_terms() #2265
• Make sure to use dev at the end of the admiraldev url to get the latest programming strategy documents (unsure if this will be impacted by multiversion update...)

New Actions

• Sophie to work on Feature Request: Use dplyr::left_join(relationship) argument #2247
• Gordon to work on Feature Request: Enable passing additional arguments to get_terms() #2265
• Edoardo to check on @gg106046 who is working on derive_vars_transposed: extra variables are treated as by_vars #2325

Previous Actions

• Edoardo to make news blurb in admiral around new Error Messaging paradigm to alert users
• Ben to make update for PR Template and Changelog section for tracking Developer updates
• Gordon to make discussion on user-defined baselines
  to update Remotes in Description for in admiral to get updates going on in admiraldev~

[bms63]

@pharmaverse/admiral hi all - threw in a few notes from today's meeting. Please add anything you think might be needed for posterity or clarity :).

[millerg23]

Apologies for abruptly dropping out of meeting, I lost my internet connection.

[manciniedoardo]

April 3rd, 2024

Agenda

• Go arounds
• Report back on Error Messaging Group
• Report back on date/time cyclomatic complexity group
• 🚨improper enviornment handling in admiral 🚨
• derive_vars_dt(preserve) removing this argument (carried over from prev meeting)
• User-defined baselines in ADLB, ADVS, ADEG, etc (Time-matched, visit-matched, etc) (carried over from prev meeting)
• Snapshot unit tests not being run on our customs checks - should we use the posit one? (carried over from prev meeting)
• Testing of non-exported functions (@nord?) (carried over from prev meeting)
• 1-1 mapping checks closes #2389 removed the typo in an example for derive_vars_locf_records #2390 (comment)
• Issues in Backlog
• 🚧 revisit derive_var_trtemfl enhancement decision
• Get Started Tab (ADSL, programming concepts)
• Numeric deCodes for Country Feature Request: Add numeric decodes for COUNTRY #2388

Notable Notes of Note

• June Release is coming!!
• Error messaging is progressing along in admiraldev, but admiral updates have stalled. @zdz2101 has offered to jump in as @bms63 has fallen off
• The Environment handling issues found by Edoardo have brought up a need to better document how we use exprs() as well as other design/WoW found in admiral
  • Decided to split the Get Started/Simple ADSL Walkthrough into two Vignettes. One focused on pure ADaM creation and the second focused on programming concepts/design/WoW
  • Current ADSL Walkthrough has a lot of extraneous material (including exprs() ) that doesn't relate to ADSL
  • ADSL Walkthrough will also include ADVS examples to showcase adding records to the dataset.
• Snapshot Testing was briefly discussed and it was observed that in admiraldev they might not be firing for R-CMD checks. This was raised to CI team and it looks like a global fix is coming.
• Several functions that involved 1-1 mapping (e.g. function using AVISIT/N) do not check for the 1-1. admiralonco had tried something similar and produced a lot of issues. We place the burden back onto the users to check for these kind of uniqueness.
  • Template checks from admiralroche could be brought over
  • Possible to add additional advice in a vignette
• The Treatment Emergent Flag has brought up some interesting discussion on what to flag and what not to flag. Stefan and Ben are going to look into which options are used in their respective companies and provide feedback to Kangie.
• Numeric decodes for Country is a new feature that will be implemented.

New Actions

• @bundfussr and @bms63 to look into Treatment Emergent process at their respective companies
• @zdz2101 to look into updating failing CI around error messaging for admiral
• @manciniedoardo to work on vignettes for Get Started
• @jeffreyad to look into implementing Country Decodes in admiral

Previous Actions

• Edoardo to make news blurb in admiral around new Error Messaging paradigm to alert users
• Ben to make update for PR Template and Changelog section for tracking Developer updates
• Gordon to make discussion on user-defined baselines
  to update Remotes in Description for in admiral to get updates going on in admiraldev~

[bms63]

@pharmaverse/admiral here are my loose notes from today's meeting. Please add anything you think might be helpful for posterity!

[bms63]

April 18th, 2024

Go arounds
Report back on Error Messaging Group
Report back on date/time cyclomatic complexity group
Get Started Vignettes: #2395
Issues in Backlog

Some Notable Notes of Note

• Short and sweet meeting!!
• Remember June is the release!!
• admiralpeds is looking to deploy in June/July! (wow)
• Error Messaging group is rounding out - a check on impact to admiral functions is needed General Issue: Ensure argument name is correct in error messages #2404
• Discussed Documentation: Break "Simple ADSL Walkthrough" into two Vignettes #2395 - Fanny to create outline to the two proposed articles and we will discuss what should go in each article in the issue.
• The trt emergent function will be implemented based on latest discussion - try to shop to the Phuse WG for further testing and possible enhancement

Actions

• @kaz462 to okay @ashachakma PR to move forward
• @Fanny-Gautier to outline proposal for two Get Started vignette content

[bms63]

@pharmaverse/admiral hi all - pretty light notes and discussion. Please add anything you think might be helpful for posterity

[bms63]

May 1, 2024

Agenda

• Go arounds/Project Board
• Use of AVALC in BDS Examples - Closes #2395: Re-vamp of get-started page #2402 (comment)
• Images in the News.md file to showcase new stuff?
• Almost to 200 Stars

Notable Notes of Note

Actions

[bms63]

May 15th, 2024

Agenda

• Amy from oak team presenting about logging in oak
• Go arounds/Project Board
• Revamp of Get Started Materials
• Use of AVALC in BDS Examples - Closes #2395: Re-vamp of get-started page #2402 (comment) (Not Discussed)
• Images in the News.md file to showcase new stuff? (Not Discussed)
• Almost to 200 Stars (Not Discussed)

Notable Notes of Note

• Amy from roak team at Roche came and presented on the roak package. This was a showcase of messaging to help drive more discussion around if this is something to include in admiral - Could admiral have a "verbose" mode where useful info is printed to the log after each function run? #2418
  • Focus is on automation and not on modular building blocks and has a black box feel to it
  • The package produces datasets regardless of errors or issues in the SDTM creation
  • Creating one variable at a time and merging on to previous datasets
  • Ingests data for creation of SDTM data - way cool!
  • Messaging is very cool and helpful, buts prints out quite a lot of stuff
  • Project is inspiration for COSA OAK R package, but taking a bit more of an admiral approach with modularity
  • DECISION - Not to implement verbosity argument for messaging for admiral functions
  • A Blog Posts with tips or a tidyadmiral could be created similar to https://github.com/elbersb/tidylog!
• Discussion around errors coming from functions that are used in wrappers - not helpful for users
  • cards R package has potential solutions
  • might implement in 1.2, 1.3 but letting percolate for a bit in cards R package
  • Keep an eye on Error Messaging: Display function the user calls rather than sub-function #2421
• Release is coming on June 3rd
  • A list of common tasks is kept in a discussion now Release 1.2: Common tasks, Dev acknowledgement, versioning, helper packages/websites, etc #2394
• Kaz and Edoardo are meeting to discuss data packages updates and release plan
  • Potential release of pharmaversesdtm on May 31st for June 3rd release of admiral
• Stefean Thoma investigating some tough issues with assert_list_elements
  • Possible update for 1.2
• New simplified Get Started to be released with 1.2 as well as a more thorough programming concepts and conventions vignette to be release. Closes #2395: Re-vamp of get-started page #2402
  • testthat addin has been moved to a new addin package just admiral developers - https://github.com/pharmaverse/pharmaverse4devs

Actions

• @manciniedoardo to look into release discussion, create branch and start making updates
• @kaz462 to chase @ashachakma and @gg106046 on issues Enhancing derive_var_trtemfl() to deal with AEs recorded on multiple lines #2302 and derive_vars_transposed: extra variables are treated as by_vars #2325 and either lend support or take over if needed

[bms63]

@pharmaverse/admiral - please add anything I missed. I don't remember a lot of actions, we all seemed to have quite a bit of things to chase already.

@pharmaverse/admiral_comm - couple of notes I thought you might be interested in following.

[manciniedoardo]

May 22nd, 2024

Agenda

• Go arounds/Project Board
• Open PRs - prioritization ahead of 1.1 release
• Use of AVALC in BDS Examples - Closes #2395: Re-vamp of get-started page #2402 (comment) (Carried over from last meeting)
• Images in the News.md file to showcase new stuff? (Carried over from last meeting)

Notable notes of note/Actions to be taken:

• Issues/PRs up for the most part are up to date with people actively still working on them
• 2404 general issue ensure argument name is correct in error messages #2431 arg names with 240+ files change, alongside similar issue in admiraldev, @ddsjoberg had a short & sweet solution that we may implement instead
• pharmaversesdtm looks good to be released ahead of time
• Use of AVALC in BDS topic, review vignettes for something of this nature, sounds like we can drop AVALC from ADVS, but check code/decode relationships, @manciniedoardo to create an appropriate issue
• Use of images in the NEWS file, action: do nothing, should be kept it boring, especially due to the nature it is up on CRAN
• Admiral abstract accepted for CDISC interchange in October
• Reminder that June release is coming shortly!

[Fanny-Gautier]

Hi @manciniedoardo ,
I don't have any invite in my calendar for the additional meeting tomorrow. Could you please forward it to me ?
Thanks.

[manciniedoardo]

thanks for flagging! i'd made the event but forgot to add the guest list 🤦 fixed now.

[bms63]

May 29th, 2024 Agenda

• Go arounds/Project Board
• Open PRs/Issues - prioritization ahead of 1.1 release
• Checking reverse dependencies
• Meeting cadence and Retrospective
• Review General Issue: Tracking updates for admiraldev #2372 (comment) for impact on Vignettes, Templates, Function Documentation
• Potential new members to team (Iain, Phillip)

Some notable notes of note

• Zelos is presenting at CDISC Interchange on admiral!!
• Ben presented at Pharmasug and was well-received. Lots of pharmaverse references and even an admiralonco presentation by someone outside the group
• Minor concerns on reverse dependencies impact to non-CRAN packages (datacutr and sdtm.oak)
• admiralvaccines has potential issues with dependencies, but Daniel ran check and seems okay
• Fanny has updated version label and thinks we have a fix!!
• Sadcla requested that we test out pharmaverse4dev pkg to see if it is working appropriately for test numbering
• Potential new members to the team coming @imccay13 and @ProfessorP-beep will update and onboard officially if they join.
• No interest from team in reviewing impact on error messaging updates to templates and vignettes - issue closed
• No Meetings until mid-July which will be a retrospective on 1.1 lead by Zelos!

Actions

• @bms63 to track down admiralonco presentation
• @ddsjoberg to check with sdtm.oak on dependencies; @manciniedoardo to check on datacutr
• @bms63 to test out version labels and see if we can get it back in action!!
• @bms63 to test out pharmaverse4dev pkg for test numbering
• @zdz2101 to set up Retrospective Document

[bms63]

@pharmaverse/admiral @pharmaverse/admiral_comm hi all - here are some of my notes. please add anything that I missed

[bms63]

@sadchla-codes the testthat addin from pharmaverse4devs is working splendid for me

[bms63]

Retrospective Pre-Planning

Hi all! Hoping to get more input for this retrospective. Even if you can't attend, please spend a few minutes identifying at least one for each category for:

• Things that are going well
• Things not going so well
• Ideas for improvement.

Get fanciful!! We all have some ideas on things for improvement or things we aren't really enthused about! We don't have to implement everything, but lets take advantage of the retrospective to build momentum for 1.2!!

Retrospective for 1.1

Please check yourself off once you entered in at least one!! I really value your feedback and ideas!!

• @bms63
• @bundfussr
• @jeffreyad
• @Fanny-Gautier
• @gg106046
• @ashachakma
• @cicdguy
• @manciniedoardo
• @Lina2689
• @sophie-gem
• @esimms999-gsk
• @millerg23
• @sadchla-codes
• @ddsjoberg
• @StefanThoma
• @ProfessorP-beep
• @kaz462
• @zdz2101
• @rossfarrugia (I just realized you are not on the DESCRIPTION file, 1.2 first issue to fix!!)

@pharmaverse/admiral_comm we also value your input - feel free to add into the document (not sure you have access), but drop here and I will add.

[bms63]

@Fanny-Gautier I check you off - feel free to add other items, but thought you might be done!

[bms63]

August 7th, 2024 Agenda

• New Working Groups and Working Group Leads
• Dummy Pull Requests and freezing admiral
• R/Pharma Workshop with admiral
• Moving deprecation forward
• Documentation: FMQs (baskets) being released by FDA #2486
• lab grading: 2.0 Roadmap (or 1.1) #2191 (comment)
• pharmaverseadam: [Feature Request] Missing variables in the ADCM dataset pharmaverseadam#77

Notable Notes of Note

• Daniel is leading some pharmaverse-related workshops at Posit Con this year! Very exciting
• There is an R/Pharma Summit and an R/Pharma Conference
  • The Summit happens at Posit Con and is a 1 day pre-conference get together. https://rinpharma.com/post/2024-03-25-announcement/
  • The Conference is annual online/free conference with workshops! https://rinpharma.com/post/2024-03-25-announcement/
• Welcome to newest admiral member @yevhen-b from Atorus. @zdz2101 is staying with us in reduced capacity, but still with us!! Yay!
• Refresh of admiraldiscovery by @jsaltane123 ! Many thanks for the thorough update!
• Data packages: adam and sdtm continued to be worked on to help align to needs of NEST
• Request from @manciniedoardo to add orchid IDs to the DESCRIPTION File - no objections
• @bms63 proposed a new working group around a thorough review of the ADaM IG as well as other CDISC documents
  • @millerg23 and @StefanThoma expressed interest but have limited time
  • Everyone is welcomed and more will be posted on slack channel
  • Looking for co-lead if anyone is interested!
• Possible new working group around CI updates/maintenance proposed
  • Tabled as @cicdguy has a bunch of updates coming to harmonize CI between admiral and NEST
  • Some outstanding CI issues to be flagged
• Try to adhere to a two week pause/freeze on dev work when 1.2 release happens
• Inconclusive discussion on how to help identify bugs/broken things trickling down to extension packages
• R/Pharma Workshop using admiral and metatools/metacore
  • 3 hour workshop
  • @Fanny-Gautier and @bms63 to lead
  • @manciniedoardo to support in chat
  • Others are welcome to join to help lead portion of the workshop or help out in chat
• FMQs briefly discussed
• Moving forward with updates to lab grading
• ATC, whodrug dictionary discussed around requested updates in [Feature Request] Missing variables in the ADCM dataset pharmaverseadam#77
  • Ongoing

Actions

• @bms63 to find any outstanding CI issues that could be fixed/addressed in the coming updates
• @sadchla-codes and @StefanThoma to discuss deprecation and move forward
• @millerg23 to expand on issue with recommendations - Documentation: FMQs (baskets) being released by FDA #2486
• @bms63 to look into snapsh**t testing :) j/k

[bms63]

@pharmaverse/admiral and @pharmaverse/admiral_comm brief notes around our first meeting for the 1.2 release. Those on the core team - please feel free to add anything I might of missed or anything that should be expanded upon!

Thanks again all! It was great to see everyone!!

[bms63]

August 21st 2024 Agenda

• 1.2 Release is in January 2025

Actions from previous meeting

• @bms63 to find any outstanding CI issues that could be fixed/addressed in the coming updates
• @sadchla-codes and @StefanThoma to discuss deprecation and move forward
• @millerg23 to expand on issue with recommendations - Documentation: FMQs (baskets) being released by FDA #2486
• @bms63 to look into snapsh**t testing :) j/k

New Topics

• admiral community meeting and posit conferences
• Environment handling working group
• Resources on Teams / Add new members / Still useful?
• ADaM IG Working Group
• Add orchid IDs

Notes

• Fanny and Ben met to discuss admiral workshop for R/Pharma. Focus will be on ADSL and ADVS with a brief intro to extension packages.
• Stefan is working on {callstores} - he is going to present a PoC at a future core meeting.
• Daniel and Stefan have been "volunteered" to start an Environment Working Group. Core team slack channel will have something posted soon about it.
• admiralpeds is up on CRAN - whew! https://cran.r-project.org/web//packages/admiralpeds/index.html
• Sadchla encourages everyone to check out {pharmaverse4devs} to help with blogs and testings
• Everyone is encouraged to make orchid IDs and add in.
• We mostly review outstanding Pull Requests and made sure critical issues are being addressed (e.g. deprecation, bugs)
• Short meeting as a lot of folks were out of town!

Actions

• Fanny to follow up with Steven about CHG/PCHG updates
• @bundfussr and @manciniedoardo to revisit the options issue as the PR got a bit out of hand!
• Daniel and Ben to work together to ensure snapshots testing's are being checked

[bms63]

@pharmaverse/admiral @pharmaverse/admiral_comm hi all! Some brief notes. The meeting was short as we had small headcount. Focus was more on ensuring PRs and Issues are not getting stale. We are at 18 Issues and I am starting to panice.

[bms63]

September 4tht 2024 Agenda

• 1.2.0 Release is in January 2025

Actions from previous meeting

• @bundfussr and @manciniedoardo to revisit the options issue as the PR got a bit out of hand!

New Topics

• call stores demo @bundfussr
• ADaM IG Working Group
• Feature Request: Function for creating variable pairs like MCRITyML/MCRITyMN #2480 (comment)
• General Issue: Make subject keys flexible in all functions #2415 (comment)
• FMQs Discussion (More needed?)
• Blog Post Requests

Notes

• Milestone achieved! No deprecation...so far...in 1.2!
• Demo of @bundfussr https://github.com/bundfussr/scriptr package for generating code templates! Very intriguing. Lots of discussion on usefulness, ideas for how to improve, concerns on what is already out there for templating. Stefan is going to progress along, but is looking for others to check it out! Very PoC!!
• FMQs moved to discussion and waiting on updates from FDA
• Minor note - if you reference a document in admiral documentation, be sure to list out the full title so it is easier for us to track down if the link goes 404 on us.
• Ben makes a plea for blog posts! Always looking for quick content!!
• That's it!!

Actions

No new Actions

[bundfussr]

@bms63 , I can do a short demo

[bms63]

September 18th, 2024 Agenda

• 1.2 slated to be released in January 2025

Agenda

• Move up release of admiral to early December
• Review of all Issues - can we clean it to 1?
  • Flexible Keys
• Review of Discussion topics: consolidate, rework, working groups, close

Some Notable notes of note

• Locked in to January 2025 Release date! We should alert the other developers of packages
• admiraldiscovery has had a nice update courtesy of Fanny - not sure if it is live yet (@Fanny-Gautier)
• We did a good run through of the Issues and every Issue has been assigned or moved to a Discussion
• Edoardo and Ben will meet to discuss moving Discussion Thread forward
• Light discussion on Ben's wanting of a function to pull out the sorting key of a dataset - DENIED :) Probably will be orphaned.
• Edoardo is going to set up Environment Handling Working Group
• Phil is going to take on the flexible keys update...again! Thanks @ProfessorP-beep
• Edoardo requested that Feature Request: Function for creating variable pairs like MCRITyML/MCRITyMN #2480 (comment) be merged in soon so he can make updates in admiraloptha

Actions

• Update Readme Release Schedule to January (@bms63)
• PR Feature Request: Function for creating variable pairs like MCRITyML/MCRITyMN #2480 (comment) to be completed as function without updates to vignettes. That is to come later (@StefanThoma)

[bms63]

@pharmaverse/admiral - did I miss anything? 37 minute meeting so notes were pretty light. Curious about reducing to 30 minutes.

@ddsjoberg highly recommends this show to watch while coding - https://en.wikipedia.org/wiki/The_Secret_Lives_of_Mormon_Wives

[ddsjoberg]

OMG I can't claim I didn't make some kind of recommendation 🤦🏼‍♀️🤦🏼‍♀️🤦🏼‍♀️ 😆

[ddsjoberg]

Regarding the 30 minute meetings. I think it's a great idea, and we can always extend as needed. Perhaps for the next meeting, keep it to 60 minutes and we can review the open discussions to see which can be closed?

[bms63]

Will put on agenda for next meeting :) Reduction of time for meetings and Secret Lives Report back

[bms63]

October 2nd, 2024

• admiral 1.2 to be release in January 2025
• PR Titles are nice and help us later!!
• Edoardo to take notes

Agenda

• https://en.wikipedia.org/wiki/The_Secret_Lives_of_Mormon_Wives
• Codify the Deprecation Strategy into Bronze Tables Deprecation 2.0 #2329
• Small issues brought up by users - See Issues Tab
• admiral community meeting
• admiral 1.2 Blog Post
• Checking on the Working Groups
• 100% Test Coverage Outsourced
• Remove .devcontainer as no longer being maintained

Some Notable Notes of Note

Actions

Remove .devcontainer

Decision: drop!

100% Test Coverage Outsourced

• Could we make issues to enhance the test coverage and outsource that to the RPharma group (@ddsjoberg leading)?
• A lot of these are very niche lines deep in admiral functions. Might be hard to execute them in a test.
• But could be good to get folks involved in making small but meaningful contributions to admiral.
• Aside: the test coverage CICD check is probably broken in admiral.

Decision: Yes, make issues, but label them as low priority

Working groups update

• ADAM IG WG:

  • @bms63 has set this up.

• Env WG:

  • will be a bit of a book club to begin with, we'll read over the env-related chapters and then apply learnings to admiral
  • @ddsjoberg to make a post on Slack once schedule is figured out by @manciniedoardo

1.2 blog post

• good opportunity for anyone interested! Let @bms63 or @manciniedoardo know

admiral community meetings

• These quarterly meetings have run their purpose and were more useful when we were releasing quarterly and often breaking things.
• Now not as well-attended and not as much to say in them.

Decision: After the final community meeting in Q42024, only run these ad-hoc. @manciniedoardo to announce this during the final community meeting and on slack.

Issue discussion

• Feature Request from admiralmetabolic: Wrapper for derive_param_calculated() to derive Ratio parameters #2514 (Ratio function) decision not to implement intermediate function for ratios. Instead, put keywords "ratio" etc into derive_param_computed() and derive_vars_computed() documentation so that users might find it easier to find the function.
• Ask Andrii for specific example to add in derive_var_joined_exist_flag().
• Bug: derive_var_atoxgr_dir() derives baseline CTCAE grade relative to baseline (if baseline abnormal) #2512 - @bms63 to spruce up issue, @millerg23 to implement.
• For other discussion - see notes within specific issues

Deprecation strategy

• Mimic 3-year deprecation strategy from @ddsjoberg and gtsummary
• @bms63 to formalise and include in admiraldev documentation
• Include new strategy in 1.2 blog post

[bms63]

Nice summary of our latest meeting - @pharmaverse/admiral @pharmaverse/admiral_comm

[bms63]

October 16th, 2024

• admiral 1.2 to be release in January 2025

• Edoardo to take notes

• New Member

Agenda

• Small issues brought up by users - See Issues Tab
• R/Pharma
• Working Groups
• admiral 1.2 Blog Post

Some Notable Notes of Note

Actions

• @manciniedoardo to make an issue to finish up subject_keys options work. Decision is to implement options in templates but not vignettes.
• @bms63 to make R in Pharma issue to add badges to main website (instead of just dev website)
• @ddsjoberg to review environments-related PR on admiraldev

[bms63]

November 13th, 2024

admiral 1.2 will be released in January 2025

Agenda

• Review of outstanding Pull Requests
• Updating ADEG script ([Question] regarding pharmaverseadam adeg data where ANL01FL == "Y" #2559)?
• Should we catch warning in derive_vars_atc() (see https://pharmaverse.github.io/admiral/dev/articles/occds.html#atc)?
• Automating add in Remotes to DESCRPITON file in each Release Cycle
• Review Release procedures

Outstanding Actions

Notes

• Issue created for the ADEG script: Update ADEG Template #2561
• Issue created for the derive_vars_atc() issue: General Issue: derive_vars_transposed() shouldn't produce list columns #2563
• The last two items of the agenda were skipped.

Actions

[bms63]

December 2nd, 2024

admiral 1.2 will be released in January 2025

Agenda

• Review of outstanding Pull Requests and Issues
• Slack Discussions: FMQs, U---, DOSECUMP/A
• Automating Template Update checks
  • Easy win: Identify keys for each dataset and compare CRAN to main
• Review Release procedures
• Should we deprecate the superseded functions?
• Remove specific calls to IG version - just say latest or not at all
• How should we document non-exported functions? I think for most of them we use @keyword internal but sometimes @noRd is used, e.g., for filter_date_source(). Do we need to update the programming strategy?
• Should we prioritize General Issue: Improve derive_*_joined_*() functions #2590?
• Should we clean up "New Features" section in NEWS.md?
• Remove use of rlang in examples
• Meetings in 2025: retro, bi-weekly

Outstanding Actions

• Issue created for the derive_vars_atc() issue: General Issue: derive_vars_transposed() shouldn't produce list columns #2563

Notes

Actions

• @bms63 to clean up "New features" section close to release, will take care of removing any updates deemed too small.
• @bms63 to make an issue to remove library(rlang) from examples sections as we import {rlang} functions with {admiral}
• agree to prioritise General Issue: Improve derive_*_joined_*() functions #2590 - @bundfussr to try get this in for Jan release, otherwise we could explore getting it in an intermediate 1.2.1 release.
• agree to stop using "@nord==RD" in documentation - document every function even if internal, just don't export it. @bms63 to make issue to update programming strategy to reflect this.
• agree to stop quoting specific version number for ADaM IG - make issue to remove any references to 1.3, etc.
• agree to deprecate superseded functions
• FMQ discussion: @bms63 to look into GSK approach and ping @nbrucken17 for comment
• retro end of january, pick back up end of february. @manciniedoardo to make calendar invites and run
• fortnightly meetings in 2025 updated to Mondays.
• @millerg23 to make issue to change format of lab metadata (maybe .json).
• @manciniedoardo to make blog post to connect with other internal admiral extensions.

[jimrothstein]

Low Priority

Thank you for your Pull Request!"

Growing appreciation for all this document touches! This leads to questions and debate: why this way, not that way?

• For pros, discussion may not be very illuminating.

• For beginners, just trying to follow the steps is enough.

• But for those somewhere in between, could some sort of followup discussion be fruitful?
  Sort of Why we do things the way we do and explore specific examples of test strategy, common functions and structure, proper documentation and whatever nuances begin to appear.

[bms63]

Thanks @jimrothstein - always excited to discuss the Pull Request Template and refining it.

Since time is limited in our meetings (hopefully just 30 minutes) please ask away. Happy to provide more context. Others might appreciate it!

[bms63]

@pharmaverse/admiral and @pharmaverse/admiral_comm for anyone interested in the bi-weekly meeting happenings