Final CRAN prep

[rafdoodle]

Hello Doug,

Hope all is well. After spending the last few days with Claude improving test coverage and documentation, I have prepared one final pull request for you to review chmsflow before we submit it to CRAN for the first time.

Your main tasks are to:

• Check if information in LICENSE and DESCRIPTION are correct.
• Check if PR Medications updates + new variable names #10 is necessary for CRAN submission and if it needs to be dealt with first.
• Check if the is_taking_drug_class function is needed for the package, as its use in the cycles1to2_* medication functions was removed during function vectorization.
• Check if package looks good and is working on your end (perhaps more in detail if you have the time).

Upon your approval, I will merge all these changes to main, from which I will submit the tarball (.tar.gz) to CRAN. Then, upon CRAN approval, I will create a release (branch) on GitHub for the packages's first version (0.1.0).

From my end already, devtools::check() passes with no errors, warnings, and notes, and I already confirmed with Claude that chmsflow meets the CRAN guidelines outlined for source packages.

Please let me know what you think.

Sincerely,
Rafidul

[DougManuel]

Review summary

Nice work on test coverage, NA handling, and documentation improvements. devtools::check() passing clean is a solid milestone.

I've created separate issues for the items that need discussion or are CRAN-blocking:

P0 (CRAN-blocking)

• anymed2 and diab_drug2 have self-referential metadata — breaks rec_with_table() #13 — anymed2/diab_drug2 self-referential metadata breaks rec_with_table()
• Role column still present in variables.csv #14 — Role column still present in variables.csv

P1 (should fix before CRAN)

• No automated workflow for medication variables in cycles 3-6 (long format) #15 — No automated workflow for cycles 3-6 medication variables
• Standardize variable naming conventions before CRAN #16 — Standardize variable naming conventions before CRAN
• Function naming uses 8+ verb prefixes with no documented taxonomy #17 — Function naming uses 8+ verb prefixes with no documented taxonomy

Additional items (smaller, can address in this PR)

Description column empty: The description column in variables.csv exists but is blank for every variable. Worth populating with brief plain-language descriptions.

Parameter case mixing: Function parameters use inconsistent case — ANYMED2 (uppercase) in determine_hypertension() but diab_drug2 (lowercase) in determine_inclusive_diabetes(). Should pick a convention and apply consistently.

Typo in variable-details.csv: dummyVariable field for anymed2 reads amymed2_cat2_3 — missing the n. Should be anymed2_cat2_3.

Re: your checklist questions

• LICENSE and DESCRIPTION: Will review separately.
• PR Medications updates + new variable names #10: Yes, the naming conventions in PR Medications updates + new variable names #10 should be resolved before CRAN (see Standardize variable naming conventions before CRAN #16, Function naming uses 8+ verb prefixes with no documented taxonomy #17). Renaming after publication requires deprecation cycles.
• is_taking_drug_class: Will review whether it's still needed given the cycles1to2_* refactoring.

[DougManuel]

Follow-up: Full review and CRAN readiness assessment

Answers to your checklist

LICENSE and DESCRIPTION

• LICENSE lists only Rafidul Islam as copyright holder, but DESCRIPTION has three authors with aut role (Rafidul, Doug, Therese). Let's confirm whether all three should be copyright holders.
• recodeflow is in Suggests — need to confirm it's on CRAN. If not, the submission will be rejected.
• Everything else looks good (version 0.1.0, title, citation, URLs, dependencies).

PR #10
PR #10 doesn't need to be merged first. It's mostly the AI.md style guide (discussion only, no code implementing the proposals) plus minor CSV changes that conflict with your more extensive PR #12 work. The AI.md can be added after this PR merges. We can close PR #10.

is_taking_drug_class
Keep it. The cycles1to2_* functions no longer call it (they use is_* helpers directly), but it's a useful public API for advanced users defining custom drug classes. It's exported, documented, and tested — fine to ship.

CRAN-blocking decision

All five issues (#13–#17) need to be addressed before CRAN submission. The naming issues (#16, #17) would require deprecation cycles if changed after publication, so better to get them right now.

Must fix before CRAN:

• anymed2 and diab_drug2 have self-referential metadata — breaks rec_with_table() #13 — anymed2/diab_drug2 self-referential metadata
• Role column still present in variables.csv #14 — Role column in variables.csv
• No automated workflow for medication variables in cycles 3-6 (long format) #15 — Cycles 3-6 medication workflow automation
• Standardize variable naming conventions before CRAN #16 — Variable naming conventions (snake_case, consistent suffixes)
• Function naming uses 8+ verb prefixes with no documented taxonomy #17 — Function naming taxonomy (reduce verb prefixes, document conventions)

Plus the smaller items from my previous comment (empty descriptions, parameter case, amymed2 typo).

Suggested sequence

1. Agree on naming conventions (Standardize variable naming conventions before CRAN #16, Function naming uses 8+ verb prefixes with no documented taxonomy #17) — this drives everything else
2. Rename variables and functions across codebase
3. Fix anymed2/diab_drug2 architecture (anymed2 and diab_drug2 have self-referential metadata — breaks rec_with_table() #13)
4. Add cycles 3-6 wrapper (No automated workflow for medication variables in cycles 3-6 (long format) #15)
5. Clean up metadata (Role column still present in variables.csv #14, descriptions, typo)
6. Update vignette, tests, and documentation to match

Let's schedule a discussion to align on the naming conventions — that's the key decision that unblocks the rest.