update, remove fda02 table by shajoezhu · Pull Request #363 · pharmaverse/cardinal

shajoezhu · 2026-09-04T03:13:24Z

Pull Request

GitHub Issue

Closes #nnn

Include a Screenshot of the TLG

Screenshot of TLG template from source document (e.g. FDA integrated guide)

TODO: Add screenshot here

Developer To-Dos

Add quarto file quarto/catalog/[TLG-ID]/index.qmd with your TLG template.
Ensure that the title, subtitle, and categories fields at the top of the TLG template are correct.
Add a screenshot of your TLG named result.png to the quarto/catalog/[TLG-ID] folder.
Branch has all updates from the main branch.
Request a reviewer.

Reviewer To-Dos

Confirm that all GitHub CI/CD pipelines pass with a ✅.
Confirm that the TLG screenshot above matches the template output screenshot (result.png).
Confirm that branch has all updates from the main branch.
Approve PR once all of the above have been confirmed.

Copilot

🟡 Changes recommended

The PR description still contains required-review placeholders/TODOs (issue link and screenshot), and the namespace now contains a stale import that should be cleaned up via roxygen regeneration.

Once you've addressed the issues Copilot identified, you can request another Copilot review.

Pull request overview

This PR removes the public make_table_02() API (FDA Table 2 helper) from the package by deleting its implementation, namespace export/imports, and generated documentation, while keeping an archived implementation under R/archive. It also includes a no-op-ish snapshot update (trailing blank line) for the fda-table_02 template test output.

Changes:

Removed make_table_02() implementation and its generated Rd documentation.
Updated NAMESPACE to drop the export and related imports tied to make_table_02().
Renamed the archived gtsummary helper in R/archive/fda-table_02.R to make_table_02() and updated the snapshot file formatting.

File summaries

File	Description
tests/testthat/_snaps/fda-table_02.md	Adds a trailing blank line in the snapshot output.
R/fda-table_02.R	Deletes the exported `make_table_02()` implementation entirely.
R/archive/fda-table_02.R	Renames the archived gtsummary implementation function to `make_table_02()`.
NAMESPACE	Removes `export(make_table_02)` and related imports previously needed by the deleted function.
man/make_table_02.Rd	Removes generated documentation for `make_table_02()`.

Review details

Files reviewed: 5/5 changed files
Comments generated: 2
Review effort level: Lite

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github-actions · 2026-09-04T03:17:29Z

Unit Tests Summary

1 files 30 suites 22s ⏱️
42 tests 15 ✅ 27 💤 0 ❌
53 runs 26 ✅ 27 💤 0 ❌

Results for commit af576f9.

♻️ This comment has been updated with latest results.

github-actions · 2026-09-04T03:17:59Z

Code Coverage Summary

Filename            Stmts    Miss  Cover    Missing
----------------  -------  ------  -------  ---------
R/cardinalfda.R         5       5  0.00%    18-22
R/run_template.R        5       0  100.00%
R/utils.R              40       0  100.00%
TOTAL                  50       5  90.00%

Diff against main

Filename            Stmts    Miss  Cover
----------------  -------  ------  --------
R/cardinalfda.R        +5      +5  +100.00%
R/run_template.R        0      -1  +20.00%
R/utils.R               0     -40  +100.00%
TOTAL                  +5     -36  +84.29%

Results for commit: af576f9

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

github-actions · 2026-09-04T04:54:02Z

Unit Test Performance Difference

Test Suite	$Status$	Time on `main`	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
run_template	👶		$+1.39$	$+4$	$0$	$0$	$0$
utils	👶		$+0.47$	$+21$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	$±Time$	Test Case
run_template	👶	$+0.68$	run_template_does_not_leak_objects_into_the_caller
run_template	👶	$+0.03$	run_template_errors_for_an_unknown_template
run_template	👶	$+0.68$	run_template_sources_a_template_and_returns_its_environment
utils	👶	$+0.01$	alt_counts_df_preproc_errors_when_required_variables_are_missing
utils	👶	$+0.32$	alt_counts_df_preproc_filters_to_the_safety_population
utils	👶	$+0.01$	alt_counts_df_preproc_returns_NULL_when_input_is_NULL
utils	👶	$+0.01$	alt_counts_df_preproc_validates_the_flag_variable
utils	👶	$+0.01$	alt_counts_df_preproc_works_without_a_safety_flag
utils	👶	$+0.01$	assert_flag_variables_accepts_a_custom_na_level
utils	👶	$+0.03$	assert_flag_variables_accepts_valid_flag_values
utils	👶	$+0.01$	assert_flag_variables_errors_on_invalid_values
utils	👶	$+0.03$	basic_table_annot_returns_a_layout_with_and_without_annotations
utils	👶	$+0.02$	split_cols_by_arm_splits_with_and_without_an_overall_column
utils	👶	$+0.02$	split_cols_by_arm_supports_risk_difference_columns

Results for commit a437903

♻️ This comment has been updated with latest results.

Melkiades · 2026-09-04T12:41:11Z

 #' @keywords internal
 #' @importFrom cards ard_continuous
 #' @importFrom cardx ard_continuous_ci
+#' @importFrom crane tbl_demographics


tbl_roche_summary?

@copilot change tbl_demographics to tbl_roche_summary in this file

Done — replaced tbl_demographics with tbl_roche_summary in both R/cardinalfda.R and NAMESPACE, and removed the stale gtsummary::tbl_summary import.

…NAMESPACE Co-authored-by: shajoezhu <3692541+shajoezhu@users.noreply.github.com>

gtsummary was in Depends but not imported, which trips the CI note-blocklist. Add it to the ignore_unused_imports() shim and NAMESPACE alongside the other Depends packages used by inst/templates. Also correct the crane import to tbl_listing (the symbol actually used; tbl_roche_summary was never called) and refresh the stale make_table_02 NEWS entry.

Melkiades

lgtm!! I added a couple of minor fixes ;)

update, remove fda02 table

e7d7217

shajoezhu requested review from Melkiades and a lite review from Copilot September 4, 2026 03:13

Copilot started reviewing on behalf of shajoezhu September 4, 2026 03:14 View session

Copilot AI reviewed Sep 4, 2026

View reviewed changes

Comment thread NAMESPACE

Comment thread NAMESPACE

ading testings

b7d4878

shajoezhu added 2 commits September 4, 2026 13:55

updaet

aa9f3c0

update

848e9d5

Melkiades reviewed Sep 4, 2026

View reviewed changes

Copilot started work on behalf of shajoezhu September 4, 2026 12:58 View session

Replace tbl_demographics with tbl_roche_summary in cardinalfda.R and …

a49af00

…NAMESPACE Co-authored-by: shajoezhu <3692541+shajoezhu@users.noreply.github.com>

Copilot finished work on behalf of shajoezhu September 4, 2026 12:59

shajoezhu and others added 2 commits September 4, 2026 21:03

Merge branch 'main' into drop_make_fda2_function

6107ab6

Melkiades reviewed Sep 4, 2026

View reviewed changes

Comment thread R/cardinalfda.R

Melkiades approved these changes Sep 4, 2026

View reviewed changes

shajoezhu merged commit 0ff116e into main Sep 4, 2026
26 of 27 checks passed

shajoezhu deleted the drop_make_fda2_function branch September 4, 2026 15:20

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update, remove fda02 table - #363

update, remove fda02 table#363
shajoezhu merged 7 commits into
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drop_make_fda2_function

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shajoezhu commented Sep 4, 2026

Pull Request

GitHub Issue

Include a Screenshot of the TLG

Screenshot of TLG template from source document (e.g. FDA integrated guide)

Developer To-Dos

Reviewer To-Dos

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🟡 Changes recommended

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Unit Test Performance Difference

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